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
NCOA3	8202	hgsc.bcm.edu	37	20	46279815	46279823	+	In_Frame_Del	DEL	GCAGCAGCA	GCAGCAGCA	-	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	GCAGCAGCA	GCAGCAGCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	16	107	.	0.174	.	.	.	none	.	NCOA3	156	.	NM_181659	exon20	c.3740_3748del	p.1247_1250del	.	.	PASS	Pindel,Atlas-Indel
FAM90A1	55138	hgsc.bcm.edu	37	12	8374781	8374782	+	In_Frame_Ins	INS	-	-	ACG	rs71265055	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	83	20	91	.	0.241	.	-|0.250;ACG|0.750	0.750	strong	.	FAM90A1	68	.	NM_018088	exon7	c.1032_1033insCGT	p.T344delinsTV	.	.	PASS	Pindel,Atlas-Indel
C9orf43	257169	hgsc.bcm.edu	37	9	116187645	116187646	+	In_Frame_Ins	INS	-	-	GCA	rs371732185		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	61	22	79	.	0.361	.	.	.	weak	C9orf43,colon,carcinoma,0,1	C9orf43	49	1	NM_152786	exon10	c.887_888insGCA	p.R296delinsRQ	.	.	PASS	Pindel,Atlas-Indel
PCSK9	255738	hgsc.bcm.edu	37	1	55505552	55505553	+	In_Frame_Ins	INS	-	-	CTG	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	20	65	.	0.206	.	.	.	none	.	PCSK9	76	.	NM_174936	exon1	c.42_43insCTG	p.P14delinsPL	.	.	PASS	Pindel,Atlas-Indel
POLI	11201	hgsc.bcm.edu	37	18	51795958	51795960	+	In_Frame_Del	DEL	CGA	CGA	-	rs10584411	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	CGA	CGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	63	31	72	.	0.492	.	CGA|0.254;-|0.746	0.746	strong	.	POLI	132	.	NM_007195	exon1	c.41_43del	p.14_15del	.	.	PASS	Pindel,Atlas-Indel
VWA3A	146177	hgsc.bcm.edu	37	16	22144375	22144375	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	27	91	0	0.391304	0	.	.	none	.	VWA3A	115	.	NM_173615	exon20	c.2026delA	p.T676fs	.	.	PASS	Atlas-Indel
DAAM2	23500	hgsc.bcm.edu	37	6	39869657	39869659	+	In_Frame_Del	DEL	GGA	GGA	-	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	GGA	GGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	45	22	57	.	0.489	.	.	.	none	.	DAAM2	101	.	NM_001201427	exon25	c.3050_3052del	p.1017_1018del	.	.	PASS	Pindel,Atlas-Indel
ACOT4	122970	hgsc.bcm.edu	37	14	74060511	74060512	+	Frame_Shift_Ins	INS	-	-	TCAA	rs373880503	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	12	100	0	0.146341	0	.	.	weak	.	ACOT4	25	.	NM_152331	exon2	c.563_564insTCAA	p.L188fs	.	.	PASS	Atlas-Indel
CNKSR1	10256	hgsc.bcm.edu	37	1	26510311	26510311	+	Frame_Shift_Del	DEL	C	C	-	rs201305445	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	25	77	.	0.272	.	C|0.980;-|0.020	0.020	strong	.	CNKSR1	66	.	NM_006314	exon9	c.844delA	p.T282fs	.	.	PASS	Pindel,Atlas-Indel
RP1L1	94137	hgsc.bcm.edu	37	8	10467681	10467686	+	In_Frame_Del	DEL	TCCTTC	TCCTTC	-	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	TCCTTC	TCCTTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	18	83	0	0.230769	0	.	.	none	.	RP1L1	453	.	NM_178857	exon4	c.3923_3928del	p.1308_1310del	.	.	PASS	Atlas-Indel
SLC28A1	9154	hgsc.bcm.edu	37	15	85438311	85438312	+	In_Frame_Ins	INS	-	-	TTG	rs151038463	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	89	33	67	.	0.371	.	-|0.732;TTG|0.268	0.268	strong	.	SLC28A1	118	.	NM_004213	exon6	c.418_419insTTG	p.L140delinsLV	.	.	PASS	Pindel,Atlas-Indel
ODF1	4956	hgsc.bcm.edu	37	8	103573011	103573037	+	In_Frame_Del	DEL	TGCAACCCCTGCAGCCCCTGCAACCCG	TGCAACCCCTGCAGCCCCTGCAACCCG	-	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	TGCAACCCCTGCAGCCCCTGCAACCCG	TGCAACCCCTGCAGCCCCTGCAACCCG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	103	19	130	0	0.184466	0	.	.	none	.	ODF1	55	.	NM_024410	exon2	c.651_677del	p.217_226del	.	.	PASS	Atlas-Indel
KRTAP10-2	386679	hgsc.bcm.edu	37	21	45970760	45970774	+	In_Frame_Del	DEL	CTTGCAGCAGACAGG	CTTGCAGCAGACAGG	-	rs67692969	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	CTTGCAGCAGACAGG	CTTGCAGCAGACAGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	103	21	103	0	0.203883	0	CTTGCAGCAGACAGG|0.758;-|0.242	0.242	strong	.	KRTAP10-2	21	.	NM_198693	exon1	c.569_583del	p.190_195del	.	.	PASS	Atlas-Indel
ANKRD36	375248	hgsc.bcm.edu	37	2	97779488	97779488	+	Frame_Shift_Del	DEL	C	C	-	rs141447363	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	118	38	129	.	0.322	.	C|0.967;-|0.033	0.033	strong	ANKRD36_ENST00000420699,right_lower_lobe,carcinoma,0,2	ANKRD36	170	2	NM_001164315	exon1	c.11delG	p.G4fs	.	.	PASS	Pindel,Atlas-Indel
AKAP3	10566	hgsc.bcm.edu	37	12	4735970	4735970	+	Frame_Shift_Del	DEL	A	A	-	rs67512580	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	11	103	0	0.141026	0	A|0.868;-|0.132	0.132	strong	.	AKAP3	212	.	NM_006422	exon4	c.2099delC	p.S700fs	.	.	PASS	Atlas-Indel
CELA1	1990	hgsc.bcm.edu	37	12	51740413	51740414	+	Frame_Shift_Ins	INS	-	-	C	rs17860279	byfrequency;alternate_allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	15	154	0	0.163043	0	-|0.426;TGGACCATATCCACTTACCATAAAGGAC|0.574	.	alt	CELA1,NS,carcinoma,+1,1	CELA1	39	1	NM_001971	exon1	c.10_11insG	p.L4fs	.	.	PASS	Atlas-Indel
CDCP2	200008	hgsc.bcm.edu	37	1	54605318	54605319	+	Frame_Shift_Ins	INS	-	-	GG	rs76608277	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	13	86	.	0.186	.	-|0.500;GG|0.500	0.500	strong	.	CDCP2	52	.	NM_201546	exon4	c.1225_1226insCC	p.M409fs	.	.	PASS	Pindel,Atlas-Indel
SYT14	255928	hgsc.bcm.edu	37	1	210267894	210267896	+	In_Frame_Del	DEL	GAA	GAA	-	rs144713062	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	120	40	181	.	0.333	.	GAA|0.912;-|0.088	0.088	strong	.	SYT14	89	.	NM_001146264	exon6	c.804_806del	p.268_269del	.	.	PASS	Pindel,Atlas-Indel
TMPRSS3	64699	hgsc.bcm.edu	37	21	43803308	43803309	+	Splice_Site	INS	-	-	TA	rs56283966	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	88	29	65	.	0.330	.	-|0.840;TA|0.160	0.160	strong	TMPRSS3,NS,carcinoma,0,2	TMPRSS3	40	2	NM_024022	exon9	c.617-1->TA	.	.	.	PASS	Pindel,Atlas-Indel
SKA3	221150	hgsc.bcm.edu	37	13	21746601	21746601	+	Frame_Shift_Del	DEL	G	G	-	rs151272242	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	137	14	130	0	0.10219	0	.	.	strong	.	SKA3	76	.	NM_145061	exon3	c.209delA	p.Q70fs	.	.	PASS	Atlas-Indel
OR51F1	256892	hgsc.bcm.edu	37	11	4790874	4790874	+	Frame_Shift_Del	DEL	G	G	-	rs34672924	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	109	24	106	0	0.220183	0	G|0.772;-|0.228	0.228	strong	OR51F1,NS,carcinoma,-1,1	OR51F1	60	1	NM_001004752	exon1	c.275delG	p.R92fs	.	.	PASS	Atlas-Indel
TAF1L	138474	hgsc.bcm.edu	37	9	32633583	32633584	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	234	16	377	0	0.0683761	0	.	.	none	.	TAF1L	382	.	NM_153809	exon1	c.1995_1996insA	p.K665fs	.	.	PASS	Atlas-Indel
C1orf173	127254	hgsc.bcm.edu	37	1	75037858	75037860	+	In_Frame_Del	DEL	CCT	CCT	-	rs10539747	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	CCT	CCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	147	50	128	.	0.340	.	CCT|0.871;-|0.129	0.129	strong	C1orf173,NS,carcinoma,-1,1	C1orf173	380	1	NM_001002912	exon14	c.3535_3537del	p.1179_1179del	.	.	PASS	Pindel,Atlas-Indel
DNAH8	1769	hgsc.bcm.edu	37	6	38840427	38840428	+	Frame_Shift_Del	DEL	AT	AT	-	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	AT	AT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	128	43	117	.	0.336	.	.	.	none	.	DNAH8	1239	.	NM_001206927	exon50	c.7105_7106del	p.2369_2369del	.	.	PASS	Pindel,Atlas-Indel
ABP1	26	hgsc.bcm.edu	37	7	150558156	150558156	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	81	17	95	.	0.210	.	.	.	none	.	ABP1	92	.	NM_001272072	exon5	c.2171delA	p.D724fs	.	.	PASS	Pindel,Atlas-Indel
CIB1	10519	hgsc.bcm.edu	37	15	90774448	90774451	+	Splice_Site	DEL	AGAG	AGAG	-	rs34604050	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	AGAG	AGAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	59	27	60	.	0.458	.	AGAG|0.433;-|0.567	0.567	strong	.	CIB1	8	.	.	.	.	.	.	.	PASS	Pindel,Atlas-Indel
ZNF880	400713	hgsc.bcm.edu	37	19	52887146	52887146	+	Frame_Shift_Del	DEL	A	A	-	rs34470614	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	74	47	118	.	0.635	.	A|0.672;-|0.328	0.328	strong	.	ZNF880	45	.	NM_001145434	exon4	c.312delT	p.L104fs	.	.	PASS	Pindel,Atlas-Indel
PLAC9	219348	hgsc.bcm.edu	37	10	81904097	81904098	+	In_Frame_Ins	INS	-	-	AGA	rs149506488	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	25	11	23	.	0.440	.	.	.	strong	.	PLAC9	9	.	NM_001012973	exon3	c.281_282insAGA	p.G94delinsGE	.	.	PASS	Pindel,Atlas-Indel
CYP4B1	1580	hgsc.bcm.edu	37	1	47280747	47280748	+	Frame_Shift_Del	DEL	AT	AT	-	rs3215983	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	AT	AT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	24	108	.	0.414	.	AT|0.822;-|0.178	0.178	strong	.	CYP4B1	81	.	NM_001099772	exon8	c.883_884del	p.295_295del	.	.	PASS	Pindel,Atlas-Indel
GPR112	139378	hgsc.bcm.edu	37	X	135474445	135474447	+	In_Frame_Del	DEL	GAT	GAT	-	rs3030295	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	GAT	GAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	198	102	356	.	0.515	.	GAT|0.500;-|0.500	0.500	strong	.	GPR112	459	.	NM_153834	exon17	c.7965_7967del	p.2655_2656del	.	.	PASS	Pindel,Atlas-Indel
KRTAP10-11	386678	hgsc.bcm.edu	37	21	46067225	46067226	+	Frame_Shift_Ins	INS	-	-	G	rs148239295	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	132	14	98	0	0.106061	0	.	.	strong	.	KRTAP10-11	36	.	NM_198692	exon1	c.850_851insG	p.R284fs	.	.	PASS	Atlas-Indel
ZFHX3	463	hgsc.bcm.edu	37	16	72822564	72822569	+	In_Frame_Del	DEL	TGCTGC	TGCTGC	-	rs376311468	alternate_allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	TGCTGC	TGCTGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	105	24	106	.	0.229	.	.	.	alt	.	ZFHX3	404	.	NM_006885	exon10	c.9607_9612del	p.3203_3204del	.	.	PASS	Pindel,Atlas-Indel
SYNJ1	8867	hgsc.bcm.edu	37	21	34003928	34003929	+	In_Frame_Ins	INS	-	-	AGTATT	rs71640263	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	151	31	174	.	0.205	.	-|0.489;AGTATT|0.511	0.511	strong	.	SYNJ1	253	.	NM_003895	exon32	c.4216_4217insAATACT	p.L1406delinsNTL	.	.	PASS	Pindel,Atlas-Indel
L1TD1	54596	hgsc.bcm.edu	37	1	62672389	62672390	+	In_Frame_Ins	INS	-	-	AACAGA	rs150799576	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	127	38	215	.	0.299	.	-|0.971;AACAGA|0.029	0.029	strong	.	L1TD1	114	.	NM_001164835	exon4	c.89_90insAACAGA	p.L30delinsLTE	.	.	PASS	Pindel,Atlas-Indel
ANKRD20A3	441425	hgsc.bcm.edu	37	9	43121655	43121658	+	Frame_Shift_Del	DEL	TAAG	TAAG	-	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	TAAG	TAAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	359	25	352	0	0.0696379	0	.	.	none	.	.	.	.	NM_001012419	exon6	c.776_779del	p.259_260del	.	.	PASS	Atlas-Indel
DOC2A	8448	hgsc.bcm.edu	37	16	30018351	30018353	+	Frame_Shift_Del	DEL	CCT	CCT	-	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	CCT	CCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	184	32	139	.	0.174	.	.	.	none	.	DOC2A	40	.	NM_003586	exon7	c.714_714del	p.238_238del	.	.	PASS	Pindel,Atlas-Indel
CLCA4	22802	hgsc.bcm.edu	37	1	87045897	87045902	+	In_Frame_Del	DEL	CCTACA	CCTACA	-	rs4001061	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	CCTACA	CCTACA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	169	40	226	.	0.237	.	CCTACA|0.284;-|0.716	0.716	strong	.	CLCA4	131	.	NM_012128	exon14	c.2628_2633del	p.876_878del	.	.	PASS	Pindel,Atlas-Indel
FAM22F	54754	hgsc.bcm.edu	37	9	97080945	97080947	+	In_Frame_Del	DEL	AGA	AGA	-	rs150455117	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	270	51	411	.	0.189	.	.	.	strong	.	FAM22F	72	.	NM_017561	exon7	c.2072_2074del	p.691_692del	.	.	PASS	Pindel,Atlas-Indel
CPS1	1373	hgsc.bcm.edu	37	2	211421452	211421453	+	In_Frame_Ins	INS	-	-	TCT	rs3835047	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	123	35	169	.	0.285	.	-|0.556;TCT|0.444	0.444	strong	.	CPS1	485	.	NM_001122633	exon2	c.13_14insTCT	p.I5delinsIF	.	.	PASS	Pindel,Atlas-Indel
ZNF527	84503	hgsc.bcm.edu	37	19	37879852	37879853	+	Frame_Shift_Ins	INS	-	-	TGTG	rs376931538	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	35	122	0	0.380435	0	.	.	weak	.	ZNF527	78	.	NM_032453	exon5	c.901_902insTGTG	p.P301fs	.	.	PASS	Atlas-Indel
GRAMD1A	57655	hgsc.bcm.edu	37	19	35505282	35505282	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	143	43	158	.	0.301	.	.	.	none	.	GRAMD1A	39	.	NM_020895	exon10	c.1059delT	p.T353fs	.	.	PASS	Pindel,Atlas-Indel
SCN3A	6328	hgsc.bcm.edu	37	2	166032776	166032778	+	In_Frame_Del	DEL	ATT	ATT	-	rs72471101	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	ATT	ATT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	229	49	227	.	0.214	.	ATT|0.949;-|0.051	0.051	strong	.	SCN3A	544	.	NM_001081677	exon3	c.128_130del	p.43_44del	.	.	PASS	Pindel,Atlas-Indel
FBXW10	10517	hgsc.bcm.edu	37	17	18682351	18682352	+	Frame_Shift_Del	DEL	AA	AA	-	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	AA	AA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	153	43	343	0	0.281046	0	.	.	none	.	FBXW10	82	.	NM_001267585	exon14	c.2898_2899del	p.966_967del	.	.	PASS	Atlas-Indel
ZNF527	84503	hgsc.bcm.edu	37	19	37879855	37879855	+	Frame_Shift_Del	DEL	T	T	-	rs200420244	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	83	35	118	0	0.421687	0	T|0.910;-|0.090	0.090	strong	.	ZNF527	78	.	NM_032453	exon5	c.903delA	p.P301fs	.	.	PASS	Atlas-Indel
MSI2	124540	hgsc.bcm.edu	37	17	55693404	55693405	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	51	11	52	.	0.216	.	.	.	none	.	MSI2	52	.	NM_138962	exon9	c.611_612insT	p.P204fs	.	.	PASS	Pindel,Atlas-Indel
GPRIN1	114787	hgsc.bcm.edu	37	5	176026136	176026146	+	Frame_Shift_Del	DEL	CCTCCTTCCTC	CCTCCTTCCTC	-	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	CCTCCTTCCTC	CCTCCTTCCTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	140	20	170	0	0.142857	0	.	.	none	.	GPRIN1	77	.	NM_052899	exon2	c.691_701del	p.231_234del	.	.	PASS	Atlas-Indel
RPGR	6103	hgsc.bcm.edu	37	X	38145805	38145805	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	38	17	209	0	0.447368	0	.	.	none	.	RPGR	175	.	NM_001034853	exon15	c.2448delA	p.G816fs	.	.	PASS	Atlas-Indel
ADRA2B	151	hgsc.bcm.edu	37	2	96780986	96780987	+	In_Frame_Ins	INS	-	-	TCCTCCTCT	rs34667759	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	38	121	.	0.437	.	-|0.500;TCCTCCTCT|0.500	0.500	strong	.	ADRA2B	115	.	NM_000682	exon1	c.903_904insAGAGGAGGA	p.E301delinsEEEE	.	.	PASS	Pindel,Atlas-Indel
TDG	6996	hgsc.bcm.edu	37	12	104373728	104373729	+	Frame_Shift_Ins	INS	-	-	A	rs151041931	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	194	73	114	0	0.376289	0	.	.	strong	.	TDG	43	.	NM_003211	exon3	c.286_287insA	p.E96fs	.	.	PASS	Atlas-Indel
MUC4	4585	hgsc.bcm.edu	37	3	195512373	195512374	+	In_Frame_Ins	INS	-	-	GAT	rs112774151	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	104	21	64	0	0.201923	0	-|0.500;GAT|0.500	0.500	strong	.	MUC4	1505	.	NM_018406	exon2	c.6078_6079insATC	p.S2026delinsSS	.	.	PASS	Atlas-Indel
USP2	9099	hgsc.bcm.edu	37	11	119228548	119228549	+	Splice_Site	DEL	GA	GA	-	rs45619639	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	GA	GA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	81	39	113	.	0.481	.	GA|0.963;-|0.037	0.037	strong	.	USP2	71	.	.	.	.	.	.	.	PASS	Pindel,Atlas-Indel
TRIOBP	11078	hgsc.bcm.edu	37	22	38120176	38120178	+	In_Frame_Del	DEL	CCT	CCT	-	rs36219868	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	CCT	CCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	305	47	355	0	0.154098	0	.	.	strong	.	TRIOBP	262	.	NM_001039141	exon7	c.1612_1614del	p.538_538del	.	.	PASS	Atlas-Indel
KRTAP4-5	85289	hgsc.bcm.edu	37	17	39305775	39305776	+	In_Frame_Ins	INS	-	-	GGCAGCAGCTGGGGC	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	47	10	48	0	0.212766	0	.	.	none	KRTAP4-5,NS,carcinoma,+1,1	KRTAP4-5	34	1	NM_033188	exon1	c.245_246insGCCCCAGCTGCTGCC	p.Q82delinsRPSCCQ	.	.	PASS	Atlas-Indel
TSPYL6	388951	hgsc.bcm.edu	37	2	54482704	54482709	+	In_Frame_Del	DEL	GGGCCC	GGGCCC	-	rs76397255	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	GGGCCC	GGGCCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	131	51	68	.	0.389	.	GGGCCC|0.831;-|0.169	0.169	strong	.	TSPYL6	54	.	NM_001003937	exon1	c.581_586del	p.194_196del	.	.	PASS	Pindel,Atlas-Indel
GEN1	348654	hgsc.bcm.edu	37	2	17962994	17962998	+	Frame_Shift_Del	DEL	AAGTT	AAGTT	-	rs149936944	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	AAGTT	AAGTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	43	83	.	0.426	.	AAGTT|0.926;-|0.074	0.074	strong	.	GEN1	79	.	NM_182625	exon14	c.2514_2518del	p.838_840del	.	.	PASS	Pindel,Atlas-Indel
WDR60	55112	hgsc.bcm.edu	37	7	158664075	158664077	+	In_Frame_Del	DEL	GAA	GAA	-	rs145233696	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	33	13	44	.	0.394	.	GAA|0.880;-|0.120	0.120	strong	.	WDR60	94	.	NM_018051	exon3	c.311_313del	p.104_105del	.	.	PASS	Pindel,Atlas-Indel
PRSS16	10279	hgsc.bcm.edu	37	6	27223065	27223079	+	In_Frame_Del	DEL	AAGGAGAGCCAGATT	AAGGAGAGCCAGATT	-	rs141138864	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	AAGGAGAGCCAGATT	AAGGAGAGCCAGATT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	55	44	100	.	0.800	.	AAGGAGAGCCAGATT|0.883;-|0.117	0.117	strong	.	PRSS16	66	.	NM_005865	exon12	c.1515_1529del	p.505_510del	.	.	PASS	Pindel,Atlas-Indel
AGAP1	116987	hgsc.bcm.edu	37	2	236761414	236761415	+	Frame_Shift_Ins	INS	-	-	CAGG	rs142341634	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	269	66	319	.	0.245	.	-|0.857;CAGG|0.143	0.143	strong	.	AGAP1	95	.	NM_001244888	exon10	c.1135_1136insCAGG	p.P379fs	.	.	PASS	Pindel,Atlas-Indel
ZFYVE19	84936	hgsc.bcm.edu	37	15	41099899	41099900	+	Frame_Shift_Ins	INS	-	-	GGGGC	rs142730574	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	95	23	138	0	0.242105	0	-|0.663;GGGGC|0.337	0.337	strong	.	ZFYVE19	31	.	NM_001077268	exon1	c.112_113insGGGGC	p.W38fs	.	.	PASS	Atlas-Indel
HLA-L	3139	hgsc.bcm.edu	37	6	30229034	30229035	+	RNA	INS	-	-	T	rs111358359	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	130	24	129	.	0.185	.	-|0.500;T|0.500	0.500	strong	.	.	.	.	.	.	.	.	.	.	PASS	Pindel,Atlas-Indel
WWC1	23286	hgsc.bcm.edu	37	5	167881030	167881032	+	In_Frame_Del	DEL	GGA	GGA	-	rs111457550	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	GGA	GGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	194	41	139	.	0.211	.	GGA|0.612;-|0.388	0.388	strong	WWC1,colon,carcinoma,0,1	WWC1	98	1	NM_015238	exon18	c.2582_2584del	p.861_862del	.	.	PASS	Pindel,Atlas-Indel
PRR25	388199	hgsc.bcm.edu	37	16	855518	855523	+	In_Frame_Del	DEL	GCAGCT	GCAGCT	-	rs137876084	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	GCAGCT	GCAGCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	25	11	45	.	0.440	.	GCAGCT|0.922;-|0.078	0.078	strong	.	PRR25	27	.	NM_001013638	exon1	c.75_80del	p.25_27del	.	.	PASS	Pindel,Atlas-Indel
CTU2	348180	hgsc.bcm.edu	37	16	88780635	88780640	+	Frame_Shift_Del	DEL	GGTGTG	GGTGTG	-	rs11278302	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	GGTGTG	GGTGTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	105	46	102	.	0.438	.	GGTGTG|0.183;-|0.817	0.817	strong	.	CTU2	66	.	NM_001012759	exon10	c.1096_1097del	p.366_366del	.	.	PASS	Pindel,Atlas-Indel
CTAGE5	4253	hgsc.bcm.edu	37	14	39784005	39784006	+	Splice_Site	DEL	TA	TA	-	rs75318507	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	TA	TA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	125	77	135	0	0.616	0	.	.	strong	.	CTAGE5	75	.	.	.	.	.	.	.	PASS	Atlas-Indel
TRIM13	10206	hgsc.bcm.edu	37	13	50590292	50590293	+	RNA	INS	-	-	CTC	rs10675754	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	116	34	136	.	0.293	.	-|0.500;CTC|0.500	0.500	strong	.	TRIM13	30	.	.	.	.	.	.	.	PASS	Pindel,Atlas-Indel
APLF	200558	hgsc.bcm.edu	37	2	68805143	68805143	+	Frame_Shift_Del	DEL	A	A	-	rs149897324	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	50	20	79	.	0.400	.	A|0.991;-|0.009	0.009	strong	.	APLF	69	.	NM_173545	exon10	c.1524delG	p.M508fs	.	.	PASS	Pindel,Atlas-Indel
FAM194B	220081	hgsc.bcm.edu	37	13	46170720	46170737	+	In_Frame_Del	DEL	CCAGATACTCTTCCTCCT	CCAGATACTCTTCCTCCT	-	rs142875900	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	CCAGATACTCTTCCTCCT	CCAGATACTCTTCCTCCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	79	14	88	.	0.177	.	.	.	strong	.	FAM194B	42	.	NM_182542	exon3	c.405_422del	p.135_141del	.	.	PASS	Pindel,Atlas-Indel
CELA1	1990	hgsc.bcm.edu	37	12	51740415	51740416	+	Frame_Shift_Del	DEL	AC	AC	-	rs370927847		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	15	152	0	0.163043	0	.	.	weak	.	CELA1	39	.	NM_001971	exon1	c.8_9del	p.3_3del	.	.	PASS	Atlas-Indel
TTN	7273	hgsc.bcm.edu	37	2	179514942	179514959	+	In_Frame_Del	DEL	TTTCCTCTTCAGGAGCAA	TTTCCTCTTCAGGAGCAA	-	rs139512154	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	TTTCCTCTTCAGGAGCAA	TTTCCTCTTCAGGAGCAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	159	34	230	.	0.214	.	TTTCCTCTTCAGGAGCAA|0.972;-|0.028	0.028	strong	.	TTN	18412	.	NM_001267550	exon210	c.39750_39767del	p.13250_13256del	.	.	PASS	Pindel,Atlas-Indel
OR8J1	219477	hgsc.bcm.edu	37	11	56128673	56128674	+	Frame_Shift_Ins	INS	-	-	T	rs34649252	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	50	23	68	.	0.460	.	-|0.931;T|0.069	0.069	strong	.	OR8J1	87	.	NM_001005205	exon1	c.951_952insT	p.X317delinsX	.	.	PASS	Pindel,Atlas-Indel
MYO7A	4647	hgsc.bcm.edu	37	11	76895771	76895792	+	Frame_Shift_Del	DEL	GGAGGCGGGGACACCAGGGCCT	GGAGGCGGGGACACCAGGGCCT	-	rs143953991	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	GGAGGCGGGGACACCAGGGCCT	GGAGGCGGGGACACCAGGGCCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	98	75	132	.	0.765	.	GGAGGCGGGGACACCAGGGCCT|0.573;-|0.427	0.427	strong	.	MYO7A	164	.	NM_001127179	exon27	c.3513_3534del	p.1171_1178del	.	.	PASS	Pindel,Atlas-Indel
CCDC71	64925	hgsc.bcm.edu	37	3	49200611	49200616	+	In_Frame_Del	DEL	GCCTTG	GCCTTG	-	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	GCCTTG	GCCTTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	21	69	.	0.244	.	.	.	none	.	CCDC71	33	.	NM_022903	exon2	c.1027_1032del	p.343_344del	.	.	PASS	Pindel,Atlas-Indel
TBCK	93627	hgsc.bcm.edu	37	4	107171638	107171642	+	Splice_Site	DEL	AAATA	AAATA	-	rs139991421	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	AAATA	AAATA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	49	22	66	.	0.449	.	AAATA|0.864;-|0.136	0.136	strong	.	TBCK	89	.	.	.	.	.	.	.	PASS	Pindel,Atlas-Indel
HOMEZ	57594	hgsc.bcm.edu	37	14	23744827	23744829	+	In_Frame_Del	DEL	TCC	TCC	-	rs67447855	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	TCC	TCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	81	13	102	.	0.160	.	TCC|0.500;-|0.500	0.500	weak	.	HOMEZ	80	.	NM_020834	exon2	c.1609_1611del	p.537_537del	.	.	PASS	Pindel,Atlas-Indel
HAVCR1	26762	hgsc.bcm.edu	37	5	156479558	156479572	+	In_Frame_Del	DEL	TTGGAACAGTCGTCA	TTGGAACAGTCGTCA	-	rs141023871	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	TTGGAACAGTCGTCA	TTGGAACAGTCGTCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	228	82	428	.	0.360	.	.	.	strong	.	HAVCR1	84	.	NM_001099414	exon4	c.474_488del	p.158_163del	.	.	PASS	Pindel,Atlas-Indel
ATAD5	79915	hgsc.bcm.edu	37	17	29161956	29161961	+	In_Frame_Del	DEL	CAATGT	CAATGT	-	rs72427574	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	CAATGT	CAATGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	30	135	.	0.309	.	CAATGT|0.874;-|0.126	0.126	strong	ATAD5,NS,carcinoma,0,1	ATAD5	150	1	NM_024857	exon2	c.856_861del	p.286_287del	.	.	PASS	Pindel,Atlas-Indel
ANKRD20A4	728747	hgsc.bcm.edu	37	9	69393857	69393860	+	Frame_Shift_Del	DEL	TACT	TACT	-	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	TACT	TACT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	363	22	321	0	0.0606061	0	.	.	none	.	ANKRD20A4	38	.	NM_001098805	exon6	c.772_775del	p.258_259del	.	.	PASS	Atlas-Indel
RFPL1	5988	hgsc.bcm.edu	37	22	29837567	29837569	+	In_Frame_Del	DEL	TCC	TCC	-	rs71324764	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	TCC	TCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	190	54	286	.	0.284	.	TCC|0.697;-|0.303	0.303	strong	.	RFPL1	43	.	NM_021026	exon2	c.409_411del	p.137_137del	.	.	PASS	Pindel,Atlas-Indel
PI4KAP2	375133	hgsc.bcm.edu	37	22	21841122	21841126	+	RNA	DEL	TCTTA	TCTTA	-	rs200598591	by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	TCTTA	TCTTA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	109	14	130	0	0.12844	0	TCTTA|0.738;-|0.262	0.262	strong	.	PI4KAP2	11	.	.	.	.	.	.	.	PASS	Atlas-Indel
DNAH5	1767	hgsc.bcm.edu	37	5	13883045	13883045	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	164	26	142	0	0.158537	0	.	.	none	.	DNAH5	868	.	NM_001369	exon20	c.3143delT	p.V1048fs	.	.	PASS	Atlas-Indel
BAIAP2L2	80115	hgsc.bcm.edu	37	22	38483174	38483175	+	In_Frame_Ins	INS	-	-	CATGGAGGT	rs200930717	by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	39	13	49	.	0.333	.	-|0.896;CATGGAGGT|0.104	0.104	strong	.	BAIAP2L2	39	.	NM_025045	exon11	c.1216_1217insACCTCCATG	p.S406delinsTSMS	.	.	PASS	Pindel,Atlas-Indel
ANKRD30B	374860	hgsc.bcm.edu	37	18	14851887	14851888	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	192	13	230	0	0.0677083	0	.	.	none	.	ANKRD30B	237	.	NM_001145029	exon36	c.3587_3588insA	p.R1196fs	.	.	PASS	Atlas-Indel
AGAP6	414189	hgsc.bcm.edu	37	10	51768675	51768676	+	Frame_Shift_Del	DEL	AA	AA	-	rs113234838		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	AA	AA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	55	36	71	.	0.655	.	AA|0.500;-|0.500	0.500	weak	.	AGAP6	53	.	NM_001077665	exon8	c.789_790del	p.263_264del	.	.	PASS	Pindel,Atlas-Indel
FAM90A1	55138	hgsc.bcm.edu	37	12	8377368	8377368	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	24	13	11	.	0.542	.	.	.	none	.	FAM90A1	68	.	NM_018088	exon4	c.62delA	p.Q21fs	.	.	PASS	Pindel,Atlas-Indel
CCR8	1237	hgsc.bcm.edu	37	3	39374514	39374516	+	In_Frame_Del	DEL	ACA	ACA	-	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	ACA	ACA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	296	57	372	.	0.193	.	.	.	none	.	CCR8	34	.	NM_005201	exon2	c.691_693del	p.231_231del	.	.	PASS	Pindel,Atlas-Indel
CARD8	22900	hgsc.bcm.edu	37	19	48735017	48735018	+	Frame_Shift_Ins	INS	-	-	TT	rs140826611	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	84	24	84	.	0.286	.	-|0.962;TT|0.038	0.038	strong	.	CARD8	53	.	NM_001184900	exon5	c.442_443insAA	p.V148fs	.	.	PASS	Pindel,Atlas-Indel
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057613	46057627	+	In_Frame_Del	DEL	CTGCTGTGTGCCTGT	CTGCTGTGTGCCTGT	-	rs66931310	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	CTGCTGTGTGCCTGT	CTGCTGTGTGCCTGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	103	50	155	.	0.485	.	CTGCTGTGTGCCTGT|0.469;-|0.531	0.531	strong	.	KRTAP10-10	37	.	NM_181688	exon1	c.278_292del	p.93_98del	.	.	PASS	Pindel,Atlas-Indel
AXDND1	126859	hgsc.bcm.edu	37	1	179504026	179504028	+	In_Frame_Del	DEL	AAG	AAG	-	rs141228272	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	162	40	212	.	0.247	.	AAG|0.640;-|0.360	0.360	strong	.	AXDND1	142	.	NM_144696	exon25	c.2959_2961del	p.987_987del	.	.	PASS	Pindel,Atlas-Indel
PDE4DIP	9659	hgsc.bcm.edu	37	1	144873963	144873963	+	Frame_Shift_Del	DEL	T	T	-	rs11341221	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	305	49	272	.	0.161	.	-|0.272;A|0.364	0.272	strong	.	PDE4DIP	817	.	NM_014644	exon31	c.4995delG	p.Q1665fs	.	.	PASS	Pindel,Atlas-Indel
SYT15	83849	hgsc.bcm.edu	37	10	46965887	46965888	+	Splice_Site	INS	-	-	G	rs112965082	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	49	10	45	.	0.204	.	-|0.500;G|0.500	0.500	weak	.	SYT15	165	.	NM_181519	exon6	c.652-2->C	.	.	.	PASS	Pindel,Atlas-Indel
HSP90B1	7184	hgsc.bcm.edu	37	12	104341188	104341190	+	In_Frame_Del	DEL	GAA	GAA	-	rs5800607	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	142	41	142	.	0.289	.	GAA|0.865;-|0.135	0.135	strong	.	HSP90B1	72	.	NM_003299	exon17	c.2361_2363del	p.787_788del	.	.	PASS	Pindel,Atlas-Indel
GTF3C1	2975	hgsc.bcm.edu	37	16	27499956	27499956	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	46	13	44	.	0.283	.	.	.	none	.	GTF3C1	210	.	NM_001520	exon22	c.3431delA	p.E1144fs	.	.	PASS	Pindel,Atlas-Indel
CCDC9	26093	hgsc.bcm.edu	37	19	47774666	47774668	+	In_Frame_Del	DEL	GAG	GAG	-	rs138370983	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	GAG	GAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	51	15	47	.	0.294	.	GAG|0.916;-|0.084	0.084	strong	.	CCDC9	37	.	NM_015603	exon12	c.1326_1328del	p.442_443del	.	.	PASS	Pindel,Atlas-Indel
MUC6	4588	hgsc.bcm.edu	37	11	1031058	1031059	+	Splice_Site	INS	-	-	G	rs71464128	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	160	65	135	.	0.406	.	-|0.878;G|0.122	0.122	strong	.	MUC6	408	.	NM_005961	exon7	c.575-2->C	.	.	.	PASS	Pindel,Atlas-Indel
ALPK2	115701	hgsc.bcm.edu	37	18	56203253	56203255	+	In_Frame_Del	DEL	AAG	AAG	-	rs141586980	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	79	30	148	.	0.380	.	AAG|0.927;-|0.073	0.073	strong	.	ALPK2	487	.	NM_052947	exon5	c.4165_4167del	p.1389_1389del	.	.	PASS	Pindel,Atlas-Indel
ETFB	2109	hgsc.bcm.edu	37	19	51857614	51857615	+	Frame_Shift_Ins	INS	-	-	G	rs141529162	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	36	14	43	0	0.388889	0	-|0.980;G|0.020	0.020	strong	.	ETFB	46	.	NM_001014763	exon1	c.279_280insC	p.P93fs	.	.	PASS	Atlas-Indel
CELA1	1990	hgsc.bcm.edu	37	12	51723598	51723599	+	Frame_Shift_Ins	INS	-	-	G	rs17860363	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	61	18	48	.	0.295	.	-|0.851;G|0.149	0.149	strong	.	CELA1	39	.	NM_001971	exon7	c.629_630insC	p.L210fs	.	.	PASS	Pindel,Atlas-Indel
CFTR	1080	hgsc.bcm.edu	37	7	117199645	117199647	+	In_Frame_Del	DEL	TCT	TCT	-	rs199826652	by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	TCT	TCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	49	17	81	.	0.347	.	TCT|0.994;-|0.006	0.006	strong	.	CFTR	171	.	NM_000492	exon11	c.1519_1521del	p.507_507del	.	.	PASS	Pindel,Atlas-Indel
CDSN	1041	hgsc.bcm.edu	37	6	31084943	31084945	+	In_Frame_Del	DEL	CTT	CTT	-	rs34182778	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	50	20	46	.	0.400	.	CTT|0.500;-|0.500	0.500	strong	.	CDSN	48	.	NM_001264	exon2	c.448_450del	p.150_150del	.	.	PASS	Pindel,Atlas-Indel
RNH1	6050	hgsc.bcm.edu	37	11	502130	502144	+	In_Frame_Del	DEL	CTGGATGTCCAGGCT	CTGGATGTCCAGGCT	-	rs71462090	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	CTGGATGTCCAGGCT	CTGGATGTCCAGGCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	45	21	47	.	0.467	.	CTGGATGTCCAGGCT|0.938;-|0.062	0.062	strong	.	RNH1	24	.	NM_203386	exon3	c.20_34del	p.7_12del	.	.	PASS	Pindel,Atlas-Indel
GFM2	84340	hgsc.bcm.edu	37	5	74021847	74021852	+	In_Frame_Del	DEL	ACTCAA	ACTCAA	-	rs5868753	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	ACTCAA	ACTCAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	105	42	113	.	0.400	.	ACTCAA|0.643;-|0.357	0.357	strong	.	GFM2	38	.	NM_032380	exon18	c.1827_1832del	p.609_611del	.	.	PASS	Pindel,Atlas-Indel
ZNF568	374900	hgsc.bcm.edu	37	19	37440852	37440852	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	45	11	30	0	0.244444	0	.	.	none	.	ZNF568	106	.	NM_198539	exon7	c.796delA	p.I266fs	.	.	PASS	Atlas-Indel
OR13A1	79290	hgsc.bcm.edu	37	10	45799065	45799066	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	52	19	81	.	0.365	.	.	.	none	.	OR13A1	49	.	NM_001004297	exon4	c.806_807insT	p.Y269fs	.	.	PASS	Pindel,Atlas-Indel
NFKBIE	4794	hgsc.bcm.edu	37	6	44232739	44232742	+	Frame_Shift_Del	DEL	GTAA	GTAA	-	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	GTAA	GTAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	35	11	44	0	0.314286	0	.	.	none	.	NFKBIE	31	.	NM_004556	exon1	c.760_763del	p.254_255del	.	.	PASS	Atlas-Indel
CASP8AP2	9994	hgsc.bcm.edu	37	6	90577712	90577728	+	Frame_Shift_Del	DEL	CTTTGCCCAGACATGGA	CTTTGCCCAGACATGGA	-	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	CTTTGCCCAGACATGGA	CTTTGCCCAGACATGGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	49	18	74	0	0.367347	0	.	.	none	.	CASP8AP2	108	.	NM_012115	exon8	c.4702_4718del	p.1568_1573del	.	.	PASS	Atlas-Indel
TRMT2A	27037	hgsc.bcm.edu	37	22	20100166	20100167	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	367	87	387	.	0.237	.	.	.	none	.	TRMT2A	34	.	NM_022727	exon12	c.1798_1799insG	p.P600fs	.	.	PASS	Pindel,Atlas-Indel
FASTKD1	79675	hgsc.bcm.edu	37	2	170387132	170387133	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	206	69	213	.	0.335	.	.	.	none	.	FASTKD1	86	.	NM_024622	exon14	c.2407_2408insA	p.R803fs	.	.	PASS	Pindel,Atlas-Indel
KRTAP19-6	337973	hgsc.bcm.edu	37	21	31913982	31913982	+	Frame_Shift_Del	DEL	G	G	-	rs5843453	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	17	66	.	0.293	.	-|0.758;G|0.242	0.758	strong	.	KRTAP19-6	16	.	NM_181612	exon1	c.172delT	p.Y58fs	.	.	PASS	Pindel,Atlas-Indel
COL12A1	1303	hgsc.bcm.edu	37	6	75887427	75887436	+	Frame_Shift_Del	DEL	AATATTCAGG	AATATTCAGG	-	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	AATATTCAGG	AATATTCAGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	155	16	155	0	0.103226	0	.	.	none	.	COL12A1	385	.	NM_004370	exon12	c.2381_2390del	p.794_797del	.	.	PASS	Atlas-Indel
GPRIN1	114787	hgsc.bcm.edu	37	5	176026122	176026134	+	Frame_Shift_Del	DEL	CAAAGACCCAGGA	CAAAGACCCAGGA	-	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	CAAAGACCCAGGA	CAAAGACCCAGGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	125	20	168	0	0.16	0	.	.	none	.	GPRIN1	77	.	NM_052899	exon2	c.703_715del	p.235_239del	.	.	PASS	Atlas-Indel
NR1H2	7376	hgsc.bcm.edu	37	19	50881820	50881821	+	In_Frame_Ins	INS	-	-	AAC	rs55652650	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	81	46	96	.	0.568	.	-|0.132;AAC|0.868	0.868	strong	.	NR1H2	47	.	NM_007121	exon6	c.514_515insAAC	p.K172delinsKQ	.	.	PASS	Pindel,Atlas-Indel
TAF1	6872	hgsc.bcm.edu	37	X	70612454	70612455	+	In_Frame_Ins	INS	-	-	ATT	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	118	27	127	.	0.229	.	.	.	none	.	TAF1	439	.	NM_004606	exon19	c.2877_2878insATT	p.F959delinsFI	.	.	PASS	Pindel,Atlas-Indel
KANK3	256949	hgsc.bcm.edu	37	19	8389893	8389895	+	In_Frame_Del	DEL	TCC	TCC	-	rs111905975	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	TCC	TCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	84	26	79	.	0.310	.	TCC|0.852;-|0.148	0.148	strong	.	KANK3	35	.	NM_198471	exon8	c.2023_2025del	p.675_675del	.	.	PASS	Pindel,Atlas-Indel
OR6Q1	219952	hgsc.bcm.edu	37	11	57799109	57799109	+	Frame_Shift_Del	DEL	C	C	-	rs34846253	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	167	73	204	.	0.437	.	C|0.867;-|0.133	0.133	strong	.	OR6Q1	58	.	NM_001005186	exon1	c.684delA	p.T228fs	.	.	PASS	Pindel,Atlas-Indel
CD200R1L	344807	hgsc.bcm.edu	37	3	112545911	112545911	+	Frame_Shift_Del	DEL	T	T	-	rs58161637	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	110	37	134	.	0.336	.	T|0.815;-|0.185	0.185	strong	CD200R1L,NS,carcinoma,-1,1	CD200R1L	47	1	NM_001008784	exon4	c.609delC	p.H203fs	.	.	PASS	Pindel,Atlas-Indel
GNRH2	2797	hgsc.bcm.edu	37	20	3026345	3026346	+	Frame_Shift_Ins	INS	-	-	GCCCC	rs16996832	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	61	11	100	.	0.180	.	-|0.814;GCCCC|0.186	0.186	strong	.	GNRH2	15	.	NM_001501	exon4	c.326_327insGCCCC	p.E109fs	.	.	PASS	Pindel,Atlas-Indel
DUSP18	150290	hgsc.bcm.edu	37	22	31059499	31059500	+	Frame_Shift_Del	DEL	CA	CA	-	rs71788033		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	CA	CA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	119	32	128	.	0.269	.	.	.	weak	.	DUSP18	10	.	NM_152511	exon2	c.492_493del	p.164_165del	.	.	PASS	Pindel,Atlas-Indel
KCNN3	3782	hgsc.bcm.edu	37	1	154842199	154842200	+	In_Frame_Ins	INS	-	-	GCTGCTGCTGCTGCT	rs3831942	alternate_allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	11	63	0	0.189655	0	.	.	alt	KCNN3,colon,carcinoma,0,1	KCNN3	141	1	NM_001204087	exon1	c.242_243insAGCAGCAGCAGCAGC	p.P81delinsQQQQQP	.	.	PASS	Atlas-Indel
FAM157A	728262	hgsc.bcm.edu	37	3	197880131	197880133	+	In_Frame_Del	DEL	GCA	GCA	-	rs3061423		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	GCA	GCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	362	22	157	0	0.0607735	0	.	.	weak	.	FAM157A	4	.	NM_001145248	exon2	c.209_211del	p.70_71del	.	.	PASS	Atlas-Indel
SCN9A	6335	hgsc.bcm.edu	37	2	167144980	167144980	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	79	12	78	0	0.151899	0	.	.	none	.	SCN9A	296	.	NM_002977	exon10	c.1282delG	p.D428fs	.	.	PASS	Atlas-Indel
IST1	9798	hgsc.bcm.edu	37	16	71956512	71956517	+	In_Frame_Del	DEL	ATGCCC	ATGCCC	-	rs148848854	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	ATGCCC	ATGCCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	112	17	90	.	0.152	.	.	.	strong	.	.	.	.	NM_001270976	exon8	c.726_731del	p.242_244del	.	.	PASS	Pindel,Atlas-Indel
PITRM1	10531	hgsc.bcm.edu	37	10	3193558	3193570	+	Splice_Site	DEL	AAAAAAGAAACAA	AAAAAAGAAACAA	-	rs60985673	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	AAAAAAGAAACAA	AAAAAAGAAACAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	38	13	70	0	0.342105	0	AAAAAAGAAACAA|0.500;-|0.500	0.500	strong	.	PITRM1	109	.	.	.	.	.	.	.	PASS	Atlas-Indel
CCDC87	55231	hgsc.bcm.edu	37	11	66358631	66358633	+	In_Frame_Del	DEL	TCT	TCT	-	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	TCT	TCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	180	78	229	.	0.433	.	.	.	none	.	CCDC87	83	.	NM_018219	exon1	c.1855_1857del	p.619_619del	.	.	PASS	Pindel,Atlas-Indel
NLGN4Y	22829	hgsc.bcm.edu	37	Y	16952663	16952663	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	79	41	3	.	0.519	.	.	.	none	.	NLGN4Y	44	.	NM_014893	exon6	c.1971delG	p.G657fs	.	.	PASS	Pindel,Atlas-Indel
TRIOBP	11078	hgsc.bcm.edu	37	22	38119755	38119757	+	In_Frame_Del	DEL	CAA	CAA	-	rs67890459	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	CAA	CAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	28	103	.	0.406	.	-|0.368;CAA|0.632	0.368	strong	.	TRIOBP	262	.	NM_001039141	exon7	c.1191_1193del	p.397_398del	.	.	PASS	Pindel,Atlas-Indel
HTR3E	285242	hgsc.bcm.edu	37	3	183818222	183818222	+	Frame_Shift_Del	DEL	G	G	-	rs5855015	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	68	18	107	.	0.265	.	G|0.951;-|0.049	0.049	strong	.	HTR3E	65	.	NM_182589	exon1	c.61delA	p.R21fs	.	.	PASS	Pindel,Atlas-Indel
KIAA1751	85452	hgsc.bcm.edu	37	1	1900106	1900107	+	In_Frame_Ins	INS	-	-	CTC	rs145742571	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	114	30	183	.	0.263	.	.	.	strong	.	KIAA1751	92	.	NM_001080484	exon11	c.1213_1214insGAG	p.K405delinsEK	.	.	PASS	Pindel,Atlas-Indel
M6PR	4074	hgsc.bcm.edu	37	12	9098995	9098996	+	In_Frame_Ins	INS	-	-	AAC	rs149871778	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	52	124	.	0.598	.	-|0.877;AAC|0.123	0.123	strong	M6PR,NS,carcinoma,0,1	M6PR	33	1	NM_001207024	exon2	c.6_7insGTT	p.F2delinsLF	.	.	PASS	Pindel,Atlas-Indel
AKAP3	10566	hgsc.bcm.edu	37	12	4735965	4735966	+	Frame_Shift_Ins	INS	-	-	C	rs200178782	by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	11	108	0	0.134146	0	-|0.868;C|0.132	0.132	strong	.	AKAP3	212	.	NM_006422	exon4	c.2103_2104insG	p.G701fs	.	.	PASS	Atlas-Indel
RYR3	6263	hgsc.bcm.edu	37	15	34137080	34137082	+	In_Frame_Del	DEL	AGA	AGA	-	rs3217346	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	114	48	108	.	0.421	.	AGA|0.918;-|0.082	0.082	strong	.	RYR3	760	.	NM_001036	exon93	c.13313_13315del	p.4438_4439del	.	.	PASS	Pindel,Atlas-Indel
ACOT4	122970	hgsc.bcm.edu	37	14	74060514	74060517	+	Frame_Shift_Del	DEL	CTTA	CTTA	-	rs375801976		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	CTTA	CTTA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	74	12	97	0	0.162162	0	.	.	weak	.	ACOT4	25	.	NM_152331	exon2	c.565_568del	p.189_190del	.	.	PASS	Atlas-Indel
HLA-C	3107	hgsc.bcm.edu	37	6	31238973	31238986	+	Frame_Shift_Del	DEL	TCTGAGCCGCGGTG	TCTGAGCCGCGGTG	-	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	TCTGAGCCGCGGTG	TCTGAGCCGCGGTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	151	29	123	0	0.192053	0	.	.	none	.	HLA-C	92	.	NM_002117	exon3	c.484_497del	p.162_166del	.	.	PASS	Atlas-Indel
ALMS1	7840	hgsc.bcm.edu	37	2	73613032	73613037	+	In_Frame_Del	DEL	GGAGGA	GGAGGA	-	rs66480235	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	GGAGGA	GGAGGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	21	10	11	0	0.47619	0	-|0.500;GGAGGA|0.500	0.500	weak	.	ALMS1	384	.	NM_015120	exon1	c.35_40del	p.12_14del	.	.	PASS	Atlas-Indel
SRSF2	6427	hgsc.bcm.edu	37	17	74732390	74732395	+	In_Frame_Del	DEL	GGACTT	GGACTT	-	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	GGACTT	GGACTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	67	14	72	.	0.209	.	.	.	none	.	SRSF2	544	.	NM_001195427	exon2	c.515_520del	p.172_174del	.	.	PASS	Pindel,Atlas-Indel
PTCHD3	374308	hgsc.bcm.edu	37	10	27702256	27702257	+	Frame_Shift_Ins	INS	-	-	C	rs112067123	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	46	85	.	0.590	.	-|0.732;C|0.268	0.268	strong	.	PTCHD3	140	.	NM_001034842	exon1	c.924_925insG	p.G308fs	.	.	PASS	Pindel,Atlas-Indel
HK3	3101	hgsc.bcm.edu	37	5	176314086	176314086	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	121	41	86	.	0.339	.	.	.	none	.	HK3	210	.	NM_002115	exon13	c.1775delA	p.Q592fs	.	.	PASS	Pindel,Atlas-Indel
ANKRD30B	374860	hgsc.bcm.edu	37	18	14837637	14837637	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	736	142	694	0	0.192935	0	.	.	none	.	ANKRD30B	237	.	NM_001145029	exon30	c.2592delA	p.L864fs	.	.	PASS	Atlas-Indel
TRIM52	84851	hgsc.bcm.edu	37	5	180687429	180687431	+	In_Frame_Del	DEL	TCT	TCT	-	rs33972170	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	TCT	TCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	157	50	136	.	0.318	.	TCT|0.580;-|0.420	0.420	strong	.	TRIM52	20	.	NM_032765	exon1	c.385_387del	p.129_129del	.	.	PASS	Pindel,Atlas-Indel
CRIPAK	285464	hgsc.bcm.edu	37	4	1388375	1388376	+	Frame_Shift_Ins	INS	-	-	CA	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	95	19	124	0	0.2	0	.	.	none	.	CRIPAK	185	.	NM_175918	exon1	c.76_77insCA	p.S26fs	.	.	PASS	Atlas-Indel
VSIG10	54621	hgsc.bcm.edu	37	12	118506328	118506333	+	In_Frame_Del	DEL	TCCTCC	TCCTCC	-	rs72125532	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	TCCTCC	TCCTCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	207	56	269	0	0.270531	0	.	.	strong	.	VSIG10	41	.	NM_019086	exon8	c.1417_1422del	p.473_474del	.	.	PASS	Atlas-Indel
TTBK1	84630	hgsc.bcm.edu	37	6	43250726	43250728	+	In_Frame_Del	DEL	GAA	GAA	-	rs113160341	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	55	18	56	0	0.327273	0	GAA|0.806;-|0.194	0.194	strong	TTBK1,NS,carcinoma,0,1	TTBK1	124	1	NM_032538	exon14	c.2247_2249del	p.749_750del	.	.	PASS	Atlas-Indel
NINL	22981	hgsc.bcm.edu	37	20	25457050	25457055	+	In_Frame_Del	DEL	CTCCCA	CTCCCA	-	rs68078266	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	CTCCCA	CTCCCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	59	14	95	.	0.237	.	CTCCCA|0.450;-|0.550	0.550	strong	.	NINL	148	.	NM_025176	exon17	c.2873_2878del	p.958_960del	.	.	PASS	Pindel,Atlas-Indel
GLT6D1	360203	hgsc.bcm.edu	37	9	138516347	138516347	+	Frame_Shift_Del	DEL	A	A	-	rs34217442	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	77	24	104	.	0.312	.	A|0.829;-|0.171	0.171	strong	.	GLT6D1	56	.	NM_182974	exon5	c.428delG	p.W143fs	.	.	PASS	Pindel,Atlas-Indel
CASP8AP2	9994	hgsc.bcm.edu	37	6	90577707	90577707	+	Frame_Shift_Del	DEL	G	G	-	rs202116886	alternate_allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	66	33	79	0	0.5	0	.	.	alt	.	CASP8AP2	108	.	NM_012115	exon8	c.4697delT	p.L1566X	.	.	PASS	Atlas-Indel
ZNF880	400713	hgsc.bcm.edu	37	19	52887246	52887247	+	In_Frame_Ins	INS	-	-	CAA	rs34678014	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	102	73	168	.	0.716	.	-|0.657;CAA|0.343	0.343	strong	.	ZNF880	45	.	NM_001145434	exon4	c.413_414insCAA	p.I138delinsIN	.	.	PASS	Pindel,Atlas-Indel
THAP2	83591	hgsc.bcm.edu	37	12	72070506	72070508	+	In_Frame_Del	DEL	GTT	GTT	-	rs140783391	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	GTT	GTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	95	30	114	.	0.316	.	GTT|0.969;-|0.031	0.031	strong	.	THAP2	29	.	NM_031435	exon3	c.304_306del	p.102_102del	.	.	PASS	Pindel,Atlas-Indel
RP1L1	94137	hgsc.bcm.edu	37	8	10467579	10467581	+	In_Frame_Del	DEL	TTC	TTC	-	rs143686100	by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	TTC	TTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	120	21	134	0	0.175	0	.	.	strong	.	RP1L1	453	.	NM_178857	exon4	c.4028_4030del	p.1343_1344del	.	.	PASS	Atlas-Indel
C18orf25	147339	hgsc.bcm.edu	37	18	43833701	43833702	+	In_Frame_Ins	INS	-	-	CTG	rs34068795	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	126	35	134	.	0.278	.	-|0.306;CTG|0.694	0.694	strong	C18orf25,NS,carcinoma,0,1	C18orf25	27	1	NM_145055	exon4	c.937_938insCTG	p.S313delinsSA	.	.	PASS	Pindel,Atlas-Indel
KRTAP4-8	728224	hgsc.bcm.edu	37	17	39254335	39254336	+	Frame_Shift_Ins	INS	-	-	T	rs201764113	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	169	52	253	0	0.307692	0	-|0.420;T|0.580	0.580	strong	.	KRTAP4-8	57	.	NM_031960	exon1	c.2_3insA	p.M1fs	.	.	PASS	Atlas-Indel
HIST1H4J	8363	hgsc.bcm.edu	37	6	27792127	27792128	+	Frame_Shift_Ins	INS	-	-	CACGC	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	199	13	242	0	0.0653266	0	.	.	none	HIST1H4J,NS,carcinoma,+2,1	HIST1H4J	11	1	NM_021968	exon1	c.225_226insCACGC	p.E75fs	.	.	PASS	Atlas-Indel
VWA3A	146177	hgsc.bcm.edu	37	16	22144376	22144378	+	In_Frame_Del	DEL	CCG	CCG	-	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	CCG	CCG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	21	90	.	0.296	.	.	.	none	.	VWA3A	115	.	NM_173615	exon20	c.2027_2029del	p.676_677del	.	.	PASS	Pindel
DSPP	1834	hgsc.bcm.edu	37	4	88535832	88535833	+	In_Frame_Ins	INS	-	-	TAGCAGTGACAGCAGCAG	rs200486992	alternate_allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	109	21	117	.	0.193	.	.	.	alt	.	DSPP	174	.	NM_014208	exon5	c.2018_2019insTAGCAGTGACAGCAGCAG	p.D673delinsDSSDSSS	.	.	PASS	Pindel
ACOT4	122970	hgsc.bcm.edu	37	14	74060512	74060517	+	In_Frame_Del	DEL	AGCTTA	AGCTTA	-	rs373880503	bycluster;alternate_allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	AGCTTA	AGCTTA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	16	97	.	0.188	.	.	.	alt	.	ACOT4	25	.	NM_152331	exon2	c.563_568del	p.188_190del	.	.	PASS	Pindel
RPGR	6103	hgsc.bcm.edu	37	X	38145791	38145805	+	In_Frame_Del	DEL	CCTCTACTTCCCCTC	CCTCTACTTCCCCTC	-	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	CCTCTACTTCCCCTC	CCTCTACTTCCCCTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	33	18	197	.	0.545	.	.	.	none	.	RPGR	175	.	NM_001034853	exon15	c.2448_2462del	p.816_821del	.	.	PASS	Pindel
CELA1	1990	hgsc.bcm.edu	37	12	51740388	51740416	+	In_Frame_Del	DEL	CTGGACCATATCCACTTACCATAAAGGAC	CTGGACCATATCCACTTACCATAAAGGAC	-	rs372974824	byfrequency;alternate_allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	CTGGACCATATCCACTTACCATAAAGGAC	CTGGACCATATCCACTTACCATAAAGGAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	93	19	157	.	0.204	.	-|0.574;CACCAGGAAGCG|0.426	0.574	alt	.	CELA1	39	.	NM_001971	exon1	c.8_16del	p.3_6del	.	.	PASS	Pindel
SELPLG	6404	hgsc.bcm.edu	37	12	109017651	109017680	+	In_Frame_Del	DEL	GAGTGGTCTGTGCCTCCGTGGGCACTGGTT	GAGTGGTCTGTGCCTCCGTGGGCACTGGTT	-	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	GAGTGGTCTGTGCCTCCGTGGGCACTGGTT	GAGTGGTCTGTGCCTCCGTGGGCACTGGTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	107	17	127	.	0.159	.	.	.	none	.	SELPLG	138	.	NM_001206609	exon2	c.453_482del	p.151_161del	.	.	PASS	Pindel
TMIE	259236	hgsc.bcm.edu	37	3	46751074	46751076	+	In_Frame_Del	DEL	AAG	AAG	-	rs10578999	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	177	51	156	.	0.288	.	.	.	strong	.	TMIE	16	.	NM_147196	exon4	c.366_368del	p.122_123del	.	.	PASS	Pindel
SOX2	6657	hgsc.bcm.edu	37	3	181431226	181431227	+	RNA	INS	-	-	A	rs201617684	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	42	10	43	.	0.238	.	.	.	weak	.	SOX2	28	.	.	.	.	.	.	.	PASS	Pindel
OR5P2	120065	hgsc.bcm.edu	37	11	7818383	7818384	+	In_Frame_Ins	INS	-	-	ATATGGTTACCAGGTAGATGC	rs138967151	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	47	18	48	.	0.383	.	.	.	strong	.	OR5P2	68	.	NM_153444	exon1	c.107_108insGCATCTACCTGGTAACCATAT	p.S36delinsCIYLVTIS	.	.	PASS	Pindel
YEATS2	55689	hgsc.bcm.edu	37	3	183493744	183493746	+	In_Frame_Del	DEL	GGA	GGA	-	rs146705467	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	GGA	GGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	14	97	.	0.163	.	.	.	strong	YEATS2,NS,carcinoma,+2,1	YEATS2	111	1	NM_018023	exon18	c.2409_2411del	p.803_804del	.	.	PASS	Pindel
TCHH	7062	hgsc.bcm.edu	37	1	152084175	152084176	+	In_Frame_Ins	INS	-	-	TGCTGCTCGCGCCTCTCC	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	103	19	123	.	0.184	.	.	.	none	.	TCHH	275	.	NM_007113	exon3	c.1518_1519insGGAGAGGCGCGAGCAGCA	p.Q506delinsQERREQQ	.	.	PASS	Pindel
OR51T1	401665	hgsc.bcm.edu	37	11	4903673	4903674	+	Frame_Shift_Ins	INS	-	-	ACCACCCC	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	139	59	238	.	0.424	.	.	.	none	.	OR51T1	92	.	NM_001004759	exon1	c.625_626insACCACCCC	p.Y209fs	.	.	PASS	Pindel
ZNF527	84503	hgsc.bcm.edu	37	19	37879853	37879855	+	In_Frame_Del	DEL	CAT	CAT	-	rs376931538	bycluster;alternate_allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	CAT	CAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	89	24	119	.	0.270	.	.	.	alt	.	ZNF527	78	.	NM_032453	exon5	c.901_903del	p.301_301del	.	.	PASS	Pindel
CEP68	23177	hgsc.bcm.edu	37	2	65298647	65298649	+	In_Frame_Del	DEL	AAC	AAC	-	rs147392467	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	AAC	AAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	401	137	207	.	0.342	.	AAC|0.932;-|0.068	0.068	strong	.	CEP68	69	.	NM_015147	exon3	c.416_418del	p.139_140del	.	.	PASS	Pindel
PLEKHG5	57449	hgsc.bcm.edu	37	1	6529183	6529185	+	In_Frame_Del	DEL	TCC	TCC	-	rs113541584	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	TCC	TCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	79	15	72	.	0.190	.	TCC|0.500;-|0.500	0.500	strong	.	PLEKHG5	66	.	NM_001265592	exon20	c.2404_2406del	p.802_802del	.	.	PASS	Pindel
LOXHD1	125336	hgsc.bcm.edu	37	18	44140280	44140282	+	In_Frame_Del	DEL	TCT	TCT	-	rs142960762	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	TCT	TCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	91	27	96	.	0.297	.	TCT|0.982;-|0.018	0.018	strong	.	LOXHD1	367	.	NM_144612	exon19	c.2826_2828del	p.942_943del	.	.	PASS	Pindel
CASP8AP2	9994	hgsc.bcm.edu	37	6	90577707	90577728	+	Frame_Shift_Del	DEL	GACATCTTTGCCCAGACATGGA	GACATCTTTGCCCAGACATGGA	-	rs202116886	alternate_allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	GACATCTTTGCCCAGACATGGA	GACATCTTTGCCCAGACATGGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	59	25	76	.	0.424	.	.	.	alt	.	CASP8AP2	108	.	NM_012115	exon8	c.4697_4718del	p.1566_1573del	.	.	PASS	Pindel
RPTN	126638	hgsc.bcm.edu	37	1	152129066	152129101	+	In_Frame_Del	DEL	TGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCA	TGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCA	-	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	TGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCA	TGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	192	36	285	.	0.188	.	.	.	none	.	RPTN	123	.	NM_001122965	exon3	c.475_510del	p.159_170del	.	.	PASS	Pindel
SPRR1B	6699	hgsc.bcm.edu	37	1	153004942	153005013	+	In_Frame_Del	DEL	TGCCACCCCAAGGTGCCTGAGCCCTGCCACCCCAAAGTGCCCGAGCCCTGCCAGCCCAAGGTTCCAGAGCCA	TGCCACCCCAAGGTGCCTGAGCCCTGCCACCCCAAAGTGCCCGAGCCCTGCCAGCCCAAGGTTCCAGAGCCA	-	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	TGCCACCCCAAGGTGCCTGAGCCCTGCCACCCCAAAGTGCCCGAGCCCTGCCAGCCCAAGGTTCCAGAGCCA	TGCCACCCCAAGGTGCCTGAGCCCTGCCACCCCAAAGTGCCCGAGCCCTGCCAGCCCAAGGTTCCAGAGCCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	23	104	.	0.295	.	.	.	none	.	SPRR1B	18	.	NM_003125	exon2	c.120_191del	p.40_64del	.	.	PASS	Pindel
ASPN	54829	hgsc.bcm.edu	37	9	95237025	95237027	+	In_Frame_Del	DEL	TCA	TCA	-	rs111419727	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	TCA	TCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	100	31	135	.	0.310	.	TCA|0.500;-|0.500	0.500	strong	.	ASPN	52	.	NM_001193335	exon2	c.154_156del	p.52_52del	.	.	PASS	Pindel
SH3BGR	6450	hgsc.bcm.edu	37	21	40883671	40883672	+	In_Frame_Ins	INS	-	-	AGA	rs3831201	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	55	81	.	0.671	.	.	.	strong	SH3BGR,colon,carcinoma,0,1	SH3BGR	29	1	NM_007341	exon6	c.689_690insAGA	p.G230delinsGE	.	.	PASS	Pindel
MAML2	84441	hgsc.bcm.edu	37	11	95825375	95825383	+	In_Frame_Del	DEL	TGCTGCTGC	TGCTGCTGC	-	rs141671766	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	TGCTGCTGC	TGCTGCTGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	95	19	114	.	0.200	.	.	.	strong	MAML2,NS,carcinoma,0,1	MAML2	94	1	NM_032427	exon2	c.1813_1821del	p.605_607del	.	.	PASS	Pindel
GPRIN1	114787	hgsc.bcm.edu	37	5	176026115	176026138	+	In_Frame_Del	DEL	CCTTTCTCAAAGACCCAGGATCCT	CCTTTCTCAAAGACCCAGGATCCT	-	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	CCTTTCTCAAAGACCCAGGATCCT	CCTTTCTCAAAGACCCAGGATCCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	168	48	168	.	0.286	.	.	.	none	.	GPRIN1	77	.	NM_052899	exon2	c.699_722del	p.233_241del	.	.	PASS	Pindel
LCE1F	353137	hgsc.bcm.edu	37	1	152749008	152749009	+	In_Frame_Ins	INS	-	-	CAGCTCTGGGGGCTGCTG	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	100	17	88	.	0.170	.	.	.	none	LCE1F,colon,carcinoma,0,2	LCE1F	42	2	NM_178354	exon1	c.161_162insCAGCTCTGGGGGCTGCTG	p.S54delinsSSSGGCC	.	.	PASS	Pindel
TEKT4	150483	hgsc.bcm.edu	37	2	95537380	95537381	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	21	112	.	0.247	.	.	.	none	.	TEKT4	72	.	NM_144705	exon1	c.56_57insT	p.R19fs	.	.	PASS	Pindel
TMEM255B	348013	hgsc.bcm.edu	37	13	114503876	114503957	+	Frame_Shift_Del	DEL	CCTGCGGGAGGTGAGGGGCACCGGGGACCCCCATATCTACACCTGCGGGAGGTGAGGGGCGCTGGGGACCCCCGTATCTACA	CCTGCGGGAGGTGAGGGGCACCGGGGACCCCCATATCTACACCTGCGGGAGGTGAGGGGCGCTGGGGACCCCCGTATCTACA	-	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	CCTGCGGGAGGTGAGGGGCACCGGGGACCCCCATATCTACACCTGCGGGAGGTGAGGGGCGCTGGGGACCCCCGTATCTACA	CCTGCGGGAGGTGAGGGGCACCGGGGACCCCCATATCTACACCTGCGGGAGGTGAGGGGCGCTGGGGACCCCCGTATCTACA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	98	25	117	.	0.255	.	.	.	none	.	.	.	.	NM_182614	exon6	c.499_509del	p.167_170del	.	.	PASS	Pindel
SIPA1	6494	hgsc.bcm.edu	37	11	65412467	65412467	+	Silent	SNP	G	G	A	rs2306364	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	110	24	102	0	0.218182	0	G|0.637;A|0.363	0.363	strong	.	SIPA1	45	.	NM_006747	exon5	c.G1026A	p.A342A	CCGGGCGGGCCAG	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	8999044	8999044	+	Silent	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	100	22	107	0	0.22	0	.	.	none	.	MUC16	4315	.	NM_024690	exon57	c.C40800T	p.S13600S	CACAGAGCTCCGC	.	PASS	Atlas-SNP
VILL	50853	hgsc.bcm.edu	37	3	38038982	38038982	+	Silent	SNP	T	T	C	rs6809649	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	65	65	72	0	1	0	T|0.768;C|0.232	0.232	strong	.	VILL	61	.	NM_015873	exon6	c.T570C	p.A190A	GCTGGCTTTGACC	.	PASS	Atlas-SNP
TNFRSF10A	8797	hgsc.bcm.edu	37	8	23059324	23059324	+	Missense_Mutation	SNP	C	C	G	rs20575	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	19	107	0	0.260274	0	C|0.521;G|0.478	0.478	strong	.	TNFRSF10A	40	.	NM_003844	exon4	c.G626C	p.R209T	CACCCTCTGCTGC	.	PASS	Atlas-SNP
NUDCD3	23386	hgsc.bcm.edu	37	7	44530193	44530193	+	Missense_Mutation	SNP	T	T	G	rs307007	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	42	34	31	0	0.809524	0	C|0.000;G|0.171;T|0.828	0.171	strong	.	NUDCD3	20	.	NM_015332	exon1	c.A7C	p.T3P	CCCCTGTCTCCAT	.	PASS	Atlas-SNP
TTC39B	158219	hgsc.bcm.edu	37	9	15189791	15189791	+	Splice_Site	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	57	11	59	0	0.192982	0	.	.	none	.	TTC39B	83	.	NM_001168339	exon13	c.1100-1G>A	.	CTGTACCTAGAAA	.	PASS	Atlas-SNP
ABCA7	10347	hgsc.bcm.edu	37	19	1044712	1044712	+	Missense_Mutation	SNP	A	A	G	rs3764647	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	33	78	0	0.452055	0	A|0.886;G|0.114	0.114	strong	.	ABCA7	174	.	NM_019112	exon11	c.A1184G	p.H395R	TGGGGCACCTGGT	.	PASS	Atlas-SNP
PHOX2B	8929	hgsc.bcm.edu	37	4	41747899	41747899	+	Silent	SNP	G	G	T	rs17885864	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	45	21	32	0	0.466667	0	G|0.972;T|0.028	0.028	strong	.	PHOX2B	53	.	NM_003924	exon3	c.C870A	p.P290P	GGCGAAGGGACCC	.	PASS	Atlas-SNP
MYO1H	283446	hgsc.bcm.edu	37	12	109835590	109835590	+	Silent	SNP	A	A	G	rs11611358	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	81	41	99	0	0.506173	0	A|0.742;G|0.258	0.258	strong	MYO1H,colon,carcinoma,0,1	MYO1H	98	1	NM_001101421	exon4	c.A495G	p.K165K	TGGGAAATACATG	.	PASS	Atlas-SNP
RGPD4	285190	hgsc.bcm.edu	37	2	108475928	108475928	+	Missense_Mutation	SNP	C	C	T	rs2912841		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	262	91	198	0	0.347328	0	.	.	weak	RGPD4,extremity,malignant_melanoma,0,1	RGPD4	112	1	NM_182588	exon11	c.C1552T	p.L518F	CTGCCCCTTCCTG	.	scavenged	Atlas-SNP
DSC1	1823	hgsc.bcm.edu	37	18	28710619	28710619	+	Missense_Mutation	SNP	C	C	A	rs985861	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	198	85	240	0	0.429293	0	C|0.914;A|0.086	0.086	strong	.	DSC1	240	.	NM_024421	exon16	c.G2543T	p.C848F	TACGAACAAACGT	.	PASS	Atlas-SNP
EIF4ENIF1	56478	hgsc.bcm.edu	37	22	31838085	31838085	+	Silent	SNP	G	G	A	rs5997988	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	133	57	170	0	0.428571	0	G|0.611;A|0.389	0.389	strong	.	EIF4ENIF1	80	.	NM_019843	exon17	c.C2226T	p.S742S	TACAGAGCTGGAT	.	PASS	Atlas-SNP
PPL	5493	hgsc.bcm.edu	37	16	4934777	4934777	+	Silent	SNP	C	C	T	rs61744951	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	136	100	189	0	0.735294	0	C|0.918;T|0.082	0.082	strong	.	PPL	168	.	NM_002705	exon22	c.G3879A	p.Q1293Q	GATCTCCTGGACC	.	PASS	Atlas-SNP
HLTF	6596	hgsc.bcm.edu	37	3	148759325	148759325	+	Silent	SNP	T	T	C	rs2290725	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	126	60	155	0	0.47619	0	T|0.692;C|0.308	0.308	strong	.	HLTF	87	.	NM_139048	exon20	c.A2328G	p.A776A	TACATGTGCACAA	.	PASS	Atlas-SNP
STT3A	3703	hgsc.bcm.edu	37	11	125476252	125476252	+	Silent	SNP	C	C	G	rs34964592	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	191	154	193	0	0.806283	0	C|0.891;G|0.109	0.109	strong	.	STT3A	52	.	NM_152713	exon8	c.C672G	p.L224L	CGTCCTCGTGCTG	.	PASS	Atlas-SNP
SUPT16H	11198	hgsc.bcm.edu	37	14	21831419	21831419	+	Silent	SNP	C	C	T	rs61746713	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	64	35	81	0	0.546875	0	C|0.925;T|0.075	0.075	strong	SUPT16H,NS,carcinoma,-1,1	SUPT16H	84	1	NM_007192	exon12	c.G1368A	p.R456R	TGCTGCCCGAGAA	.	PASS	Atlas-SNP
APOBEC2	10930	hgsc.bcm.edu	37	6	41029342	41029342	+	Missense_Mutation	SNP	T	T	C	rs2076472	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	98	46	110	0	0.469388	0	T|0.816;C|0.184	0.184	strong	.	APOBEC2	30	.	NM_006789	exon2	c.T407C	p.I136T	GCATTATCAAAAC	.	PASS	Atlas-SNP
PER3	8863	hgsc.bcm.edu	37	1	7887248	7887248	+	Silent	SNP	G	G	A	rs2859387	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	72	64	0	0.986301	0	G|0.567;A|0.433	0.433	strong	PER3,NS,carcinoma,+1,1	PER3	95	1	NM_016831	exon17	c.G2235A	p.P745P	GCTGCCGGAGCCG	.	PASS	Atlas-SNP
C16orf3	750	hgsc.bcm.edu	37	16	90095561	90095561	+	Missense_Mutation	SNP	C	C	T	rs3785183	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	121	48	90	0	0.396694	0	C|0.676;T|0.324	0.324	strong	C16orf3,NS,carcinoma,0,1	C16orf3	14	1	NM_001214	exon1	c.G190A	p.V64I	AGCCTACGGGGCA	.	PASS	Atlas-SNP
PREP	5550	hgsc.bcm.edu	37	6	105776866	105776866	+	Missense_Mutation	SNP	A	A	C	rs12192054	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	80	39	135	0	0.4875	0	A|0.879;C|0.121	0.121	strong	.	PREP	65	.	NM_002726	exon9	c.T1051G	p.L351V	AGCATAAGACCAA	.	PASS	Atlas-SNP
GFPT2	9945	hgsc.bcm.edu	37	5	179740827	179740827	+	Missense_Mutation	SNP	T	T	C	rs2303007	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	57	16	48	0	0.280702	0	T|0.789;C|0.211	0.211	strong	GFPT2,NS,carcinoma,0,1	GFPT2	74	1	NM_005110	exon14	c.A1411G	p.I471V	CGCCGATCTCCGG	.	PASS	Atlas-SNP
HMGXB3	22993	hgsc.bcm.edu	37	5	149390148	149390148	+	Missense_Mutation	SNP	G	G	A	rs2241698	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	56	27	85	0	0.482143	0	G|0.869;A|0.131	0.131	strong	.	HMGXB3	31	.	NM_014983	exon4	c.G787A	p.V263I	GAGAGTGTATCAG	.	PASS	Atlas-SNP
CCDC111	201973	hgsc.bcm.edu	37	4	185599489	185599489	+	Silent	SNP	G	G	A	rs34985821	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	356	183	427	0	0.514045	0	G|0.904;A|0.096	0.096	strong	.	CCDC111	43	.	NM_152683	exon8	c.G948A	p.Q316Q	TATACAGTCAAAA	.	PASS	Atlas-SNP
PPP1R32	220004	hgsc.bcm.edu	37	11	61253841	61253841	+	Missense_Mutation	SNP	C	C	A	rs11230707	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	143	107	194	0	0.748252	0	C|0.955;A|0.045	0.045	strong	.	.	.	.	NM_145017	exon8	c.C713A	p.T238N	GTGTCACCAAGTC	.	PASS	Atlas-SNP
OR51S1	119692	hgsc.bcm.edu	37	11	4870284	4870284	+	Missense_Mutation	SNP	G	G	C	rs35918613	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	255	59	187	0	0.231373	0	G|0.898;C|0.102	0.102	strong	.	OR51S1	83	.	NM_001004758	exon1	c.C155G	p.T52S	AGGATGGTGCCAT	.	PASS	Atlas-SNP
T	6862	hgsc.bcm.edu	37	6	166580188	166580188	+	Silent	SNP	G	G	A	rs1056048	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	74	19	116	0	0.256757	0	G|0.749;A|0.251	0.251	strong	.	T	77	.	NM_003181	exon3	c.C363T	p.S121S	GACGCAGCTGGGC	.	PASS	Atlas-SNP
SEMA6B	10501	hgsc.bcm.edu	37	19	4558431	4558431	+	Silent	SNP	C	C	G	rs2304213	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	20	12	15	0	0.6	0	C|0.510;G|0.490	0.490	strong	SEMA6B,NS,carcinoma,0,2	SEMA6B	51	2	NM_032108	exon2	c.G39C	p.L13L	AAGCAGCAGGGCC	.	PASS	Atlas-SNP
KRT32	3882	hgsc.bcm.edu	37	17	39623363	39623363	+	Missense_Mutation	SNP	T	T	C	rs3744786	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	65	65	103	0	1	0	C|0.286;N|0.000	0.286	strong	.	KRT32	57	.	NM_002278	exon1	c.A215G	p.Q72R	GCTGCCTGGCAGG	.	PASS	Atlas-SNP
IGSF1	3547	hgsc.bcm.edu	37	X	130408745	130408745	+	Silent	SNP	G	G	A	rs6529473	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	169	167	233	0	0.988166	0	0|0.003;A|0.363	0.363	strong	.	IGSF1	231	.	NM_001170961	exon18	c.C3594T	p.V1198V	TTCTAGGACAAAT	.	PASS	Atlas-SNP
UNC13D	201294	hgsc.bcm.edu	37	17	73836162	73836162	+	Silent	SNP	C	C	G	rs7223416	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	39	80	0	0.565217	0	C|0.507;G|0.493	0.493	strong	.	UNC13D	68	.	NM_199242	exon11	c.G888C	p.P296P	GTAGCTCGGCTGC	.	PASS	Atlas-SNP
TMEM184A	202915	hgsc.bcm.edu	37	7	1595068	1595068	+	Missense_Mutation	SNP	G	G	A	rs17852421	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	90	21	94	0	0.233333	0	G|0.778;A|0.222	0.222	strong	.	TMEM184A	35	.	NM_001097620	exon2	c.C53T	p.A18V	CAGTTCGCTGACA	.	PASS	Atlas-SNP
ITIH1	3697	hgsc.bcm.edu	37	3	52820981	52820981	+	Missense_Mutation	SNP	A	A	T	rs678	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	126	113	151	0	0.896825	0	A|0.681;T|0.319	0.319	strong	.	ITIH1	108	.	NM_002215	exon14	c.A1754T	p.E585V	GGGAGGAGAGGGC	.	PASS	Atlas-SNP
KRT73	319101	hgsc.bcm.edu	37	12	53012053	53012053	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	118	69	108	0	0.584746	0	.	.	none	.	KRT73	101	.	NM_175068	exon1	c.T256G	p.F86V	TGCCAAACATGCT	.	PASS	Atlas-SNP
MAGEB3	4114	hgsc.bcm.edu	37	X	30254530	30254530	+	Silent	SNP	A	A	G	rs2071310	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	240	238	402	0	0.991667	0	A|0.567;0|0.003	.	strong	.	MAGEB3	54	.	NM_002365	exon5	c.A489G	p.V163V	GGTGGTATTTGGT	.	PASS	Atlas-SNP
SPTLC3	55304	hgsc.bcm.edu	37	20	13134768	13134768	+	Silent	SNP	T	T	C	rs6078938	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	141	50	168	0	0.35461	0	T|0.826;C|0.174	0.174	strong	.	SPTLC3	78	.	NM_018327	exon10	c.T1398C	p.Y466Y	TCTTTATATGCCT	.	PASS	Atlas-SNP
CD101	9398	hgsc.bcm.edu	37	1	117554247	117554247	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	141	60	168	0	0.425532	0	.	.	none	.	CD101	95	.	NM_001256109	exon3	c.C500T	p.T167I	CCCTCACCTGTGA	.	PASS	Atlas-SNP
GALNT8	26290	hgsc.bcm.edu	37	12	4835882	4835882	+	Silent	SNP	T	T	G	rs2286578	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	57	29	58	0	0.508772	0	T|0.649;G|0.351	0.351	strong	.	GALNT8	89	.	NM_017417	exon2	c.T396G	p.L132L	GGATCTTTCTGAG	.	PASS	Atlas-SNP
FAM200B	285550	hgsc.bcm.edu	37	4	15689632	15689632	+	Silent	SNP	G	G	A	rs11729955	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	191	93	218	0	0.486911	0	G|0.683;A|0.317	0.317	strong	FAM200B_ENST00000422728,NS,carcinoma,0,2	FAM200B	56	2	NM_001145191	exon2	c.G1032A	p.E344E	CATGGAGGTATTG	.	PASS	Atlas-SNP
C1orf173	127254	hgsc.bcm.edu	37	1	75055419	75055419	+	Missense_Mutation	SNP	T	T	C	rs2305549	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	240	107	265	0	0.445833	0	T|0.909;C|0.091	0.091	strong	.	C1orf173	380	.	NM_001002912	exon12	c.A2072G	p.H691R	GAAACATGTTTCC	.	PASS	Atlas-SNP
EXOC1	55763	hgsc.bcm.edu	37	4	56756531	56756531	+	Silent	SNP	T	T	C	rs2290016	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	70	104	0	0.985915	0	T|0.688;C|0.312	0.312	strong	.	EXOC1	103	.	NM_018261	exon12	c.T1518C	p.A506A	TGTTGCTGACAGG	.	PASS	Atlas-SNP
PIGG	54872	hgsc.bcm.edu	37	4	527677	527677	+	Missense_Mutation	SNP	T	T	C	rs34623004	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	125	60	134	0	0.48	0	T|0.799;C|0.201	0.201	strong	PIGG,colon,carcinoma,0,5	PIGG	86	5	NM_001127178	exon12	c.T2642C	p.I881T	TGGAAATCCCAGC	.	PASS	Atlas-SNP
COASY	80347	hgsc.bcm.edu	37	17	40714804	40714804	+	Missense_Mutation	SNP	C	C	A	rs615942	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	76	30	64	0	0.394737	0	C|0.512;A|0.488	0.488	strong	COASY,colon,carcinoma,0,1	COASY	45	1	NM_001042532	exon3	c.C251A	p.S84Y	CCCAGTCCAGCCC	.	PASS	Atlas-SNP
RECQL4	9401	hgsc.bcm.edu	37	8	145742879	145742879	+	Silent	SNP	T	T	C	rs2306386	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	10	10	4	0	1	0	T|0.468;C|0.532	0.532	strong	.	RECQL4	75	.	NM_004260	exon3	c.A132G	p.E44E	GCGGTATTCCCGG	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1264767	1264767	+	Silent	SNP	G	G	A	rs74447707	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	306	7	213	1	0.0228758	0.00469484	.	.	weak	MUC5B,NS,neuroblastoma,0,2	MUC5B	473	2	NM_002458	exon31	c.G6657A	p.S2219S	CACCTCGGGCATC	.	scavenged	Atlas-SNP
ASIC4	55515	hgsc.bcm.edu	37	2	220402671	220402671	+	Missense_Mutation	SNP	G	G	T	rs11689281	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	62	37	60	0	0.596774	0	G|0.523;T|0.477	0.477	strong	.	.	.	.	NM_182847	exon9	c.G1847T	p.R616L	CGAGCCGGGGCCG	.	PASS	Atlas-SNP
ACAN	176	hgsc.bcm.edu	37	15	89400339	89400339	+	Missense_Mutation	SNP	A	A	C	rs2882676	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	95	95	57	0	1	0	A|0.565;C|0.435	0.435	strong	.	ACAN	220	.	NM_001135	exon12	c.A4523C	p.E1508A	TCAGTGAACTTCC	.	PASS	Atlas-SNP
UNC5CL	222643	hgsc.bcm.edu	37	6	40998141	40998141	+	Silent	SNP	G	G	A	rs736795	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	125	50	156	0	0.4	0	G|0.767;A|0.233	0.233	strong	.	UNC5CL	52	.	NM_173561	exon8	c.C1320T	p.C440C	CATGCCGCAAAGC	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105416254	105416254	+	Missense_Mutation	SNP	G	G	A	rs201136817	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	182	8	196	1	0.043956	0.00510204	G|0.992;A|0.008	0.008	strong	AHNAK2_ENST00000333244,colon,carcinoma,+1,1	AHNAK2	719	1	NM_138420	exon7	c.C5534T	p.S1845L	TCCACCGAGGCCT	.	scavenged	Atlas-SNP
CCDC168	643677	hgsc.bcm.edu	37	13	103388015	103388015	+	Missense_Mutation	SNP	C	C	G	rs17507841	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	180	93	183	0	0.516667	0	C|0.984;G|0.016	0.016	strong	.	.	.	.	NM_001146197	exon4	c.G15032C	p.G5011A	TCTTCTCCCTGTG	.	PASS	Atlas-SNP
IQGAP2	10788	hgsc.bcm.edu	37	5	75932869	75932869	+	Silent	SNP	C	C	T	rs2910819	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	120	119	114	0	0.991667	0	C|0.441;T|0.559	0.559	strong	IQGAP2,NS,carcinoma,0,1	IQGAP2	186	1	NM_006633	exon16	c.C1791T	p.D597D	TAGTGACGGTTCA	.	PASS	Atlas-SNP
PRKCQ	5588	hgsc.bcm.edu	37	10	6553071	6553071	+	Silent	SNP	T	T	C	rs17555072	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	252	125	268	0	0.496032	0	T|0.958;C|0.042	0.042	strong	.	PRKCQ	113	.	NM_006257	exon3	c.A204G	p.R68R	CATGACTCTTCCC	.	PASS	Atlas-SNP
NUP214	8021	hgsc.bcm.edu	37	9	134021630	134021630	+	Silent	SNP	A	A	G	rs2296710	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	113	54	109	0	0.477876	0	T|0.000;G|0.312;A|0.687	0.312	strong	NUP214,NS,carcinoma,0,1	NUP214	166	1	NM_005085	exon13	c.A1884G	p.T628T	CCCCACACCTCTC	.	PASS	Atlas-SNP
RCOR3	55758	hgsc.bcm.edu	37	1	211451467	211451467	+	Silent	SNP	T	T	C	rs11577985	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	59	59	92	0	1	0	T|0.830;C|0.170	0.170	strong	RCOR3,NS,carcinoma,0,1	RCOR3	51	1	NM_001136223	exon6	c.T525C	p.D175D	TCCAGATAAGACA	.	PASS	Atlas-SNP
FAM179A	165186	hgsc.bcm.edu	37	2	29240673	29240673	+	Missense_Mutation	SNP	G	G	A	rs35166194	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	242	111	232	0	0.458678	0	G|0.779;A|0.221	0.221	strong	.	FAM179A	106	.	NM_199280	exon10	c.G1211A	p.R404Q	CCCTCCGGGGCAG	.	PASS	Atlas-SNP
NUP88	4927	hgsc.bcm.edu	37	17	5289580	5289580	+	Silent	SNP	A	A	G	rs11209	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	214	96	229	0	0.448598	0	A|0.526;G|0.474	0.474	strong	.	NUP88	47	.	NM_002532	exon17	c.T2172C	p.H724H	CCTTATATGTTCA	.	PASS	Atlas-SNP
AKD1	221264	hgsc.bcm.edu	37	6	109886005	109886005	+	Silent	SNP	T	T	C	rs7757895	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	102	102	120	0	1	0	T|0.802;C|0.198	0.198	strong	.	AKD1	223	.	NM_001145128	exon22	c.A2388G	p.P796P	TCCTTTTGGGATT	.	PASS	Atlas-SNP
FRMPD4	9758	hgsc.bcm.edu	37	X	12725701	12725701	+	Silent	SNP	C	C	G	rs6641078	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	173	173	236	1	1	0.00423729	C|0.852;G|0.148	0.148	strong	.	FRMPD4	214	.	NM_014728	exon13	c.C1401G	p.V467V	CCACGTCAACAGG	.	PASS	Atlas-SNP
ZSCAN29	146050	hgsc.bcm.edu	37	15	43661802	43661802	+	Missense_Mutation	SNP	T	T	C	rs3809482	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	192	65	188	0	0.338542	0	T|0.485;C|0.515	0.515	strong	.	ZSCAN29	57	.	NM_152455	exon1	c.A310G	p.R104G	AAGATCTAGGTCT	.	PASS	Atlas-SNP
OR5P2	120065	hgsc.bcm.edu	37	11	7818190	7818190	+	Silent	SNP	C	C	T	rs73406607	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	44	34	45	0	0.772727	0	C|0.738;T|0.262	0.262	strong	OR5P2,brain,glioma,0,2	OR5P2	68	2	NM_153444	exon1	c.G300A	p.A100A	GAAAGCCGCTGAA	.	PASS	Atlas-SNP
FHAD1	114827	hgsc.bcm.edu	37	1	15653563	15653563	+	Silent	SNP	C	C	T	rs3765357	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	212	98	248	0	0.462264	0	C|0.799;T|0.201	0.201	strong	.	FHAD1	78	.	NM_052929	exon12	c.C1482T	p.H494H	GGAGCACTTCAGA	.	PASS	Atlas-SNP
SLC5A8	160728	hgsc.bcm.edu	37	12	101560328	101560328	+	Missense_Mutation	SNP	C	C	A	rs164365	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	118	63	138	0	0.533898	0	C|0.767;A|0.233	0.233	strong	.	SLC5A8	102	.	NM_145913	exon12	c.G1470T	p.M490I	GGTTGTCATCAAA	.	PASS	Atlas-SNP
SRD5A1	6715	hgsc.bcm.edu	37	5	6656210	6656210	+	Silent	SNP	G	G	A	rs55789931		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	133	77	124	0	0.578947	0	.	.	weak	SRD5A1,NS,carcinoma,0,1	SRD5A1	31	1	NM_001047	exon3	c.G480A	p.T160T	GTTAACGGGCATG	.	PASS	Atlas-SNP
DDX4	54514	hgsc.bcm.edu	37	5	55082474	55082474	+	Silent	SNP	C	C	T	rs957459	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	230	75	201	0	0.326087	0	C|0.565;T|0.435	0.435	strong	.	DDX4	194	.	NM_024415	exon14	c.C993T	p.C331C	GGCTTGCGCTCAA	.	PASS	Atlas-SNP
ASCC3	10973	hgsc.bcm.edu	37	6	101049748	101049748	+	Silent	SNP	C	C	T	rs61746540	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	44	96	0	0.586667	0	C|0.969;T|0.031	0.031	strong	.	ASCC3	205	.	NM_006828	exon34	c.G5241A	p.K1747K	ATCTTGCTTAGAT	.	PASS	Atlas-SNP
POM121L12	285877	hgsc.bcm.edu	37	7	53103571	53103571	+	Silent	SNP	G	G	A	rs11238248	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	43	22	38	0	0.511628	0	G|0.585;A|0.415	0.415	strong	.	POM121L12	146	.	NM_182595	exon1	c.G207A	p.G69G	GTGGGGGCGCCCG	.	PASS	Atlas-SNP
FASTKD1	79675	hgsc.bcm.edu	37	2	170403106	170403106	+	Silent	SNP	G	G	A	rs16857030	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	220	92	225	0	0.418182	0	G|0.902;A|0.098	0.098	strong	.	FASTKD1	86	.	NM_024622	exon8	c.C1323T	p.A441A	TAAAACGGCTTCA	.	PASS	Atlas-SNP
ZPLD1	131368	hgsc.bcm.edu	37	3	102181131	102181131	+	Missense_Mutation	SNP	A	A	G	rs12054046	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	91	45	88	0	0.494505	0	A|0.884;G|0.116	0.116	strong	.	ZPLD1	82	.	NM_175056	exon6	c.A637G	p.T213A	GATTCAACCTACA	.	PASS	Atlas-SNP
BCKDHA	593	hgsc.bcm.edu	37	19	41928927	41928927	+	Silent	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	108	2	130	0	0.0185185	0	.	.	none	BCKDHA,NS,carcinoma,0,1	BCKDHA	36	1	NM_000709	exon8	c.C1020T	p.D340D	CAGTGACGACAGT	.	scavenged	Atlas-SNP
ANKRD36	375248	hgsc.bcm.edu	37	2	97790211	97790211	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	198	13	200	2	0.0656566	0.01	.	.	none	ANKRD36_ENST00000420699,extremity,malignant_melanoma,0,2	ANKRD36	170	2	NM_001164315	exon5	c.A608T	p.H203L	TCATACATGCTGT	.	scavenged	Atlas-SNP
MYO7A	4647	hgsc.bcm.edu	37	11	76910766	76910766	+	Silent	SNP	C	C	T	rs7927472	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	92	106	1	1	0.00943396	C|0.511;T|0.489	0.489	strong	.	MYO7A	164	.	NM_000260	exon35	c.C4755T	p.S1585S	CTCCAGCAATGCT	.	PASS	Atlas-SNP
C11orf21	29125	hgsc.bcm.edu	37	11	2323022	2323022	+	Missense_Mutation	SNP	C	C	T	rs12276847	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	80	16	69	0	0.2	0	C|0.750;T|0.250	0.250	strong	.	C11orf21	11	.	NM_001142946	exon1	c.G70A	p.V24M	ATCCCACACCAGG	.	PASS	Atlas-SNP
ZSCAN5B	342933	hgsc.bcm.edu	37	19	56703286	56703286	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	33	90	0	0.37931	0	.	.	none	.	ZSCAN5B	160	.	NM_001080456	exon2	c.C521T	p.P174L	GTCCCCGGATGCA	.	PASS	Atlas-SNP
FSIP2	401024	hgsc.bcm.edu	37	2	186672527	186672527	+	Missense_Mutation	SNP	T	T	A	rs72900086	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	107	59	150	0	0.551402	0	T|0.836;A|0.164	0.164	strong	.	FSIP2	251	.	NM_173651	exon17	c.T18761A	p.L6254Q	TGCCCCTACCTAA	.	PASS	Atlas-SNP
PGLYRP2	114770	hgsc.bcm.edu	37	19	15586672	15586672	+	Missense_Mutation	SNP	A	A	T	rs892145	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	62	30	60	0	0.483871	0	A|0.632;T|0.368	0.368	strong	PGLYRP2_ENST00000292609,NS,carcinoma,0,4	PGLYRP2	116	4	NM_052890	exon2	c.T809A	p.M270K	AAGGCCATGGTTA	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	145	144	237	0	0.993103	0	C|0.629;T|0.371	0.371	strong	.	LIPI	95	.	NM_198996	exon9	c.G1354A	p.E452K	ACCTTTCTGGGTA	.	PASS	Atlas-SNP
LIMD2	80774	hgsc.bcm.edu	37	17	61775992	61775992	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	102	27	94	0	0.264706	0	.	.	none	.	LIMD2	6	.	NM_030576	exon5	c.T304A	p.Y102N	CGTCGTAGTTGCC	.	PASS	Atlas-SNP
CDRT1	374286	hgsc.bcm.edu	37	17	15496727	15496727	+	Missense_Mutation	SNP	T	T	G	rs79385100	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	211	209	227	0	0.990521	0	T|0.825;G|0.175	0.175	strong	.	CDRT1	83	.	NM_006382	exon11	c.A1930C	p.N644H	TCCCATTGAAGAA	.	PASS	Atlas-SNP
KANK4	163782	hgsc.bcm.edu	37	1	62713246	62713246	+	Silent	SNP	G	G	A	rs10889315	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	121	60	114	0	0.495868	0	G|0.637;A|0.363	0.363	strong	KANK4,NS,carcinoma,0,1	KANK4	135	1	NM_181712	exon9	c.C2781T	p.H927H	TCCATCGTGGTCC	.	PASS	Atlas-SNP
MYO6	4646	hgsc.bcm.edu	37	6	76576290	76576290	+	Silent	SNP	C	C	T	rs11756446	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	175	88	208	0	0.502857	0	C|0.959;T|0.041	0.041	strong	MYO6,NS,carcinoma,+2,1	MYO6	124	1	NM_004999	exon17	c.C1722T	p.D574D	AGACGACGAAGGC	.	PASS	Atlas-SNP
TMEM231	79583	hgsc.bcm.edu	37	16	75574030	75574030	+	Silent	SNP	C	C	T	rs2242406	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	28	51	0	0.4	0	C|0.752;T|0.248	0.248	strong	.	TMEM231	13	.	NM_001077416	exon6	c.G972A	p.V324V	ATACTGCACCCAG	.	PASS	Atlas-SNP
PCDHGA9	56107	hgsc.bcm.edu	37	5	140784895	140784895	+	Silent	SNP	C	C	T	rs4912606	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	151	73	190	0	0.483444	0	C|0.975;T|0.025	0.025	strong	.	PCDHGA9	110	.	NM_032089	exon1	c.C2376T	p.C792C	TTTGTGCGTCTCT	.	PASS	Atlas-SNP
PXDNL	137902	hgsc.bcm.edu	37	8	52233408	52233408	+	Missense_Mutation	SNP	C	C	T	rs7827446	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	12	98	0	0.146341	0	C|0.679;T|0.321	0.321	strong	PXDNL_ENST00000356297,caecum,carcinoma,0,1	PXDNL	414	1	NM_144651	exon22	c.G4196A	p.R1399K	ACCCCTCTAACAT	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228469870	228469870	+	Missense_Mutation	SNP	C	C	T	rs3795785	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	187	94	192	0	0.502674	0	C|0.882;T|0.118	0.118	strong	.	OBSCN	2142	.	NM_001271223	exon36	c.C9721T	p.R3241W	TCTGTGCGGGGCC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195508418	195508418	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	4	92	2	0.0547945	0.0217391	.	.	none	MUC4_ENST00000463781,rectum,carcinoma,+2,1	MUC4	1505	1	NM_018406	exon2	c.G10033C	p.V3345L	CAGGCACAGGGGT	.	scavenged	Atlas-SNP
TRMT12	55039	hgsc.bcm.edu	37	8	125463250	125463250	+	Missense_Mutation	SNP	T	T	C	rs3812475	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	85	92	0	1	0	T|0.442;C|0.558	0.558	strong	.	TRMT12	28	.	NM_017956	exon1	c.T82C	p.W28R	GAGCCTTGGTTTA	.	PASS	Atlas-SNP
SYNE1	23345	hgsc.bcm.edu	37	6	152746593	152746593	+	Missense_Mutation	SNP	A	A	T	rs111250109	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	142	95	230	0	0.669014	0	A|0.951;T|0.049	0.049	strong	.	SYNE1	3227	.	NM_033071	exon39	c.T5211A	p.D1737E	CACATCATCTTTG	.	PASS	Atlas-SNP
ERCC2	2068	hgsc.bcm.edu	37	19	45855478	45855478	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	114	30	91	0	0.263158	0	.	.	none	.	ERCC2	78	.	NM_000400	exon22	c.C2179T	p.P727S	GGAAGGGCTGTGC	.	PASS	Atlas-SNP
ALPP	250	hgsc.bcm.edu	37	2	233245026	233245026	+	Missense_Mutation	SNP	G	G	A	rs71421640		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	228	102	380	3	0.447368	0.00789474	G|0.500;A|0.500	0.500	weak	ALPP,NS,carcinoma,+1,1	ALPP	53	1	NM_001632	exon6	c.G788A	p.R263H	CGAAGCGCCAGGT	.	scavenged	Atlas-SNP
FBN3	84467	hgsc.bcm.edu	37	19	8191401	8191401	+	Silent	SNP	G	G	A	rs3813778	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	64	64	65	1	1	0.0153846	G|0.684;A|0.316	0.316	strong	FBN3,NS,carcinoma,0,1	FBN3	300	1	NM_032447	exon19	c.C2505T	p.C835C	GGTGGCGCAGCAC	.	scavenged	Atlas-SNP
HSPD1	3329	hgsc.bcm.edu	37	2	198363534	198363534	+	Silent	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	199	2	259	1	0.0100503	0.003861	.	.	none	HSPD1_ENST00000426480,NS,haematopoietic_neoplasm,0,3	HSPD1	68	3	NM_002156	exon2	c.G39A	p.P13P	GGACACCGGTCTC	.	scavenged	Atlas-SNP
NOL6	65083	hgsc.bcm.edu	37	9	33464897	33464897	+	Missense_Mutation	SNP	T	T	C	rs142747625	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	77	34	79	0	0.441558	0	T|0.998;C|0.002	0.002	strong	.	NOL6	85	.	NM_022917	exon21	c.A2759G	p.N920S	TTGAGGTTGACAA	.	PASS	Atlas-SNP
PKDREJ	10343	hgsc.bcm.edu	37	22	46657894	46657894	+	Silent	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	183	47	199	0	0.256831	0	.	.	none	.	PKDREJ	195	.	NM_006071	exon1	c.G1326A	p.A442A	AGAAAACGCTGTC	.	PASS	Atlas-SNP
TCP11	6954	hgsc.bcm.edu	37	6	35108553	35108553	+	Missense_Mutation	SNP	T	T	G	rs35693439	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	59	25	59	0	0.423729	0	T|0.833;G|0.167	0.167	strong	.	TCP11	94	.	NM_001093728	exon2	c.A134C	p.D45A	CTCTTGTCTTCCT	.	PASS	Atlas-SNP
OPLAH	26873	hgsc.bcm.edu	37	8	145112983	145112983	+	Missense_Mutation	SNP	C	C	T	rs55916375	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	74	73	131	0	0.986486	0	C|0.947;T|0.053	0.053	strong	.	OPLAH	78	.	NM_017570	exon8	c.G1018A	p.V340I	GGGTGACGCCAGC	.	PASS	Atlas-SNP
CDHR5	53841	hgsc.bcm.edu	37	11	617519	617519	+	Silent	SNP	A	A	G	rs34889521	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	52	85	0	0.732394	0	A|0.664;G|0.336	0.336	strong	.	CDHR5	77	.	NM_021924	exon15	c.T2370C	p.A790A	CCAGACAGCCTTG	.	PASS	Atlas-SNP
CAMK2G	818	hgsc.bcm.edu	37	10	75574956	75574956	+	Silent	SNP	G	G	A	rs55640406	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	143	142	195	0	0.993007	0	G|0.988;A|0.012	0.012	strong	.	CAMK2G	79	.	NM_172171	exon20	c.C1488T	p.H496H	GTGGACGTGTGGG	.	PASS	Atlas-SNP
CDC14A	8556	hgsc.bcm.edu	37	1	100928418	100928418	+	Silent	SNP	C	C	G	rs28364884	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	43	92	0	0.467391	0	C|0.997;G|0.003	0.003	strong	.	CDC14A	65	.	NM_033313	exon9	c.C819G	p.A273A	AGGGGCCATCGCC	.	PASS	Atlas-SNP
COL18A1	80781	hgsc.bcm.edu	37	21	46896312	46896312	+	Silent	SNP	G	G	T	rs2230688	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	104	33	104	0	0.317308	0	A|0.000;C|0.000;G|0.800;T|0.199	0.199	strong	.	COL18A1	129	.	NM_030582	exon5	c.G1386T	p.T462T	CACCACGCCACCC	.	PASS	Atlas-SNP
AGAP6	414189	hgsc.bcm.edu	37	10	51769799	51769799	+	Silent	SNP	C	C	T	rs61848275	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	108	57	89	0	0.527778	0	C|0.500;T|0.500	0.500	weak	AGAP6,NS,carcinoma,0,1	AGAP6	53	1	NM_001077665	exon8	c.C1914T	p.V638V	TGTGGTCCTGGCG	.	scavenged	Atlas-SNP
IL17RD	54756	hgsc.bcm.edu	37	3	57138419	57138419	+	Missense_Mutation	SNP	G	G	A	rs6780995	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	81	38	116	0	0.469136	0	G|0.431;A|0.569	0.569	strong	.	IL17RD	93	.	NM_017563	exon8	c.C764T	p.T255M	CTGGTCGTCTCTG	.	PASS	Atlas-SNP
SLC12A3	6559	hgsc.bcm.edu	37	16	56913513	56913513	+	Silent	SNP	C	C	T	rs5801	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	33	71	0	0.358696	0	C|0.858;T|0.142	0.142	strong	.	SLC12A3	99	.	NM_001126108	exon11	c.C1395T	p.T465T	GGCCACCCTCTCC	.	PASS	Atlas-SNP
NUSAP1	51203	hgsc.bcm.edu	37	15	41634588	41634588	+	Missense_Mutation	SNP	C	C	A	rs7178777	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	106	42	140	0	0.396226	0	C|0.686;A|0.314	0.314	strong	NUSAP1,NS,carcinoma,+1,2	NUSAP1	32	2	NM_018454	exon2	c.C98A	p.T33N	AGGCAACCAAGTT	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105416823	105416823	+	Silent	SNP	G	G	A	rs2582504	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	149	74	153	0	0.496644	0	G|0.883;A|0.117	0.117	strong	AHNAK2_ENST00000333244,NS,carcinoma,-2,1	AHNAK2	719	1	NM_138420	exon7	c.C4965T	p.D1655D	CTTGCTGTCTTTG	.	PASS	Atlas-SNP
AKAP6	9472	hgsc.bcm.edu	37	14	33015082	33015082	+	Missense_Mutation	SNP	A	A	G	rs17099240	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	96	94	163	0	0.979167	0	A|0.861;G|0.139	0.139	strong	.	AKAP6	308	.	NM_004274	exon4	c.A1223G	p.N408S	AAGGCAATGGTGG	.	PASS	Atlas-SNP
IDUA	3425	hgsc.bcm.edu	37	4	995305	995305	+	Silent	SNP	T	T	C	rs6815946	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	68	30	92	0	0.441176	0	T|0.821;C|0.179	0.179	strong	.	IDUA	33	.	NM_000203	exon5	c.T543C	p.N181N	GTGGAATGAGCCA	.	PASS	Atlas-SNP
FSIP1	161835	hgsc.bcm.edu	37	15	39910052	39910052	+	Missense_Mutation	SNP	C	C	G	rs16969386	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	139	62	169	0	0.446043	0	C|0.858;G|0.142	0.142	strong	FSIP1,NS,carcinoma,0,1	FSIP1	53	1	NM_152597	exon11	c.G1583C	p.G528A	CCAATGCCAAGAG	.	PASS	Atlas-SNP
FCGBP	8857	hgsc.bcm.edu	37	19	40368330	40368330	+	Missense_Mutation	SNP	C	C	T	rs74540349	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	152	53	203	0	0.348684	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
IL10RA	3587	hgsc.bcm.edu	37	11	117869642	117869642	+	Missense_Mutation	SNP	C	C	A	rs369418818		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	53	43	47	0	0.811321	0	.	.	weak	.	IL10RA	46	.	NM_001558	exon7	c.C1023A	p.H341Q	CCCTCACCCCCAG	.	PASS	Atlas-SNP
KRTAP4-8	728224	hgsc.bcm.edu	37	17	39253956	39253956	+	Silent	SNP	G	G	A	rs76327324	byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	30	10	64	1	0.333333	0.015625	G|0.500;A|0.500	0.500	strong	KRTAP4-8,NS,carcinoma,0,1	KRTAP4-8	57	1	NM_031960	exon1	c.C381T	p.P127P	GCAGCTGGGGCGG	.	scavenged	Atlas-SNP
MX2	4600	hgsc.bcm.edu	37	21	42771176	42771176	+	Silent	SNP	T	T	C	rs2301803	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	197	117	212	0	0.593909	0	T|0.946;C|0.054	0.054	strong	.	MX2	84	.	NM_002463	exon10	c.T1326C	p.V442V	AGAAGTTGTAAGG	.	PASS	Atlas-SNP
HEATR3	55027	hgsc.bcm.edu	37	16	50106594	50106594	+	Silent	SNP	T	T	C	rs2287197	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	224	222	169	1	0.991071	0.00591716	T|0.405;C|0.595	0.595	strong	.	HEATR3	59	.	NM_182922	exon5	c.T591C	p.F197F	TAGGTTTCCTACC	.	PASS	Atlas-SNP
SLC14A2	8170	hgsc.bcm.edu	37	18	43252883	43252883	+	Missense_Mutation	SNP	G	G	A	rs1123617	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	180	86	177	0	0.477778	0	G|0.840;T|0.001	.	strong	.	SLC14A2	121	.	NM_001242692	exon18	c.G2248A	p.V750I	ATCCCCGTTGGAA	.	PASS	Atlas-SNP
ZNF286A	57335	hgsc.bcm.edu	37	17	15620481	15620481	+	Silent	SNP	C	C	T	rs74608540		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	142	44	185	0	0.309859	0	C|0.250;T|0.750	0.750	weak	ZNF286A,NS,carcinoma,0,1	ZNF286A	58	1	NM_020652	exon6	c.C1443T	p.L481L	AGCTCTCATTCAA	.	PASS	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	93	49	112	0	0.526882	0	T|0.794;N|0.000	.	strong	.	.	.	.	NM_030899	exon2	c.A148T	p.T50S	CAGGAGTCTCTTG	.	PASS	Atlas-SNP
ST3GAL4	6484	hgsc.bcm.edu	37	11	126278075	126278075	+	Silent	SNP	C	C	T	rs2230279	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	217	155	205	0	0.714286	0	C|0.657;T|0.343	0.343	strong	.	ST3GAL4	25	.	NM_001254757	exon7	c.C423T	p.Y141Y	CAAGTACGATGTG	.	PASS	Atlas-SNP
ESRRG	2104	hgsc.bcm.edu	37	1	216692669	216692669	+	Silent	SNP	C	C	T	rs945453	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	57	26	81	0	0.45614	0	C|0.442;T|0.558	0.558	strong	.	ESRRG	111	.	NM_001243518	exon7	c.G993A	p.S331S	CTCAAACGAAAGA	.	PASS	Atlas-SNP
ZDHHC19	131540	hgsc.bcm.edu	37	3	195938177	195938177	+	Silent	SNP	A	A	G	rs1522394	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	31	65	0	0.43662	0	A|0.742;G|0.258	0.258	strong	.	ZDHHC19	25	.	NM_001039617	exon1	c.T10C	p.L4L	CCGTTAAGAGTGT	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228528563	228528563	+	Missense_Mutation	SNP	C	C	G	rs1188710	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	62	62	89	0	1	0	C|0.442;G|0.558	0.558	strong	OBSCN_ENST00000570156,NS,carcinoma,0,4	OBSCN	2142	4	NM_001271223	exon83	c.C20542G	p.Q6848E	ACCCTGCAGGCCC	.	PASS	Atlas-SNP
CACNA1H	8912	hgsc.bcm.edu	37	16	1254369	1254369	+	Missense_Mutation	SNP	C	C	T	rs3751664	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	209	156	207	0	0.746412	0	C|0.927;T|0.073	0.073	strong	.	CACNA1H	317	.	NM_021098	exon10	c.C2362T	p.R788C	CTGCGCCGCATCG	.	PASS	Atlas-SNP
AGAP7	653268	hgsc.bcm.edu	37	10	51465366	51465366	+	Missense_Mutation	SNP	G	G	C	rs191741842	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	125	63	170	0	0.504	0	G|0.983;C|0.017	0.017	strong	.	AGAP7	33	.	NM_001077685	exon7	c.C1090G	p.P364A	GCTTGGGGATGGT	.	PASS	Atlas-SNP
ZIC2	7546	hgsc.bcm.edu	37	13	100635377	100635377	+	Silent	SNP	C	C	T	rs1831992	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	54	21	56	0	0.388889	0	C|0.922;T|0.078	0.078	strong	.	ZIC2	25	.	NM_007129	exon1	c.C1059T	p.H353H	GATCCACAAAAGG	.	PASS	Atlas-SNP
TTC30A	92104	hgsc.bcm.edu	37	2	178482698	178482698	+	Silent	SNP	A	A	G	rs3813256	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	190	106	214	1	0.557895	0.0046729	A|0.915;G|0.085	0.085	strong	.	TTC30A	60	.	NM_152275	exon1	c.T732C	p.V244V	ATGGAGAACTAAG	.	PASS	Atlas-SNP
PSG1	5669	hgsc.bcm.edu	37	19	43372386	43372386	+	Silent	SNP	T	T	C	rs1064491	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	140	60	131	0	0.428571	0	T|0.797;C|0.203	0.203	strong	.	PSG1	196	.	NM_001184826	exon5	c.A1110G	p.E370E	AAACTTTTCATTA	.	PASS	Atlas-SNP
SDC3	9672	hgsc.bcm.edu	37	1	31349647	31349647	+	Missense_Mutation	SNP	C	C	T	rs2491132	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	38	52	0	0.535211	0	C|0.879;G|0.000;T|0.121	0.121	strong	.	SDC3	45	.	NM_014654	exon3	c.G622A	p.V208I	TCCGTACGCCAGT	.	PASS	Atlas-SNP
PCNT	5116	hgsc.bcm.edu	37	21	47817316	47817316	+	Missense_Mutation	SNP	G	G	A	rs143796569	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	100	27	93	0	0.27	0	G|0.999;A|0.001	0.001	strong	PCNT,NS,carcinoma,-2,1	PCNT	283	1	NM_006031	exon22	c.G4354A	p.G1452R	CATCGCGGGTGTG	.	PASS	Atlas-SNP
FAM228A	653140	hgsc.bcm.edu	37	2	24413298	24413298	+	Missense_Mutation	SNP	A	A	G	rs2288073	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	221	87	188	1	0.393665	0.00531915	A|0.776;G|0.224	0.224	strong	C2orf84,NS,carcinoma,+1,1	.	.	1	NM_001040710	exon6	c.A419G	p.Y140C	TCATCTATGCAGA	.	scavenged	Atlas-SNP
HIST1H2AD	3013	hgsc.bcm.edu	37	6	26199222	26199222	+	Silent	SNP	G	G	A	rs113561314	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	165	79	171	0	0.478788	0	G|0.897;A|0.103	0.103	strong	.	HIST1H2AD	20	.	NM_021065	exon1	c.C250T	p.L84L	GCTGCAGGTGTCG	.	PASS	Atlas-SNP
MYO10	4651	hgsc.bcm.edu	37	5	16794916	16794916	+	Silent	SNP	G	G	A	rs396514	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	35	59	0	0.507246	0	G|0.708;A|0.292	0.292	strong	.	MYO10	198	.	NM_012334	exon4	c.C306T	p.S102S	GTTCACGGAGGCC	.	PASS	Atlas-SNP
FAM21A	387680	hgsc.bcm.edu	37	10	51853633	51853633	+	Missense_Mutation	SNP	C	C	T	rs199520696	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	893	144	701	1	0.161254	0.00142653	C|0.796;T|0.205	0.205	strong	FAM21A,NS,carcinoma,0,4	FAM21A	32	4	NM_001005751	exon13	c.C1136T	p.T379M	TCTTCACGGAAGC	.	scavenged	Atlas-SNP
PCDHB4	56131	hgsc.bcm.edu	37	5	140502343	140502343	+	Missense_Mutation	SNP	C	C	T	rs3733698	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	107	51	144	0	0.476636	0	C|0.827;T|0.173	0.173	strong	.	PCDHB4	177	.	NM_018938	exon1	c.C763T	p.P255S	AACAGCCCCCTAG	.	PASS	Atlas-SNP
GPR157	80045	hgsc.bcm.edu	37	1	9165685	9165685	+	Missense_Mutation	SNP	G	G	A	rs72637739	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	199	196	225	0	0.984925	0	G|0.839;A|0.161	0.161	strong	.	GPR157	14	.	NM_024980	exon3	c.C652T	p.R218C	AGTGGCGCAGCAG	.	PASS	Atlas-SNP
SLC47A2	146802	hgsc.bcm.edu	37	17	19584752	19584752	+	Silent	SNP	G	G	C	rs34416664	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	33	122	0	0.402439	0	G|0.993;C|0.007	0.007	strong	.	SLC47A2	61	.	NM_152908	exon15	c.C1428G	p.A476A	GACACAGGCCAGC	.	PASS	Atlas-SNP
ALPK2	115701	hgsc.bcm.edu	37	18	56202120	56202120	+	Missense_Mutation	SNP	G	G	A	rs7234999	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	179	88	229	0	0.49162	0	G|0.907;A|0.093	0.093	strong	.	ALPK2	487	.	NM_052947	exon5	c.C5299T	p.H1767Y	CTGTGTGTGATAA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195506499	195506499	+	Silent	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	42	10	51	7	0.238095	0.137255	.	.	none	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.C11952T	p.P3984P	AGGAAGGGGGGTG	.	scavenged	Atlas-SNP
SLC22A4	6583	hgsc.bcm.edu	37	5	131663062	131663062	+	Missense_Mutation	SNP	T	T	C	rs272893	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	135	71	160	0	0.525926	0	T|0.373;G|0.001	.	strong	.	SLC22A4	45	.	NM_003059	exon5	c.T917C	p.I306T	ACAACATAGCTGT	.	PASS	Atlas-SNP
AKD1	221264	hgsc.bcm.edu	37	6	109954518	109954518	+	Silent	SNP	T	T	C	rs9374111	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	38	38	44	0	1	0	C|0.211;N|0.000	0.211	strong	AKD1_ENST00000424296,NS,carcinoma,0,2	AKD1	223	2	NM_145025	exon11	c.A942G	p.L314L	ACGAAATAGCTCA	.	PASS	Atlas-SNP
ANAPC1	64682	hgsc.bcm.edu	37	2	112592265	112592265	+	Missense_Mutation	SNP	T	T	C	rs71277799	alternate_allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	426	54	391	0	0.126761	0	CGAAGAACG|0.500;TGAAGAACA|0.500	.	alt	ANAPC1,NS,carcinoma,0,1	ANAPC1	116	1	NM_022662	exon19	c.A2300G	p.H767R	ACAAGGTGAAGAA	.	scavenged	Atlas-SNP
NQO2	4835	hgsc.bcm.edu	37	6	3017138	3017138	+	Silent	SNP	C	C	T	rs1130428	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	81	30	57	0	0.37037	0	C|0.960;T|0.040	0.040	strong	.	NQO2	21	.	NM_000904	exon6	c.C438T	p.S146S	CCTTTCCGTAACC	.	PASS	Atlas-SNP
OSBPL10	114884	hgsc.bcm.edu	37	3	32022622	32022622	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	21	12	8	0	0.571429	0	.	.	none	.	OSBPL10	160	.	NM_017784	exon1	c.G50A	p.S17N	CGGCTGCTGCTGT	.	PASS	Atlas-SNP
ZNF248	57209	hgsc.bcm.edu	37	10	38121631	38121631	+	Missense_Mutation	SNP	T	T	C	rs11011379	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	56	29	90	0	0.517857	0	T|0.986;C|0.014	0.014	strong	.	ZNF248	61	.	NM_001267597	exon6	c.A652G	p.K218E	CATTTTTACTATA	.	PASS	Atlas-SNP
NSMCE1	197370	hgsc.bcm.edu	37	16	27246617	27246617	+	Missense_Mutation	SNP	T	T	C	rs17856580	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	46	25	49	0	0.543478	0	T|0.754;C|0.246	0.246	strong	.	NSMCE1	28	.	NM_145080	exon3	c.A140G	p.N47S	GTGGCATTGCCTG	.	PASS	Atlas-SNP
RAI14	26064	hgsc.bcm.edu	37	5	34811131	34811131	+	Silent	SNP	G	G	A	rs35607113	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	147	81	141	0	0.55102	0	G|0.872;A|0.128	0.128	strong	.	RAI14	100	.	NM_001145525	exon10	c.G474A	p.P158P	TATACCGCTGCTT	.	PASS	Atlas-SNP
GOLGA6L6	727832	hgsc.bcm.edu	37	15	20740252	20740252	+	Nonsense_Mutation	SNP	C	C	A	rs199807662	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	33	27	6	0	0.818182	0	.	.	weak	.	GOLGA6L6	37	.	NM_001145004	exon8	c.G1498T	p.E500X	CCTGCTCGTGCAT	.	PASS	Atlas-SNP
TAF1L	138474	hgsc.bcm.edu	37	9	32631518	32631518	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	338	86	433	1	0.254438	0.00230947	.	.	none	.	TAF1L	382	.	NM_153809	exon1	c.G4060C	p.E1354Q	GAACCTCATGCAC	.	PASS	Atlas-SNP
TMEM63A	9725	hgsc.bcm.edu	37	1	226055595	226055595	+	Silent	SNP	G	G	A	rs2292564	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	52	30	71	0	0.576923	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
PDIA2	64714	hgsc.bcm.edu	37	16	334580	334580	+	Silent	SNP	G	G	C	rs432925	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	52	70	0	0.693333	0	G|0.756;C|0.244	0.244	strong	.	PDIA2	51	.	NM_006849	exon2	c.G393C	p.P131P	GCACCCGGAGGAG	.	PASS	Atlas-SNP
TNS1	7145	hgsc.bcm.edu	37	2	218712726	218712726	+	Silent	SNP	A	A	G	rs1364642	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	89	42	113	0	0.47191	0	A|0.591;G|0.409	0.409	strong	.	TNS1	251	.	NM_022648	exon17	c.T2139C	p.N713N	CAGCATATTGAGT	.	PASS	Atlas-SNP
SLC18A2	6571	hgsc.bcm.edu	37	10	119003564	119003564	+	Silent	SNP	T	T	G	rs363387	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	66	41	96	0	0.621212	0	T|0.932;G|0.068	0.068	strong	.	SLC18A2	58	.	NM_003054	exon3	c.T204G	p.T68T	GCACACTGCCTCC	.	PASS	Atlas-SNP
NEFH	4744	hgsc.bcm.edu	37	22	29886043	29886043	+	Missense_Mutation	SNP	A	A	C	rs165602	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	43	20	38	0	0.465116	0	A|0.871;C|0.129	0.129	strong	.	NEFH	178	.	NM_021076	exon4	c.A2414C	p.E805A	TGAAGGAGGATGC	.	PASS	Atlas-SNP
PCDHB8	56128	hgsc.bcm.edu	37	5	140559914	140559914	+	Missense_Mutation	SNP	T	T	C	rs2740583	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	46	133	0	0.528736	0	A|0.000;C|0.223;N|0.000;T|0.776	0.223	strong	.	PCDHB8	199	.	NM_019120	exon1	c.T2299C	p.F767L	TTCCAGTTCCTGA	.	PASS	Atlas-SNP
MLC1	23209	hgsc.bcm.edu	37	22	50515843	50515843	+	Missense_Mutation	SNP	C	C	A	rs6010260	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	134	63	158	0	0.470149	0	C|0.898;A|0.102	0.102	strong	.	MLC1	48	.	NM_015166	exon6	c.G512T	p.C171F	TTCTTGCAGTCCT	.	PASS	Atlas-SNP
ARID4B	51742	hgsc.bcm.edu	37	1	235416122	235416122	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	172	36	168	0	0.209302	0	.	.	none	.	ARID4B	142	.	NM_016374	exon6	c.T277C	p.F93L	CATCAAAAACTAT	.	PASS	Atlas-SNP
ZNF623	9831	hgsc.bcm.edu	37	8	144733176	144733176	+	Silent	SNP	C	C	T	rs141224385	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	35	5	32	0	0.142857	0	C|0.999;T|0.001	0.001	strong	ZNF623,NS,carcinoma,0,1	ZNF623	63	1	NM_014789	exon1	c.C1134T	p.N378N	ATGTAACGAGTGT	.	scavenged	Atlas-SNP
ABCB8	11194	hgsc.bcm.edu	37	7	150739054	150739054	+	Missense_Mutation	SNP	G	G	A	rs56198402	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	42	26	31	0	0.619048	0	G|0.969;A|0.031	0.031	strong	.	ABCB8	65	.	NM_007188	exon14	c.G1624A	p.V542I	GAGCCCGTCCTGT	.	PASS	Atlas-SNP
RFX8	731220	hgsc.bcm.edu	37	2	102018908	102018908	+	Missense_Mutation	SNP	A	A	G	rs2175968	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	83	38	94	0	0.457831	0	A|0.523;G|0.477	0.477	strong	.	RFX8	16	.	NM_001145664	exon11	c.T1235C	p.M412T	TTGCCCATGGCAG	.	PASS	Atlas-SNP
LCORL	254251	hgsc.bcm.edu	37	4	17886146	17886146	+	Missense_Mutation	SNP	A	A	G	rs17526944	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	153	64	151	0	0.418301	0	A|0.972;G|0.028	0.028	strong	.	LCORL	60	.	NM_001166139	exon7	c.T1006C	p.Y336H	CCTTATATGAATA	.	PASS	Atlas-SNP
ZNF746	155061	hgsc.bcm.edu	37	7	149191460	149191460	+	Silent	SNP	G	G	A	rs61744226	byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	208	97	180	0	0.466346	0	G|0.714;A|0.286	0.286	strong	.	ZNF746	68	.	NM_001163474	exon2	c.C159T	p.A53A	CTCCACGGCTGTC	.	PASS	Atlas-SNP
FRAS1	80144	hgsc.bcm.edu	37	4	79353587	79353587	+	Missense_Mutation	SNP	C	C	G	rs35219594	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	120	59	174	0	0.491667	0	C|0.998;G|0.002	0.002	strong	FRAS1_ENST00000325942,NS,carcinoma,+2,3	FRAS1	779	3	NM_001166133	exon38	c.C5046G	p.D1682E	GGAAGACAGCATG	.	PASS	Atlas-SNP
PRX	57716	hgsc.bcm.edu	37	19	40901614	40901614	+	Missense_Mutation	SNP	A	A	G	rs268671	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	65	21	69	0	0.323077	0	A|0.446;G|0.554	0.554	strong	.	PRX	151	.	NM_181882	exon7	c.T2645C	p.V882A	CCCTCCACCCGCT	.	PASS	Atlas-SNP
STAB1	23166	hgsc.bcm.edu	37	3	52558133	52558133	+	Silent	SNP	T	T	C	rs13621	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	126	125	152	0	0.992063	0	A|0.000;C|0.428;G|0.000;T|0.572	0.428	strong	.	STAB1	178	.	NM_015136	exon68	c.T7560C	p.D2520D	TGCTGATGACGAC	.	PASS	Atlas-SNP
KRT1	3848	hgsc.bcm.edu	37	12	53070145	53070145	+	Silent	SNP	G	G	A	rs936958	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	128	59	154	0	0.460938	0	G|0.554;A|0.446	0.446	strong	KRT1,NS,carcinoma,-2,1	KRT1	110	1	NM_006121	exon7	c.C1389T	p.R463R	GTAGTCGCGCAGC	.	PASS	Atlas-SNP
GFM2	84340	hgsc.bcm.edu	37	5	74055209	74055209	+	Missense_Mutation	SNP	T	T	C	rs957680	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	201	98	222	0	0.487562	0	T|0.820;G|0.001	.	strong	.	GFM2	38	.	NM_032380	exon4	c.A191G	p.N64S	GGAGGATTGATGA	.	PASS	Atlas-SNP
SRRM5	100170229	hgsc.bcm.edu	37	19	44118353	44118353	+	Missense_Mutation	SNP	G	G	A	rs2302421	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	64	29	85	0	0.453125	0	G|0.833;A|0.167	0.167	strong	.	SRRM5	38	.	NM_001145641	exon1	c.G2080A	p.D694N	CAAGCCGACGCCA	.	PASS	Atlas-SNP
LDLR	3949	hgsc.bcm.edu	37	19	11230881	11230881	+	Silent	SNP	T	T	C	rs5925	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	102	57	108	0	0.558824	0	T|0.656;C|0.344	0.344	strong	.	LDLR	72	.	NM_001195798	exon13	c.T1959C	p.V653V	TATGGTTCTCTTC	.	PASS	Atlas-SNP
SLC9B2	133308	hgsc.bcm.edu	37	4	103964529	103964529	+	Missense_Mutation	SNP	A	A	C	rs2276976	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	68	33	57	0	0.485294	0	A|0.893;C|0.107	0.107	strong	.	.	.	.	NM_178833	exon9	c.T1070G	p.F357C	AAACCAAAATGCA	.	PASS	Atlas-SNP
SNX9	51429	hgsc.bcm.edu	37	6	158330765	158330765	+	Silent	SNP	G	G	A	rs3211067	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	88	34	159	0	0.386364	0	G|0.778;A|0.222	0.222	strong	.	SNX9	43	.	NM_016224	exon8	c.G774A	p.R258R	TCCCAGGAAAGGC	.	PASS	Atlas-SNP
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33037611	33037611	+	Silent	SNP	C	C	T	rs1062481	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	95	30	142	0	0.315789	0	T|0.111;G|0.000;C|0.889	0.111	strong	.	HLA-DPA1	20	.	NM_033554	exon2	c.G153A	p.G51G	AAACTCCCCTGTT	.	PASS	Atlas-SNP
MLLT4	4301	hgsc.bcm.edu	37	6	168352105	168352105	+	Silent	SNP	G	G	A	rs2076664	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	33	17	78	0	0.515152	0	G|0.852;A|0.148	0.148	strong	MLLT4,NS,carcinoma,+1,1	MLLT4	351	1	NM_001040000	exon29	c.G4050A	p.P1350P	CATACCGGCCACC	.	PASS	Atlas-SNP
PTPRZ1	5803	hgsc.bcm.edu	37	7	121513561	121513561	+	Missense_Mutation	SNP	T	T	G	rs740965	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	49	22	55	0	0.44898	0	T|0.868;G|0.132	0.132	strong	.	PTPRZ1	605	.	NM_001206838	exon1	c.T8G	p.I3S	TGCGAATCCTAAA	.	PASS	Atlas-SNP
SEC14L1	6397	hgsc.bcm.edu	37	17	75190962	75190962	+	Silent	SNP	C	C	T	rs674402	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	106	104	103	0	0.981132	0	C|0.643;T|0.357	0.357	strong	.	SEC14L1	81	.	NM_001204408	exon9	c.C678T	p.S226S	CCCCAGCGCACCT	.	PASS	Atlas-SNP
TRIO	7204	hgsc.bcm.edu	37	5	14330940	14330940	+	Silent	SNP	T	T	C	rs2277045	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	119	75	107	0	0.630252	0	T|0.952;C|0.048	0.048	strong	.	TRIO	305	.	NM_007118	exon10	c.T1785C	p.G595G	TACAGGTGTGGGG	.	PASS	Atlas-SNP
CPZ	8532	hgsc.bcm.edu	37	4	8616096	8616096	+	Silent	SNP	T	T	C	rs1131140	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	107	106	99	0	0.990654	0	T|0.457;C|0.543	0.543	strong	.	CPZ	95	.	NM_001014447	exon9	c.T1374C	p.D458D	GTCCGATTTCAAC	.	PASS	Atlas-SNP
CCR2	729230	hgsc.bcm.edu	37	3	46399798	46399798	+	Silent	SNP	T	T	C	rs1799865	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	276	126	220	0	0.456522	0	T|0.668;C|0.332	0.332	strong	.	CCR2	103	.	NM_001123041	exon2	c.T780C	p.N260N	CTATAATATTGTC	.	PASS	Atlas-SNP
AKD1	221264	hgsc.bcm.edu	37	6	109827528	109827528	+	Splice_Site	SNP	A	A	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	24	131	0	0.307692	0	.	.	none	C6orf224,NS,carcinoma,-2,2	AKD1	223	2	NM_001145128	exon36	c.4849+2T>C	.	TATCTTACCTGCT	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29912852	29912852	+	Silent	SNP	T	T	C	rs1137296	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	119	46	237	0	0.386555	0	T|0.347;C|0.653	0.653	strong	.	HLA-A	89	.	NM_001242758	exon6	c.T1029C	p.S343S	AGGGAGTTACACT	.	PASS	Atlas-SNP
LILRB2	10288	hgsc.bcm.edu	37	19	54778587	54778587	+	Missense_Mutation	SNP	T	T	C	rs146683137	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	236	127	282	1	0.538136	0.0035461	T|0.983;C|0.017	0.017	strong	.	LILRB2	94	.	NM_005874	exon14	c.A1747G	p.R583G	GTTCCCTTTCCTG	.	PASS	Atlas-SNP
ANKRD20A2	441430	hgsc.bcm.edu	37	9	42368549	42368549	+	Silent	SNP	C	C	T	rs77881930		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	221	98	263	1	0.443439	0.00380228	.	.	weak	ANKRD20A2,bladder,carcinoma,+2,2	ANKRD20A2	9	2	NM_001012421	exon1	c.C135T	p.D45D	AGGCGACGCCGCG	.	scavenged	Atlas-SNP
N4BP3	23138	hgsc.bcm.edu	37	5	177547336	177547336	+	Missense_Mutation	SNP	G	G	A	rs3812082	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	18	10	16	0	0.555556	0	G|0.832;A|0.168	0.168	strong	N4BP3,NS,carcinoma,0,2	N4BP3	25	2	NM_015111	exon3	c.G488A	p.R163Q	GGCCCCGGGCCAG	.	scavenged	Atlas-SNP
FLRT3	23767	hgsc.bcm.edu	37	20	14306896	14306896	+	Silent	SNP	G	G	A	rs6042672	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	108	55	96	0	0.509259	0	G|0.677;A|0.323	0.323	strong	.	FLRT3	67	.	NM_013281	exon2	c.C1257T	p.T419T	ATCAGAGGTGACA	.	PASS	Atlas-SNP
FZD3	7976	hgsc.bcm.edu	37	8	28384712	28384712	+	Silent	SNP	A	A	G	rs2241802	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	216	214	316	1	0.990741	0.00316456	A|0.459;G|0.541	0.541	strong	.	FZD3	65	.	NM_017412	exon5	c.A435G	p.L145L	GAATTTAGCTGGA	.	PASS	Atlas-SNP
CD48	962	hgsc.bcm.edu	37	1	160654758	160654758	+	Missense_Mutation	SNP	C	C	G	rs2295615	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	160	113	254	0	0.70625	0	C|0.882;G|0.118	0.118	strong	CD48,NS,carcinoma,0,1	CD48	31	1	NM_001256030	exon2	c.G304C	p.E102Q	TGTCCTCTTTCTG	.	PASS	Atlas-SNP
ABP1	26	hgsc.bcm.edu	37	7	150557622	150557622	+	Silent	SNP	G	G	A	rs12179	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	33	103	0	0.471429	0	G|0.580;A|0.420	0.420	strong	ABP1,NS,carcinoma,0,1	ABP1	92	1	NM_001272072	exon4	c.G1947A	p.S649S	GGAGTCGGAGCTG	.	PASS	Atlas-SNP
SLC51A	200931	hgsc.bcm.edu	37	3	195955762	195955762	+	Missense_Mutation	SNP	G	G	A	rs939885	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	162	67	164	0	0.41358	0	G|0.554;A|0.446	0.446	strong	.	.	.	.	NM_152672	exon6	c.G604A	p.V202I	TTTCTCGTCCCCG	.	PASS	Atlas-SNP
OR5H14	403273	hgsc.bcm.edu	37	3	97868959	97868959	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	140	73	181	0	0.521429	0	.	.	none	.	OR5H14	56	.	NM_001005514	exon1	c.C730A	p.H244N	GGAGCTCATCTCT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195511911	195511911	+	Silent	SNP	G	G	A	rs200732241		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	94	3	118	0	0.0319149	0	G|0.998;A|0.002	0.002	weak	MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	NM_018406	exon2	c.C6540T	p.T2180T	AGTGTCGGTGACA	.	scavenged	Atlas-SNP
HRAS	3265	hgsc.bcm.edu	37	11	534242	534242	+	Silent	SNP	A	A	G	rs12628	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	139	104	124	0	0.748201	0	A|0.663;G|0.337	0.337	strong	HRAS,arm,benign_melanocytic_nevus,0,26	HRAS	1232	26	NM_001130442	exon2	c.T81C	p.H27H	CACAAAATGGTTC	.	PASS	Atlas-SNP
MRPL28	10573	hgsc.bcm.edu	37	16	419154	419154	+	Silent	SNP	G	G	A	rs1802752	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	167	165	212	0	0.988024	0	G|0.881;A|0.119	0.119	strong	MRPL28,colon,carcinoma,0,1	MRPL28	15	1	NM_006428	exon3	c.C355T	p.L119L	TGTCCAGGATCTC	.	PASS	Atlas-SNP
DCLRE1A	9937	hgsc.bcm.edu	37	10	115609915	115609915	+	Missense_Mutation	SNP	C	C	G	rs3750898	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	103	103	123	0	1	0	C|0.339;G|0.661	0.661	strong	.	DCLRE1A	80	.	NM_014881	exon2	c.G949C	p.D317H	AATCATCCGGTTT	.	PASS	Atlas-SNP
GET4	51608	hgsc.bcm.edu	37	7	930689	930689	+	Silent	SNP	C	C	T	rs13171	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	251	71	313	0	0.282869	0	C|0.831;T|0.169	0.169	strong	GET4,NS,carcinoma,0,1	GET4	17	1	NM_015949	exon5	c.C591T	p.A197A	CGTGGCCCAGGCC	.	PASS	Atlas-SNP
HIPK4	147746	hgsc.bcm.edu	37	19	40886993	40886993	+	Missense_Mutation	SNP	C	C	T	rs11670988	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	62	20	72	0	0.322581	0	C|0.921;T|0.079	0.079	strong	HIPK4_ENST00000291823,larynx,carcinoma,-1,1	HIPK4	100	1	NM_144685	exon3	c.G905A	p.R302Q	GTTAGCCGACTGG	.	PASS	Atlas-SNP
KCNMB1	3779	hgsc.bcm.edu	37	5	169810796	169810796	+	Missense_Mutation	SNP	C	C	T	rs11739136	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	59	83	0	0.584158	0	C|0.910;T|0.090	0.090	strong	.	KCNMB1	38	.	NM_004137	exon3	c.T193A	p.S65T	TCAGCTCCTCCTG	.	PASS	Atlas-SNP
PTPN13	5783	hgsc.bcm.edu	37	4	87696470	87696470	+	Silent	SNP	A	A	G	rs12507034	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	135	53	144	0	0.392593	0	A|0.906;G|0.094	0.094	strong	.	PTPN13	203	.	NM_080685	exon34	c.A5670G	p.T1890T	CATAACACTAACG	.	PASS	Atlas-SNP
APOL6	80830	hgsc.bcm.edu	37	22	36054944	36054944	+	Silent	SNP	C	C	T	rs34527373	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	41	67	0	0.594203	0	C|0.975;T|0.025	0.025	strong	.	APOL6	26	.	NM_030641	exon3	c.C333T	p.T111T	CTCCACCGCTGGT	.	PASS	Atlas-SNP
NCAN	1463	hgsc.bcm.edu	37	19	19351431	19351431	+	Silent	SNP	G	G	A	rs2229851	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	67	36	75	0	0.537313	0	G|0.956;A|0.044	0.044	strong	.	NCAN	277	.	NM_004386	exon12	c.G3429A	p.T1143T	AAACACGTGGATC	.	PASS	Atlas-SNP
PIGH	5283	hgsc.bcm.edu	37	14	68060574	68060574	+	Silent	SNP	G	G	A	rs45474396	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	125	63	114	0	0.504	0	G|0.905;A|0.095	0.095	strong	.	PIGH	13	.	NM_004569	exon2	c.C276T	p.I92I	ATCAATGATTAAC	.	PASS	Atlas-SNP
SIVA1	10572	hgsc.bcm.edu	37	14	105222988	105222988	+	Missense_Mutation	SNP	G	G	A	rs144031294	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	135	73	134	0	0.540741	0	G|0.998;A|0.002	0.002	strong	.	SIVA1	12	.	NM_006427	exon3	c.G361A	p.V121M	CGAGCCGTGGATG	.	PASS	Atlas-SNP
OR10H1	26539	hgsc.bcm.edu	37	19	15918654	15918654	+	Missense_Mutation	SNP	G	G	A	rs74729097		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	79	17	207	0	0.21519	0	A|1.000;|0.000	1.000	weak	OR10H1,colon,carcinoma,-1,2	OR10H1	59	2	NM_013940	exon1	c.C194T	p.A65V	GAGAGGGCGCACA	.	scavenged	Atlas-SNP
PCDHB1	29930	hgsc.bcm.edu	37	5	140432602	140432602	+	Missense_Mutation	SNP	C	C	T	rs116101801	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	98	2	122	1	0.0204082	0.00819672	C|0.999;T|0.001	0.001	strong	PCDHB1,colon,carcinoma,+1,3	PCDHB1	148	3	NM_013340	exon1	c.C1547T	p.A516V	TCTACGCGCTGAG	.	scavenged	Atlas-SNP
RGS3	5998	hgsc.bcm.edu	37	9	116346118	116346118	+	Missense_Mutation	SNP	G	G	A	rs41305473	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	74	46	91	0	0.621622	0	G|0.884;A|0.116	0.116	strong	.	RGS3	251	.	NM_144488	exon21	c.G2426A	p.R809Q	CCACCCGGGACCT	.	PASS	Atlas-SNP
RTP4	64108	hgsc.bcm.edu	37	3	187089031	187089031	+	Missense_Mutation	SNP	C	C	A	rs1003995	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	30	20	36	0	0.666667	0	C|0.721;A|0.278	0.278	strong	.	RTP4	20	.	NM_022147	exon2	c.C611A	p.A204D	AGTCAGCTGAGGC	.	PASS	Atlas-SNP
CEP192	55125	hgsc.bcm.edu	37	18	13001523	13001523	+	Missense_Mutation	SNP	G	G	A	rs11080618	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	39	15	43	0	0.384615	0	G|0.697;A|0.303	0.303	strong	.	CEP192	340	.	NM_032142	exon3	c.G232A	p.G78R	TCTCCCGGAAGCC	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	196	112	273	0	0.571429	0	C|0.767;T|0.233	0.233	strong	.	SPATA22	49	.	NM_032598	exon6	c.G442A	p.V148M	AACTCACTGGACA	.	PASS	Atlas-SNP
THNSL1	79896	hgsc.bcm.edu	37	10	25314005	25314005	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	139	30	149	0	0.215827	0	.	.	none	.	THNSL1	70	.	NM_024838	exon3	c.G1853A	p.W618X	CTGACTGGTGCTC	.	PASS	Atlas-SNP
PLEKHG2	64857	hgsc.bcm.edu	37	19	39911451	39911451	+	Missense_Mutation	SNP	C	C	G	rs34975345	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	54	29	59	0	0.537037	0	C|0.979;G|0.021	0.021	strong	.	PLEKHG2	329	.	NM_022835	exon13	c.C1358G	p.P453R	CTCGACCTCGAGA	.	PASS	Atlas-SNP
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057393	46057393	+	Missense_Mutation	SNP	T	T	A	rs2838602	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	88	86	119	1	0.977273	0.00840336	T|0.231;A|0.769	0.769	strong	KRTAP10-10,NS,carcinoma,-1,1	KRTAP10-10	37	1	NM_181688	exon1	c.T59A	p.V20D	GGGTAGTCGACTG	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	46	102	0	0.541176	0	A|0.738;G|0.262	0.262	strong	.	FAM71C	48	.	NM_153364	exon1	c.A211G	p.M71V	GTAACAATGGGCA	.	PASS	Atlas-SNP
MYH4	4622	hgsc.bcm.edu	37	17	10346781	10346781	+	Missense_Mutation	SNP	T	T	C	rs3744554	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	173	84	183	0	0.485549	0	T|0.573;C|0.427	0.427	strong	.	MYH4	349	.	NM_017533	exon40	c.A5731G	p.K1911E	GTTCCTTGGCCTC	.	PASS	Atlas-SNP
LAMC2	3918	hgsc.bcm.edu	37	1	183206573	183206573	+	Silent	SNP	G	G	A	rs1047981	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	267	150	362	1	0.561798	0.00276243	G|0.694;A|0.306	0.306	strong	LAMC2,NS,carcinoma,+2,1	LAMC2	113	1	NM_005562	exon18	c.G2688A	p.Q896Q	TACACAGAAGAAT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195515141	195515141	+	Missense_Mutation	SNP	A	A	G	rs71321850	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	62	14	49	0	0.225806	0	A|0.250;G|0.750	0.750	weak	.	MUC4	1505	.	NM_018406	exon2	c.T3310C	p.S1104P	GAAGAGAGGTGGC	.	PASS	Atlas-SNP
NLGN1	22871	hgsc.bcm.edu	37	3	173997153	173997153	+	Silent	SNP	G	G	A	rs7646919	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	146	58	177	1	0.39726	0.00564972	G|0.797;A|0.203	0.203	strong	NLGN1,caecum,carcinoma,0,1	NLGN1	209	1	NM_014932	exon6	c.G1362A	p.K454K	AAGAAAGACATTA	.	scavenged	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195511238	195511238	+	Missense_Mutation	SNP	C	C	T	rs3103956		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	133	8	150	0	0.0601504	0	.	.	weak	MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	NM_018406	exon2	c.G7213A	p.D2405N	AAGTGTCGGTGAC	.	scavenged	Atlas-SNP
RTN4IP1	84816	hgsc.bcm.edu	37	6	107019880	107019880	+	Silent	SNP	A	A	G	rs9486410	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	104	52	148	0	0.5	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
PARD3B	117583	hgsc.bcm.edu	37	2	206364737	206364737	+	Silent	SNP	T	T	C	rs10197347	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	64	36	83	0	0.5625	0	T|0.587;C|0.413	0.413	strong	.	PARD3B	314	.	NM_152526	exon20	c.T2976C	p.S992S	GCCATCTGAGTAT	.	PASS	Atlas-SNP
CER1	9350	hgsc.bcm.edu	37	9	14720361	14720361	+	Silent	SNP	T	T	C	rs17289263	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	98	44	101	0	0.44898	0	T|0.907;C|0.093	0.093	strong	.	CER1	41	.	NM_005454	exon2	c.A531G	p.E177E	TACTTTTTCACAG	.	PASS	Atlas-SNP
LRRN3	54674	hgsc.bcm.edu	37	7	110764596	110764596	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	22	62	0	0.318841	0	.	.	none	.	LRRN3	132	.	NM_018334	exon2	c.A1768G	p.K590E	GAGTATAAAATTT	.	PASS	Atlas-SNP
OR1L4	254973	hgsc.bcm.edu	37	9	125486686	125486686	+	Missense_Mutation	SNP	T	T	A	rs149895531	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	209	111	218	1	0.5311	0.00458716	A|0.023;T|0.977	0.023	strong	.	OR1L4	38	.	NM_001005235	exon1	c.T418A	p.W140R	AAACCATGGCATT	.	PASS	Atlas-SNP
C20orf96	140680	hgsc.bcm.edu	37	20	259969	259969	+	Silent	SNP	G	G	C	rs7271033	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	22	12	32	0	0.545455	0	G|0.353;C|0.647	0.647	strong	.	C20orf96	28	.	NM_153269	exon5	c.C309G	p.T103T	GAGCGAGGTCTGC	.	PASS	Atlas-SNP
KIAA0317	9870	hgsc.bcm.edu	37	14	75142606	75142606	+	Silent	SNP	G	G	A	rs35864766	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	79	39	82	0	0.493671	0	G|0.985;A|0.015	0.015	strong	.	KIAA0317	68	.	NM_001039479	exon8	c.C876T	p.G292G	GCTCACGCCTGAA	.	PASS	Atlas-SNP
EBF4	57593	hgsc.bcm.edu	37	20	2739583	2739583	+	Silent	SNP	T	T	C	rs2073125	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	128	58	135	0	0.453125	0	T|0.647;C|0.353	0.353	strong	.	.	.	.	NM_001110514	exon17	c.T1755C	p.F585F	CAAGTTTCACTCT	.	PASS	Atlas-SNP
WDR73	84942	hgsc.bcm.edu	37	15	85189464	85189464	+	Silent	SNP	T	T	G	rs2271431	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	42	29	47	0	0.690476	0	T|0.830;G|0.170	0.170	strong	.	WDR73	15	.	NM_032856	exon6	c.A468C	p.R156R	CAGACTTCGGAGC	.	PASS	Atlas-SNP
DNAH10	196385	hgsc.bcm.edu	37	12	124417889	124417889	+	Silent	SNP	C	C	T	rs4930721	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	59	33	53	0	0.559322	0	C|0.719;T|0.281	0.281	strong	.	DNAH10	888	.	NM_207437	exon76	c.C12954T	p.S4318S	CGAGAGCGAGCCC	.	PASS	Atlas-SNP
AASDH	132949	hgsc.bcm.edu	37	4	57248716	57248716	+	Missense_Mutation	SNP	G	G	C	rs34228795	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	133	68	192	1	0.511278	0.00520833	G|0.967;C|0.033	0.033	strong	AASDH,NS,osteosarcoma,0,1	AASDH	101	1	NM_181806	exon3	c.C278G	p.P93R	GACGGTGGTGAAT	.	scavenged	Atlas-SNP
CEP192	55125	hgsc.bcm.edu	37	18	13069782	13069782	+	Missense_Mutation	SNP	C	C	T	rs6505780	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	65	33	84	0	0.507692	0	C|0.258;T|0.742	0.742	strong	.	CEP192	340	.	NM_032142	exon27	c.C5101T	p.L1701F	AATCTACTCCTTA	.	PASS	Atlas-SNP
FER	2241	hgsc.bcm.edu	37	5	108281909	108281909	+	Missense_Mutation	SNP	C	C	G	rs2229086	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	59	27	72	0	0.457627	0	C|0.956;G|0.044	0.044	strong	.	FER	100	.	NM_005246	exon11	c.C1315G	p.L439V	TCTGCACTGGGCT	.	PASS	Atlas-SNP
EIF2AK3	9451	hgsc.bcm.edu	37	2	88926522	88926522	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	24	59	0	0.338028	0	.	.	none	.	EIF2AK3	160	.	NM_004836	exon1	c.G271T	p.E91X	CTGGTTCCGGACC	.	PASS	Atlas-SNP
CARS2	79587	hgsc.bcm.edu	37	13	111298392	111298392	+	Silent	SNP	A	A	G	rs436462	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	84	45	95	0	0.535714	0	A|0.580;G|0.420	0.420	strong	.	CARS2	37	.	NM_024537	exon12	c.T1239C	p.D413D	GTCAAAATCATCT	.	PASS	Atlas-SNP
FAM35A	54537	hgsc.bcm.edu	37	10	88911841	88911841	+	Missense_Mutation	SNP	A	A	G	rs77879311	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	83	50	115	0	0.60241	0	A|0.850;G|0.150	0.150	strong	.	FAM35A	48	.	NM_019054	exon3	c.A730G	p.S244G	TTTCTCAGTATAA	.	PASS	Atlas-SNP
CRTAC1	55118	hgsc.bcm.edu	37	10	99664456	99664456	+	Silent	SNP	T	T	C	rs7068503	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	62	27	72	0	0.435484	0	T|0.914;C|0.086	0.086	strong	.	CRTAC1	86	.	NM_001206528	exon7	c.A966G	p.Q322Q	GCTCATTTGCAGA	.	PASS	Atlas-SNP
GDPGP1	390637	hgsc.bcm.edu	37	15	90784250	90784250	+	Missense_Mutation	SNP	T	T	C	rs7171194	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	161	159	107	0	0.987578	0	T|0.225;C|0.775	0.775	strong	.	.	.	.	NM_001013657	exon4	c.T110C	p.M37T	ATCTCATGGCAGA	.	PASS	Atlas-SNP
LRRTM1	347730	hgsc.bcm.edu	37	2	80529956	80529956	+	Missense_Mutation	SNP	T	T	C	rs6733871	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	150	81	195	0	0.54	0	C|0.316;N|0.000	0.316	strong	.	LRRTM1	251	.	NM_178839	exon2	c.A989G	p.N330S	AAGTTGTTGAGCC	.	PASS	Atlas-SNP
FRAS1	80144	hgsc.bcm.edu	37	4	79455733	79455733	+	Silent	SNP	C	C	T	rs4975139	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	112	58	151	0	0.517857	0	C|0.484;T|0.516	0.516	strong	.	FRAS1	779	.	NM_025074	exon71	c.C11056T	p.L3686L	ATGTCACTAGCAG	.	PASS	Atlas-SNP
ARHGEF19	128272	hgsc.bcm.edu	37	1	16534255	16534255	+	Missense_Mutation	SNP	C	C	G	rs221057	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	107	49	120	0	0.457944	0	C|0.778;G|0.222	0.222	strong	.	ARHGEF19	49	.	NM_153213	exon4	c.G712C	p.E238Q	GAGCCTCCATTCC	.	PASS	Atlas-SNP
C1orf106	55765	hgsc.bcm.edu	37	1	200867492	200867492	+	Silent	SNP	C	C	G	rs2271018	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	62	33	85	0	0.532258	0	C|0.788;G|0.212	0.212	strong	.	C1orf106	59	.	NM_018265	exon2	c.C261G	p.P87P	TCCCCCCTCCCTG	.	PASS	Atlas-SNP
CD3E	916	hgsc.bcm.edu	37	11	118178007	118178007	+	Silent	SNP	C	C	T	rs1126924	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	41	28	65	0	0.682927	0	C|0.768;T|0.232	0.232	strong	CD3E,NS,carcinoma,0,1	CD3E	23	1	NM_000733	exon3	c.C54T	p.G18G	AGTTGGCGTTTGG	.	PASS	Atlas-SNP
GJD2	57369	hgsc.bcm.edu	37	15	35044757	35044757	+	Silent	SNP	C	C	T	rs34964522	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	41	92	0	0.546667	0	C|0.925;T|0.075	0.075	strong	GJD2,bladder,carcinoma,-2,1	GJD2	49	1	NM_020660	exon2	c.G888A	p.E296E	ACGAATCTCATAG	.	PASS	Atlas-SNP
PHLPP2	23035	hgsc.bcm.edu	37	16	71682830	71682830	+	Missense_Mutation	SNP	C	C	T	rs61733124	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	191	110	184	0	0.575916	0	C|0.917;T|0.083	0.083	strong	.	PHLPP2	96	.	NM_015020	exon18	c.G3935A	p.R1312Q	TCGGTCCGATCCT	.	PASS	Atlas-SNP
FSD2	123722	hgsc.bcm.edu	37	15	83428192	83428192	+	Missense_Mutation	SNP	C	C	T	rs1108134	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	98	44	83	0	0.44898	0	C|0.869;T|0.131	0.131	strong	.	FSD2	45	.	NM_001007122	exon13	c.G2158A	p.E720K	CAAATTCGTGAAG	.	PASS	Atlas-SNP
EPHB3	2049	hgsc.bcm.edu	37	3	184299167	184299167	+	Silent	SNP	T	T	C	rs1138510	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	217	110	242	1	0.506912	0.00413223	T|0.632;C|0.368	0.368	strong	.	EPHB3	114	.	NM_004443	exon15	c.T2859C	p.S953S	TGCATCTTTTGAC	.	PASS	Atlas-SNP
DCHS2	54798	hgsc.bcm.edu	37	4	155295076	155295076	+	Missense_Mutation	SNP	A	A	G	rs11721758	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	96	39	92	0	0.40625	0	A|0.641;G|0.359	0.359	strong	.	DCHS2	594	.	NM_017639	exon4	c.T458C	p.V153A	ACCTTCACCAGGG	.	PASS	Atlas-SNP
CSF3R	1441	hgsc.bcm.edu	37	1	36938235	36938235	+	Silent	SNP	G	G	A	rs3918017	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	150	85	158	0	0.566667	0	G|0.987;A|0.013	0.013	strong	.	CSF3R	157	.	NM_156039	exon7	c.C726T	p.A242A	GGGAGGGGCCGCT	.	PASS	Atlas-SNP
NLRP8	126205	hgsc.bcm.edu	37	19	56485077	56485077	+	Missense_Mutation	SNP	A	A	G	rs61740015	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	77	43	101	0	0.558442	0	A|0.941;G|0.059	0.059	strong	.	NLRP8	225	.	NM_176811	exon7	c.A2594G	p.Q865R	TCAGGCAGAGTAA	.	PASS	Atlas-SNP
ADIRF	10974	hgsc.bcm.edu	37	10	88730312	88730312	+	Silent	SNP	T	T	C	rs4869	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	139	65	134	0	0.467626	0	T|0.489;C|0.511	0.511	strong	C10orf116,NS,carcinoma,0,1	.	.	1	NM_006829	exon3	c.T204C	p.I68I	TGGGATTGGGAAA	.	PASS	Atlas-SNP
MOCS2	4338	hgsc.bcm.edu	37	5	52397199	52397199	+	Missense_Mutation	SNP	G	G	A	rs2233218	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	148	71	126	0	0.47973	0	G|0.995;A|0.005	0.005	strong	.	MOCS2	28	.	NM_004531	exon5	c.C367T	p.H123Y	GTCTATGGAACAC	.	PASS	Atlas-SNP
TCOF1	6949	hgsc.bcm.edu	37	5	149776232	149776232	+	Missense_Mutation	SNP	C	C	T	rs15251	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	88	44	108	0	0.5	0	C|0.790;T|0.210	0.210	strong	.	TCOF1	154	.	NM_001135243	exon24	c.C4169T	p.A1390V	GGAAAGCAAAGAG	.	PASS	Atlas-SNP
HIST1H2BK	85236	hgsc.bcm.edu	37	6	27114289	27114289	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	105	34	90	0	0.32381	0	.	.	none	.	HIST1H2BK	68	.	NM_080593	exon1	c.A289G	p.T97A	CGGCCGTCTGGAT	.	PASS	Atlas-SNP
GALNT18	374378	hgsc.bcm.edu	37	11	11292700	11292700	+	Silent	SNP	G	G	C	rs10831567	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	64	12	46	0	0.1875	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
HSPG2	3339	hgsc.bcm.edu	37	1	22163402	22163402	+	Silent	SNP	G	G	A	rs41310390	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	43	16	41	0	0.372093	0	G|0.954;A|0.046	0.046	strong	.	HSPG2	311	.	NM_005529	exon75	c.C10248T	p.S3416S	CTCAACGCTGGCC	.	PASS	Atlas-SNP
PPP1R26	9858	hgsc.bcm.edu	37	9	138376972	138376972	+	Missense_Mutation	SNP	A	A	G	rs3928777	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	43	22	46	0	0.511628	0	A|0.724;G|0.276	0.276	strong	.	.	.	.	NM_014811	exon4	c.A616G	p.K206E	TCCAGCAAGGACC	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100684650	100684650	+	Missense_Mutation	SNP	C	C	G	rs12673753	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	63	37	72	0	0.587302	0	C|0.967;G|0.033	0.033	strong	.	MUC17	804	.	NM_001040105	exon3	c.C9953G	p.A3318G	CTCAAGCCAGTTC	.	PASS	Atlas-SNP
CCDC169	728591	hgsc.bcm.edu	37	13	36857639	36857639	+	Silent	SNP	T	T	C	rs1998800	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	107	50	142	0	0.46729	0	T|0.714;C|0.286	0.286	strong	.	CCDC169	20	.	NM_001144981	exon4	c.A282G	p.L94L	AGAAGATAGTCTA	.	PASS	Atlas-SNP
ARSD	414	hgsc.bcm.edu	37	X	2836041	2836041	+	Missense_Mutation	SNP	A	A	T	rs67272620	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	93	7	101	0	0.0752688	0	A|0.500;T|0.500	0.500	strong	.	ARSD	47	.	NM_001669	exon5	c.T667A	p.F223I	CAGAGAAGAAACC	.	PASS	Atlas-SNP
FCGBP	8857	hgsc.bcm.edu	37	19	40363926	40363926	+	Missense_Mutation	SNP	C	C	G	rs3746013	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	118	68	130	0	0.576271	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
CLN5	1203	hgsc.bcm.edu	37	13	77574983	77574983	+	Missense_Mutation	SNP	A	A	G	rs1800209	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	94	46	134	0	0.489362	0	A|0.774;G|0.226	0.226	strong	.	CLN5	32	.	NM_006493	exon4	c.A1103G	p.K368R	TGCACAAACAGTT	.	PASS	Atlas-SNP
AZU1	566	hgsc.bcm.edu	37	19	830820	830820	+	Missense_Mutation	SNP	G	G	A	rs28626600	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	42	14	36	0	0.333333	0	G|0.933;A|0.067	0.067	strong	AZU1,rectum,carcinoma,0,2	AZU1	31	2	NM_001700	exon4	c.G473A	p.R158H	GCCAGCGCAGTGG	.	PASS	Atlas-SNP
KLK2	3817	hgsc.bcm.edu	37	19	51379893	51379893	+	Silent	SNP	C	C	T	rs198972	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	37	87	0	0.451219	0	C|0.585;T|0.415	0.415	strong	.	KLK2	66	.	NM_001002231	exon3	c.C372T	p.L124L	GCTGCTCCGCCTG	.	PASS	Atlas-SNP
C5orf60	285679	hgsc.bcm.edu	37	5	179071958	179071958	+	Missense_Mutation	SNP	C	C	G	rs7731123	bycluster;byfrequency;by2hit2allele;byhapmap	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	276	51	316	0	0.184783	0	C|0.147;G|0.853	0.853	strong	C5orf60,NS,carcinoma,0,1	C5orf60	24	1	NM_001142306	exon1	c.G64C	p.D22H	CACTGTCCAGAGG	.	PASS	Atlas-SNP
ADAM32	203102	hgsc.bcm.edu	37	8	39091526	39091526	+	Silent	SNP	T	T	C	rs4515515	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	25	108	0	0.247525	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
LY75	4065	hgsc.bcm.edu	37	2	160676350	160676350	+	Missense_Mutation	SNP	T	T	C	rs17827158	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	145	65	196	0	0.448276	0	T|0.915;C|0.085	0.085	strong	.	LY75	151	.	NM_002349	exon29	c.A4040G	p.K1347R	AAAAACTTCTCAT	.	PASS	Atlas-SNP
DOCK4	9732	hgsc.bcm.edu	37	7	111503547	111503547	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	81	27	75	0	0.333333	0	.	.	none	.	DOCK4	365	.	NM_014705	exon23	c.A2354G	p.N785S	ACCAAGTTGGCTA	.	PASS	Atlas-SNP
CYTH3	9265	hgsc.bcm.edu	37	7	6227341	6227341	+	Silent	SNP	A	A	G	rs41282682	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	80	58	89	0	0.725	0	A|0.986;G|0.014	0.014	strong	.	CYTH3	44	.	NM_004227	exon3	c.T129C	p.Y43Y	AATTTCATATTTC	.	PASS	Atlas-SNP
AOX1	316	hgsc.bcm.edu	37	2	201501687	201501687	+	Silent	SNP	A	A	G	rs149839944	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	156	75	132	0	0.480769	0	A|0.999;G|0.001	0.001	strong	.	AOX1	152	.	NM_001159	exon22	c.A2400G	p.V800V	CCATGTAAGGCGT	.	PASS	Atlas-SNP
DOCK1	1793	hgsc.bcm.edu	37	10	129242515	129242515	+	Silent	SNP	G	G	A	rs11371	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	54	54	58	0	1	0	G|0.667;A|0.333	0.333	strong	.	DOCK1	188	.	NM_001380	exon50	c.G5322A	p.R1774R	ACCAAGGGCCAAG	.	PASS	Atlas-SNP
SNX30	401548	hgsc.bcm.edu	37	9	115598610	115598610	+	Missense_Mutation	SNP	A	A	G	rs76424583	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	59	26	100	0	0.440678	0	A|0.922;G|0.078	0.078	strong	.	SNX30	32	.	NM_001012994	exon5	c.A735G	p.I245M	TGCCATAGGTGAC	.	PASS	Atlas-SNP
GP2	2813	hgsc.bcm.edu	37	16	20335325	20335325	+	Silent	SNP	G	G	A	rs12930599	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	136	51	112	0	0.375	0	G|0.865;A|0.135	0.135	strong	.	GP2	122	.	NM_001007240	exon3	c.C348T	p.D116D	GGGAGCGTCTGTC	.	PASS	Atlas-SNP
CAMK1G	57172	hgsc.bcm.edu	37	1	209782343	209782343	+	Silent	SNP	A	A	G	rs11119314	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	122	67	126	0	0.54918	0	A|0.485;G|0.515	0.515	strong	CAMK1G,NS,adenoma,0,2	CAMK1G	49	2	NM_020439	exon8	c.A654G	p.P218P	CCCCCCATTCTAT	.	PASS	Atlas-SNP
INPP4A	3631	hgsc.bcm.edu	37	2	99172243	99172243	+	Silent	SNP	C	C	T	rs41486345	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	56	56	56	0	1	0	C|0.954;T|0.046	0.046	strong	.	INPP4A	205	.	NM_001134224	exon17	c.C1809T	p.S603S	GCCCTCCACTGCA	.	PASS	Atlas-SNP
TOM1	10043	hgsc.bcm.edu	37	22	35742925	35742925	+	Silent	SNP	T	T	G	rs743810	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	52	26	40	1	0.5	0.025	T|0.655;G|0.345	0.345	strong	TOM1,NS,carcinoma,0,1	TOM1	43	1	NM_001135732	exon14	c.T1287G	p.G429G	CCAGGGTAATGAT	.	scavenged	Atlas-SNP
GPSM2	29899	hgsc.bcm.edu	37	1	109446750	109446750	+	Missense_Mutation	SNP	G	G	A	rs61754640	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	156	71	144	0	0.455128	0	G|0.978;A|0.022	0.022	strong	.	GPSM2	56	.	NM_013296	exon10	c.G1066A	p.G356R	TAGGTTGGGGATA	.	PASS	Atlas-SNP
BNIP2	663	hgsc.bcm.edu	37	15	59963488	59963488	+	Silent	SNP	A	A	G	rs1135148	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	53	30	56	0	0.566038	0	A|0.703;G|0.297	0.297	strong	.	BNIP2	27	.	NM_004330	exon7	c.T964C	p.L322L	CTACTAATAGCTC	.	PASS	Atlas-SNP
LRRC16B	90668	hgsc.bcm.edu	37	14	24527220	24527220	+	Silent	SNP	C	C	T	rs4982853	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	71	86	0	0.986111	0	C|0.898;T|0.102	0.102	strong	.	LRRC16B	120	.	NM_138360	exon16	c.C1269T	p.Y423Y	CGCCTACACACTG	.	PASS	Atlas-SNP
LRP2	4036	hgsc.bcm.edu	37	2	170103351	170103351	+	Silent	SNP	G	G	T	rs2075249	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	175	80	194	0	0.457143	0	G|0.583;T|0.417	0.417	strong	.	LRP2	751	.	NM_004525	exon21	c.C3054A	p.T1018T	TTCATTGGTTGGG	.	PASS	Atlas-SNP
PCYT1A	5130	hgsc.bcm.edu	37	3	195965760	195965760	+	Silent	SNP	A	A	G	rs116712058	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	50	25	42	0	0.5	0	A|0.988;G|0.012	0.012	strong	.	PCYT1A	34	.	NM_005017	exon10	c.T903C	p.H301H	CAGCATATGTTTC	.	PASS	Atlas-SNP
KIAA0319	9856	hgsc.bcm.edu	37	6	24576706	24576706	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	359	65	490	0	0.181058	0	.	.	none	.	KIAA0319	117	.	NM_001168377	exon10	c.C1624T	p.P542S	TTTGGGGCAAAGT	.	PASS	Atlas-SNP
KRTAP4-12	83755	hgsc.bcm.edu	37	17	39279944	39279944	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	55	16	60	0	0.290909	0	.	.	none	.	KRTAP4-12	32	.	NM_031854	exon1	c.G431C	p.S144T	CAGCAGCTGGGGC	.	PASS	Atlas-SNP
LPA	4018	hgsc.bcm.edu	37	6	160952838	160952838	+	Missense_Mutation	SNP	G	G	A	rs3124784	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	323	322	521	0	0.996904	0	G|0.770;A|0.230	0.230	strong	.	LPA	237	.	NM_005577	exon40	c.C6046T	p.R2016C	TGGGGCGTGCACA	.	PASS	Atlas-SNP
ITGB2	3689	hgsc.bcm.edu	37	21	46320313	46320313	+	Silent	SNP	C	C	T	rs2230528	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	262	145	213	0	0.553435	0	T|0.201;G|0.000;C|0.798;N|0.001;A|0.000	0.201	strong	ITGB2,NS,malignant_melanoma,-2,1	ITGB2	107	1	NM_000211	exon7	c.G819A	p.G273G	CAGCTTCCCGTCG	.	PASS	Atlas-SNP
CA14	23632	hgsc.bcm.edu	37	1	150234657	150234657	+	Silent	SNP	G	G	T	rs34714364	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	99	45	111	0	0.454545	0	G|0.897;T|0.103	0.103	strong	.	CA14	37	.	NM_012113	exon4	c.G357T	p.G119G	CCCAGGGGGGTCA	.	PASS	Atlas-SNP
ZNF584	201514	hgsc.bcm.edu	37	19	58928786	58928786	+	Missense_Mutation	SNP	A	A	G	rs7257872	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	102	38	80	0	0.372549	0	A|0.686;G|0.314	0.314	strong	.	ZNF584	31	.	NM_173548	exon4	c.A901G	p.T301A	GAGTGTACAGAAT	.	PASS	Atlas-SNP
C6	729	hgsc.bcm.edu	37	5	41181578	41181578	+	Silent	SNP	T	T	A	rs61734263	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	154	94	146	0	0.61039	0	T|0.980;A|0.020	0.020	strong	.	C6	197	.	NM_001115131	exon7	c.A810T	p.S270S	TGAGAATGAGCCT	.	PASS	Atlas-SNP
UGT2A1	10941	hgsc.bcm.edu	37	4	70512787	70512787	+	Nonsense_Mutation	SNP	A	A	T	rs111696697	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	45	89	0	0.6	0	A|0.971;T|0.029	0.029	strong	.	UGT2A1	131	.	NM_001252274	exon2	c.T576A	p.Y192X	AGGAACATAGGAA	.	PASS	Atlas-SNP
KRT23	25984	hgsc.bcm.edu	37	17	39081713	39081713	+	Silent	SNP	A	A	G	rs8037	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	232	127	303	1	0.547414	0.00330033	A|0.501;G|0.499	0.499	strong	.	KRT23	59	.	NM_015515	exon7	c.T1035C	p.H345H	CAGTTCATGGCGT	.	PASS	Atlas-SNP
CACNA1E	777	hgsc.bcm.edu	37	1	181548341	181548341	+	Silent	SNP	A	A	G	rs17443123	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	181	78	237	0	0.430939	0	A|0.910;G|0.090	0.090	strong	CACNA1E,NS,carcinoma,+2,1	CACNA1E	778	1	NM_001205293	exon5	c.A750G	p.A250A	TCGAGCATGCTTC	.	PASS	Atlas-SNP
CDCP2	200008	hgsc.bcm.edu	37	1	54605769	54605769	+	Silent	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	138	68	177	0	0.492754	0	.	.	none	.	CDCP2	52	.	NM_201546	exon4	c.G774A	p.Q258Q	TACCTCCTGGCAT	.	PASS	Atlas-SNP
LENG8	114823	hgsc.bcm.edu	37	19	54967408	54967408	+	Missense_Mutation	SNP	C	C	T	rs75472495	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	128	68	140	0	0.53125	0	C|0.998;T|0.002	0.002	strong	LENG8,colon,carcinoma,-1,1	LENG8	73	1	NM_052925	exon9	c.C1288T	p.R430C	CCGACGCGCCACT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195508537	195508537	+	Missense_Mutation	SNP	A	A	G	rs73891106	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	30	24	119	0	0.8	0	A|0.500;G|0.500	0.500	strong	MUC4_ENST00000463781,NS,carcinoma,-1,3	MUC4	1505	3	NM_018406	exon2	c.T9914C	p.V3305A	GTGGATACTGAGG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195509346	195509346	+	Silent	SNP	G	G	T	rs371492604		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	102	12	39	4	0.117647	0.102564	.	.	weak	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.C9105A	p.T3035T	GTGACCGGTGGAT	.	scavenged	Atlas-SNP
OR10AD1	121275	hgsc.bcm.edu	37	12	48596484	48596484	+	Missense_Mutation	SNP	A	A	T	rs75413005	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	42	75	0	0.488372	0	A|0.934;T|0.066	0.066	strong	.	OR10AD1	24	.	NM_001004134	exon1	c.T592A	p.W198R	TTGCCCACAGACT	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1092843	1092843	+	Silent	SNP	C	C	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	67	5	48	0	0.0746269	0	.	.	none	MUC2_ENST00000441003,trunk,malignant_melanoma,+1,2	MUC2	614	2	NM_002457	exon30	c.C4662G	p.G1554G	CACCGGCACACAG	.	PASS	Atlas-SNP
OR2T35	403244	hgsc.bcm.edu	37	1	248801592	248801592	+	Missense_Mutation	SNP	C	C	T	rs78622116	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	11	4	33	3	0.363636	0.0909091	C|0.245;T|0.755	0.755	strong	OR2T35,caecum,carcinoma,0,1	OR2T35	19	1	NM_001001827	exon1	c.G968A	p.G323D	TGCTAGCCCTTCC	.	scavenged	Atlas-SNP
AMPH	273	hgsc.bcm.edu	37	7	38431511	38431511	+	Silent	SNP	C	C	T	rs2229922	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	102	27	93	0	0.264706	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
MUC4	4585	hgsc.bcm.edu	37	3	195505960	195505960	+	Missense_Mutation	SNP	G	G	C	rs376166		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	5	48	0	0.0694444	0	.	.	weak	MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	NM_018406	exon2	c.C12491G	p.T4164S	GCGTCGGTGACAG	.	scavenged	Atlas-SNP
OR8D1	283159	hgsc.bcm.edu	37	11	124179835	124179835	+	Silent	SNP	C	C	T	rs4936918	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	123	23	208	0	0.186992	0	C|0.669;T|0.331	0.331	strong	.	OR8D1	53	.	NM_001002917	exon1	c.G828A	p.V276V	GTAGAACACAGAG	.	PASS	Atlas-SNP
ATP9B	374868	hgsc.bcm.edu	37	18	77097360	77097360	+	Missense_Mutation	SNP	A	A	T	rs585033	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	38	20	64	0	0.526316	0	A|0.943;T|0.057	0.057	strong	.	ATP9B	96	.	NM_198531	exon19	c.A2194T	p.M732L	AGGGAGATGGAAC	.	PASS	Atlas-SNP
CCDC60	160777	hgsc.bcm.edu	37	12	119909961	119909961	+	Silent	SNP	C	C	T	rs17482508	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	31	63	0	0.534483	0	C|0.976;T|0.024	0.024	strong	.	CCDC60	84	.	NM_178499	exon3	c.C333T	p.T111T	GGACACCTTATTG	.	PASS	Atlas-SNP
TTC40	54777	hgsc.bcm.edu	37	10	134649709	134649709	+	Missense_Mutation	SNP	C	C	T	rs76581191	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	42	20	44	0	0.47619	0	C|0.990;T|0.010	0.010	strong	TTC40,NS,carcinoma,0,2	TTC40	100	2	NM_001200049	exon46	c.G6550A	p.G2184S	CAGCGCCGTACAG	.	PASS	Atlas-SNP
KCTD16	57528	hgsc.bcm.edu	37	5	143586416	143586416	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	129	3	208	0	0.0232558	0	.	.	none	KCTD16,scalp,carcinoma,0,1	KCTD16	70	1	NM_020768	exon3	c.C139T	p.P47S	AGCATCCCTCATT	.	scavenged	Atlas-SNP
NTAN1	123803	hgsc.bcm.edu	37	16	15133889	15133889	+	Silent	SNP	T	T	G	rs14347	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	55	42	81	0	0.763636	0	T|0.710;G|0.290	0.290	strong	.	NTAN1	21	.	NM_173474	exon8	c.A576C	p.A192A	AAAGGATGCTCTG	.	PASS	Atlas-SNP
LGALS2	3957	hgsc.bcm.edu	37	22	37966649	37966649	+	Silent	SNP	G	G	A	rs115686288	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	196	89	207	0	0.454082	0	G|0.993;A|0.007	0.007	strong	.	LGALS2	16	.	NM_006498	exon3	c.C183T	p.D61D	GCTGCCGTCCAAT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195515422	195515422	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	74	23	65	0	0.310811	0	.	.	none	.	MUC4	1505	.	NM_018406	exon2	c.C3029A	p.P1010H	GTGACAGGAAGAG	.	PASS	Atlas-SNP
FAT1	2195	hgsc.bcm.edu	37	4	187516880	187516880	+	Silent	SNP	A	A	G	rs1298865	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	107	50	103	0	0.46729	0	A|0.468;G|0.532	0.532	strong	.	FAT1	500	.	NM_005245	exon26	c.T13101C	p.S4367S	GCTCAGAGACTGC	.	PASS	Atlas-SNP
ARVCF	421	hgsc.bcm.edu	37	22	19965563	19965563	+	Missense_Mutation	SNP	C	C	T	rs16982871	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	95	36	104	0	0.378947	0	C|0.995;T|0.005	0.005	strong	.	ARVCF	54	.	NM_001670	exon8	c.G1616A	p.R539Q	CGGAGTCGCCGCC	.	PASS	Atlas-SNP
MACF1	23499	hgsc.bcm.edu	37	1	39549983	39549983	+	Silent	SNP	G	G	A	rs3736890	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	54	20	79	0	0.37037	0	G|0.867;A|0.133	0.133	strong	.	MACF1	909	.	NM_012090	exon3	c.G93A	p.S31S	GCGGTCGGGGAGC	.	PASS	Atlas-SNP
C14orf159	80017	hgsc.bcm.edu	37	14	91633706	91633706	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	106	20	107	0	0.188679	0	.	.	none	.	C14orf159	57	.	NM_001102366	exon6	c.G241A	p.A81T	CAAGGTGCTATCT	.	PASS	Atlas-SNP
TIAM1	7074	hgsc.bcm.edu	37	21	32638549	32638549	+	Missense_Mutation	SNP	C	C	A	rs2070417	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	96	59	109	0	0.614583	0	C|0.874;A|0.119	0.119	strong	.	TIAM1	522	.	NM_003253	exon5	c.G740T	p.G247V	GGCCCCCCGTTTG	.	PASS	Atlas-SNP
GCSAM	257144	hgsc.bcm.edu	37	3	111844089	111844089	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	41	8	60	0	0.195122	0	.	.	none	.	.	.	.	NM_001190259	exon5	c.C209A	p.S70X	GTAGATGACATTC	.	PASS	Atlas-SNP
LILRB1	10859	hgsc.bcm.edu	37	19	55148088	55148088	+	Silent	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	194	10	153	10	0.0515464	0.0653595	.	.	none	LILRB1,NS,carcinoma,0,1	LILRB1	140	1	NM_001081637	exon14	c.G1797A	p.R599R	GGACAGGCAGATG	.	scavenged	Atlas-SNP
TRIM48	79097	hgsc.bcm.edu	37	11	55029787	55029787	+	Missense_Mutation	SNP	G	G	A	rs12799381	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	88	61	115	0	0.693182	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
TJP2	9414	hgsc.bcm.edu	37	9	71862987	71862987	+	Silent	SNP	G	G	A	rs2095876	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	56	37	78	0	0.660714	0	G|0.763;A|0.237	0.237	strong	TJP2,colon,carcinoma,+2,1	TJP2	120	1	NM_001170416	exon19	c.G2820A	p.A940A	GGGCGCGGACTAT	.	PASS	Atlas-SNP
PCDHA8	56140	hgsc.bcm.edu	37	5	140221098	140221098	+	Missense_Mutation	SNP	C	C	G	rs62624460	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	49	22	55	0	0.44898	0	C|0.929;G|0.071	0.071	strong	.	PCDHA8	366	.	NM_031856	exon1	c.C192G	p.F64L	CCTGTTCCGGGTG	.	PASS	Atlas-SNP
RHOBTB2	23221	hgsc.bcm.edu	37	8	22863614	22863614	+	Silent	SNP	C	C	T	rs139953909	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	54	101	0	0.72	0	C|0.990;T|0.010	0.010	strong	.	RHOBTB2	67	.	NM_001160036	exon6	c.C504T	p.Y168Y	GCGCTACGCTGAC	.	PASS	Atlas-SNP
ZNF883	169834	hgsc.bcm.edu	37	9	115760345	115760345	+	Silent	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	53	9	80	0	0.169811	0	.	.	none	.	.	.	.	NM_001101338	exon5	c.A195G	p.G65G	TTTCTCTCCAGTA	.	PASS	Atlas-SNP
ZNF469	84627	hgsc.bcm.edu	37	16	88501386	88501386	+	Missense_Mutation	SNP	C	C	A	rs141218390	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	16	11	15	0	0.6875	0	C|0.923;A|0.077	0.077	strong	.	ZNF469	121	.	NM_001127464	exon2	c.C7424A	p.A2475E	CCCCCGCGGAGCC	.	PASS	Atlas-SNP
ANO7	50636	hgsc.bcm.edu	37	2	242163359	242163359	+	Missense_Mutation	SNP	G	G	A	rs7590653	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	42	103	0	0.482759	0	G|0.808;A|0.192	0.192	strong	.	ANO7	136	.	NM_001001891	exon24	c.G2734A	p.E912K	CAGCCCGAGGGCT	.	PASS	Atlas-SNP
ZSCAN32	54925	hgsc.bcm.edu	37	16	3434699	3434699	+	Missense_Mutation	SNP	A	A	G	rs27230	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	198	150	182	0	0.757576	0	A|0.885;G|0.115	0.115	strong	.	.	.	.	NM_017810	exon5	c.T358C	p.Y120H	CCTCATAAAAGAT	.	PASS	Atlas-SNP
NCAN	1463	hgsc.bcm.edu	37	19	19329924	19329924	+	Missense_Mutation	SNP	C	C	T	rs2228603	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	108	56	102	0	0.518519	0	C|0.950;T|0.050	0.050	strong	NCAN_ENST00000539499,NS,carcinoma,0,4	NCAN	277	4	NM_004386	exon3	c.C274T	p.P92S	GACTTGCCCATCC	.	PASS	Atlas-SNP
PASK	23178	hgsc.bcm.edu	37	2	242072357	242072357	+	Silent	SNP	G	G	A	rs34401965	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	112	52	106	0	0.464286	0	G|0.925;A|0.075	0.075	strong	.	PASK	230	.	NM_015148	exon9	c.C1395T	p.T465T	AGTCCCGGTGAAG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195505801	195505801	+	Missense_Mutation	SNP	G	G	A	rs200432267		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	111	24	73	0	0.216216	0	.	.	weak	MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	NM_018406	exon2	c.C12650T	p.A4217V	GTGGATGCTGAGG	.	scavenged	Atlas-SNP
OR2B2	81697	hgsc.bcm.edu	37	6	27879982	27879982	+	Missense_Mutation	SNP	A	A	G	rs61742093	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	39	91	0	0.52	0	A|0.943;G|0.057	0.057	strong	.	OR2B2	54	.	NM_033057	exon1	c.T116C	p.I39T	CCAAAGATTGTCA	.	PASS	Atlas-SNP
ZNF341	84905	hgsc.bcm.edu	37	20	32379263	32379263	+	Silent	SNP	T	T	C	rs2626551	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	52	51	59	0	0.980769	0	T|0.235;C|0.765	0.765	strong	ZNF341,rectum,carcinoma,0,1	ZNF341	73	1	NM_032819	exon15	c.T2484C	p.A828A	GCAGGCTGGGGCC	.	PASS	Atlas-SNP
PDE4DIP	9659	hgsc.bcm.edu	37	1	144952207	144952207	+	Missense_Mutation	SNP	C	C	T	rs55945104		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	790	135	808	0	0.170886	0	.	.	weak	.	PDE4DIP	817	.	NM_022359	exon7	c.G923A	p.R308K	TTGTCCCTCTGGG	.	PASS	Atlas-SNP
COL13A1	1305	hgsc.bcm.edu	37	10	71678058	71678058	+	Silent	SNP	C	C	G	rs2274181	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	35	18	28	0	0.514286	0	C|0.804;G|0.196	0.196	strong	COL13A1_ENST00000398978,NS,carcinoma,+2,2	COL13A1	133	2	NM_001130103	exon19	c.C1014G	p.A338A	AATTGCCGTGGCT	.	PASS	Atlas-SNP
CDC42BPG	55561	hgsc.bcm.edu	37	11	64601933	64601933	+	Silent	SNP	T	T	C	rs7933683	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	27	19	32	0	0.703704	0	T|0.722;C|0.278	0.278	strong	.	CDC42BPG	101	.	NM_017525	exon19	c.A2292G	p.T764T	CACCTGTGTCAGC	.	PASS	Atlas-SNP
HS3ST6	64711	hgsc.bcm.edu	37	16	1962132	1962132	+	Missense_Mutation	SNP	G	G	A	rs8055325	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	43	62	0	0.623188	0	G|0.549;A|0.451	0.451	strong	.	HS3ST6	26	.	NM_001009606	exon2	c.C395T	p.A132V	CGGGGGGCCTCTC	.	PASS	Atlas-SNP
PCSK9	255738	hgsc.bcm.edu	37	1	55505668	55505668	+	Missense_Mutation	SNP	C	C	T	rs11583680	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	102	55	90	0	0.539216	0	C|0.912;T|0.088	0.088	strong	PCSK9,NS,carcinoma,0,1	PCSK9	76	1	NM_174936	exon1	c.C158T	p.A53V	GCCTGGCCGAAGC	.	PASS	Atlas-SNP
ZDHHC13	54503	hgsc.bcm.edu	37	11	19184916	19184916	+	Missense_Mutation	SNP	A	A	G	rs12798330	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	102	21	87	0	0.205882	0	A|0.987;G|0.013	0.013	strong	.	ZDHHC13	40	.	NM_019028	exon11	c.A1175G	p.Y392C	TTTTCTATAAGAC	.	PASS	Atlas-SNP
FAM120B	84498	hgsc.bcm.edu	37	6	170627797	170627797	+	Missense_Mutation	SNP	A	A	G	rs9366138	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	35	11	52	0	0.314286	0	A|0.870;G|0.130	0.130	strong	.	FAM120B	108	.	NM_032448	exon2	c.A1319G	p.Y440C	CCATGTATACAGA	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	88	44	106	0	0.5	0	A|0.812;G|0.188	0.188	strong	.	PASK	230	.	NM_015148	exon10	c.T2706C	p.D902D	TAAGCCATCTCGA	.	PASS	Atlas-SNP
VTI1A	143187	hgsc.bcm.edu	37	10	114427978	114427978	+	Silent	SNP	G	G	A	rs17353359	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	193	84	255	0	0.435233	0	G|0.980;A|0.020	0.020	strong	.	VTI1A	15	.	NM_145206	exon6	c.G429A	p.E143E	CGTAGAGCAAATT	.	PASS	Atlas-SNP
PTPRN2	5799	hgsc.bcm.edu	37	7	157931119	157931119	+	Silent	SNP	A	A	G	rs1130500	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	91	90	124	1	0.989011	0.00806452	A|0.625;G|0.375	0.375	strong	.	PTPRN2	243	.	NM_130843	exon7	c.T999C	p.A333A	CAGCTCAGCCATG	.	PASS	Atlas-SNP
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057711	46057711	+	Missense_Mutation	SNP	G	G	C	rs4818948	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	156	44	128	1	0.282051	0.0078125	G|0.711;C|0.289	0.289	strong	KRTAP10-10,NS,carcinoma,0,1	KRTAP10-10	37	1	NM_181688	exon1	c.G377C	p.C126S	CTTCATGCTGCCA	.	scavenged	Atlas-SNP
MCMBP	79892	hgsc.bcm.edu	37	10	121596498	121596498	+	Silent	SNP	C	C	T	rs34118671	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	56	22	91	0	0.392857	0	C|0.887;T|0.113	0.113	strong	.	MCMBP	49	.	NM_024834	exon13	c.G1458A	p.Q486Q	CACCTTCTGCCAC	.	PASS	Atlas-SNP
WDR90	197335	hgsc.bcm.edu	37	16	708308	708308	+	Silent	SNP	G	G	A	rs369151964	alternate_allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	27	121	0	0.385714	0	.	.	alt	.	WDR90	107	.	NM_145294	exon22	c.G2730A	p.V910V	AGTCGTGGTGCTG	.	PASS	Atlas-SNP
IRG1	730249	hgsc.bcm.edu	37	13	77527764	77527764	+	Silent	SNP	T	T	A	rs17385627	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	148	64	191	0	0.432432	0	T|0.884;A|0.116	0.116	strong	.	IRG1	1	.	NM_001258406	exon2	c.T192A	p.V64V	CACTGTTTGGGGT	.	PASS	Atlas-SNP
MKI67	4288	hgsc.bcm.edu	37	10	129899922	129899922	+	Missense_Mutation	SNP	T	T	C	rs34750407	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	99	43	115	0	0.434343	0	T|0.926;C|0.074	0.074	strong	MKI67,right_upper_lobe,carcinoma,+1,1	MKI67	363	1	NM_002417	exon14	c.A9305G	p.E3102G	TGCTGTTCTGCCT	.	PASS	Atlas-SNP
COLGALT1	79709	hgsc.bcm.edu	37	19	17670201	17670201	+	Silent	SNP	C	C	T	rs62119894	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	103	53	124	0	0.514563	0	C|0.942;T|0.058	0.058	strong	.	.	.	.	NM_024656	exon2	c.C342T	p.S114S	CCATTCCGTGGAG	.	PASS	Atlas-SNP
MUC7	4589	hgsc.bcm.edu	37	4	71339723	71339723	+	Splice_Site	SNP	G	G	A	rs2306949	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	55	33	94	0	0.6	0	G|0.840;A|0.160	0.160	strong	.	MUC7	91	.	.	.	.	.	TTCCCAGGAGACA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195507379	195507379	+	Missense_Mutation	SNP	G	G	C	rs371423143		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	43	16	63	0	0.372093	0	.	.	weak	MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	NM_018406	exon2	c.C11072G	p.T3691R	TGACCTGTGGATG	.	scavenged	Atlas-SNP
LCT	3938	hgsc.bcm.edu	37	2	136547204	136547204	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	32	156	0	0.316832	0	.	.	none	.	LCT	309	.	NM_002299	exon16	c.G5500A	p.V1834M	GGACCACAGAGGC	.	PASS	Atlas-SNP
GEMIN5	25929	hgsc.bcm.edu	37	5	154287275	154287275	+	Silent	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	199	2	255	1	0.0100503	0.00392157	.	.	none	GEMIN5,colon,carcinoma,0,4	GEMIN5	120	4	NM_015465	exon16	c.G2271A	p.S757S	ATCAATCGATTCC	.	scavenged	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179462494	179462494	+	Silent	SNP	A	A	G	rs35833641	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	131	57	185	0	0.435115	0	A|0.821;G|0.179	0.179	strong	.	TTN	18412	.	NM_001267550	exon294	c.T57315C	p.H19105H	TCCAGCATGGACA	.	PASS	Atlas-SNP
MUC20	200958	hgsc.bcm.edu	37	3	195452805	195452805	+	Missense_Mutation	SNP	T	T	C	rs138659995	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	473	123	456	0	0.260042	0	T|0.856;C|0.144	0.144	strong	MUC20,NS,carcinoma,0,1	MUC20	84	1	NM_152673	exon3	c.T818C	p.L273P	CAGATCTCATCCC	.	PASS	Atlas-SNP
NOS1	4842	hgsc.bcm.edu	37	12	117685270	117685270	+	Silent	SNP	G	G	A	rs1047735	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	108	61	124	0	0.564815	0	G|0.652;A|0.348	0.348	strong	.	NOS1	240	.	NM_001204218	exon19	c.C2808T	p.H936H	CACAGCGTGTCCG	.	PASS	Atlas-SNP
PKHD1	5314	hgsc.bcm.edu	37	6	51483961	51483961	+	Missense_Mutation	SNP	T	T	C	rs9381994	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	86	87	0	0.988506	0	T|0.458;C|0.542	0.542	strong	PKHD1,colon,carcinoma,0,2	PKHD1	927	2	NM_138694	exon67	c.A12143G	p.Q4048R	TTCTCTTGGGAAA	.	PASS	Atlas-SNP
FBXO8	26269	hgsc.bcm.edu	37	4	175180938	175180938	+	Missense_Mutation	SNP	T	T	C	rs61748174	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	212	99	248	0	0.466981	0	T|0.997;C|0.003	0.003	strong	.	FBXO8	34	.	NM_012180	exon3	c.A368G	p.N123S	TTCTTATTGTATA	.	PASS	Atlas-SNP
MCMDC2	157777	hgsc.bcm.edu	37	8	67796120	67796120	+	Missense_Mutation	SNP	C	C	G	rs17332410	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	64	158	0	0.695652	0	C|0.950;G|0.050	0.050	strong	.	MCMDC2	84	.	NM_173518	exon9	c.C964G	p.L322V	AATTTGCTCAAGC	.	PASS	Atlas-SNP
OR10H2	26538	hgsc.bcm.edu	37	19	15839459	15839459	+	Silent	SNP	G	G	A	rs11669315	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	147	69	180	0	0.469388	0	G|0.839;A|0.161	0.161	strong	.	OR10H2	59	.	NM_013939	exon1	c.G606A	p.L202L	GGGCTTGGTATGT	.	PASS	Atlas-SNP
SETX	23064	hgsc.bcm.edu	37	9	135173685	135173685	+	Missense_Mutation	SNP	T	T	C	rs2296871	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	94	40	105	0	0.425532	0	C|0.380;N|0.000;T|0.620	0.380	strong	.	SETX	234	.	NM_015046	exon13	c.A5563G	p.T1855A	ACTCAGTTTTCCC	.	PASS	Atlas-SNP
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33037626	33037626	+	Silent	SNP	C	C	G	rs1042174	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	81	26	129	0	0.320988	0	C|0.687;G|0.313	0.313	strong	.	HLA-DPA1	20	.	NM_033554	exon2	c.G138C	p.T46T	TCTATGCGTCTGT	.	PASS	Atlas-SNP
ZNF423	23090	hgsc.bcm.edu	37	16	49671218	49671218	+	Silent	SNP	C	C	T	rs16947741	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	241	95	212	0	0.394191	0	C|0.973;T|0.027	0.027	strong	ZNF423_ENST00000262383,NS,carcinoma,0,2	ZNF423	463	2	NM_015069	exon4	c.G1845A	p.P615P	CCGCTTCGGGGAA	.	PASS	Atlas-SNP
HOXA11	3207	hgsc.bcm.edu	37	7	27222437	27222437	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	63	27	68	0	0.428571	0	.	.	none	.	HOXA11	29	.	NM_005523	exon2	c.A920G	p.Y307C	GCTGAGTAGTACT	.	PASS	Atlas-SNP
CACNA1H	8912	hgsc.bcm.edu	37	16	1254064	1254064	+	Missense_Mutation	SNP	C	C	T	rs145376050	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	13	70	0	0.178082	0	C|0.998;T|0.002	0.002	strong	.	CACNA1H	317	.	NM_021098	exon10	c.C2057T	p.P686L	CCCTGCCCAGCCC	.	PASS	Atlas-SNP
OR5L2	26338	hgsc.bcm.edu	37	11	55595116	55595116	+	Missense_Mutation	SNP	G	G	C	rs75822385	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	208	144	257	0	0.692308	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
CTBP2	1488	hgsc.bcm.edu	37	10	126714714	126714714	+	Missense_Mutation	SNP	G	G	C	rs2946994	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	148	69	161	0	0.466216	0	G|0.533;C|0.467	0.467	strong	CTBP2,colon,carcinoma,0,1	CTBP2	100	1	NM_022802	exon1	c.C1615G	p.Q539E	CCTTCTGGTACGG	.	PASS	Atlas-SNP
ZNF469	84627	hgsc.bcm.edu	37	16	88494604	88494604	+	Silent	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	100	64	113	0	0.64	0	.	.	none	.	ZNF469	121	.	NM_001127464	exon1	c.C726T	p.S242S	GAATAGCTTCCCA	.	PASS	Atlas-SNP
MYOF	26509	hgsc.bcm.edu	37	10	95111005	95111005	+	Silent	SNP	T	T	C	rs35669278	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	93	40	119	0	0.430108	0	T|0.950;C|0.050	0.050	strong	.	MYOF	177	.	NM_013451	exon35	c.A3870G	p.L1290L	CATGTATAGATTT	.	PASS	Atlas-SNP
PDE1C	5137	hgsc.bcm.edu	37	7	31920395	31920395	+	Silent	SNP	G	G	A	rs61729940	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	62	9	107	0	0.145161	0	A|0.094;G|0.906;T|0.000	0.094	strong	.	PDE1C	465	.	NM_001191058	exon4	c.C387T	p.A129A	CACTGTGGCTGCA	.	PASS	Atlas-SNP
LILRB1	10859	hgsc.bcm.edu	37	19	55143156	55143156	+	Silent	SNP	T	T	C	rs34880987	alternate_allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	149	148	200	0	0.993289	0	.	.	alt	.	LILRB1	140	.	NM_001081637	exon4	c.T276C	p.H92H	GGAACATGCAGGG	.	PASS	Atlas-SNP
ANKK1	255239	hgsc.bcm.edu	37	11	113266821	113266821	+	Missense_Mutation	SNP	G	G	A	rs7118900	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	119	24	128	0	0.201681	0	G|0.714;A|0.286	0.286	strong	.	ANKK1	83	.	NM_178510	exon5	c.G715A	p.A239T	CGAGTGGCGGCAG	.	PASS	Atlas-SNP
RYR3	6263	hgsc.bcm.edu	37	15	33905410	33905410	+	Missense_Mutation	SNP	A	A	G	rs2229116	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	115	55	138	1	0.478261	0.00724638	A|0.790;G|0.210	0.210	strong	RYR3,colon,carcinoma,0,1	RYR3	760	1	NM_001243996	exon19	c.A2191G	p.I731V	GCTTCCATCAACC	.	scavenged	Atlas-SNP
MAP1A	4130	hgsc.bcm.edu	37	15	43816917	43816917	+	Silent	SNP	G	G	A	rs1060939	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	141	43	118	0	0.304965	0	G|0.497;A|0.503	0.503	strong	.	MAP1A	189	.	NM_002373	exon4	c.G3246A	p.G1082G	TGAGGGGCTTACA	.	PASS	Atlas-SNP
HGFAC	3083	hgsc.bcm.edu	37	4	3451109	3451109	+	Missense_Mutation	SNP	G	G	A	rs2498323	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	217	99	234	0	0.456221	0	G|0.909;A|0.091	0.091	strong	HGFAC,NS,carcinoma,0,1	HGFAC	69	1	NM_001528	exon14	c.G1931A	p.R644Q	ACGACCGGATACG	.	PASS	Atlas-SNP
ENTPD6	955	hgsc.bcm.edu	37	20	25193949	25193949	+	Silent	SNP	G	G	A	rs2076561	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	66	36	83	0	0.545455	0	G|0.708;A|0.292	0.292	strong	ENTPD6,face,carcinoma,+2,1	ENTPD6	57	1	NM_001247	exon5	c.G504A	p.P168P	CATTCCGTTCGAC	.	PASS	Atlas-SNP
RTN3	10313	hgsc.bcm.edu	37	11	63486204	63486204	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	42	12	67	0	0.285714	0	.	.	none	.	RTN3	104	.	NM_001265589	exon3	c.C230T	p.P77L	ATGAGCCATCTTC	.	PASS	Atlas-SNP
MYOM2	9172	hgsc.bcm.edu	37	8	2037833	2037833	+	Silent	SNP	G	G	C	rs2294061	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	90	63	107	0	0.7	0	G|0.783;C|0.217	0.217	strong	.	MYOM2	251	.	NM_003970	exon15	c.G1647C	p.S549S	GTAGTCGGTGGTG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195513397	195513397	+	Missense_Mutation	SNP	C	C	T	rs201019164		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	156	14	240	0	0.0897436	0	.	.	weak	MUC4_ENST00000463781,NS,carcinoma,-1,3	MUC4	1505	3	NM_018406	exon2	c.G5054A	p.G1685D	GAAAGGCCGGTGA	.	PASS	Atlas-SNP
SLC7A6OS	84138	hgsc.bcm.edu	37	16	68336360	68336360	+	Silent	SNP	A	A	G	rs35736950	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	323	191	280	1	0.591331	0.00357143	A|0.965;G|0.035	0.035	strong	.	SLC7A6OS	22	.	NM_032178	exon4	c.T723C	p.D241D	CTCGTCATCTTCA	.	PASS	Atlas-SNP
PCDHB11	56125	hgsc.bcm.edu	37	5	140580772	140580772	+	Silent	SNP	T	T	C	rs57636116	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	119	63	122	0	0.529412	0	T|0.869;C|0.131	0.131	strong	.	PCDHB11	162	.	NM_018931	exon1	c.T1425C	p.A475A	CAGCGCTACAGAC	.	PASS	Atlas-SNP
ILDR1	286676	hgsc.bcm.edu	37	3	121712051	121712051	+	Silent	SNP	A	A	C	rs2877561	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	249	246	222	0	0.987952	0	A|0.224;C|0.776	0.776	strong	.	ILDR1	120	.	NM_001199799	exon7	c.T1545G	p.L515L	GATATCAAGTGAG	.	PASS	Atlas-SNP
DEFB110	245913	hgsc.bcm.edu	37	6	49986788	49986788	+	Nonsense_Mutation	SNP	T	T	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	168	40	181	0	0.238095	0	.	.	none	.	DEFB110	5	.	NM_001037497	exon2	c.A106T	p.R36X	CTATTCTGCACTC	.	PASS	Atlas-SNP
ZKSCAN2	342357	hgsc.bcm.edu	37	16	25263278	25263278	+	Missense_Mutation	SNP	G	G	A	rs2112811	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	186	79	171	0	0.424731	0	G|0.696;N|0.000	.	strong	ZKSCAN2,NS,adenoma,0,2	ZKSCAN2	90	2	NM_001012981	exon4	c.C757T	p.L253F	GGTAGAGGTCCCT	.	PASS	Atlas-SNP
ATXN1	6310	hgsc.bcm.edu	37	6	16327330	16327330	+	Silent	SNP	T	T	C	rs2075974	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	45	20	63	0	0.444444	0	T|0.695;C|0.305	0.305	strong	.	ATXN1	117	.	NM_001128164	exon7	c.A1212G	p.E404E	GGAGGCTTCACGA	.	PASS	Atlas-SNP
KRTAP12-3	386683	hgsc.bcm.edu	37	21	46077946	46077946	+	Missense_Mutation	SNP	A	A	G	rs9306111	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	146	144	165	0	0.986301	0	A|0.246;G|0.754	0.754	strong	.	KRTAP12-3	18	.	NM_198697	exon1	c.A50G	p.H17R	GCATACACAGCCC	.	PASS	Atlas-SNP
FSCB	84075	hgsc.bcm.edu	37	14	44975349	44975349	+	Missense_Mutation	SNP	G	G	A	rs139581441	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	89	37	109	0	0.41573	0	G|0.997;A|0.003	0.003	strong	FSCB,NS,carcinoma,0,1	FSCB	173	1	NM_032135	exon1	c.C842T	p.A281V	GGCTCCGCTTTAG	.	PASS	Atlas-SNP
ZNF14	7561	hgsc.bcm.edu	37	19	19823270	19823270	+	Missense_Mutation	SNP	T	T	A	rs12973901	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	44	29	33	0	0.659091	0	T|0.808;A|0.192	0.192	strong	.	ZNF14	89	.	NM_021030	exon4	c.A820T	p.T274S	CTCCAGTGTGAGT	.	PASS	Atlas-SNP
ANO8	57719	hgsc.bcm.edu	37	19	17439450	17439450	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	22	4	25	0	0.181818	0	.	.	none	.	ANO8	67	.	NM_020959	exon13	c.G1747A	p.E583K	CGTCCTCCTCCTT	.	PASS	Atlas-SNP
HOXD3	3232	hgsc.bcm.edu	37	2	177036754	177036754	+	Silent	SNP	T	T	C	rs1051929	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	22	56	0	0.37931	0	T|0.243;C|0.757	0.757	strong	HOXD3,NS,carcinoma,0,3	HOXD3	65	3	NM_006898	exon3	c.T1051C	p.L351L	GCCAACTTGCAGG	.	PASS	Atlas-SNP
BAZ2B	29994	hgsc.bcm.edu	37	2	160294842	160294842	+	Missense_Mutation	SNP	A	A	G	rs3213790	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	205	104	264	0	0.507317	0	A|0.860;G|0.140	0.140	strong	.	BAZ2B	196	.	NM_013450	exon8	c.T1265C	p.L422S	GTCAATAAACTAG	.	PASS	Atlas-SNP
GEMIN4	50628	hgsc.bcm.edu	37	17	650518	650518	+	Silent	SNP	G	G	A	rs35696687	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	122	56	130	0	0.459016	0	G|0.897;A|0.103	0.103	strong	.	GEMIN4	116	.	NM_015721	exon2	c.C765T	p.D255D	GGGGTCGTCCTCT	.	PASS	Atlas-SNP
THBS1	7057	hgsc.bcm.edu	37	15	39879717	39879717	+	Silent	SNP	G	G	A	rs2229364	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	54	29	58	0	0.537037	0	G|0.874;A|0.126	0.126	strong	.	THBS1	106	.	NM_003246	exon8	c.G1290A	p.K430K	TGACAAGAGATGT	.	PASS	Atlas-SNP
ADCYAP1R1	117	hgsc.bcm.edu	37	7	31142970	31142970	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	116	3	150	0	0.0258621	0	.	.	none	ADCYAP1R1,right_lower_lobe,carcinoma,0,1	ADCYAP1R1	78	1	NM_001199635	exon15	c.G1250A	p.G417D	GGCTGGGCTCCTT	.	scavenged	Atlas-SNP
CCDC168	643677	hgsc.bcm.edu	37	13	103394421	103394421	+	Missense_Mutation	SNP	T	T	C	rs111294175	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	191	96	202	0	0.502618	0	T|0.998;C|0.002	0.002	strong	.	.	.	.	NM_001146197	exon4	c.A8626G	p.K2876E	TGTCTTTTGGCTT	.	PASS	Atlas-SNP
GUCY2D	3000	hgsc.bcm.edu	37	17	7909890	7909890	+	Silent	SNP	C	C	T	rs61749678	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	79	37	91	0	0.468354	0	C|0.999;T|0.001	0.001	strong	.	GUCY2D	82	.	NM_000180	exon4	c.C1236T	p.D412D	GGGAGACCGGCTT	.	PASS	Atlas-SNP
CWC27	10283	hgsc.bcm.edu	37	5	64273018	64273018	+	Silent	SNP	G	G	A	rs1309581	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	262	146	269	0	0.557252	0	G|0.631;A|0.369	0.369	strong	.	CWC27	47	.	NM_005869	exon13	c.G1209A	p.T403T	TGAAACGCCTGAA	.	PASS	Atlas-SNP
KLHL32	114792	hgsc.bcm.edu	37	6	97580539	97580539	+	Silent	SNP	A	A	G	rs13208956	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	47	24	71	0	0.510638	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
PTPRB	5787	hgsc.bcm.edu	37	12	71029733	71029733	+	Missense_Mutation	SNP	C	C	T	rs2584021	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	260	130	261	0	0.5	0	C|0.773;T|0.227	0.227	strong	.	PTPRB	676	.	NM_001109754	exon2	c.G169A	p.D57N	TTTCATCCTCAGT	.	PASS	Atlas-SNP
SDK2	54549	hgsc.bcm.edu	37	17	71426656	71426656	+	Missense_Mutation	SNP	G	G	T	rs1105353	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	23	13	44	0	0.565217	0	G|0.817;N|0.000	.	strong	.	SDK2	219	.	NM_001144952	exon12	c.C1577A	p.T526N	CTGATGGTTACTC	.	PASS	Atlas-SNP
TGM5	9333	hgsc.bcm.edu	37	15	43545728	43545728	+	Silent	SNP	G	G	A	rs555001	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	52	21	65	0	0.403846	0	G|0.539;A|0.461	0.461	strong	.	TGM5	88	.	NM_201631	exon5	c.C660T	p.Y220Y	GCTGACGTAGACG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195509974	195509974	+	Missense_Mutation	SNP	A	A	G	rs200426444	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	141	30	110	1	0.212766	0.00909091	.	.	weak	MUC4_ENST00000463781,brain,glioma,0,2	MUC4	1505	2	NM_018406	exon2	c.T8477C	p.F2826S	CCTGTGAACACTG	.	scavenged	Atlas-SNP
CDHR5	53841	hgsc.bcm.edu	37	11	617420	617420	+	Silent	SNP	A	A	G	rs61877857	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	66	48	79	1	0.727273	0.0126582	A|0.675;G|0.325	0.325	strong	CDHR5,rectum,carcinoma,0,2	CDHR5	77	2	NM_021924	exon15	c.T2469C	p.D823D	GCCCTCATCGCCG	.	scavenged	Atlas-SNP
EPHX1	2052	hgsc.bcm.edu	37	1	226019633	226019633	+	Missense_Mutation	SNP	T	T	C	rs1051740	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	39	70	0	0.557143	0	C|0.290;N|0.000	0.290	strong	.	EPHX1	57	.	NM_001136018	exon3	c.T337C	p.Y113H	AACAGATACCCTC	.	PASS	Atlas-SNP
PSG8	440533	hgsc.bcm.edu	37	19	43259169	43259169	+	Missense_Mutation	SNP	C	C	T	rs140722778	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	28	15	55	0	0.535714	0	C|0.998;T|0.002	0.002	strong	PSG8_ENST00000404209,NS,carcinoma,0,5	PSG8	101	5	NM_001130167	exon4	c.G959A	p.R320H	TAACTGCGGATGC	.	PASS	Atlas-SNP
NRCAM	4897	hgsc.bcm.edu	37	7	107834734	107834734	+	Silent	SNP	C	C	T	rs404287	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	354	353	479	2	0.997175	0.00417537	C|0.299;T|0.701	0.701	strong	.	NRCAM	267	.	NM_001037132	exon13	c.G1602A	p.A534A	ATTCTTCGCCATC	.	PASS	Atlas-SNP
FCGBP	8857	hgsc.bcm.edu	37	19	40366374	40366374	+	Silent	SNP	G	G	C	rs2053089	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	163	71	127	0	0.435583	0	G|0.828;C|0.172	0.172	strong	FCGBP,NS,carcinoma,-1,1	FCGBP	416	1	NM_003890	exon30	c.C13860G	p.P4620P	GTCTGCGGGGTCC	.	PASS	Atlas-SNP
NR1I2	8856	hgsc.bcm.edu	37	3	119531709	119531709	+	Silent	SNP	C	C	T	rs61755051	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	33	60	0	0.458333	0	C|0.993;T|0.007	0.007	strong	.	NR1I2	44	.	NM_022002	exon5	c.C813T	p.G271G	CAGTGGCGGGAAA	.	PASS	Atlas-SNP
ACAD8	27034	hgsc.bcm.edu	37	11	134128923	134128923	+	Missense_Mutation	SNP	C	C	G	rs113488591	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	138	26	121	0	0.188406	0	C|0.985;G|0.015	0.015	strong	.	ACAD8	33	.	NM_014384	exon5	c.C512G	p.S171C	CTGCCTCTCTTCT	.	PASS	Atlas-SNP
AASDH	132949	hgsc.bcm.edu	37	4	57221348	57221348	+	Missense_Mutation	SNP	T	T	C	rs3796543	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	63	29	82	0	0.460317	0	T|0.950;C|0.050	0.050	strong	.	AASDH	101	.	NM_181806	exon6	c.A1103G	p.K368R	CCTTACTTGAGAG	.	PASS	Atlas-SNP
MAP2K2	5605	hgsc.bcm.edu	37	19	4101062	4101062	+	Silent	SNP	G	G	T	rs11539507		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	145	68	160	0	0.468966	0	.	.	weak	MAP2K2_ENST00000262948,NS,carcinoma,0,2	MAP2K2	72	2	NM_030662	exon6	c.C660A	p.I220I	GGAGTCGATGAGC	.	PASS	Atlas-SNP
VCAN	1462	hgsc.bcm.edu	37	5	82816190	82816190	+	Missense_Mutation	SNP	A	A	G	rs61754531	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	64	34	88	0	0.53125	0	A|0.993;G|0.007	0.007	strong	.	VCAN	498	.	NM_004385	exon7	c.A2065G	p.T689A	ACAGAAACACTAA	.	PASS	Atlas-SNP
PTBP1	5725	hgsc.bcm.edu	37	19	804642	804642	+	Silent	SNP	C	C	T	rs3170451	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	66	66	54	0	1	0	C|0.860;T|0.140	0.140	strong	PTBP1,NS,carcinoma,0,1	PTBP1	43	1	NM_031990	exon6	c.C546T	p.P182P	GAGCCCCGTGCTC	.	PASS	Atlas-SNP
COL6A3	1293	hgsc.bcm.edu	37	2	238243292	238243292	+	Missense_Mutation	SNP	G	G	A	rs1131296	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	44	111	0	0.435644	0	G|0.635;A|0.365	0.365	strong	.	COL6A3	608	.	NM_004369	exon41	c.C9206T	p.T3069I	TGGTAGGTGGCTC	.	PASS	Atlas-SNP
PROM2	150696	hgsc.bcm.edu	37	2	95947085	95947085	+	Missense_Mutation	SNP	A	A	G	rs12992066	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	77	76	72	0	0.987013	0	A|0.207;C|0.000;G|0.793;T|0.000	0.793	strong	.	PROM2	78	.	NM_001165977	exon12	c.A1523G	p.Q508R	TGTGCCAGAGCTG	.	PASS	Atlas-SNP
SLITRK3	22865	hgsc.bcm.edu	37	3	164905688	164905688	+	Silent	SNP	G	G	A	rs17449404	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	102	50	119	0	0.490196	0	G|0.914;A|0.086	0.086	strong	.	SLITRK3	263	.	NM_014926	exon2	c.C2931T	p.F977F	CTGTTAGAACCTG	.	PASS	Atlas-SNP
RALGAPA2	57186	hgsc.bcm.edu	37	20	20493222	20493222	+	Silent	SNP	G	G	A	rs35039408	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	96	96	119	0	1	0	G|0.683;A|0.317	0.317	strong	RALGAPA2_ENST00000202677,NS,carcinoma,0,3	RALGAPA2	274	3	NM_020343	exon32	c.C4791T	p.P1597P	TCCTCGGGGCTCC	.	PASS	Atlas-SNP
LY75	4065	hgsc.bcm.edu	37	2	160711045	160711045	+	Missense_Mutation	SNP	G	G	C	rs3951216	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	170	75	182	0	0.441176	0	G|0.536;C|0.464	0.464	strong	.	LY75	151	.	NM_002349	exon18	c.C2421G	p.D807E	AGCACGGTCTAAA	.	PASS	Atlas-SNP
ARSD	414	hgsc.bcm.edu	37	X	2835964	2835964	+	Silent	SNP	G	G	A	rs73632972	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	148	16	166	0	0.108108	0	G|0.500;A|0.500	0.500	strong	.	ARSD	47	.	NM_001669	exon5	c.C744T	p.F248F	AAACCCGAAGGAG	.	PASS	Atlas-SNP
RP1L1	94137	hgsc.bcm.edu	37	8	10467571	10467571	+	Missense_Mutation	SNP	C	C	T	rs200175359		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	107	8	138	1	0.0747664	0.00724638	.	.	weak	RP1L1,NS,carcinoma,-1,1	RP1L1	453	1	NM_178857	exon4	c.G4037A	p.G1346E	CCTTCTCCTTCTG	.	scavenged	Atlas-SNP
SORCS1	114815	hgsc.bcm.edu	37	10	108389111	108389111	+	Silent	SNP	A	A	G	rs3802553	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	39	77	0	0.47561	0	A|0.841;G|0.159	0.159	strong	.	SORCS1	534	.	NM_001206572	exon19	c.T2511C	p.F837F	ATCGCCAAAGTCC	.	PASS	Atlas-SNP
KCNJ18	100134444	hgsc.bcm.edu	37	17	21319399	21319399	+	Missense_Mutation	SNP	A	A	G	rs4985866	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	148	29	178	0	0.195946	0	A|0.625;G|0.375	0.375	strong	KCNJ12,NS,neuroblastoma,0,1	.	.	1	NM_001194958	exon3	c.A745G	p.I249V	GACCAGATCGACA	.	PASS	Atlas-SNP
CD207	50489	hgsc.bcm.edu	37	2	71058184	71058184	+	Silent	SNP	C	C	T	rs13421115	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	93	93	124	0	1	0	C|0.806;T|0.194	0.194	strong	.	CD207	47	.	NM_015717	exon6	c.G984A	p.P328P	CTGTCACGGTTCT	.	PASS	Atlas-SNP
UBXN11	91544	hgsc.bcm.edu	37	1	26608877	26608877	+	Silent	SNP	G	G	A	rs1134582	byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	29	12	25	1	0.413793	0.04	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
PLCB2	5330	hgsc.bcm.edu	37	15	40590134	40590134	+	Silent	SNP	G	G	A	rs2229690	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	90	43	96	0	0.477778	0	G|0.349;A|0.651	0.651	strong	PLCB2_ENST00000260402,NS,carcinoma,0,2	PLCB2	177	2	NM_004573	exon12	c.C1182T	p.S394S	AAAGGCGCTTTCT	.	PASS	Atlas-SNP
ALMS1	7840	hgsc.bcm.edu	37	2	73717656	73717656	+	Missense_Mutation	SNP	A	A	G	rs10193972	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	136	136	137	1	1	0.00729927	A|0.675;G|0.325	0.325	strong	.	ALMS1	384	.	NM_015120	exon10	c.A8567G	p.N2856S	GAGTAAACAGATC	.	PASS	Atlas-SNP
SHANK3	85358	hgsc.bcm.edu	37	22	51153371	51153371	+	Missense_Mutation	SNP	G	G	A	rs61729471	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	32	65	0	0.551724	0	G|0.988;A|0.012	0.012	strong	.	SHANK3	96	.	NM_033517	exon19	c.G2119A	p.A707T	GCAGCCGCCGCAG	.	PASS	Atlas-SNP
ZNF217	7764	hgsc.bcm.edu	37	20	52193542	52193542	+	Silent	SNP	C	C	T	rs61748380	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	122	68	126	0	0.557377	0	C|0.998;T|0.002	0.002	strong	.	ZNF217	227	.	NM_006526	exon3	c.G1761A	p.L587L	GCTGCCCAGAACA	.	PASS	Atlas-SNP
HTRA1	5654	hgsc.bcm.edu	37	10	124249118	124249118	+	Silent	SNP	C	C	T	rs17624021	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	98	46	139	0	0.469388	0	C|0.966;T|0.034	0.034	strong	.	HTRA1	40	.	NM_002775	exon3	c.C753T	p.I251I	AGACATCGCACTC	.	PASS	Atlas-SNP
APOA5	116519	hgsc.bcm.edu	37	11	116662407	116662407	+	Missense_Mutation	SNP	G	G	C	rs3135506	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	133	32	122	0	0.240602	0	G|0.891;C|0.109	0.109	strong	APOA5,colon,carcinoma,0,1	APOA5	34	1	NM_001166598	exon3	c.C56G	p.S19W	GTGGCCGAAAACG	.	PASS	Atlas-SNP
MS4A6E	245802	hgsc.bcm.edu	37	11	60102507	60102507	+	Missense_Mutation	SNP	G	G	T	rs2304933	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	129	90	175	0	0.697674	0	G|0.705;T|0.295	0.295	strong	.	MS4A6E	22	.	NM_139249	exon1	c.G139T	p.V47F	GTCAAAGTTATTG	.	PASS	Atlas-SNP
SLC15A2	6565	hgsc.bcm.edu	37	3	121641693	121641693	+	Silent	SNP	G	G	A	rs2293616	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	29	108	0	0.408451	0	G|0.524;A|0.476	0.476	strong	.	SLC15A2	92	.	NM_021082	exon9	c.G852A	p.A284A	CTGGGCGGCTGAG	.	PASS	Atlas-SNP
MRPL43	84545	hgsc.bcm.edu	37	10	102746503	102746503	+	Silent	SNP	C	C	T	rs2863095	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	46	17	68	0	0.369565	0	C|0.704;T|0.296	0.296	strong	.	MRPL43	16	.	NM_032112	exon3	c.G468A	p.V156V	TGCTTGCACCTGG	.	PASS	Atlas-SNP
WDR35	57539	hgsc.bcm.edu	37	2	20131079	20131079	+	Missense_Mutation	SNP	T	T	C	rs1191778	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	168	96	168	0	0.571429	0	T|0.710;C|0.290	0.290	strong	WDR35,NS,carcinoma,-1,1	WDR35	92	1	NM_001006657	exon25	c.A2948G	p.E983G	ATCTGTTCATGGT	.	PASS	Atlas-SNP
TNFRSF6B	8771	hgsc.bcm.edu	37	20	62328829	62328829	+	Silent	SNP	C	C	G	rs1291205	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	109	65	127	0	0.59633	0	C|0.792;G|0.208	0.208	strong	TNFRSF6B,caecum,carcinoma,0,1	TNFRSF6B	22	1	NM_003823	exon2	c.C573G	p.T191T	TGACACCCTGTGC	.	PASS	Atlas-SNP
SBNO1	55206	hgsc.bcm.edu	37	12	123794104	123794104	+	Silent	SNP	G	G	T	rs3825141	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	44	128	1	0.478261	0.0078125	G|0.932;T|0.068	0.068	strong	SBNO1,NS,carcinoma,+1,2	SBNO1	138	2	NM_001167856	exon26	c.C3469A	p.R1157R	TTTTCCGCACTTT	.	scavenged	Atlas-SNP
PRKAA2	5563	hgsc.bcm.edu	37	1	57158051	57158051	+	Silent	SNP	G	G	A	rs17848595	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	190	108	146	0	0.568421	0	G|0.891;A|0.109	0.109	strong	.	PRKAA2	177	.	NM_006252	exon4	c.G351A	p.R117R	AGCCAGGCGGCTC	.	PASS	Atlas-SNP
USHBP1	83878	hgsc.bcm.edu	37	19	17366278	17366278	+	Silent	SNP	T	T	C	rs4430871	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	56	56	70	0	1	0	T|0.284;C|0.716	0.716	strong	.	USHBP1	85	.	NM_031941	exon10	c.A1608G	p.A536A	GAGCTCTGCCCGT	.	PASS	Atlas-SNP
ZNF446	55663	hgsc.bcm.edu	37	19	58991900	58991900	+	Missense_Mutation	SNP	G	G	A	rs882610	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	91	27	78	1	0.296703	0.0128205	G|0.697;A|0.303	0.303	strong	ZNF446,NS,carcinoma,+1,1	ZNF446	22	1	NM_017908	exon7	c.G1160A	p.R387H	CCCGACGCTCACT	.	scavenged	Atlas-SNP
KIAA1217	56243	hgsc.bcm.edu	37	10	24813585	24813585	+	Silent	SNP	G	G	A	rs145162894	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	61	32	63	0	0.52459	0	G|0.996;A|0.004	0.004	strong	.	KIAA1217	235	.	NM_019590	exon13	c.G2790A	p.S930S	GATGTCGCAGGCT	.	PASS	Atlas-SNP
IMMT	10989	hgsc.bcm.edu	37	2	86385728	86385728	+	Silent	SNP	C	C	T	rs1131071	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	110	109	104	0	0.990909	0	T|0.180;G|0.013	0.180	strong	.	IMMT	65	.	NM_006839	exon10	c.G1149A	p.G383G	TTTCCACCCAGGA	.	PASS	Atlas-SNP
TMTC4	84899	hgsc.bcm.edu	37	13	101287365	101287365	+	Silent	SNP	T	T	C	rs946838	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	122	122	121	1	1	0.00826446	T|0.170;C|0.830	0.830	strong	.	TMTC4	103	.	NM_032813	exon11	c.A1287G	p.A429A	ACGCTCTGCGACC	.	PASS	Atlas-SNP
FFAR4	338557	hgsc.bcm.edu	37	10	95347041	95347041	+	Missense_Mutation	SNP	G	G	A	rs116454156	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	59	112	0	0.608247	0	G|0.987;A|0.013	0.013	strong	.	.	.	.	NM_181745	exon4	c.G809A	p.R270H	AGATCCGCGTGTC	.	PASS	Atlas-SNP
CA5B	11238	hgsc.bcm.edu	37	X	15800751	15800751	+	Silent	SNP	G	G	A	rs1808	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	95	95	155	1	1	0.00645161	G|0.655;0|0.003	.	strong	.	CA5B	23	.	NM_007220	exon8	c.G918A	p.A306A	ACAAGCGAAACCC	.	PASS	Atlas-SNP
FAT4	79633	hgsc.bcm.edu	37	4	126336201	126336201	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	156	15	137	0	0.0961538	0	.	.	none	.	FAT4	1752	.	NM_024582	exon5	c.C6083T	p.A2028V	TTCCAGCCTCCAG	.	PASS	Atlas-SNP
ECHDC3	79746	hgsc.bcm.edu	37	10	11805339	11805339	+	Silent	SNP	C	C	T	rs17850531	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	35	19	32	0	0.542857	0	C|0.831;T|0.169	0.169	strong	.	ECHDC3	12	.	NM_024693	exon5	c.C708T	p.I236I	GCGGATCGCTAGG	.	PASS	Atlas-SNP
ZNF142	7701	hgsc.bcm.edu	37	2	219508372	219508372	+	Missense_Mutation	SNP	A	A	T	rs3770213	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	84	48	87	0	0.571429	0	A|0.741;N|0.000	.	strong	.	ZNF142	190	.	NM_001105537	exon8	c.T2867A	p.L956H	GTGGCAAGAGGCT	.	PASS	Atlas-SNP
COBL	23242	hgsc.bcm.edu	37	7	51094269	51094269	+	Missense_Mutation	SNP	G	G	A	rs61737954	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	56	27	92	0	0.482143	0	G|0.947;A|0.053	0.053	strong	.	COBL	167	.	NM_015198	exon11	c.C3478T	p.H1160Y	CGCTGTGCCCGCG	.	PASS	Atlas-SNP
SIN3B	23309	hgsc.bcm.edu	37	19	16976289	16976289	+	Silent	SNP	T	T	C	rs2303091	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	121	121	129	0	1	0	T|0.859;C|0.141	0.141	strong	.	SIN3B	90	.	NM_015260	exon12	c.T1548C	p.S516S	GCTATCTCGGATG	.	PASS	Atlas-SNP
NOP58	51602	hgsc.bcm.edu	37	2	203139844	203139844	+	Silent	SNP	T	T	C	rs80282360	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	198	102	277	0	0.515152	0	T|0.904;C|0.096	0.096	strong	NOP58,NS,carcinoma,0,1	NOP58	41	1	NM_015934	exon2	c.T54C	p.N18N	TCTAAATGAGAAG	.	PASS	Atlas-SNP
SLC35G6	643664	hgsc.bcm.edu	37	17	7386272	7386272	+	Silent	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	96	8	115	1	0.0833333	0.00869565	.	.	none	POLR2A_ENST00000412468,NS,carcinoma,0,1	.	.	1	NM_001102614	exon2	c.C969T	p.I323I	CATCATCACAGCC	.	scavenged	Atlas-SNP
DCLK1	9201	hgsc.bcm.edu	37	13	36385031	36385031	+	Silent	SNP	G	G	T	rs2322807	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	102	35	129	0	0.343137	0	G|0.713;T|0.287	0.287	strong	.	DCLK1	350	.	NM_004734	exon12	c.C1629A	p.P543P	GTACAGGGGGCCG	.	PASS	Atlas-SNP
CASQ2	845	hgsc.bcm.edu	37	1	116310967	116310967	+	Missense_Mutation	SNP	T	T	C	rs4074536	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	155	76	164	0	0.490323	0	T|0.631;C|0.369	0.369	strong	CASQ2,colon,carcinoma,0,1	CASQ2	54	1	NM_001232	exon1	c.A196G	p.T66A	TTTGCGTGACCTT	.	PASS	Atlas-SNP
GPS2	2874	hgsc.bcm.edu	37	17	7217463	7217463	+	Silent	SNP	T	T	C	rs2292064	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	208	101	231	0	0.485577	0	T|0.494;C|0.506	0.506	strong	GPS2,NS,carcinoma,0,2	GPS2	44	2	NM_004489	exon5	c.A333G	p.L111L	TGATGTTAGGGTG	.	PASS	Atlas-SNP
ZNF578	147660	hgsc.bcm.edu	37	19	53015384	53015384	+	Missense_Mutation	SNP	A	A	G	rs4802965	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	30	15	38	0	0.5	0	A|0.687;G|0.313	0.313	strong	.	.	.	.	NM_001099694	exon6	c.A1750G	p.I584V	TCATCAATCAAGC	.	PASS	Atlas-SNP
MYH7B	57644	hgsc.bcm.edu	37	20	33584289	33584289	+	Silent	SNP	C	C	T	rs3746438	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	89	42	88	0	0.47191	0	C|0.542;T|0.458	0.458	strong	.	MYH7B	145	.	NM_020884	exon29	c.C3210T	p.T1070T	GCTGACCAAGGCC	.	PASS	Atlas-SNP
LAMC2	3918	hgsc.bcm.edu	37	1	183201970	183201970	+	Missense_Mutation	SNP	G	G	C	rs2296303	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	37	24	49	0	0.648649	0	G|0.841;C|0.159	0.159	strong	.	LAMC2	113	.	NM_005562	exon14	c.G2198C	p.S733T	CAGAAAGTGAAGC	.	PASS	Atlas-SNP
XPC	7508	hgsc.bcm.edu	37	3	14187449	14187449	+	Missense_Mutation	SNP	G	G	T	rs2228001	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	74	42	84	0	0.567568	0	G|0.341;T|0.659	0.659	strong	.	XPC	60	.	NM_004628	exon16	c.C2815A	p.Q939K	ACAGCTGCTCAAA	.	PASS	Atlas-SNP
CCDC60	160777	hgsc.bcm.edu	37	12	119866533	119866533	+	Missense_Mutation	SNP	A	A	G	rs1064319	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	36	93	0	0.439024	0	A|0.720;G|0.280	0.280	strong	CCDC60,NS,carcinoma,0,1	CCDC60	84	1	NM_178499	exon2	c.A136G	p.I46V	AAGGAAATAATAA	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	45	45	63	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
DOC2A	8448	hgsc.bcm.edu	37	16	30021402	30021402	+	Missense_Mutation	SNP	C	C	T	rs1140239	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	161	159	96	0	0.987578	0	C|0.733;T|0.267	0.267	strong	.	DOC2A	40	.	NM_003586	exon2	c.G142A	p.G48S	CGCCGCCCCCGCC	.	PASS	Atlas-SNP
KREMEN1	83999	hgsc.bcm.edu	37	22	29533572	29533572	+	Missense_Mutation	SNP	C	C	G	rs34920087	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	55	33	61	0	0.6	0	C|0.862;G|0.138	0.138	strong	.	KREMEN1	46	.	NM_001039570	exon6	c.C874G	p.L292V	CCACCTCTGTCCT	.	PASS	Atlas-SNP
KIF2B	84643	hgsc.bcm.edu	37	17	51901385	51901385	+	Silent	SNP	C	C	T	rs3803826	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	59	26	87	0	0.440678	0	C|0.677;T|0.323	0.323	strong	.	KIF2B	254	.	NM_032559	exon1	c.C991T	p.L331L	TATGCTCTGGTGG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195506982	195506982	+	Silent	SNP	G	G	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	52	12	73	1	0.230769	0.0136986	.	.	none	MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	NM_018406	exon2	c.C11469G	p.T3823T	AAGAGGGGTGGTG	.	scavenged	Atlas-SNP
ZNF701	55762	hgsc.bcm.edu	37	19	53085813	53085813	+	Silent	SNP	T	T	C	rs3745101	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	85	131	0	0.988372	0	T|0.704;C|0.296	0.296	strong	.	ZNF701	44	.	NM_001172655	exon5	c.T699C	p.A233A	GAAGGCTATCAAC	.	PASS	Atlas-SNP
IPO4	79711	hgsc.bcm.edu	37	14	24653523	24653523	+	Missense_Mutation	SNP	G	G	C	rs11550452	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	109	49	103	0	0.449541	0	G|0.693;C|0.307	0.307	strong	.	IPO4	74	.	NM_024658	exon17	c.C1738G	p.P580A	AGTCAGGGTCGTC	.	PASS	Atlas-SNP
DHX38	9785	hgsc.bcm.edu	37	16	72130203	72130203	+	Silent	SNP	C	C	G	rs1050361	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	170	64	124	0	0.376471	0	C|0.490;G|0.510	0.510	strong	DHX38,NS,carcinoma,0,1	DHX38	91	1	NM_014003	exon2	c.C147G	p.L49L	ATTACTCGGACTG	.	PASS	Atlas-SNP
LAMC2	3918	hgsc.bcm.edu	37	1	183192304	183192304	+	Silent	SNP	T	T	G	rs1047980	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	139	73	138	0	0.52518	0	T|0.692;G|0.308	0.308	strong	LAMC2,NS,carcinoma,0,1	LAMC2	113	1	NM_005562	exon7	c.T798G	p.G266G	CTATGGTCAAAGC	.	PASS	Atlas-SNP
ROBO2	6092	hgsc.bcm.edu	37	3	77607099	77607099	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	103	32	109	0	0.31068	0	.	.	none	.	ROBO2	527	.	NM_002942	exon9	c.G1236C	p.L412F	AGTTTTGACAGAT	.	PASS	Atlas-SNP
CCDC13	152206	hgsc.bcm.edu	37	3	42787469	42787469	+	Silent	SNP	A	A	G	rs2240859	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	38	81	0	0.550725	0	A|0.512;G|0.488	0.488	strong	.	CCDC13	71	.	NM_144719	exon7	c.T771C	p.S257S	TGGCGAAGATAGG	.	PASS	Atlas-SNP
RET	5979	hgsc.bcm.edu	37	10	43615633	43615633	+	Silent	SNP	C	C	G	rs1800863	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	90	40	102	0	0.444444	0	C|0.844;G|0.156	0.156	strong	.	RET	916	.	NM_020630	exon15	c.C2712G	p.S904S	GGATTCCTACGTG	.	PASS	Atlas-SNP
OR52R1	119695	hgsc.bcm.edu	37	11	4825349	4825349	+	Missense_Mutation	SNP	A	A	G	rs17327254	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	117	27	108	0	0.230769	0	A|0.937;G|0.063	0.063	strong	.	OR52R1	81	.	NM_001005177	exon1	c.T262C	p.F88L	ACCAGAATATGGC	.	PASS	Atlas-SNP
PTGER1	5731	hgsc.bcm.edu	37	19	14583582	14583582	+	Silent	SNP	C	C	T	rs11668633	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	37	20	36	1	0.540541	0.0277778	C|0.862;T|0.138	0.138	strong	PTGER1,NS,carcinoma,0,1	PTGER1	5	1	NM_000955	exon3	c.G999A	p.L333L	CAGGAACAGTGGC	.	scavenged	Atlas-SNP
HHIPL2	79802	hgsc.bcm.edu	37	1	222713631	222713631	+	Missense_Mutation	SNP	G	G	C	rs3748666	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	88	30	82	0	0.340909	0	G|0.678;C|0.322	0.322	strong	.	HHIPL2	122	.	NM_024746	exon4	c.C1171G	p.H391D	TGCCATGTGAGCC	.	PASS	Atlas-SNP
CNBD2	140894	hgsc.bcm.edu	37	20	34560609	34560609	+	Missense_Mutation	SNP	G	G	A	rs17347958	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	140	73	160	0	0.521429	0	G|0.966;A|0.034	0.034	strong	.	.	.	.	NM_080834	exon2	c.G110A	p.R37H	TGTTCCGCCAAGG	.	PASS	Atlas-SNP
TPTE	7179	hgsc.bcm.edu	37	21	10942927	10942927	+	Silent	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	250	5	340	0	0.02	0	.	.	none	TPTE_ENST00000361285,NS,carcinoma,-2,2	TPTE	513	2	NM_199261	exon12	c.A660G	p.R220R	CCGCCTTCTTATC	.	scavenged	Atlas-SNP
ZNF426	79088	hgsc.bcm.edu	37	19	9646898	9646898	+	Missense_Mutation	SNP	G	G	A	rs2042200	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	59	26	59	0	0.440678	0	G|0.820;A|0.180	0.180	strong	.	ZNF426	56	.	NM_024106	exon3	c.C11T	p.A4V	AAATCAGCAGCTG	.	PASS	Atlas-SNP
SEMA3A	10371	hgsc.bcm.edu	37	7	83634713	83634713	+	Silent	SNP	A	A	G	rs7804122	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	133	56	126	0	0.421053	0	A|0.771;G|0.229	0.229	strong	SEMA3A,colon,carcinoma,0,1	SEMA3A	121	1	NM_006080	exon11	c.T1302C	p.I434I	TACGACAATTTGT	.	PASS	Atlas-SNP
PLEKHG4B	153478	hgsc.bcm.edu	37	5	163300	163300	+	Missense_Mutation	SNP	C	C	T	rs138837556	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	96	53	99	0	0.552083	0	C|0.999;T|0.001	0.001	strong	.	PLEKHG4B	167	.	NM_052909	exon11	c.C2045T	p.S682F	CACTGTCCCTCCT	.	PASS	Atlas-SNP
DHX34	9704	hgsc.bcm.edu	37	19	47878858	47878858	+	Missense_Mutation	SNP	C	C	T	rs61751860	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	10	9	3	0	0.9	0	C|0.904;T|0.096	0.096	strong	DHX34,NS,carcinoma,0,1	DHX34	98	1	NM_014681	exon10	c.C2200T	p.R734C	GCGGGGCGCAGGC	.	PASS	Atlas-SNP
NR4A3	8013	hgsc.bcm.edu	37	9	102595069	102595069	+	Silent	SNP	G	G	A	rs41274654	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	99	43	152	0	0.434343	0	G|0.892;A|0.108	0.108	strong	.	NR4A3	80	.	NM_173200	exon5	c.G1083A	p.Q361Q	ATTTCAGAAGTGT	.	PASS	Atlas-SNP
OR5H2	79310	hgsc.bcm.edu	37	3	98001777	98001777	+	Missense_Mutation	SNP	G	G	C	rs72487753	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	156	84	211	0	0.538462	0	G|0.858;C|0.142	0.142	strong	.	OR5H2	63	.	NM_001005482	exon1	c.G46C	p.E16Q	CTGACAGAGTTTG	.	PASS	Atlas-SNP
FN1	2335	hgsc.bcm.edu	37	2	216242917	216242917	+	Silent	SNP	T	T	A	rs1132741	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	41	14	46	0	0.341463	0	T|0.728;A|0.272	0.272	strong	FN1,NS,carcinoma,0,1	FN1	521	1	NM_212482	exon35	c.A5691T	p.G1897G	GACAACTCCCTGA	.	PASS	Atlas-SNP
HTT	3064	hgsc.bcm.edu	37	4	3215835	3215835	+	Missense_Mutation	SNP	T	T	C	rs362331	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	98	98	110	0	1	0	C|0.453;N|0.000	0.453	strong	HTT,NS,carcinoma,0,1	HTT	221	1	NM_002111	exon50	c.T6925C	p.Y2309H	CTCATCTACTGTG	.	PASS	Atlas-SNP
HOXC11	3227	hgsc.bcm.edu	37	12	54367690	54367690	+	Missense_Mutation	SNP	C	C	T	rs12427129	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	17	10	16	0	0.588235	0	C|0.931;T|0.069	0.069	strong	.	HOXC11	32	.	NM_014212	exon1	c.C665T	p.A222V	AGCCGGCCAAAGG	.	PASS	Atlas-SNP
NTRK1	4914	hgsc.bcm.edu	37	1	156848946	156848946	+	Missense_Mutation	SNP	G	G	T	rs6339	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	157	70	146	0	0.44586	0	G|0.965;T|0.035	0.035	strong	.	NTRK1	287	.	NM_002529	exon15	c.G1838T	p.G613V	TGGCTGGTGGGGA	.	PASS	Atlas-SNP
NRAP	4892	hgsc.bcm.edu	37	10	115389366	115389366	+	Missense_Mutation	SNP	G	G	A	rs2286735	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	93	46	98	0	0.494624	0	G|0.726;N|0.001	.	strong	.	NRAP	208	.	NM_001261463	exon19	c.C2021T	p.A674V	CCATAGGCCTTCT	.	PASS	Atlas-SNP
TGM4	7047	hgsc.bcm.edu	37	3	44948479	44948479	+	Missense_Mutation	SNP	C	C	T	rs3749195	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	95	42	111	0	0.442105	0	C|0.414;T|0.586	0.586	strong	.	TGM4	82	.	NM_003241	exon10	c.C1114T	p.R372C	GCCATCCGCAAAG	.	PASS	Atlas-SNP
DNPH1	10591	hgsc.bcm.edu	37	6	43193877	43193877	+	Silent	SNP	G	G	A	rs7832	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	27	6	40	0	0.222222	0	G|0.942;A|0.058	0.058	strong	C6orf108_ENST00000393987,NS,carcinoma,0,2	.	.	2	NM_006443	exon3	c.C270T	p.V90V	TGCCACGACCACT	.	PASS	Atlas-SNP
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33036548	33036548	+	Missense_Mutation	SNP	G	G	A	rs56046206	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	119	42	143	0	0.352941	0	G|0.995;A|0.005	0.005	strong	.	HLA-DPA1	20	.	NM_033554	exon4	c.C662T	p.T221M	GTCTCCGTTGTCT	.	PASS	Atlas-SNP
ABCA7	10347	hgsc.bcm.edu	37	19	1042809	1042809	+	Missense_Mutation	SNP	A	A	G	rs3764645	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	51	30	45	0	0.588235	0	A|0.609;G|0.391	0.391	strong	.	ABCA7	174	.	NM_019112	exon7	c.A563G	p.E188G	CCGCTGAGGACCT	.	PASS	Atlas-SNP
RTP2	344892	hgsc.bcm.edu	37	3	187416666	187416666	+	Missense_Mutation	SNP	C	C	T	rs61748316	byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	216	100	203	1	0.462963	0.00492611	C|0.839;T|0.161	0.161	strong	RTP2,NS,carcinoma,0,1	RTP2	38	1	NM_001004312	exon2	c.G298A	p.G100S	CCGTGCCGCACTC	.	scavenged	Atlas-SNP
SUPT20HL2	170067	hgsc.bcm.edu	37	X	24330386	24330386	+	Silent	SNP	G	G	A	rs73205129	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	519	517	707	1	0.996146	0.00141443	G|0.929;A|0.071	0.071	strong	.	.	.	.	NM_001136233	exon1	c.C1047T	p.D349D	CTTGGTGTCCCAG	.	PASS	Atlas-SNP
FAM179A	165186	hgsc.bcm.edu	37	2	29240783	29240783	+	Missense_Mutation	SNP	A	A	G	rs1109758	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	134	63	125	0	0.470149	0	A|0.599;G|0.401	0.401	strong	.	FAM179A	106	.	NM_199280	exon10	c.A1321G	p.I441V	ATCCCCATCAGCC	.	PASS	Atlas-SNP
CNTRL	11064	hgsc.bcm.edu	37	9	123903840	123903840	+	Missense_Mutation	SNP	G	G	A	rs17292952	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	33	22	38	0	0.666667	0	G|0.976;A|0.024	0.024	strong	.	CNTRL	161	.	NM_007018	exon16	c.G2665A	p.A889T	AGGCAGGCCTGTG	.	PASS	Atlas-SNP
LTN1	26046	hgsc.bcm.edu	37	21	30341891	30341891	+	Missense_Mutation	SNP	A	A	G	rs2254796	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	38	84	0	0.487179	0	A|0.317;G|0.683	0.683	strong	.	LTN1	141	.	NM_015565	exon9	c.T1346C	p.L449S	GACTCTAAAGAGC	.	PASS	Atlas-SNP
COL28A1	340267	hgsc.bcm.edu	37	7	7398423	7398423	+	Silent	SNP	C	C	T	rs373840985		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	166	40	201	0	0.240964	0	.	.	weak	.	COL28A1	113	.	NM_001037763	exon35	c.G3219A	p.L1073L	GGCTTCCAAACAT	.	PASS	Atlas-SNP
PHRF1	57661	hgsc.bcm.edu	37	11	609353	609353	+	Silent	SNP	G	G	A	rs11539530	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	83	57	85	0	0.686747	0	G|0.798;A|0.202	0.202	strong	.	PHRF1	188	.	NM_020901	exon14	c.G3894A	p.P1298P	TTCCCCGGAGCGA	.	PASS	Atlas-SNP
MYH11	4629	hgsc.bcm.edu	37	16	15850204	15850204	+	Silent	SNP	A	A	G	rs2272554	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	113	24	140	0	0.212389	0	A|0.465;G|0.535	0.535	strong	.	MYH11	520	.	NM_001040114	exon15	c.T1764C	p.A588A	CTTCCCAGCATAA	.	PASS	Atlas-SNP
OR5L1	219437	hgsc.bcm.edu	37	11	55578991	55578991	+	Silent	SNP	C	C	T	rs66537410	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	64	46	74	0	0.71875	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
ATP2C1	27032	hgsc.bcm.edu	37	3	130718472	130718472	+	Silent	SNP	G	G	A	rs16835513	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	88	88	149	1	1	0.00671141	G|0.886;A|0.114	0.114	strong	.	ATP2C1	94	.	NM_001199181	exon26	c.G2700A	p.K900K	TCAGAAGGTTTTT	.	PASS	Atlas-SNP
SYNE1	23345	hgsc.bcm.edu	37	6	152771849	152771849	+	Silent	SNP	G	G	A	rs17082701	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	77	53	144	0	0.688312	0	G|0.931;A|0.069	0.069	strong	.	SYNE1	3227	.	NM_033071	exon27	c.C3327T	p.H1109H	AGTCACGTGACAG	.	PASS	Atlas-SNP
CLPTM1	1209	hgsc.bcm.edu	37	19	45490570	45490570	+	Silent	SNP	A	A	G	rs3786505	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	79	41	52	0	0.518987	0	A|0.596;G|0.404	0.404	strong	.	CLPTM1	109	.	NM_001294	exon8	c.A927G	p.P309P	CTGCCCACTCTCG	.	PASS	Atlas-SNP
PLXNC1	10154	hgsc.bcm.edu	37	12	94575307	94575307	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	214	7	249	0	0.0327103	0	.	.	none	PLXNC1,caecum,carcinoma,0,2	PLXNC1	135	2	NM_005761	exon3	c.T1289C	p.V430A	AACTCGTTCCTGA	.	scavenged	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195515194	195515194	+	Missense_Mutation	SNP	G	G	C	rs201370057	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	60	12	43	1	0.2	0.0232558	G|0.939;C|0.061	0.061	strong	MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	NM_018406	exon2	c.C3257G	p.T1086S	GGGGTGGTGTCAC	.	scavenged	Atlas-SNP
ZNF169	169841	hgsc.bcm.edu	37	9	97062981	97062981	+	Missense_Mutation	SNP	C	C	T	rs12236219	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	46	16	66	1	0.347826	0.0151515	C|0.894;T|0.106	0.106	strong	ZNF169,NS,carcinoma,-1,1	ZNF169	60	1	NM_194320	exon5	c.C1141T	p.R381C	TGTGGGCGTAGCT	.	scavenged	Atlas-SNP
ESRRA	2101	hgsc.bcm.edu	37	11	64081445	64081445	+	Silent	SNP	G	G	A	rs2276014	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	137	107	128	0	0.781022	0	G|0.895;A|0.105	0.105	strong	.	ESRRA	56	.	NM_004451	exon3	c.G348A	p.P116P	CTGTCCGGCCTCC	.	PASS	Atlas-SNP
PDE4DIP	9659	hgsc.bcm.edu	37	1	144859792	144859792	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	151	10	143	0	0.0662252	0	.	.	none	.	PDE4DIP	817	.	NM_014644	exon38	c.A6292G	p.T2098A	GGTCAGTGCTGGC	.	PASS	Atlas-SNP
CTXN3	613212	hgsc.bcm.edu	37	5	126993282	126993282	+	Missense_Mutation	SNP	G	G	A	rs2280170	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	42	87	0	0.512195	0	G|0.917;A|0.083	0.083	strong	.	CTXN3	19	.	NM_001048252	exon3	c.G69A	p.M23I	TAGCATGTCCCTG	.	PASS	Atlas-SNP
COL6A5	256076	hgsc.bcm.edu	37	3	130129322	130129322	+	Missense_Mutation	SNP	G	G	C	rs35886424	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	45	129	0	0.48913	0	G|0.888;C|0.112	0.112	strong	.	COL6A5	205	.	NM_153264	exon20	c.G4616C	p.S1539T	GTAGAAGTGGACA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195515411	195515411	+	Missense_Mutation	SNP	G	G	C	rs55803325	bycluster;byfrequency;alternate_allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	26	61	0	0.361111	0	G|0.993;T|0.007	.	alt	.	MUC4	1505	.	NM_018406	exon2	c.C3040G	p.P1014A	AGGAAGGGCTGGT	.	PASS	Atlas-SNP
CPA4	51200	hgsc.bcm.edu	37	7	129962414	129962414	+	Silent	SNP	C	C	T	rs2306848	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	118	62	122	0	0.525424	0	C|0.941;T|0.059	0.059	strong	.	CPA4	47	.	NM_016352	exon11	c.C1164T	p.T388T	CGGGACCTATGGC	.	PASS	Atlas-SNP
PRODH	5625	hgsc.bcm.edu	37	22	18910355	18910355	+	Missense_Mutation	SNP	G	G	T	rs5747933	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	123	58	165	0	0.471545	0	G|0.951;T|0.049	0.049	strong	.	PRODH	42	.	NM_016335	exon7	c.C824A	p.T275N	AGCTTGGTGTCCA	.	PASS	Atlas-SNP
AKAP10	11216	hgsc.bcm.edu	37	17	19812541	19812541	+	Missense_Mutation	SNP	T	T	C	rs203462	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	89	48	64	0	0.539326	0	T|0.572;G|0.003	.	strong	.	AKAP10	47	.	NM_007202	exon14	c.A1936G	p.I646V	GCATAATGTCACT	.	PASS	Atlas-SNP
KRTAP4-8	728224	hgsc.bcm.edu	37	17	39254142	39254142	+	Silent	SNP	A	A	G	rs375280428		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	36	5	50	1	0.138889	0.02	.	.	weak	KRTAP4-8,rectum,carcinoma,0,2	KRTAP4-8	57	2	NM_031960	exon1	c.T195C	p.C65C	GGGGCGACAGCAG	.	scavenged	Atlas-SNP
EFCAB4B	84766	hgsc.bcm.edu	37	12	3788188	3788188	+	Silent	SNP	C	C	T	rs3803135	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	108	48	109	0	0.444444	0	C|0.862;T|0.138	0.138	strong	.	EFCAB4B	100	.	NM_001144958	exon6	c.G417A	p.K139K	ATACACCTTCTCT	.	PASS	Atlas-SNP
BCL11A	53335	hgsc.bcm.edu	37	2	60687959	60687959	+	Silent	SNP	A	A	G	rs7569946	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	115	115	55	0	1	0	A|0.278;G|0.722	0.722	strong	.	BCL11A	298	.	NM_018014	exon4	c.T2088C	p.S696S	GCGCAAACTCCCG	.	PASS	Atlas-SNP
PPL	5493	hgsc.bcm.edu	37	16	4935985	4935985	+	Missense_Mutation	SNP	C	C	G	rs35869286	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	59	49	72	0	0.830508	0	C|0.942;G|0.058	0.058	strong	PPL,NS,carcinoma,0,1	PPL	168	1	NM_002705	exon22	c.G2671C	p.E891Q	ACGCCTCCTCCAC	.	PASS	Atlas-SNP
STYXL1	51657	hgsc.bcm.edu	37	7	75630274	75630274	+	Silent	SNP	T	T	C	rs8565	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	117	66	128	1	0.564103	0.0078125	T|0.318;C|0.682	0.682	strong	STYXL1,NS,carcinoma,-2,1	STYXL1	35	1	NM_016086	exon8	c.A744G	p.Q248Q	GATACCTTGGGTG	.	scavenged	Atlas-SNP
GIT2	9815	hgsc.bcm.edu	37	12	110383141	110383141	+	Missense_Mutation	SNP	G	G	A	rs11068997	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	47	22	52	0	0.468085	0	G|0.941;A|0.059	0.059	strong	.	GIT2	81	.	NM_057169	exon16	c.C1655T	p.A552V	ACAAGTGCACTCC	.	PASS	Atlas-SNP
MFHAS1	9258	hgsc.bcm.edu	37	8	8748013	8748013	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	53	30	61	0	0.566038	0	.	.	none	.	MFHAS1	58	.	NM_004225	exon1	c.C2556G	p.C852W	CACATAGCATGGG	.	PASS	Atlas-SNP
KCNG4	93107	hgsc.bcm.edu	37	16	84270476	84270476	+	Missense_Mutation	SNP	G	G	A	rs11646443	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	130	71	97	0	0.546154	0	G|0.721;A|0.279	0.279	strong	.	KCNG4	71	.	NM_172347	exon2	c.C616T	p.R206W	GCAGCCGGTTCAT	.	PASS	Atlas-SNP
OR56A4	120793	hgsc.bcm.edu	37	11	6024031	6024031	+	Silent	SNP	G	G	A	rs143488149	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	160	110	132	0	0.6875	0	G|0.999;A|0.001	0.001	strong	.	OR56A4	66	.	NM_001005179	exon1	c.C348T	p.Y116Y	GAGCAGGTAGTAC	.	PASS	Atlas-SNP
LCMT2	9836	hgsc.bcm.edu	37	15	43621947	43621947	+	Silent	SNP	A	A	G	rs3742969	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	53	26	53	0	0.490566	0	A|0.668;G|0.332	0.332	strong	.	LCMT2	48	.	NM_014793	exon1	c.T741C	p.R247R	AGGAAAACGCTCC	.	PASS	Atlas-SNP
NTRK1	4914	hgsc.bcm.edu	37	1	156846233	156846233	+	Silent	SNP	G	G	A	rs6334	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	176	86	188	0	0.488636	0	G|0.804;A|0.196	0.196	strong	.	NTRK1	287	.	NM_002529	exon14	c.G1674A	p.Q558Q	CTTCCAGCGTGAG	.	PASS	Atlas-SNP
GLP2R	9340	hgsc.bcm.edu	37	17	9792768	9792768	+	Missense_Mutation	SNP	G	G	A	rs17681684	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	37	93	0	0.474359	0	G|0.822;A|0.178	0.178	strong	.	GLP2R	90	.	NM_004246	exon13	c.G1408A	p.D470N	GGGAAGGACTTCC	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	74	34	94	0	0.459459	0	G|0.775;A|0.225	0.225	strong	.	SSH2	107	.	NM_033389	exon15	c.C2228T	p.S743L	TTTTCCGAGTGAG	.	PASS	Atlas-SNP
ZNF319	57567	hgsc.bcm.edu	37	16	58032026	58032026	+	Silent	SNP	G	G	A	rs56347618	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	30	31	0	0.422535	0	G|0.970;A|0.030	0.030	strong	.	ZNF319	42	.	NM_020807	exon2	c.C144T	p.A48A	ATAGACGGCACAG	.	PASS	Atlas-SNP
CERS2	29956	hgsc.bcm.edu	37	1	150940625	150940625	+	Missense_Mutation	SNP	T	T	G	rs267738	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	54	53	56	0	0.981481	0	T|0.878;G|0.122	0.122	strong	LASS2,colon,carcinoma,0,1	.	.	1	NM_022075	exon4	c.A344C	p.E115A	CAACGCTCTACCT	.	PASS	Atlas-SNP
ZCCHC2	54877	hgsc.bcm.edu	37	18	60231851	60231851	+	Silent	SNP	A	A	G	rs12956093	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	167	81	216	0	0.48503	0	A|0.878;G|0.122	0.122	strong	.	ZCCHC2	64	.	NM_017742	exon10	c.A1734G	p.G578G	GAAAGGAAAGCCA	.	PASS	Atlas-SNP
THRB	7068	hgsc.bcm.edu	37	3	24184995	24184995	+	Silent	SNP	G	G	A	rs3752874	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	132	73	160	0	0.55303	0	G|0.858;A|0.142	0.142	strong	.	THRB	52	.	NM_000461	exon7	c.C735T	p.F245F	TACCAGGAATTTC	.	PASS	Atlas-SNP
CLHC1	130162	hgsc.bcm.edu	37	2	55449464	55449464	+	Silent	SNP	T	T	C	rs17852670	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	394	80	209	0	0.203046	0	T|0.796;C|0.204	0.204	strong	.	.	.	.	NM_152385	exon3	c.A84G	p.Q28Q	GTATCTTTGCACA	.	PASS	Atlas-SNP
SMC1B	27127	hgsc.bcm.edu	37	22	45767369	45767369	+	Silent	SNP	A	A	G	rs470062	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	193	94	240	0	0.487047	0	A|0.862;G|0.138	0.138	strong	.	SMC1B	215	.	NM_148674	exon14	c.T2295C	p.F765F	TTCTTGAAATTCT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195509429	195509429	+	Missense_Mutation	SNP	A	A	G	rs28542401	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	60	58	30	2	0.966667	0.0666667	A|0.389;C|0.096;G|0.515	0.515	strong	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.T9022C	p.S3008P	GAAGAGAGGTGGC	.	scavenged	Atlas-SNP
OR5I1	10798	hgsc.bcm.edu	37	11	55703728	55703728	+	Missense_Mutation	SNP	A	A	G	rs4367963	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	80	55	108	0	0.6875	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
RASGRP4	115727	hgsc.bcm.edu	37	19	38912764	38912764	+	Missense_Mutation	SNP	A	A	G	rs892055	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	88	87	90	0	0.988636	0	A|0.489;G|0.510	0.510	strong	.	RASGRP4	54	.	NM_001146206	exon2	c.T53C	p.I18T	CCTCCTATTTTTC	.	PASS	Atlas-SNP
FGFR2	2263	hgsc.bcm.edu	37	10	123239112	123239112	+	Silent	SNP	G	G	A	rs1047057	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	76	35	95	0	0.460526	0	G|0.609;A|0.391	0.391	strong	FGFR2_ENST00000357555,NS,carcinoma,0,1	FGFR2	758	1	NM_001144915	exon17	c.C2107T	p.L703L	CAGCCAGTACGCA	.	PASS	Atlas-SNP
AKAP10	11216	hgsc.bcm.edu	37	17	19861458	19861458	+	Missense_Mutation	SNP	C	C	T	rs2108978	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	208	100	260	1	0.480769	0.00384615	C|0.582;T|0.418	0.418	strong	.	AKAP10	47	.	NM_007202	exon4	c.G746A	p.R249H	TCAAGACGGAGAG	.	PASS	Atlas-SNP
FAAH	2166	hgsc.bcm.edu	37	1	46870761	46870761	+	Missense_Mutation	SNP	C	C	A	rs324420	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	156	82	174	0	0.525641	0	C|0.749;A|0.251	0.251	strong	.	FAAH	36	.	NM_001441	exon3	c.C385A	p.P129T	CAGGCCCCAAGGC	.	PASS	Atlas-SNP
TGM4	7047	hgsc.bcm.edu	37	3	44948590	44948590	+	Missense_Mutation	SNP	G	G	A	rs9876921	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	145	74	178	0	0.510345	0	G|0.470;A|0.530	0.530	strong	.	TGM4	82	.	NM_003241	exon10	c.G1225A	p.V409I	TTACACGTAATTT	.	PASS	Atlas-SNP
AMZ1	155185	hgsc.bcm.edu	37	7	2752152	2752152	+	Silent	SNP	G	G	A	rs798565	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	63	14	61	0	0.222222	0	G|0.793;A|0.207	0.207	strong	AMZ1,colon,carcinoma,0,3	AMZ1	41	3	NM_133463	exon7	c.G1137A	p.S379S	CGCCTCGGGGCCA	.	PASS	Atlas-SNP
PHKG2	5261	hgsc.bcm.edu	37	16	30762886	30762886	+	Silent	SNP	C	C	T	rs56029513	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	672	239	533	1	0.355655	0.00187617	C|0.997;T|0.003	0.003	strong	.	PHKG2	29	.	NM_001172432	exon4	c.C288T	p.S96S	CGATTCCTACGAG	.	PASS	Atlas-SNP
CSRP3	8048	hgsc.bcm.edu	37	11	19207841	19207841	+	Silent	SNP	C	C	T	rs13451	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	148	104	162	1	0.702703	0.00617284	T|0.065;G|0.005	0.065	strong	CSRP3,NS,adenocarcinoma,-1,1	CSRP3	24	1	NM_003476	exon5	c.G336A	p.A112A	AAACTTCGCAGTG	.	PASS	Atlas-SNP
ZSCAN12	9753	hgsc.bcm.edu	37	6	28366151	28366151	+	Missense_Mutation	SNP	A	A	G	rs2232423	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	239	124	259	0	0.518828	0	A|0.959;G|0.041	0.041	strong	.	ZSCAN12	35	.	NM_001163391	exon2	c.T32C	p.M11T	TGGTCCATGTGGG	.	PASS	Atlas-SNP
SGK1	6446	hgsc.bcm.edu	37	6	134494619	134494619	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	89	19	105	0	0.213483	0	.	.	none	.	SGK1	387	.	NM_001143676	exon6	c.G599C	p.G200A	CCCTTTCCGATCA	.	PASS	Atlas-SNP
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46058060	46058060	+	Silent	SNP	C	C	T	rs74695406		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	195	113	161	0	0.579487	0	T|1.000;|0.000	1.000	weak	.	KRTAP10-10	37	.	NM_181688	exon1	c.C726T	p.S242S	CTACAGCCTCTGC	.	PASS	Atlas-SNP
DFNB59	494513	hgsc.bcm.edu	37	2	179325714	179325714	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	4	84	0	0.056338	0	.	.	none	.	DFNB59	37	.	NM_001042702	exon7	c.A772G	p.R258G	GATAGAAGAGTGA	.	PASS	Atlas-SNP
DUOX2	50506	hgsc.bcm.edu	37	15	45402883	45402883	+	Missense_Mutation	SNP	G	G	C	rs151261408	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	249	145	216	0	0.582329	0	G|0.990;C|0.010	0.010	strong	DUOX2,NS,carcinoma,0,2	DUOX2	137	2	NM_014080	exon8	c.C908G	p.P303R	AAGCTGGGCAGCC	.	PASS	Atlas-SNP
PIM1	5292	hgsc.bcm.edu	37	6	37138345	37138345	+	Silent	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	63	15	39	0	0.238095	0	.	.	none	.	PIM1	71	.	NM_001243186	exon1	c.G267A	p.E89E	CCTGGAGGTTGGG	.	PASS	Atlas-SNP
KIAA1671	85379	hgsc.bcm.edu	37	22	25577688	25577688	+	Silent	SNP	G	G	A	rs763279	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	121	55	124	0	0.454545	0	G|0.654;A|0.346	0.346	strong	KIAA1671,NS,carcinoma,0,1	KIAA1671	28	1	NM_001145206	exon8	c.G5097A	p.E1699E	GAAGGAGGAGTCG	.	PASS	Atlas-SNP
FREM1	158326	hgsc.bcm.edu	37	9	14747412	14747412	+	Silent	SNP	A	A	G	rs4741426	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	131	63	123	0	0.480916	0	A|0.848;G|0.152	0.152	strong	.	FREM1	261	.	NM_144966	exon34	c.T5859C	p.V1953V	CAAGGAAACTATC	.	PASS	Atlas-SNP
SGK1	6446	hgsc.bcm.edu	37	6	134494661	134494661	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	14	90	0	0.2	0	.	.	none	SGK1_ENST00000367858,lymph_node,lymphoid_neoplasm,0,3	SGK1	387	3	NM_001143676	exon6	c.C557G	p.P186R	GCATGAGGATTGG	.	PASS	Atlas-SNP
CLIC5	53405	hgsc.bcm.edu	37	6	46047458	46047458	+	Silent	SNP	C	C	T	rs3734207	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	34	99	0	0.336634	0	C|0.815;T|0.185	0.185	strong	.	CLIC5	48	.	NM_001114086	exon1	c.G522A	p.E174E	GTAAATCTCAGGG	.	PASS	Atlas-SNP
FAM136A	84908	hgsc.bcm.edu	37	2	70524577	70524577	+	Silent	SNP	G	G	A	rs2618235	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	34	51	1	0.586207	0.0196078	G|0.748;A|0.252	0.252	strong	FAM136A,right_upper_lobe,carcinoma,-2,1	FAM136A	14	1	NM_032822	exon3	c.C261T	p.N87N	TTTGTCGTTGCAA	.	scavenged	Atlas-SNP
MUC20	200958	hgsc.bcm.edu	37	3	195453288	195453288	+	Missense_Mutation	SNP	A	A	C	rs3828405	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	111	40	139	4	0.36036	0.028777	A|0.928;C|0.072	0.072	strong	MUC20,NS,carcinoma,0,1	MUC20	84	1	NM_152673	exon3	c.A1301C	p.D434A	GCAGGGACCCTCT	.	scavenged	Atlas-SNP
KDR	3791	hgsc.bcm.edu	37	4	55972946	55972946	+	Missense_Mutation	SNP	A	A	G	rs34231037	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	176	89	187	0	0.505682	0	A|0.980;G|0.020	0.020	strong	KDR,middle_lobe,carcinoma,+2,1	KDR	307	1	NM_002253	exon11	c.T1444C	p.C482R	CTTCACAAGGGTA	.	PASS	Atlas-SNP
GC	2638	hgsc.bcm.edu	37	4	72618323	72618323	+	Missense_Mutation	SNP	G	G	T	rs4588	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	135	135	159	0	1	0	G|0.785;T|0.215	0.215	strong	.	GC	132	.	NM_001204307	exon12	c.C1364A	p.T455K	AGTTCCGTGGGTG	.	PASS	Atlas-SNP
SLC8A3	6547	hgsc.bcm.edu	37	14	70633998	70633998	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	148	40	139	0	0.27027	0	.	.	none	.	SLC8A3	234	.	NM_183002	exon2	c.C1142T	p.S381F	ATGCTGGAGGCCT	.	PASS	Atlas-SNP
CYP4F12	66002	hgsc.bcm.edu	37	19	15807305	15807305	+	Silent	SNP	T	T	C	rs688755	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	130	83	122	0	0.638462	0	T|0.764;C|0.236	0.236	strong	.	CYP4F12	89	.	NM_023944	exon12	c.T1380C	p.P460P	TATTCCTTTCTCC	.	PASS	Atlas-SNP
FAM111A	63901	hgsc.bcm.edu	37	11	58919813	58919813	+	Silent	SNP	A	A	G	rs10896928	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	54	12	54	0	0.222222	0	A|0.739;G|0.261	0.261	strong	.	FAM111A	57	.	NM_001142520	exon5	c.A672G	p.A224A	GGATGCACTGTGC	.	PASS	Atlas-SNP
UMODL1	89766	hgsc.bcm.edu	37	21	43510427	43510427	+	Silent	SNP	T	T	C	rs67055914	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	132	52	115	0	0.393939	0	T|0.748;C|0.252	0.252	strong	UMODL1_ENST00000408989,colon,carcinoma,0,2	UMODL1	186	2	NM_173568	exon6	c.T810C	p.Y270Y	TTTCTATGAGGAG	.	PASS	Atlas-SNP
CCDC86	79080	hgsc.bcm.edu	37	11	60610056	60610056	+	Missense_Mutation	SNP	G	G	C	rs2074421	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	72	85	0	1	0	G|0.909;C|0.091	0.091	strong	.	CCDC86	24	.	NM_024098	exon1	c.G459C	p.Q153H	GCATCAGCTACCG	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	177	95	195	1	0.536723	0.00512821	G|0.545;C|0.455	0.455	strong	.	ARSA	19	.	NM_001085426	exon8	c.C1178G	p.T393S	TTTCCAGTCCGCA	.	PASS	Atlas-SNP
MUC6	4588	hgsc.bcm.edu	37	11	1018436	1018436	+	Silent	SNP	C	C	T	rs12802800	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	355	152	331	1	0.428169	0.00302115	C|0.911;T|0.089	0.089	strong	.	MUC6	408	.	NM_005961	exon31	c.G4365A	p.V1455V	TGGAGTCACCAAG	.	PASS	Atlas-SNP
ABCA13	154664	hgsc.bcm.edu	37	7	48314279	48314279	+	Silent	SNP	G	G	A	rs6955212	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	24	146	0	0.292683	0	G|0.816;A|0.184	0.184	strong	ABCA13_ENST00000435803,NS,carcinoma,+1,2	ABCA13	1192	2	NM_152701	exon17	c.G5016A	p.K1672K	TAAGAAGGCAGAC	.	PASS	Atlas-SNP
PALLD	23022	hgsc.bcm.edu	37	4	169432673	169432673	+	Silent	SNP	C	C	T	rs61051061	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	40	21	66	0	0.525	0	C|0.791;T|0.209	0.209	strong	.	PALLD	179	.	NM_001166108	exon2	c.C18T	p.S6S	CTCCTCCCATGAG	.	PASS	Atlas-SNP
MGAT3	4248	hgsc.bcm.edu	37	22	39883736	39883736	+	Silent	SNP	G	G	C	rs9623008	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	47	31	41	0	0.659574	0	G|0.887;C|0.113	0.113	strong	MGAT3,NS,carcinoma,+1,1	MGAT3	65	1	NM_002409	exon2	c.G384C	p.P128P	GAGGCCGCCCCCG	.	PASS	Atlas-SNP
LAMA5	3911	hgsc.bcm.edu	37	20	60889385	60889385	+	Missense_Mutation	SNP	G	G	T	rs117480847	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	36	94	1	0.48	0.0106383	G|0.986;T|0.014	0.014	strong	LAMA5,NS,haematopoietic_neoplasm,0,1	LAMA5	268	1	NM_005560	exon62	c.C8479A	p.Q2827K	CGAACTGCTCCCC	.	scavenged	Atlas-SNP
SCN4A	6329	hgsc.bcm.edu	37	17	62019103	62019103	+	Silent	SNP	G	G	T	rs56342400	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	165	89	191	0	0.539394	0	A|0.000;C|0.000;G|0.831;T|0.168	0.168	strong	SCN4A,NS,carcinoma,0,1	SCN4A	205	1	NM_000334	exon24	c.C4539A	p.I1513I	ATCATCGATGCCC	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	107	21	155	0	0.196262	0	G|0.701;C|0.299	0.299	strong	.	ZNF263	58	.	NM_005741	exon6	c.G929C	p.C310S	CTGTATGCTCTGA	.	PASS	Atlas-SNP
SBNO1	55206	hgsc.bcm.edu	37	12	123799938	123799938	+	Silent	SNP	C	C	T	rs61751327	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	15	77	0	0.217391	0	C|0.943;T|0.057	0.057	strong	SBNO1,NS,carcinoma,0,1	SBNO1	138	1	NM_001167856	exon22	c.G3102A	p.R1034R	GTTGAACCTGCTC	.	PASS	Atlas-SNP
HIST1H2AI	8329	hgsc.bcm.edu	37	6	27776002	27776002	+	Silent	SNP	C	C	T	rs493283	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	225	25	223	0	0.111111	0	C|0.988;T|0.012	0.012	strong	.	HIST1H2AI	9	.	NM_003509	exon1	c.C15T	p.G5G	GCGTGGCAAGCAG	.	PASS	Atlas-SNP
PCNT	5116	hgsc.bcm.edu	37	21	47850484	47850484	+	Missense_Mutation	SNP	G	G	C	rs2070426	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	159	69	127	0	0.433962	0	G|0.520;C|0.480	0.480	strong	.	PCNT	283	.	NM_006031	exon37	c.G7977C	p.Q2659H	TGAGCAGGGGAAG	.	PASS	Atlas-SNP
FAM184B	27146	hgsc.bcm.edu	37	4	17635336	17635336	+	Missense_Mutation	SNP	G	G	A	rs61741403	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	128	47	143	0	0.367188	0	G|0.979;A|0.021	0.021	strong	.	FAM184B	38	.	NM_015688	exon17	c.C3065T	p.S1022F	TCTGTAGACTGGT	.	PASS	Atlas-SNP
GSG2	83903	hgsc.bcm.edu	37	17	3627840	3627840	+	Missense_Mutation	SNP	G	G	A	rs220462	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	103	34	162	0	0.330097	0	G|0.759;A|0.241	0.241	strong	.	GSG2	48	.	NM_031965	exon1	c.G611A	p.G204D	CGAGCGGCCTCCA	.	PASS	Atlas-SNP
MYEOV	26579	hgsc.bcm.edu	37	11	69063572	69063572	+	Missense_Mutation	SNP	A	A	G	rs17856376	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	17	102	0	0.242857	0	A|0.808;C|0.000;G|0.192	0.192	strong	.	MYEOV	42	.	NM_138768	exon3	c.A655G	p.M219V	CTCTGCATGACCC	.	PASS	Atlas-SNP
PCDHB15	56121	hgsc.bcm.edu	37	5	140626724	140626724	+	Silent	SNP	T	T	G	rs3776091	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	231	103	232	0	0.445887	0	T|0.852;G|0.148	0.148	strong	.	PCDHB15	138	.	NM_018935	exon1	c.T1578G	p.A526A	GCAGGCTTTCGAG	.	PASS	Atlas-SNP
WISP3	8838	hgsc.bcm.edu	37	6	112390565	112390565	+	Silent	SNP	A	A	G	rs17219737	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	59	29	52	0	0.491525	0	A|0.956;G|0.044	0.044	strong	.	WISP3	33	.	NM_198239	exon5	c.A861G	p.Q287Q	ATGCCAACCTACT	.	PASS	Atlas-SNP
CA6	765	hgsc.bcm.edu	37	1	9009406	9009406	+	Missense_Mutation	SNP	C	C	T	rs2274327	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	102	47	77	0	0.460784	0	C|0.706;N|0.000	.	strong	.	CA6	47	.	NM_001270500	exon2	c.C164T	p.T55M	AGAGGACGAAGGT	.	PASS	Atlas-SNP
TYR	7299	hgsc.bcm.edu	37	11	88911696	88911696	+	Missense_Mutation	SNP	C	C	A	rs1042602	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	15	101	0	0.172414	0	C|0.751;A|0.249	0.249	strong	TYR,NS,carcinoma,0,1	TYR	130	1	NM_000372	exon1	c.C575A	p.S192Y	GGGGATCTGAAAT	.	PASS	Atlas-SNP
CEP350	9857	hgsc.bcm.edu	37	1	179989742	179989742	+	Missense_Mutation	SNP	G	G	C	rs2477120	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	144	143	166	1	0.993056	0.0060241	G|0.450;C|0.550	0.550	strong	.	CEP350	418	.	NM_014810	exon12	c.G2833C	p.E945Q	AAACCAGAAGGGC	.	PASS	Atlas-SNP
LRIT2	340745	hgsc.bcm.edu	37	10	85981801	85981801	+	Missense_Mutation	SNP	T	T	G	rs6585847	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	64	28	64	0	0.4375	0	T|0.443;G|0.557	0.557	strong	LRIT2,colon,carcinoma,0,3	LRIT2	81	3	NM_001017924	exon3	c.A1528C	p.T510P	CAGGGGTGCAGCT	.	PASS	Atlas-SNP
ZNF256	10172	hgsc.bcm.edu	37	19	58453342	58453342	+	Silent	SNP	T	T	C	rs959231	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	116	77	127	0	0.663793	0	T|0.741;C|0.259	0.259	strong	.	ZNF256	117	.	NM_005773	exon3	c.A834G	p.Q278Q	AGAGCTTTGCCTA	.	PASS	Atlas-SNP
SEMA6B	10501	hgsc.bcm.edu	37	19	4555084	4555084	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	46	17	59	0	0.369565	0	.	.	none	.	SEMA6B	51	.	NM_032108	exon8	c.G586T	p.V196F	CGGTAACAGTAGC	.	PASS	Atlas-SNP
LILRB1	10859	hgsc.bcm.edu	37	19	55143157	55143157	+	Missense_Mutation	SNP	G	G	A	rs12460501	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	148	146	197	0	0.986486	0	G|0.855;A|0.145	0.145	strong	.	LILRB1	140	.	NM_001081637	exon4	c.G277A	p.A93T	GAACATGCAGGGC	.	PASS	Atlas-SNP
BMP5	653	hgsc.bcm.edu	37	6	55639028	55639028	+	Silent	SNP	G	G	A	rs41271330	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	142	59	151	0	0.415493	0	G|0.903;A|0.097	0.097	strong	BMP5,NS,carcinoma,0,1	BMP5	94	1	NM_021073	exon4	c.C846T	p.N282N	TTTTACGTTGATA	.	PASS	Atlas-SNP
ILVBL	10994	hgsc.bcm.edu	37	19	15226970	15226970	+	Silent	SNP	G	G	A	rs2074262	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	42	17	58	0	0.404762	0	G|0.577;A|0.423	0.423	strong	.	ILVBL	54	.	NM_006844	exon12	c.C1464T	p.L488L	AGGATCGAGCCAG	.	PASS	Atlas-SNP
OR52E2	119678	hgsc.bcm.edu	37	11	5080068	5080068	+	Missense_Mutation	SNP	G	G	A	rs2500052	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	92	114	0	1	0	G|0.476;A|0.524	0.524	strong	OR52E2,colon,carcinoma,0,1	OR52E2	63	1	NM_001005164	exon1	c.C790T	p.R264C	CAAAGCGATGAGT	.	PASS	Atlas-SNP
SIGLEC5	8778	hgsc.bcm.edu	37	19	52133292	52133292	+	Missense_Mutation	SNP	A	A	G	rs1973019	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	964	510	1154	5	0.529046	0.00433276	A|0.500;G|0.500	0.500	strong	SIGLEC5,NS,carcinoid-endocrine_tumour,0,1	SIGLEC5	67	1	NM_003830	exon2	c.T215C	p.V72A	GCCACAACCTCAG	.	scavenged	Atlas-SNP
NOTCH1	4851	hgsc.bcm.edu	37	9	139397707	139397707	+	Silent	SNP	G	G	A	rs10521	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	37	85	0	0.506849	0	G|0.466;A|0.534	0.534	strong	NOTCH1_ENST00000277541,colon,carcinoma,0,19	NOTCH1	1980	19	NM_017617	exon27	c.C5094T	p.D1698D	GGCCACGTCGGTG	.	PASS	Atlas-SNP
KRTAP10-6	386674	hgsc.bcm.edu	37	21	46011719	46011719	+	Missense_Mutation	SNP	G	G	A	rs202022037		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	245	18	232	0	0.0734694	0	.	.	weak	KRTAP10-6,caecum,carcinoma,-1,1	KRTAP10-6	57	1	NM_198688	exon1	c.C647T	p.P216L	CAAGTTGGCTGGC	.	scavenged	Atlas-SNP
C14orf159	80017	hgsc.bcm.edu	37	14	91671124	91671124	+	Missense_Mutation	SNP	G	G	A	rs2295524	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	83	75	0	0.976471	0	G|0.835;A|0.165	0.165	strong	.	C14orf159	57	.	NM_001102368	exon12	c.G1519A	p.D507N	CACGGGGATGTCA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195512287	195512287	+	Missense_Mutation	SNP	G	G	A	rs113602668	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	20	66	0	0.235294	0	G|0.843;A|0.157	0.157	strong	.	MUC4	1505	.	NM_018406	exon2	c.C6164T	p.S2055F	ACTGAGGAAAGGC	.	PASS	Atlas-SNP
NDUFA6	4700	hgsc.bcm.edu	37	22	42486723	42486723	+	Missense_Mutation	SNP	G	G	A	rs1801311	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	100	97	119	0	0.97	0	G|0.625;A|0.375	0.375	strong	.	NDUFA6	13	.	NM_002490	exon1	c.C104T	p.A35V	GAAGTAGCTTGGC	.	PASS	Atlas-SNP
NAV2	89797	hgsc.bcm.edu	37	11	20124807	20124807	+	Missense_Mutation	SNP	C	C	T	rs34329467	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	20	114	0	0.266667	0	C|0.997;T|0.003	0.003	strong	.	NAV2	255	.	NM_001244963	exon35	c.C6601T	p.R2201C	GAATTGCGCCAGT	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	41	152	0	0.42268	0	C|0.693;T|0.307	0.307	strong	.	TMX4	39	.	NM_021156	exon8	c.G907A	p.G303R	CCTCTCCTGGGGG	.	PASS	Atlas-SNP
KRT84	3890	hgsc.bcm.edu	37	12	52777580	52777580	+	Silent	SNP	A	A	C	rs1613929	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	90	44	110	0	0.488889	0	A|0.686;C|0.314	0.314	strong	.	KRT84	61	.	NM_033045	exon2	c.T549G	p.V183V	GAACCGAACCTAA	.	PASS	Atlas-SNP
FCHO2	115548	hgsc.bcm.edu	37	5	72347223	72347223	+	Silent	SNP	A	A	G	rs7712838	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	124	69	117	0	0.556452	0	A|0.673;G|0.327	0.327	strong	.	FCHO2	96	.	NM_138782	exon12	c.A987G	p.T329T	AGAAACAAATCAG	.	PASS	Atlas-SNP
TEDDM1	127670	hgsc.bcm.edu	37	1	182369078	182369078	+	Silent	SNP	G	G	A	rs6698722	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	190	95	191	0	0.5	0	G|0.154;A|0.846	0.846	strong	.	TEDDM1	32	.	NM_172000	exon1	c.C543T	p.P181P	AGAGACGGGTCTG	.	PASS	Atlas-SNP
SERPINF1	5176	hgsc.bcm.edu	37	17	1674429	1674429	+	Silent	SNP	T	T	C	rs8074840	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	85	92	0	1	0	T|0.735;C|0.265	0.265	strong	SERPINF1,NS,carcinoma,0,1	SERPINF1	31	1	NM_002615	exon4	c.T390C	p.T130T	GGTCACTGCCCCC	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	59	42	66	0	0.711864	0	T|0.747;C|0.253	0.253	strong	.	KLHL33	37	.	NM_001109997	exon3	c.A1034G	p.E345G	TTGAGCTCAGGGT	.	PASS	Atlas-SNP
CCDC67	159989	hgsc.bcm.edu	37	11	93103330	93103330	+	Missense_Mutation	SNP	C	C	T	rs34205920	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	115	19	123	0	0.165217	0	C|0.989;T|0.011	0.011	strong	.	CCDC67	57	.	NM_181645	exon6	c.C524T	p.S175F	TATTATCTGAGAA	.	PASS	Atlas-SNP
HRG	3273	hgsc.bcm.edu	37	3	186395572	186395572	+	Missense_Mutation	SNP	A	A	T	rs1042464	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	213	213	258	0	1	0	A|0.351;T|0.649	0.649	strong	.	HRG	81	.	NM_000412	exon7	c.A1478T	p.N493I	CAGACAATCAGCC	.	PASS	Atlas-SNP
TRIM50	135892	hgsc.bcm.edu	37	7	72732848	72732848	+	Silent	SNP	G	G	T	rs201525569		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	457	32	463	0	0.0700219	0	G|0.999;T|0.001	0.001	weak	.	TRIM50	78	.	NM_178125	exon4	c.C699A	p.G233G	CTCATTGCCGAAC	.	PASS	Atlas-SNP
MMRN2	79812	hgsc.bcm.edu	37	10	88703122	88703122	+	Silent	SNP	G	G	C	rs146872793	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	117	67	105	0	0.57265	0	G|0.998;C|0.002	0.002	strong	.	MMRN2	49	.	NM_024756	exon6	c.C1419G	p.L473L	CAGCGTGAGGTTG	.	PASS	Atlas-SNP
MFAP1	4236	hgsc.bcm.edu	37	15	44102010	44102010	+	Silent	SNP	A	A	C	rs2228368	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	210	67	242	0	0.319048	0	T|0.141;G|0.046	.	strong	.	MFAP1	36	.	NM_005926	exon7	c.T990G	p.A330A	CTTAACAGCTTTG	.	PASS	Atlas-SNP
HTR3D	200909	hgsc.bcm.edu	37	3	183756742	183756742	+	Silent	SNP	C	C	T	rs55674402	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	135	64	158	0	0.474074	0	C|0.658;T|0.342	0.342	strong	HTR3D,NS,carcinoma,0,1	HTR3D	65	1	NM_001163646	exon8	c.C1344T	p.V448V	CACCGTCATATGC	.	PASS	Atlas-SNP
MRPL52	122704	hgsc.bcm.edu	37	14	23299135	23299135	+	Missense_Mutation	SNP	G	G	T	rs1135641	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	59	32	58	0	0.542373	0	T|0.503;G|0.497;N|0.000;A|0.000	0.503	strong	.	MRPL52	7	.	NM_180982	exon1	c.G14T	p.G5V	CTTTAGGGACTGT	.	PASS	Atlas-SNP
SLC30A3	7781	hgsc.bcm.edu	37	2	27481661	27481661	+	Silent	SNP	G	G	A	rs41288821	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	91	62	84	0	0.681319	0	G|0.993;A|0.007	0.007	strong	.	SLC30A3	39	.	NM_003459	exon2	c.C237T	p.A79A	GGCACAGGCAGCA	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	106	48	106	0	0.45283	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
METTL21C	196541	hgsc.bcm.edu	37	13	103339365	103339365	+	Silent	SNP	A	A	G	rs660207	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	32	83	0	0.450704	0	A|0.483;G|0.517	0.517	strong	METTL21C,NS,carcinoma,+2,1	METTL21C	23	1	NM_001010977	exon3	c.T325C	p.L109L	AATTCAATTCCTC	.	PASS	Atlas-SNP
IWS1	55677	hgsc.bcm.edu	37	2	128244216	128244216	+	Silent	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	142	29	121	0	0.204225	0	.	.	none	.	IWS1	61	.	NM_017969	exon13	c.A2241G	p.G747G	ACAGAATCCAGGA	.	PASS	Atlas-SNP
FAT2	2196	hgsc.bcm.edu	37	5	150901630	150901630	+	Silent	SNP	G	G	T	rs3734049	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	38	10	45	0	0.263158	0	G|0.872;T|0.128	0.128	strong	.	FAT2	465	.	NM_001447	exon18	c.C10524A	p.I3508I	GGGAGGGATGCCA	.	PASS	Atlas-SNP
FREM1	158326	hgsc.bcm.edu	37	9	14801687	14801687	+	Silent	SNP	T	T	C	rs10738380	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	224	101	233	1	0.450893	0.00429185	T|0.834;C|0.166	0.166	strong	.	FREM1	261	.	NM_144966	exon21	c.A3657G	p.A1219A	AACAGGTGCATGT	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105415265	105415265	+	Missense_Mutation	SNP	A	A	T	rs201824674	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	114	19	30	0	0.166667	0	A|0.980;T|0.019	0.019	strong	AHNAK2_ENST00000333244,NS,carcinoma,+1,1	AHNAK2	719	1	NM_138420	exon7	c.T6523A	p.S2175T	CCACCGAGGCCTC	.	scavenged	Atlas-SNP
TSPAN6	7105	hgsc.bcm.edu	37	X	99890204	99890204	+	Missense_Mutation	SNP	C	C	T	rs1802288	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	134	134	195	0	1	0	0|0.015;T|0.099	0.099	strong	.	TSPAN6	23	.	NM_003270	exon3	c.G322A	p.A108T	CGATGGCAGCGAC	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	158	61	120	0	0.386076	0	G|0.811;T|0.189	0.189	strong	.	KRTAP10-2	21	.	NM_198693	exon1	c.C319A	p.P107T	ACACAGGCTTGCA	.	PASS	Atlas-SNP
SIRPG	55423	hgsc.bcm.edu	37	20	1610894	1610894	+	Silent	SNP	G	G	A	rs3746721	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	45	26	48	0	0.577778	0	G|0.742;A|0.258	0.258	strong	SIRPG,NS,carcinoma,0,1	SIRPG	61	1	NM_018556	exon5	c.C1140T	p.Y380Y	GGGGACGTAGATG	.	PASS	Atlas-SNP
FAIM3	9214	hgsc.bcm.edu	37	1	207087435	207087435	+	Silent	SNP	C	C	T	rs167082	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	55	31	63	0	0.563636	0	C|0.648;T|0.352	0.352	strong	.	FAIM3	36	.	NM_005449	exon2	c.G42A	p.S14S	GGCCCCCGATACT	.	PASS	Atlas-SNP
CCDC176	80127	hgsc.bcm.edu	37	14	74523869	74523869	+	Missense_Mutation	SNP	A	A	G	rs3742809	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	77	41	110	0	0.532468	0	G|0.185;N|0.001	0.185	strong	.	.	.	.	NM_025057	exon11	c.A1486G	p.K496E	CAAGATAAAATCT	.	PASS	Atlas-SNP
CYP4F12	66002	hgsc.bcm.edu	37	19	15789140	15789140	+	Missense_Mutation	SNP	A	A	G	rs609290	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	129	129	153	0	1	0	A|0.061;G|0.939	0.939	strong	CYP4F12,tonsil,carcinoma,0,1	CYP4F12	89	1	NM_023944	exon3	c.A268G	p.I90V	TTTACGATATGGC	.	PASS	Atlas-SNP
TTC21A	199223	hgsc.bcm.edu	37	3	39161456	39161456	+	Missense_Mutation	SNP	G	G	A	rs1274972	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	164	70	225	0	0.426829	0	G|0.555;A|0.445	0.445	strong	.	TTC21A	96	.	NM_145755	exon8	c.G869A	p.R290K	AGACAAGGGAACC	.	PASS	Atlas-SNP
USH1C	10083	hgsc.bcm.edu	37	11	17531146	17531146	+	Silent	SNP	G	G	A	rs17776775	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	29	23	29	0	0.793103	0	A|0.048;G|0.952	0.048	strong	.	USH1C	157	.	NM_153676	exon18	c.C1770T	p.A590A	GGATGAGGCGCTC	.	PASS	Atlas-SNP
GLRB	2743	hgsc.bcm.edu	37	4	158060077	158060077	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	124	20	139	0	0.16129	0	.	.	none	GLRB,caecum,carcinoma,-2,1	GLRB	74	1	NM_000824	exon7	c.T727A	p.C243S	GGTAACTGTACAA	.	PASS	Atlas-SNP
LRRC71	149499	hgsc.bcm.edu	37	1	156902259	156902259	+	Silent	SNP	G	G	A	rs822430	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	102	101	137	0	0.990196	0	G|0.286;A|0.714	0.714	strong	.	LRRC71	33	.	NM_144702	exon14	c.G1485A	p.T495T	CGCCACGGTGCAG	.	PASS	Atlas-SNP
POTEF	728378	hgsc.bcm.edu	37	2	130872791	130872791	+	Missense_Mutation	SNP	A	A	G	rs200596208	byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	188	9	199	0	0.0478723	0	A|0.951;G|0.049	0.049	strong	POTEF,brain,glioma,0,2	POTEF	140	2	NM_001099771	exon4	c.T632C	p.I211T	ACCTTTATCAGAG	.	scavenged	Atlas-SNP
TENM3	55714	hgsc.bcm.edu	37	4	183674697	183674697	+	Silent	SNP	C	C	T	rs17263582	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	157	77	171	0	0.490446	0	C|0.827;T|0.173	0.173	strong	ODZ3,NS,carcinoma,0,1	.	.	1	NM_001080477	exon20	c.C3957T	p.G1319G	TCTGGGCTCTAAC	.	PASS	Atlas-SNP
DHX33	56919	hgsc.bcm.edu	37	17	5347788	5347788	+	Missense_Mutation	SNP	G	G	A	rs75426953	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	96	54	119	1	0.5625	0.00840336	A|0.014;C|0.000;G|0.986	0.014	strong	DHX33,NS,carcinoma,0,1	DHX33	41	1	NM_020162	exon12	c.C1861T	p.R621C	AGCGGCGGACACT	.	scavenged	Atlas-SNP
FCHSD1	89848	hgsc.bcm.edu	37	5	141026182	141026182	+	Missense_Mutation	SNP	G	G	T	rs3749760	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	63	32	88	0	0.507937	0	G|0.981;T|0.019	0.019	strong	.	FCHSD1	51	.	NM_033449	exon11	c.C1032A	p.N344K	CCCATGGTTCTGG	.	PASS	Atlas-SNP
SCN2A	6326	hgsc.bcm.edu	37	2	166152389	166152389	+	Missense_Mutation	SNP	G	G	A	rs17183814	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	104	66	114	0	0.634615	0	G|0.933;A|0.067	0.067	strong	.	SCN2A	589	.	NM_001040143	exon1	c.G56A	p.R19K	TTACCAGGGAATC	.	PASS	Atlas-SNP
SENP7	57337	hgsc.bcm.edu	37	3	101085413	101085413	+	Silent	SNP	G	G	A	rs939443	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	131	130	146	0	0.992366	0	G|0.603;A|0.397	0.397	strong	.	SENP7	170	.	NM_020654	exon9	c.C1179T	p.T393T	CTCAACGGTTTCA	.	PASS	Atlas-SNP
HLA-B	3106	hgsc.bcm.edu	37	6	31324089	31324089	+	Silent	SNP	G	G	A	rs1050370	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	100	57	231	0	0.57	0	G|0.971;A|0.029	0.029	strong	.	HLA-B	54	.	NM_005514	exon3	c.C474T	p.T158T	CGCGGCGGTCCAG	.	PASS	Atlas-SNP
ELOVL5	60481	hgsc.bcm.edu	37	6	53159090	53159090	+	Silent	SNP	G	G	T	rs2294857	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	124	53	141	0	0.427419	0	G|0.922;T|0.078	0.078	strong	.	ELOVL5	25	.	NM_001242831	exon3	c.C258A	p.A86A	GGCAGGGGCATGT	.	PASS	Atlas-SNP
OR12D3	81797	hgsc.bcm.edu	37	6	29342775	29342775	+	Missense_Mutation	SNP	G	G	A	rs3749971	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	110	51	92	0	0.463636	0	G|0.942;A|0.058	0.058	strong	OR12D3,NS,carcinoma,0,3	OR12D3	55	3	NM_030959	exon1	c.C290T	p.T97I	AGCTGGGTGATAC	.	PASS	Atlas-SNP
NGFR	4804	hgsc.bcm.edu	37	17	47588000	47588000	+	Silent	SNP	C	C	T	rs11466155	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	159	155	144	0	0.974843	0	C|0.763;T|0.237	0.237	strong	NGFR,colon,carcinoma,0,2	NGFR	46	2	NM_002507	exon4	c.C795T	p.G265G	TGTGGGCCTTGTG	.	PASS	Atlas-SNP
RHOT2	89941	hgsc.bcm.edu	37	16	718514	718514	+	Silent	SNP	C	C	G	rs7204542	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	29	29	34	0	1	0	C|0.369;G|0.631	0.631	strong	RHOT2,colon,carcinoma,0,3	RHOT2	35	3	NM_138769	exon3	c.C123G	p.T41T	GATCACCATCCCC	.	PASS	Atlas-SNP
PXDNL	137902	hgsc.bcm.edu	37	8	52232487	52232487	+	Missense_Mutation	SNP	G	G	T	rs1052704	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	88	21	97	0	0.238636	0	G|0.688;T|0.312	0.312	strong	.	PXDNL	414	.	NM_144651	exon23	c.C4356A	p.D1452E	TCCTCGGTCTCTG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195510762	195510762	+	Silent	SNP	G	G	A	rs2911273	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	152	41	116	0	0.269737	0	G|0.625;A|0.375	0.375	strong	MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	NM_018406	exon2	c.C7689T	p.V2563V	GTCGGTGACAGGA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195515414	195515414	+	Missense_Mutation	SNP	T	T	C	rs200193644	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	41	61	0	0.569444	0	T|0.963;C|0.037	0.037	strong	MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	NM_018406	exon2	c.A3037G	p.S1013G	AAGGGCTGGTGAC	.	PASS	Atlas-SNP
DIRAS1	148252	hgsc.bcm.edu	37	19	2717513	2717513	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	21	84	0	0.295775	0	.	.	none	.	DIRAS1	26	.	NM_145173	exon2	c.G292C	p.G98R	TGGGCCCCAGCTC	.	PASS	Atlas-SNP
GRM6	2916	hgsc.bcm.edu	37	5	178413947	178413947	+	Silent	SNP	T	T	C	rs11746675	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	97	88	0	1	0	T|0.434;C|0.566	0.566	strong	.	GRM6	149	.	NM_000843	exon7	c.A1392G	p.G464G	CGCATCTCCGTTC	.	PASS	Atlas-SNP
KLF17	128209	hgsc.bcm.edu	37	1	44595047	44595047	+	Missense_Mutation	SNP	T	T	A	rs11210969	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	112	51	101	0	0.455357	0	T|0.767;A|0.233	0.233	strong	KLF17,NS,carcinoma,0,1	KLF17	92	1	NM_173484	exon2	c.T104A	p.I35N	CGCCCATCTTGAA	.	PASS	Atlas-SNP
USP40	55230	hgsc.bcm.edu	37	2	234442134	234442134	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	125	32	128	0	0.256	0	.	.	none	.	USP40	174	.	NM_018218	exon10	c.C1495G	p.P499A	CAGGGGGTCTCTG	.	PASS	Atlas-SNP
KCNH6	81033	hgsc.bcm.edu	37	17	61623052	61623052	+	Missense_Mutation	SNP	C	C	T	rs35819807	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	48	26	89	0	0.541667	0	C|0.804;T|0.196	0.196	strong	.	KCNH6	122	.	NM_030779	exon14	c.C2774T	p.T925M	TGGCAACGGACAA	.	PASS	Atlas-SNP
BPIFB2	80341	hgsc.bcm.edu	37	20	31596472	31596472	+	Missense_Mutation	SNP	A	A	T	rs6088066	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	134	68	132	0	0.507463	0	A|0.820;T|0.180	0.180	strong	.	.	.	.	NM_025227	exon2	c.A92T	p.K31M	TCAACAAGGCAGC	.	PASS	Atlas-SNP
GJD2	57369	hgsc.bcm.edu	37	15	35045057	35045057	+	Silent	SNP	G	G	A	rs3743123	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	161	73	247	1	0.453416	0.00404858	G|0.695;A|0.305	0.305	strong	.	GJD2	49	.	NM_020660	exon2	c.C588T	p.S196S	GAAGCGGGAGATG	.	PASS	Atlas-SNP
CPAMD8	27151	hgsc.bcm.edu	37	19	17091368	17091368	+	Silent	SNP	T	T	G	rs8103646	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	80	80	99	0	1	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
IGSF3	3321	hgsc.bcm.edu	37	1	117158745	117158745	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	216	8	292	14	0.037037	0.0479452	.	.	none	IGSF3,extremity,malignant_melanoma,0,1	IGSF3	294	1	NM_001542	exon3	c.T378G	p.D126E	TTGCTTATCAGTG	.	scavenged	Atlas-SNP
MYH8	4626	hgsc.bcm.edu	37	17	10310246	10310246	+	Silent	SNP	G	G	A	rs12936716	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	195	95	249	0	0.487179	0	G|0.945;A|0.055	0.055	strong	.	MYH8	346	.	NM_002472	exon18	c.C2016T	p.F672F	CCGTACGAAGTGA	.	PASS	Atlas-SNP
NTAN1	123803	hgsc.bcm.edu	37	16	15131974	15131974	+	Missense_Mutation	SNP	G	G	T	rs1136001	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	112	80	178	1	0.714286	0.00561798	G|0.706;T|0.294	0.294	strong	.	NTAN1	21	.	NM_173474	exon10	c.C847A	p.H283N	GTGTGTGAGCTGG	.	PASS	Atlas-SNP
STAG2	10735	hgsc.bcm.edu	37	X	123176493	123176493	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	257	68	446	1	0.264591	0.00224215	.	.	none	.	STAG2	309	.	NM_001042749	exon7	c.G460A	p.E154K	TTCGATGAGGTAA	.	PASS	Atlas-SNP
LRIT1	26103	hgsc.bcm.edu	37	10	85993910	85993910	+	Silent	SNP	G	G	A	rs3814206	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	62	62	49	0	1	0	G|0.431;A|0.569	0.569	strong	.	LRIT1	73	.	NM_015613	exon3	c.C814T	p.L272L	GTAGCAGTGCTGT	.	PASS	Atlas-SNP
POTEC	388468	hgsc.bcm.edu	37	18	14542693	14542693	+	Silent	SNP	C	C	T	rs371316587		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	370	5	393	0	0.0135135	0	.	.	weak	POTEC,NS,carcinoma,0,4	POTEC	129	4	NM_001137671	exon1	c.G453A	p.K151K	GGGGACCTTACCC	.	scavenged	Atlas-SNP
PLA2G3	50487	hgsc.bcm.edu	37	22	31533967	31533967	+	Silent	SNP	G	G	A	rs2074739	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	50	27	46	0	0.54	0	G|0.488;N|0.000	.	strong	.	PLA2G3	85	.	NM_015715	exon4	c.C795T	p.Y265Y	TGTGCCGTACATC	.	PASS	Atlas-SNP
ZNF469	84627	hgsc.bcm.edu	37	16	88500430	88500430	+	Silent	SNP	G	G	T	rs12919507	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	74	42	70	0	0.567568	0	G|0.916;T|0.084	0.084	strong	.	ZNF469	121	.	NM_001127464	exon2	c.G6468T	p.T2156T	AGCCACGACAGAT	.	PASS	Atlas-SNP
FAT4	79633	hgsc.bcm.edu	37	4	126336347	126336347	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	108	8	127	0	0.0740741	0	.	.	none	.	FAT4	1752	.	NM_024582	exon5	c.C6229A	p.P2077T	ACTGACCCAGATA	.	PASS	Atlas-SNP
FCGBP	8857	hgsc.bcm.edu	37	19	40392802	40392802	+	Missense_Mutation	SNP	C	C	T	rs149844303	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	465	75	351	0	0.16129	0	.	.	weak	FCGBP,NS,carcinoma,0,1	FCGBP	416	1	NM_003890	exon16	c.G7702A	p.A2568T	CGTAGGCCACACG	.	scavenged	Atlas-SNP
CTU2	348180	hgsc.bcm.edu	37	16	88781040	88781040	+	Missense_Mutation	SNP	A	A	G	rs8059048	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	209	207	192	0	0.990431	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
RAPGEF5	9771	hgsc.bcm.edu	37	7	22233635	22233635	+	Missense_Mutation	SNP	G	G	A	rs375862364		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	77	12	103	0	0.155844	0	.	.	weak	.	RAPGEF5	96	.	NM_012294	exon10	c.C554T	p.T185M	ACAGTCGTCACTT	.	PASS	Atlas-SNP
DOCK5	80005	hgsc.bcm.edu	37	8	25220581	25220581	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	84	47	120	0	0.559524	0	.	.	none	.	DOCK5	167	.	NM_024940	exon29	c.T2968A	p.F990I	GAAACTTTTATCA	.	PASS	Atlas-SNP
FOXQ1	94234	hgsc.bcm.edu	37	6	1313470	1313470	+	Silent	SNP	C	C	T	rs4435985	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	201	80	173	1	0.39801	0.00578035	C|0.811;T|0.189	0.189	strong	FOXQ1,NS,carcinoma,0,1	FOXQ1	8	1	NM_033260	exon1	c.C531T	p.F177F	CTGCTTCGTCAAG	.	scavenged	Atlas-SNP
SLC16A6	9120	hgsc.bcm.edu	37	17	66267691	66267691	+	Missense_Mutation	SNP	A	A	T	rs7222013	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	144	82	186	0	0.569444	0	A|0.636;T|0.364	0.364	strong	.	SLC16A6	56	.	NM_001174166	exon6	c.T610A	p.F204I	TGATAAAGATGGG	.	PASS	Atlas-SNP
HSD3B1	3283	hgsc.bcm.edu	37	1	120057158	120057158	+	Silent	SNP	C	C	T	rs6203	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	179	72	190	0	0.402235	0	C|0.647;T|0.353	0.353	strong	.	HSD3B1	53	.	NM_000862	exon4	c.C1012T	p.L338L	CGAGATCTGGCGT	.	PASS	Atlas-SNP
KRT77	374454	hgsc.bcm.edu	37	12	53091566	53091566	+	Missense_Mutation	SNP	C	C	A	rs1567759	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	142	84	190	0	0.591549	0	C|0.593;A|0.407	0.407	strong	KRT77,colon,carcinoma,0,1	KRT77	58	1	NM_175078	exon2	c.G658T	p.G220C	GGTCACCGATGTA	.	PASS	Atlas-SNP
STRC	161497	hgsc.bcm.edu	37	15	43893072	43893072	+	Silent	SNP	G	G	A	rs55877445		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	197	63	221	0	0.319797	0	.	.	weak	.	STRC	58	.	NM_153700	exon25	c.C4842T	p.F1614F	TGACCTGAACTCC	.	PASS	Atlas-SNP
TEX40	25858	hgsc.bcm.edu	37	11	64068310	64068310	+	Missense_Mutation	SNP	C	C	T	rs2286614	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	109	79	118	0	0.724771	0	C|0.899;T|0.101	0.101	strong	.	.	.	.	NM_001039496	exon2	c.C203T	p.P68L	ACAGCCCGGGGCG	.	PASS	Atlas-SNP
SIRT5	23408	hgsc.bcm.edu	37	6	13604710	13604710	+	Missense_Mutation	SNP	A	A	T	rs41273886	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	91	43	104	0	0.472527	0	A|0.989;T|0.011	0.011	strong	.	SIRT5	45	.	NM_031244	exon10	c.A860T	p.H287L	TCAGTCATTTGAT	.	PASS	Atlas-SNP
KRTAP12-2	353323	hgsc.bcm.edu	37	21	46086457	46086457	+	Missense_Mutation	SNP	G	G	A	rs12483730	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	263	110	206	0	0.418251	0	G|0.846;A|0.154	0.154	strong	.	KRTAP12-2	10	.	NM_181684	exon1	c.C347T	p.A116V	GGAGCCGCATACA	.	PASS	Atlas-SNP
USP48	84196	hgsc.bcm.edu	37	1	22109370	22109370	+	Silent	SNP	G	G	A	rs10917042	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	79	38	35	0	0.481013	0	G|0.772;A|0.228	0.228	strong	.	USP48	91	.	NM_001032730	exon1	c.C81T	p.H27H	CTCGATGTGCTCC	.	PASS	Atlas-SNP
RHBDL2	54933	hgsc.bcm.edu	37	1	39352271	39352271	+	Missense_Mutation	SNP	G	G	T	rs2147914	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	81	42	86	0	0.518519	0	G|0.652;T|0.348	0.348	strong	RHBDL2,bladder,carcinoma,+2,1	RHBDL2	28	1	NM_017821	exon8	c.C817A	p.L273M	CTTTCAGCAGTGC	.	PASS	Atlas-SNP
TLR6	10333	hgsc.bcm.edu	37	4	38829163	38829163	+	Silent	SNP	A	A	C	rs5743818	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	88	56	120	0	0.636364	0	A|0.842;C|0.158	0.158	strong	.	TLR6	67	.	NM_006068	exon2	c.T1932G	p.A644A	AATAAAAGCATGA	.	PASS	Atlas-SNP
AIRE	326	hgsc.bcm.edu	37	21	45712983	45712983	+	Silent	SNP	T	T	C	rs61737072	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	63	24	40	0	0.380952	0	T|0.951;C|0.049	0.049	strong	.	AIRE	61	.	NM_000383	exon10	c.T1203C	p.P401P	TCCGCCTTCTGCA	.	PASS	Atlas-SNP
CDH11	1009	hgsc.bcm.edu	37	16	65025718	65025718	+	Missense_Mutation	SNP	G	G	A	rs35195	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	163	163	166	0	1	0	G|0.763;A|0.237	0.237	strong	CDH11,NS,carcinoma,+1,1	CDH11	260	1	NM_001797	exon6	c.C764T	p.T255M	GTGATCGTCACTT	.	PASS	Atlas-SNP
PLIN4	729359	hgsc.bcm.edu	37	19	4511890	4511890	+	Silent	SNP	G	G	A	rs200897749	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	236	38	230	0	0.161017	0	G|0.982;A|0.018	0.018	strong	.	PLIN4	191	.	NM_001080400	exon3	c.C2040T	p.T680T	GGTGCCGGTCAGC	.	PASS	Atlas-SNP
APCDD1	147495	hgsc.bcm.edu	37	18	10471732	10471732	+	Missense_Mutation	SNP	G	G	A	rs3748415	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	49	30	60	0	0.612245	0	G|0.906;A|0.094	0.094	strong	.	APCDD1	57	.	NM_153000	exon3	c.G448A	p.V150I	CACAACGTCCAGG	.	PASS	Atlas-SNP
KDM2B	84678	hgsc.bcm.edu	37	12	121880520	121880520	+	Silent	SNP	G	G	A	rs3751131	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	33	67	0	0.388235	0	G|0.651;A|0.349	0.349	strong	KDM2B_ENST00000377071,colon,carcinoma,-2,2	KDM2B	218	2	NM_032590	exon19	c.C2724T	p.D908D	GGAGTGGTCGCTC	.	PASS	Atlas-SNP
ENDOG	2021	hgsc.bcm.edu	37	9	131584729	131584729	+	Missense_Mutation	SNP	G	G	T	rs61737988	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	143	74	147	0	0.517483	0	G|0.998;T|0.002	0.002	strong	.	ENDOG	8	.	NM_004435	exon3	c.G734T	p.R245L	AGCTCCGCACCTA	.	PASS	Atlas-SNP
GPS2	2874	hgsc.bcm.edu	37	17	7216540	7216540	+	Silent	SNP	G	G	A	rs2270981	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	110	49	93	0	0.445455	0	G|0.879;A|0.121	0.121	strong	.	GPS2	44	.	NM_004489	exon9	c.C795T	p.F265F	GTCGGAGAAGCCA	.	PASS	Atlas-SNP
NPVF	64111	hgsc.bcm.edu	37	7	25267934	25267934	+	Missense_Mutation	SNP	T	T	C	rs877834	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	103	80	158	1	0.776699	0.00632911	C|0.206;N|0.000	0.206	strong	.	NPVF	36	.	NM_022150	exon1	c.A125G	p.D42G	TATTTGTCATAAT	.	PASS	Atlas-SNP
SMIM11	54065	hgsc.bcm.edu	37	21	35757787	35757787	+	Silent	SNP	C	C	T	rs61747964	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	290	107	307	0	0.368966	0	C|0.971;T|0.029	0.029	strong	.	.	.	.	NM_058182	exon3	c.C24T	p.H8H	TGAGCACGTGCCC	.	PASS	Atlas-SNP
ZNF71	58491	hgsc.bcm.edu	37	19	57132968	57132968	+	Missense_Mutation	SNP	G	G	A	rs2072501	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	37	37	31	0	1	0	G|0.766;A|0.234	0.234	strong	.	ZNF71	69	.	NM_021216	exon3	c.G313A	p.V105I	CCACCCGTAAGGC	.	PASS	Atlas-SNP
LARP6	55323	hgsc.bcm.edu	37	15	71125339	71125339	+	Silent	SNP	G	G	A	rs28676469	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	104	39	106	0	0.375	0	G|0.929;A|0.071	0.071	strong	.	LARP6	43	.	NM_018357	exon3	c.C528T	p.F176F	GTTGGGGAACAGT	.	PASS	Atlas-SNP
ULK3	25989	hgsc.bcm.edu	37	15	75131959	75131959	+	Silent	SNP	A	A	G	rs936227	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	76	76	62	0	1	0	A|0.563;G|0.437	0.437	strong	.	ULK3	30	.	NM_001099436	exon7	c.T792C	p.F264F	CGCAAAAAAGTCC	.	PASS	Atlas-SNP
KIAA1751	85452	hgsc.bcm.edu	37	1	1896440	1896440	+	Silent	SNP	G	G	A	rs16824585	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	56	17	70	0	0.303571	0	G|0.764;A|0.236	0.236	strong	.	KIAA1751	92	.	NM_001080484	exon13	c.C1462T	p.L488L	GCTCCAGGATGTC	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100676968	100676968	+	Silent	SNP	G	G	A	rs138994021	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	29	48	0	0.5	0	G|0.991;A|0.009	0.009	strong	.	MUC17	804	.	NM_001040105	exon3	c.G2271A	p.T757T	CAAAACGCTGTTG	.	PASS	Atlas-SNP
ABCA13	154664	hgsc.bcm.edu	37	7	48287840	48287840	+	Missense_Mutation	SNP	G	G	A	rs2361519	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	32	10	94	0	0.3125	0	G|0.802;A|0.197	0.197	strong	.	ABCA13	1192	.	NM_152701	exon14	c.G1664A	p.R555H	AGGATCGTATTTT	.	PASS	Atlas-SNP
CBY1	25776	hgsc.bcm.edu	37	22	39069181	39069181	+	Silent	SNP	T	T	C	rs3747174	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	68	32	59	0	0.470588	0	T|0.702;C|0.298	0.298	strong	.	CBY1	10	.	NM_001002880	exon6	c.T450C	p.A150A	CACTGCTGAATCC	.	PASS	Atlas-SNP
THSD7A	221981	hgsc.bcm.edu	37	7	11581134	11581134	+	Silent	SNP	T	T	C	rs2074603	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	205	150	215	0	0.731707	0	T|0.532;C|0.468	0.468	strong	.	THSD7A	219	.	NM_015204	exon6	c.A1734G	p.A578A	TCTCACTGCTTTC	.	PASS	Atlas-SNP
ITGAM	3684	hgsc.bcm.edu	37	16	31336888	31336888	+	Missense_Mutation	SNP	C	C	T	rs1143683	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	76	41	75	0	0.539474	0	C|0.870;T|0.130	0.130	strong	.	ITGAM	137	.	NM_001145808	exon21	c.C2576T	p.A859V	CTGGGGCCTTGAA	.	PASS	Atlas-SNP
CRIPAK	285464	hgsc.bcm.edu	37	4	1389007	1389007	+	Silent	SNP	C	C	T	rs78871723	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	19	10	81	5	0.526316	0.0617284	C|0.918;T|0.082	0.082	strong	CRIPAK,rectum,NS,+2,1	CRIPAK	185	1	NM_175918	exon1	c.C708T	p.C236C	CCGATGCGGAGTG	.	scavenged	Atlas-SNP
DYSF	8291	hgsc.bcm.edu	37	2	71906278	71906278	+	Silent	SNP	A	A	C	rs17718530	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	89	31	112	0	0.348315	0	A|0.799;C|0.201;T|0.000	0.201	strong	.	DYSF	536	.	NM_001130987	exon53	c.A5976C	p.P1992P	CCACCCAGAATGG	.	PASS	Atlas-SNP
CAB39L	81617	hgsc.bcm.edu	37	13	49956980	49956980	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	254	63	225	0	0.248031	0	.	.	none	.	CAB39L	35	.	NM_030925	exon2	c.G67T	p.D23Y	AATTGTCTTTCAG	.	PASS	Atlas-SNP
DDB1	1642	hgsc.bcm.edu	37	11	61099072	61099072	+	Silent	SNP	G	G	A	rs2230356	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	129	41	145	0	0.317829	0	G|0.928;A|0.072	0.072	strong	.	DDB1	100	.	NM_001923	exon2	c.C153T	p.P51P	TTTGACGGGCCGA	.	PASS	Atlas-SNP
MECOM	2122	hgsc.bcm.edu	37	3	168810874	168810874	+	Silent	SNP	C	C	T	rs17466625	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	97	137	1	1	0.00729927	C|0.871;T|0.129	0.129	strong	.	MECOM	216	.	NM_004991	exon14	c.G3036A	p.S1012S	ATGAGGCGACGAT	.	PASS	Atlas-SNP
CIITA	4261	hgsc.bcm.edu	37	16	11001770	11001770	+	Silent	SNP	G	G	T	rs34654419	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	48	43	54	0	0.895833	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
A2ML1	144568	hgsc.bcm.edu	37	12	9010671	9010671	+	Silent	SNP	G	G	A	rs11612600	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	68	93	0	0.985507	0	G|0.729;A|0.271	0.271	strong	A2ML1,NS,carcinoma,0,1	A2ML1	199	1	NM_144670	exon26	c.G3237A	p.V1079V	CAACGTGGGAAAT	.	PASS	Atlas-SNP
OR1A2	26189	hgsc.bcm.edu	37	17	3100827	3100827	+	Silent	SNP	T	T	C	rs2241093	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	81	80	90	0	0.987654	0	T|0.693;C|0.307	0.307	strong	OR1A2,NS,carcinoma,0,1	OR1A2	52	1	NM_012352	exon1	c.T15C	p.N5N	AGAAAATCAATCC	.	PASS	Atlas-SNP
KNG1	3827	hgsc.bcm.edu	37	3	186435370	186435370	+	Silent	SNP	G	G	A	rs1050274	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	31	90	0	0.449275	0	G|0.637;A|0.363	0.363	strong	KNG1_ENST00000265023,NS,adenoma,0,2	KNG1	129	2	NM_000893	exon1	c.G39A	p.L13L	CAGGCTGCTACTA	.	PASS	Atlas-SNP
PPP1R18	170954	hgsc.bcm.edu	37	6	30652872	30652872	+	Silent	SNP	G	G	A	rs2269706	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	140	68	165	0	0.485714	0	G|0.875;A|0.125	0.125	strong	.	.	.	.	NM_001134870	exon2	c.C924T	p.S308S	TCCTGCGGAACTG	.	PASS	Atlas-SNP
TUB	7275	hgsc.bcm.edu	37	11	8122143	8122143	+	Missense_Mutation	SNP	C	C	T	rs139170512	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	79	55	81	0	0.696203	0	C|1.000;T|0.000	0.000	weak	TUB,NS,carcinoma,-1,1	TUB	71	1	NM_003320	exon11	c.C1375T	p.R459C	CGCCCCCGCAACG	.	PASS	Atlas-SNP
ZNF285	26974	hgsc.bcm.edu	37	19	44890651	44890651	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	18	89	0	0.206897	0	.	.	none	.	ZNF285	86	.	NM_152354	exon4	c.C1756T	p.Q586X	CTCTCTGCTCATG	.	PASS	Atlas-SNP
LAIR2	3904	hgsc.bcm.edu	37	19	55021777	55021777	+	Missense_Mutation	SNP	T	T	A	rs62131570	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	200	61	322	0	0.305	0	T|0.976;A|0.024	0.024	strong	.	LAIR2	30	.	NM_002288	exon5	c.T457A	p.X153R	GCACCATGAATGA	.	PASS	Atlas-SNP
CDHR1	92211	hgsc.bcm.edu	37	10	85978939	85978939	+	Silent	SNP	G	G	A	rs4244947	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	98	52	79	0	0.530612	0	G|0.460;A|0.540	0.540	strong	.	CDHR1	122	.	NM_001171971	exon17	c.G2145A	p.L715L	GGGTCTGTTCTTG	.	PASS	Atlas-SNP
DES	1674	hgsc.bcm.edu	37	2	220283592	220283592	+	Silent	SNP	C	C	T	rs111828114	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	111	61	103	1	0.54955	0.00970874	C|0.979;T|0.021	0.021	strong	DES,brain,glioma,0,2	DES	53	2	NM_001927	exon1	c.C408T	p.L136L	GGCGCTCGCCGCC	.	scavenged	Atlas-SNP
SLC9C1	285335	hgsc.bcm.edu	37	3	111996554	111996554	+	Missense_Mutation	SNP	T	T	C	rs9828502	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	135	135	159	0	1	0	T|0.713;C|0.287	0.287	strong	.	.	.	.	NM_183061	exon5	c.A472G	p.I158V	CTCTTATAGCAGC	.	PASS	Atlas-SNP
RNASE8	122665	hgsc.bcm.edu	37	14	21526079	21526079	+	Missense_Mutation	SNP	C	C	T	rs12437266	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	54	15	66	0	0.277778	0	C|0.481;T|0.519	0.519	strong	.	RNASE8	11	.	NM_138331	exon1	c.C28T	p.P10S	TGCTGCCCCCTGC	.	PASS	Atlas-SNP
OSBPL7	114881	hgsc.bcm.edu	37	17	45885756	45885756	+	Silent	SNP	C	C	T	rs9911983	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	125	59	158	0	0.472	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
KRT77	374454	hgsc.bcm.edu	37	12	53090190	53090190	+	Silent	SNP	C	C	T	rs7138818	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	29	16	44	1	0.551724	0.0227273	C|0.590;T|0.410	0.410	strong	KRT77,NS,carcinoma,0,1	KRT77	58	1	NM_175078	exon3	c.G783A	p.R261R	GCCAGTCCTCTTG	.	scavenged	Atlas-SNP
HLA-G	3135	hgsc.bcm.edu	37	6	29796327	29796327	+	Silent	SNP	C	C	T	rs1130356	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	83	101	0	0.976471	0	C|0.734;T|0.266	0.266	strong	.	HLA-G	90	.	NM_002127	exon4	c.C351T	p.H117H	TTCTCACACCCTC	.	PASS	Atlas-SNP
GPN1	11321	hgsc.bcm.edu	37	2	27851918	27851918	+	Missense_Mutation	SNP	G	G	A	rs3749147	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	115	65	109	0	0.565217	0	G|0.772;A|0.228	0.228	strong	.	GPN1	28	.	NM_007266	exon1	c.G35A	p.R12K	GGGCCAGGAGGAA	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	163	100	196	1	0.613497	0.00510204	T|0.680;C|0.320	0.320	strong	.	C2orf16	357	.	NM_032266	exon1	c.T2054C	p.V685A	AGGCTGTGAAATC	.	PASS	Atlas-SNP
ABCA3	21	hgsc.bcm.edu	37	16	2348528	2348528	+	Silent	SNP	G	G	C	rs323043	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	121	23	109	0	0.190083	0	G|0.858;C|0.142	0.142	strong	.	ABCA3	176	.	NM_001089	exon15	c.C1755G	p.P585P	ACTGGTGGGGGGA	.	PASS	Atlas-SNP
ZNF415	55786	hgsc.bcm.edu	37	19	53612311	53612311	+	Silent	SNP	T	T	C	rs4803051	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	36	21	42	0	0.583333	0	T|0.561;C|0.439	0.439	strong	.	ZNF415	68	.	NM_018355	exon4	c.A987G	p.T329T	TTTACATGTGTAA	.	PASS	Atlas-SNP
BRF1	2972	hgsc.bcm.edu	37	14	105722726	105722726	+	Silent	SNP	T	T	C	rs1008628	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	22	9	34	0	0.409091	0	T|0.783;C|0.217	0.217	strong	.	BRF1	102	.	NM_001242790	exon4	c.A600G	p.P200P	CCTGACTGGGCAG	.	PASS	Atlas-SNP
OSCP1	127700	hgsc.bcm.edu	37	1	36886117	36886117	+	Missense_Mutation	SNP	C	C	T	rs2275477	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	136	75	128	1	0.551471	0.0078125	C|0.755;T|0.245	0.245	strong	OSCP1,NS,carcinoma,0,1	OSCP1	48	1	NM_145047	exon8	c.G919A	p.G307R	GGAATCCGGGCTC	.	scavenged	Atlas-SNP
CSPG4	1464	hgsc.bcm.edu	37	15	75982058	75982058	+	Missense_Mutation	SNP	T	T	A	rs147116973	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	224	20	229	0	0.0892857	0	T|0.988;A|0.013	0.013	strong	CSPG4,NS,haematopoietic_neoplasm,0,1	CSPG4	175	1	NM_001897	exon3	c.A1348T	p.R450W	CATGCCTCCACTC	.	PASS	Atlas-SNP
SPATA22	84690	hgsc.bcm.edu	37	17	3343519	3343519	+	Silent	SNP	T	T	C	rs17822627	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	353	171	402	0	0.484419	0	T|0.774;C|0.226	0.226	strong	.	SPATA22	49	.	NM_032598	exon9	c.A1014G	p.E338E	TTTTTGTTCAGAA	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179482633	179482633	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	276	76	323	0	0.275362	0	.	.	none	.	TTN	18412	.	NM_001267550	exon253	c.C47445A	p.D15815E	AGACAGGTCTTCA	.	PASS	Atlas-SNP
ADAM32	203102	hgsc.bcm.edu	37	8	39044565	39044565	+	Splice_Site	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	38	18	44	0	0.473684	0	.	.	none	.	ADAM32	70	.	NM_145004	exon11	c.1052+1G>A	.	AGTTGTGTAAGTT	.	PASS	Atlas-SNP
AQP8	343	hgsc.bcm.edu	37	16	25239805	25239805	+	Missense_Mutation	SNP	G	G	C	rs2287798	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	112	42	92	1	0.375	0.0108696	G|0.599;C|0.401	0.401	strong	AQP8_ENST00000219660,NS,carcinoma,0,2	AQP8	75	2	NM_001169	exon6	c.G778C	p.A260P	CTGAAGGCTCGGT	.	scavenged	Atlas-SNP
TTLL5	23093	hgsc.bcm.edu	37	14	76156609	76156609	+	Missense_Mutation	SNP	C	C	T	rs2303345	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	112	111	147	0	0.991071	0	C|0.562;T|0.438	0.438	strong	.	TTLL5	102	.	NM_015072	exon6	c.C446T	p.A149V	TCAAGGCTTTTCA	.	PASS	Atlas-SNP
CD27	939	hgsc.bcm.edu	37	12	6554628	6554628	+	Missense_Mutation	SNP	G	G	A	rs25680	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	62	26	66	0	0.419355	0	G|0.844;A|0.156	0.156	strong	.	CD27	17	.	NM_001242	exon2	c.G175A	p.A59T	AGAAAGGCTGCTC	.	PASS	Atlas-SNP
MAP1B	4131	hgsc.bcm.edu	37	5	71495041	71495041	+	Silent	SNP	T	T	C	rs3805452	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	21	57	0	0.362069	0	T|0.749;C|0.251	0.251	strong	.	MAP1B	243	.	NM_005909	exon5	c.T5859C	p.G1953G	AGAGGGTGGGTAC	.	PASS	Atlas-SNP
KY	339855	hgsc.bcm.edu	37	3	134322742	134322742	+	Silent	SNP	A	A	G	rs2293293	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	39	62	0	0.565217	0	A|0.316;G|0.684	0.684	strong	.	KY	92	.	NM_178554	exon11	c.T1665C	p.L555L	GCATACAAGGTAA	.	PASS	Atlas-SNP
SNX15	29907	hgsc.bcm.edu	37	11	64799998	64799998	+	Silent	SNP	T	T	C	rs534236	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	53	18	61	0	0.339623	0	T|0.524;C|0.476	0.476	strong	.	SNX15	35	.	NM_147777	exon3	c.T231C	p.P77P	GTTCCCTGCTTTC	.	PASS	Atlas-SNP
SPATA18	132671	hgsc.bcm.edu	37	4	52946016	52946016	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	191	45	227	0	0.235602	0	.	.	none	.	SPATA18	222	.	NM_145263	exon9	c.C1286A	p.A429E	CCTTTGCAATGCA	.	PASS	Atlas-SNP
EPS8L2	64787	hgsc.bcm.edu	37	11	722709	722709	+	Silent	SNP	C	C	T	rs10902205	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	134	115	111	0	0.858209	0	A|0.000;C|0.882;G|0.000;T|0.118	0.118	strong	.	EPS8L2	42	.	NM_022772	exon14	c.C1245T	p.Y415Y	CCTCTACGTGCCC	.	PASS	Atlas-SNP
DHX34	9704	hgsc.bcm.edu	37	19	47883086	47883086	+	Silent	SNP	T	T	G	rs28522883	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	50	48	81	0	0.96	0	T|0.878;G|0.122	0.122	strong	.	DHX34	98	.	NM_014681	exon14	c.T2826G	p.A942A	GGCGGCTTCCCTG	.	PASS	Atlas-SNP
KRT84	3890	hgsc.bcm.edu	37	12	52778947	52778947	+	Silent	SNP	A	A	G	rs1791631	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	79	41	101	0	0.518987	0	A|0.685;G|0.315	0.315	strong	.	KRT84	61	.	NM_033045	exon1	c.T423C	p.T141T	GTTCACAGTCACA	.	PASS	Atlas-SNP
OR10G4	390264	hgsc.bcm.edu	37	11	123887175	123887175	+	Silent	SNP	G	G	A	rs61908597	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	89	69	129	0	0.775281	0	G|0.940;A|0.060	0.060	strong	OR10G4,NS,carcinoma,+2,1	OR10G4	77	1	NM_001004462	exon1	c.G894A	p.V298V	AGCTGTGTTGAAA	.	PASS	Atlas-SNP
OR5B3	441608	hgsc.bcm.edu	37	11	58170738	58170738	+	Missense_Mutation	SNP	A	A	G	rs11229413	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	60	68	0	0.697674	0	A|0.675;G|0.325	0.325	strong	.	OR5B3	65	.	NM_001005469	exon1	c.T145C	p.W49R	AATCCCAGAATAT	.	PASS	Atlas-SNP
PIEZO1	9780	hgsc.bcm.edu	37	16	88783449	88783449	+	Silent	SNP	C	C	G	rs8057031	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	108	108	118	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
CD101	9398	hgsc.bcm.edu	37	1	117554421	117554421	+	Missense_Mutation	SNP	A	A	G	rs3754112	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	150	83	165	0	0.553333	0	G|0.210;N|0.000	0.210	strong	CD101,NS,adenoma,0,1	CD101	95	1	NM_001256109	exon3	c.A674G	p.N225S	AGCTCAACAAACT	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	136	38	174	0	0.279412	0	G|0.683;C|0.317	0.317	strong	.	NOD1	79	.	NM_006092	exon4	c.C156G	p.A52A	ATCTTCGGCCGAG	.	PASS	Atlas-SNP
FYCO1	79443	hgsc.bcm.edu	37	3	46009864	46009864	+	Missense_Mutation	SNP	C	C	G	rs3733100	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	36	19	33	0	0.527778	0	C|0.537;G|0.463	0.463	strong	.	FYCO1	115	.	NM_024513	exon8	c.G962C	p.G321A	TCCAGGCCCTGCA	.	PASS	Atlas-SNP
ULK2	9706	hgsc.bcm.edu	37	17	19720109	19720109	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	113	17	161	0	0.150442	0	.	.	none	.	ULK2	142	.	NM_001142610	exon13	c.C1049T	p.T350M	TCATCCGTGTCAC	.	PASS	Atlas-SNP
SELPLG	6404	hgsc.bcm.edu	37	12	109017680	109017680	+	Missense_Mutation	SNP	T	T	G	rs200527674	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	22	119	0	0.217822	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
C8orf31	286122	hgsc.bcm.edu	37	8	144124609	144124609	+	Missense_Mutation	SNP	T	T	C	rs11136300	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	24	109	0	0.27907	0	T|0.317;C|0.683	0.683	strong	.	C8orf31	18	.	NM_173687	exon3	c.T116C	p.L39P	GGCTGCTGGCTGC	.	PASS	Atlas-SNP
OR51L1	119682	hgsc.bcm.edu	37	11	5020799	5020799	+	Missense_Mutation	SNP	C	C	T	rs10768448	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	374	373	399	1	0.997326	0.00250627	C|0.707;T|0.293	0.293	strong	.	OR51L1	60	.	NM_001004755	exon1	c.C587T	p.T196I	CCAGGACCAACAG	.	PASS	Atlas-SNP
STPG2	285555	hgsc.bcm.edu	37	4	98893437	98893437	+	Silent	SNP	A	A	G	rs783960	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	156	153	205	0	0.980769	0	A|0.578;G|0.422	0.422	strong	C4orf37,NS,carcinoma,0,2	.	.	2	NM_174952	exon7	c.T927C	p.D309D	CTGATAATCAGCA	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	49	86	0	0.485149	0	C|0.687;G|0.312	0.312	strong	.	LRRFIP1	171	.	NM_001137552	exon11	c.C2347G	p.H783D	CCAGGGCACTTCA	.	PASS	Atlas-SNP
GABRA6	2559	hgsc.bcm.edu	37	5	161119125	161119125	+	Silent	SNP	C	C	G	rs13184586	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	129	127	143	0	0.984496	0	C|0.535;G|0.465	0.465	strong	.	GABRA6	139	.	NM_000811	exon8	c.C1005G	p.A335A	GAAGGCCAAAAGG	.	PASS	Atlas-SNP
MYH14	79784	hgsc.bcm.edu	37	19	50812315	50812315	+	Silent	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	196	98	187	0	0.5	0	.	.	none	.	MYH14	261	.	NM_001145809	exon42	c.C5841T	p.A1947A	GGAGGCCGAGGAG	.	PASS	Atlas-SNP
XDH	7498	hgsc.bcm.edu	37	2	31588395	31588395	+	Silent	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	135	45	140	0	0.333333	0	.	.	none	.	XDH	191	.	NM_000379	exon23	c.G2472A	p.V824V	GCATCGCACAGGG	.	PASS	Atlas-SNP
TRPA1	8989	hgsc.bcm.edu	37	8	72975801	72975801	+	Missense_Mutation	SNP	T	T	G	rs7819749	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	56	51	87	0	0.910714	0	T|0.245;G|0.755	0.755	strong	TRPA1,NS,carcinoma,-2,1	TRPA1	256	1	NM_007332	exon5	c.A558C	p.K186N	TCCTTTTTTAAGC	.	PASS	Atlas-SNP
ARL5B	221079	hgsc.bcm.edu	37	10	18964097	18964097	+	Silent	SNP	G	G	A	rs12359433	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	129	62	129	0	0.48062	0	G|0.945;A|0.055	0.055	strong	.	ARL5B	12	.	NM_178815	exon6	c.G492A	p.G164G	GTTTAGGTTATGC	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29910719	29910719	+	Missense_Mutation	SNP	G	G	A	rs2230991	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	188	69	264	0	0.367021	0	A|0.110;C|0.022;G|0.868	0.110	strong	.	HLA-A	89	.	NM_001242758	exon2	c.G259A	p.E87K	GACCAGGAGACAC	.	PASS	Atlas-SNP
PLEKHG1	57480	hgsc.bcm.edu	37	6	151121915	151121915	+	Silent	SNP	G	G	A	rs2073061	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	59	118	0	0.641304	0	G|0.393;A|0.607	0.607	strong	PLEKHG1,NS,adenoma,0,1	PLEKHG1	97	1	NM_001029884	exon7	c.G690A	p.E230E	CAGGGAGCGTCAG	.	PASS	Atlas-SNP
LTB	4050	hgsc.bcm.edu	37	6	31549364	31549364	+	Missense_Mutation	SNP	G	G	A	rs4647186	bycluster;alternate_allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	31	144	0	0.336957	0	G|0.994;C|0.006	.	alt	LTB,NS,lymphoid_neoplasm,0,1	LTB	19	1	NM_009588	exon2	c.C206T	p.A69V	CCCGGGGCTGAGA	.	PASS	Atlas-SNP
ZNF404	342908	hgsc.bcm.edu	37	19	44376937	44376937	+	Missense_Mutation	SNP	G	G	A	rs76311065	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	36	78	0	0.62069	0	G|0.962;A|0.038	0.038	strong	.	ZNF404	46	.	NM_001033719	exon2	c.C1420T	p.R474C	TAGAACGAAAGGC	.	PASS	Atlas-SNP
DDX26B	203522	hgsc.bcm.edu	37	X	134713855	134713855	+	Silent	SNP	G	G	A	rs2298301	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	318	316	520	1	0.993711	0.00192308	G|0.877;A|0.123	0.123	strong	.	DDX26B	130	.	NM_182540	exon15	c.G2151A	p.L717L	TTCTCTGTCTGAC	.	PASS	Atlas-SNP
SNAPC4	6621	hgsc.bcm.edu	37	9	139276430	139276430	+	Silent	SNP	G	G	A	rs34850728	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	122	52	175	0	0.42623	0	G|0.876;A|0.124	0.124	strong	.	SNAPC4	82	.	NM_003086	exon17	c.C2163T	p.H721H	GGCTCTGTGCCGT	.	PASS	Atlas-SNP
BARD1	580	hgsc.bcm.edu	37	2	215632255	215632255	+	Missense_Mutation	SNP	C	C	T	rs2070094	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	198	91	192	0	0.459596	0	C|0.656;T|0.344	0.344	strong	.	BARD1	138	.	NM_000465	exon6	c.G1519A	p.V507M	TATCCACATGCCC	.	PASS	Atlas-SNP
KRT84	3890	hgsc.bcm.edu	37	12	52777502	52777502	+	Silent	SNP	A	A	G	rs1945297	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	145	70	172	0	0.482759	0	A|0.586;G|0.414	0.414	strong	.	KRT84	61	.	NM_033045	exon2	c.T627C	p.N209N	CTCCAGATTGCTC	.	PASS	Atlas-SNP
RGS3	5998	hgsc.bcm.edu	37	9	116279880	116279880	+	Silent	SNP	T	T	C	rs35270441	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	33	92	0	0.478261	0	T|0.889;C|0.111	0.111	strong	.	RGS3	251	.	NM_144488	exon17	c.T1734C	p.Y578Y	GCTGTATGAAGGG	.	PASS	Atlas-SNP
HAP1	9001	hgsc.bcm.edu	37	17	39888636	39888636	+	Missense_Mutation	SNP	G	G	T	rs142535684	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	93	43	68	0	0.462366	0	G|0.998;T|0.002	0.002	strong	.	HAP1	48	.	NM_001079870	exon3	c.C584A	p.P195H	CAGACAGGTGGGA	.	PASS	Atlas-SNP
MPP6	51678	hgsc.bcm.edu	37	7	24703298	24703298	+	Silent	SNP	G	G	A	rs1053962	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	76	18	92	0	0.236842	0	A|0.556;C|0.001	0.556	strong	.	MPP6	62	.	NM_016447	exon7	c.G741A	p.E247E	AGGAGAGATTCTT	.	PASS	Atlas-SNP
COL15A1	1306	hgsc.bcm.edu	37	9	101822220	101822220	+	Silent	SNP	C	C	T	rs4480177	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	176	88	211	0	0.5	0	C|0.706;T|0.294	0.294	strong	.	COL15A1	211	.	NM_001855	exon36	c.C3387T	p.P1129P	GCTTCCCGGATCC	.	PASS	Atlas-SNP
MYO1H	283446	hgsc.bcm.edu	37	12	109848567	109848567	+	Silent	SNP	T	T	C	rs7315991	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	57	29	57	0	0.508772	0	T|0.459;C|0.541	0.541	strong	MYO1H,NS,carcinoma,+1,1	MYO1H	98	1	NM_001101421	exon12	c.T1356C	p.S452S	CATATCTATTCTG	.	PASS	Atlas-SNP
KRTAP4-7	100132476	hgsc.bcm.edu	37	17	39240511	39240511	+	Missense_Mutation	SNP	A	A	T	rs383835	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	49	17	72	0	0.346939	0	A|0.527;T|0.473	0.473	strong	.	KRTAP4-7	49	.	NM_033061	exon1	c.A53T	p.D18V	GCCAAGACCTCTG	.	PASS	Atlas-SNP
SUN1	23353	hgsc.bcm.edu	37	7	897492	897492	+	Silent	SNP	A	A	G	rs10950789	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	16	117	0	0.186047	0	A|0.604;G|0.396	0.396	strong	.	SUN1	157	.	NM_001130965	exon13	c.A1422G	p.T474T	GCCCACAGTCGAG	.	PASS	Atlas-SNP
ZNF609	23060	hgsc.bcm.edu	37	15	64962630	64962630	+	Silent	SNP	A	A	C	rs11633399	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	208	104	214	1	0.5	0.0046729	A|0.631;C|0.369	0.369	strong	.	ZNF609	106	.	NM_015042	exon3	c.A1059C	p.P353P	ACCCCCAAGGTAA	.	PASS	Atlas-SNP
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32609874	32609874	+	Missense_Mutation	SNP	T	T	G	rs41547417	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	171	104	220	0	0.608187	0	T|0.928;G|0.072	0.072	strong	.	HLA-DQA1	52	.	NM_002122	exon3	c.T457G	p.S153A	GGGCAGTCAGTCA	.	PASS	Atlas-SNP
RNH1	6050	hgsc.bcm.edu	37	11	494942	494942	+	Silent	SNP	G	G	C	rs7983	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	295	242	263	1	0.820339	0.00380228	G|0.627;C|0.373	0.373	strong	.	RNH1	24	.	NM_203384	exon9	c.C1239G	p.A413A	GATGCCGGCGTCC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195489067	195489067	+	Silent	SNP	C	C	G	rs2246980	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	155	73	105	0	0.470968	0	C|0.619;G|0.381	0.381	strong	MUC4_ENST00000463781,colon,carcinoma,0,3	MUC4	1505	3	NM_018406	exon14	c.G14403C	p.S4801S	GCTGGCCGAGACC	.	PASS	Atlas-SNP
ZNF169	169841	hgsc.bcm.edu	37	9	97062852	97062852	+	Missense_Mutation	SNP	A	A	T	rs61154129	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	37	24	47	0	0.648649	0	A|0.985;T|0.015	0.015	strong	.	ZNF169	60	.	NM_194320	exon5	c.A1012T	p.R338W	CACCAGAGGACGC	.	PASS	Atlas-SNP
TXLNB	167838	hgsc.bcm.edu	37	6	139609755	139609755	+	Silent	SNP	T	T	C	rs6933125	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	192	68	327	0	0.354167	0	T|0.935;C|0.065	0.065	strong	.	TXLNB	96	.	NM_153235	exon2	c.A282G	p.S94S	GTCAGGTGATTCT	.	PASS	Atlas-SNP
EPS15	2060	hgsc.bcm.edu	37	1	51869184	51869184	+	Silent	SNP	T	T	G	rs144030750	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	203	104	242	0	0.512315	0	T|0.999;G|0.001	0.001	strong	.	EPS15	72	.	NM_001981	exon17	c.A1698C	p.L566L	AGGCAGTAGTTCA	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1092928	1092928	+	Missense_Mutation	SNP	T	T	A	rs376681392		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	68	12	41	8	0.176471	0.195122	.	.	weak	MUC2_ENST00000441003,rectum,carcinoma,0,4	MUC2	614	4	NM_002457	exon30	c.T4747A	p.S1583T	CCAACATCGACAC	.	scavenged	Atlas-SNP
OR5B3	441608	hgsc.bcm.edu	37	11	58170143	58170143	+	Missense_Mutation	SNP	C	C	G	rs11229409	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	61	47	100	0	0.770492	0	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	.	PASS	Atlas-SNP
ZP1	22917	hgsc.bcm.edu	37	11	60637164	60637164	+	Missense_Mutation	SNP	C	C	T	rs489172	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	122	122	123	0	1	0	C|0.222;T|0.778	0.778	strong	.	ZP1	69	.	NM_207341	exon3	c.C473T	p.T158I	TCTCAACCCCACA	.	PASS	Atlas-SNP
GBP5	115362	hgsc.bcm.edu	37	1	89732237	89732237	+	Silent	SNP	G	G	A	rs61729628	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	109	52	203	0	0.477064	0	G|0.859;A|0.141	0.141	strong	.	GBP5	65	.	NM_052942	exon7	c.C660T	p.P220P	CAGACGGGGCAAA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195515412	195515412	+	Silent	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	26	61	0	0.361111	0	.	.	none	MUC4_ENST00000463781,NS,carcinoma,-2,2	MUC4	1505	2	NM_018406	exon2	c.C3039T	p.S1013S	GGAAGGGCTGGTG	.	PASS	Atlas-SNP
TIPIN	54962	hgsc.bcm.edu	37	15	66629403	66629403	+	Missense_Mutation	SNP	C	C	A	rs3759786	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	254	94	197	0	0.370079	0	C|0.895;A|0.105	0.105	strong	.	TIPIN	23	.	NM_017858	exon8	c.G799T	p.A267S	CAATAGCATCATT	.	PASS	Atlas-SNP
PLIN4	729359	hgsc.bcm.edu	37	19	4510530	4510530	+	Missense_Mutation	SNP	G	G	A	rs7250947	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	117	57	118	0	0.487179	0	G|0.909;A|0.091	0.091	strong	.	PLIN4	191	.	NM_001080400	exon3	c.C3400T	p.R1134C	CCAAGCGTGGGGC	.	PASS	Atlas-SNP
MDGA1	266727	hgsc.bcm.edu	37	6	37626142	37626142	+	Silent	SNP	C	C	T	rs2273110	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	53	28	60	0	0.528302	0	C|0.849;T|0.151	0.151	strong	.	MDGA1	104	.	NM_153487	exon3	c.G261A	p.S87S	GAACACCGATGTC	.	PASS	Atlas-SNP
PCSK5	5125	hgsc.bcm.edu	37	9	78938043	78938043	+	Missense_Mutation	SNP	G	G	A	rs2495207	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	107	48	104	0	0.448598	0	G|0.668;A|0.332	0.332	strong	.	PCSK5	329	.	NM_001190482	exon31	c.G4097A	p.R1366H	ACTCGCGCCACTG	.	PASS	Atlas-SNP
DLG1	1739	hgsc.bcm.edu	37	3	196771513	196771513	+	Missense_Mutation	SNP	G	G	A	rs34492126	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	120	61	169	0	0.508333	0	G|0.966;A|0.034	0.034	strong	DLG1_ENST00000419354,NS,adenoma,0,3	DLG1	120	3	NM_004087	exon26	c.C2762T	p.P921L	TTTGCCGGAACCC	.	PASS	Atlas-SNP
VWA3B	200403	hgsc.bcm.edu	37	2	98928323	98928323	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	202	53	219	0	0.262376	0	.	.	none	.	VWA3B	138	.	NM_144992	exon27	c.C3563T	p.P1188L	TCTGGCCACTGAA	.	PASS	Atlas-SNP
LSP1	4046	hgsc.bcm.edu	37	11	1902793	1902793	+	Missense_Mutation	SNP	A	A	T	rs11545725	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	196	157	145	0	0.80102	0	A|0.864;T|0.136	0.136	strong	.	LSP1	59	.	NM_001242932	exon4	c.A707T	p.Q236L	CCCCCCAGTGCAG	.	PASS	Atlas-SNP
HCAR3	8843	hgsc.bcm.edu	37	12	123200693	123200693	+	Missense_Mutation	SNP	A	A	G	rs17884481	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	168	156	216	0	0.928571	0	A|0.479;G|0.521	0.521	strong	HCAR3_ENST00000528880,colon,carcinoma,0,3	HCAR3	49	3	NM_006018	exon1	c.T592C	p.F198L	GCAGGAAGAACTC	.	PASS	Atlas-SNP
APOL6	80830	hgsc.bcm.edu	37	22	36055406	36055406	+	Silent	SNP	A	A	C	rs34014315	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	31	82	0	0.442857	0	A|0.965;C|0.035	0.035	strong	.	APOL6	26	.	NM_030641	exon3	c.A795C	p.T265T	AAGGACAAAGTTT	.	PASS	Atlas-SNP
DIDO1	11083	hgsc.bcm.edu	37	20	61513649	61513649	+	Missense_Mutation	SNP	G	G	T	rs6011441	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	133	79	148	0	0.593985	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
TAMM41	132001	hgsc.bcm.edu	37	3	11871215	11871215	+	Missense_Mutation	SNP	T	T	C	rs11551661	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	29	97	0	0.39726	0	T|0.916;C|0.084	0.084	strong	.	.	.	.	NM_138807	exon4	c.A535G	p.I179V	TCTCTATGAAGAG	.	PASS	Atlas-SNP
NANOS2	339345	hgsc.bcm.edu	37	19	46417625	46417625	+	Silent	SNP	A	A	G	rs142962668	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	40	106	0	0.512821	0	A|0.993;G|0.007	0.007	strong	.	NANOS2	10	.	NM_001029861	exon1	c.T327C	p.H109H	GAGCGTATGGGCC	.	PASS	Atlas-SNP
CCDC15	80071	hgsc.bcm.edu	37	11	124857198	124857198	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	147	3	160	0	0.0204082	0	.	.	none	CCDC15_ENST00000344762,NS,carcinoma,+1,2	CCDC15	134	2	NM_025004	exon8	c.A1076G	p.D359G	AGCCAGATACCCA	.	scavenged	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195513398	195513398	+	Missense_Mutation	SNP	C	C	T	rs376864964		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	160	5	243	0	0.03125	0	.	.	weak	MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	NM_018406	exon2	c.G5053A	p.G1685S	AAAGGCCGGTGAC	.	scavenged	Atlas-SNP
APOBEC3F	200316	hgsc.bcm.edu	37	22	39445554	39445554	+	Missense_Mutation	SNP	G	G	A	rs2076101	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	40	93	1	0.45977	0.0107527	G|0.532;A|0.468	0.468	strong	APOBEC3F,NS,carcinoma,-2,1	APOBEC3F	37	1	NM_145298	exon5	c.G691A	p.V231I	TCACCTGTCTCCT	.	scavenged	Atlas-SNP
TBC1D19	55296	hgsc.bcm.edu	37	4	26585881	26585881	+	Silent	SNP	C	C	T	rs4692549	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	40	69	0	0.487805	0	C|0.679;T|0.321	0.321	strong	.	TBC1D19	53	.	NM_018317	exon1	c.C66T	p.S22S	GGGCTCCAATTTG	.	PASS	Atlas-SNP
PSD3	23362	hgsc.bcm.edu	37	8	18729496	18729496	+	Missense_Mutation	SNP	G	G	A	rs13263453	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	197	141	199	0	0.715736	0	G|0.801;A|0.199	0.199	strong	.	PSD3	142	.	NM_015310	exon3	c.C878T	p.P293L	CGGCCTGGGCGTC	.	PASS	Atlas-SNP
WNT5A	7474	hgsc.bcm.edu	37	3	55513589	55513589	+	Silent	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	105	2	104	0	0.0190476	0	.	.	none	WNT5A,colon,carcinoma,0,2	WNT5A	43	2	NM_003392	exon3	c.G144A	p.S48S	ACCTAGCGACCTG	.	scavenged	Atlas-SNP
DDHD2	23259	hgsc.bcm.edu	37	8	38095662	38095662	+	Missense_Mutation	SNP	C	C	T	rs2306899	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	248	48	301	0	0.193548	0	C|0.805;T|0.195	0.195	strong	DDHD2,NS,carcinoma,-1,1	DDHD2	60	1	NM_001164232	exon5	c.C557T	p.T186M	CACCCACGGAGCA	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	156	63	133	0	0.403846	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
COL5A3	50509	hgsc.bcm.edu	37	19	10071347	10071347	+	Missense_Mutation	SNP	C	C	T	rs2277969	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	23	14	47	0	0.608696	0	C|0.770;T|0.230	0.230	strong	.	COL5A3	243	.	NM_015719	exon66	c.G5071A	p.V1691I	GGGGGACGCTGAC	.	PASS	Atlas-SNP
SEC24D	9871	hgsc.bcm.edu	37	4	119736796	119736796	+	Silent	SNP	A	A	C	rs2389688	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	130	58	131	0	0.446154	0	T|0.108;G|0.070	.	strong	SEC24D,NS,carcinoma,0,1	SEC24D	96	1	NM_014822	exon5	c.T483G	p.P161P	AATGGAAGGCTGT	.	PASS	Atlas-SNP
AGO2	27161	hgsc.bcm.edu	37	8	141559358	141559358	+	Silent	SNP	G	G	A	rs2292781	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	133	98	127	0	0.736842	0	G|0.586;N|0.000	.	strong	.	.	.	.	NM_012154	exon12	c.C1443T	p.A481A	CATGCCGGCGTCT	.	PASS	Atlas-SNP
HIVEP2	3097	hgsc.bcm.edu	37	6	143090734	143090734	+	Silent	SNP	T	T	C	rs34530989	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	88	65	162	0	0.738636	0	T|0.858;C|0.142	0.142	strong	.	HIVEP2	225	.	NM_006734	exon5	c.A5142G	p.G1714G	GCCGGTTCCAGGC	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	158	85	170	0	0.537975	0	G|0.474;A|0.526	0.526	strong	.	MB	7	.	NM_203377	exon3	c.C204T	p.T68T	GAGCACGGTGGCA	.	PASS	Atlas-SNP
TAMM41	132001	hgsc.bcm.edu	37	3	11887991	11887991	+	Silent	SNP	C	C	G	rs408600	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	116	114	124	0	0.982759	0	C|0.543;G|0.457	0.457	strong	.	.	.	.	NM_138807	exon1	c.G120C	p.P40P	TGAACTCGGCCCT	.	PASS	Atlas-SNP
TSC22D1	8848	hgsc.bcm.edu	37	13	45147305	45147305	+	Missense_Mutation	SNP	T	T	A	rs144252895	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	90	47	91	0	0.522222	0	T|0.998;A|0.002	0.002	strong	.	TSC22D1	88	.	NM_183422	exon1	c.A2906T	p.D969V	CTCTCATCCTCGC	.	PASS	Atlas-SNP
PVRL2	5819	hgsc.bcm.edu	37	19	45391553	45391553	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	198	114	185	0	0.575758	0	.	.	none	.	PVRL2	58	.	NM_001042724	exon9	c.A1534G	p.I512V	AACCCCATCTATG	.	PASS	Atlas-SNP
IGLL1	3543	hgsc.bcm.edu	37	22	23915652	23915652	+	Missense_Mutation	SNP	G	G	A	rs73157031	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	182	92	189	0	0.505495	0	G|0.891;A|0.109	0.109	strong	IGLL1,NS,carcinoma,0,1	IGLL1	27	1	NM_020070	exon3	c.C443T	p.T148I	TTCCAGGTCACCG	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	76	40	90	0	0.526316	0	C|0.692;G|0.308	0.308	strong	.	APOL5	45	.	NM_030642	exon4	c.C1217G	p.S406C	CAGTCTCTGCCCC	.	PASS	Atlas-SNP
KIAA0368	23392	hgsc.bcm.edu	37	9	114172438	114172438	+	Silent	SNP	C	C	T	rs61744546	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	159	63	212	0	0.396226	0	C|0.993;T|0.007	0.007	strong	.	KIAA0368	144	.	NM_001080398	exon24	c.G2967A	p.L989L	TTCACCCAGGGCT	.	PASS	Atlas-SNP
FOXO1	2308	hgsc.bcm.edu	37	13	41134629	41134629	+	Silent	SNP	G	G	A	rs139436481	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	157	81	173	0	0.515924	0	G|0.996;A|0.004	0.004	strong	.	FOXO1	110	.	NM_002015	exon2	c.C999T	p.T333T	CTGTTCGGTCATA	.	PASS	Atlas-SNP
MROH2B	133558	hgsc.bcm.edu	37	5	41061715	41061715	+	Nonsense_Mutation	SNP	C	C	T	rs1023840	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	160	160	148	0	1	0	C|0.821;T|0.179	0.179	strong	.	.	.	.	NM_173489	exon6	c.G572A	p.W191X	ATATACCAGAACA	.	PASS	Atlas-SNP
CAPN13	92291	hgsc.bcm.edu	37	2	30957326	30957326	+	Missense_Mutation	SNP	A	A	G	rs2276568	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	99	110	0	0.980198	0	A|0.920;G|0.080	0.080	strong	.	CAPN13	70	.	NM_144575	exon19	c.T1787C	p.I596T	TTCTCTATGGCCT	.	PASS	Atlas-SNP
CRIPAK	285464	hgsc.bcm.edu	37	4	1388944	1388944	+	Missense_Mutation	SNP	G	G	A	rs200759023	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	12	12	61	0	1	0	.	.	weak	.	CRIPAK	185	.	NM_175918	exon1	c.G645A	p.M215I	GCCCATGTGGAGT	.	PASS	Atlas-SNP
SYMPK	8189	hgsc.bcm.edu	37	19	46329624	46329624	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	53	31	64	0	0.584906	0	.	.	none	.	SYMPK	104	.	NM_004819	exon17	c.C2189T	p.S730F	GCCTGGGAGCGCA	.	PASS	Atlas-SNP
AMACR	23600	hgsc.bcm.edu	37	5	33998768	33998768	+	Missense_Mutation	SNP	C	C	A	rs34677	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	247	115	198	0	0.465587	0	T|0.007;G|0.005	.	strong	AMACR,NS,carcinoma,0,1	AMACR	38	1	NM_014324	exon4	c.G717T	p.Q239H	GTAGAACTGGGGT	.	PASS	Atlas-SNP
TLN2	83660	hgsc.bcm.edu	37	15	62939591	62939591	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	110	7	102	0	0.0636364	0	.	.	none	.	TLN2	253	.	NM_015059	exon1	c.T82C	p.Y28H	GCTGTGTACGATG	.	PASS	Atlas-SNP
PHIP	55023	hgsc.bcm.edu	37	6	79656570	79656570	+	Silent	SNP	G	G	A	rs2275290	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	60	60	66	0	1	0	G|0.674;A|0.326	0.326	strong	.	PHIP	177	.	NM_017934	exon37	c.C4228T	p.L1410L	CAGACAGGCGCAA	.	PASS	Atlas-SNP
CCDC168	643677	hgsc.bcm.edu	37	13	103384712	103384712	+	Missense_Mutation	SNP	G	G	A	rs17507827	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	190	95	207	1	0.5	0.00483092	G|0.983;A|0.017	0.017	strong	.	.	.	.	NM_001146197	exon4	c.C18335T	p.T6112M	CGCCCCGTGATAT	.	PASS	Atlas-SNP
NUP214	8021	hgsc.bcm.edu	37	9	134073622	134073622	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	106	30	98	0	0.283019	0	.	.	none	.	NUP214	166	.	NM_005085	exon29	c.G4741C	p.A1581P	ACGGAGGCAGTAC	.	PASS	Atlas-SNP
MKLN1	4289	hgsc.bcm.edu	37	7	131082040	131082040	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	114	3	101	0	0.0263158	0	.	.	none	MKLN1,NS,carcinoma,-1,1	MKLN1	67	1	NM_013255	exon5	c.T415A	p.W139R	TTGTCCTGGGGAC	.	scavenged	Atlas-SNP
REST	5978	hgsc.bcm.edu	37	4	57796900	57796900	+	Missense_Mutation	SNP	G	G	A	rs2228991	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	100	46	100	0	0.46	0	G|0.906;A|0.094	0.094	strong	.	REST	104	.	NM_001193508	exon4	c.G1876A	p.V626I	GGGCCCGTTCAGG	.	PASS	Atlas-SNP
CCDC110	256309	hgsc.bcm.edu	37	4	186380846	186380846	+	Missense_Mutation	SNP	A	A	T	rs7698680	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	79	32	82	0	0.405063	0	A|0.555;T|0.445	0.445	strong	CCDC110,NS,carcinoma,0,1	CCDC110	78	1	NM_152775	exon6	c.T895A	p.L299M	CGTCCAAGTTTTC	.	PASS	Atlas-SNP
GATA5	140628	hgsc.bcm.edu	37	20	61040453	61040453	+	Silent	SNP	C	C	G	rs6061243	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	45	31	51	0	0.688889	0	C|0.467;G|0.533	0.533	strong	GATA5,NS,carcinoma,-1,1	GATA5	22	1	NM_080473	exon6	c.G981C	p.S327S	GGCTTTCGAAGTG	.	PASS	Atlas-SNP
GRAMD1A	57655	hgsc.bcm.edu	37	19	35504539	35504539	+	Missense_Mutation	SNP	C	C	T	rs201394899	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	57	92	0	0.564356	0	.	.	weak	.	GRAMD1A	39	.	NM_020895	exon9	c.C814T	p.R272C	GGTTCGCGCCGTG	.	PASS	Atlas-SNP
VSIG10	54621	hgsc.bcm.edu	37	12	118506186	118506186	+	Silent	SNP	A	A	T	rs67405503	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	219	102	243	0	0.465753	0	A|0.602;T|0.398	0.398	strong	.	VSIG10	41	.	NM_019086	exon8	c.T1563A	p.L521L	ACCTTGAAGATCC	.	PASS	Atlas-SNP
MUC7	4589	hgsc.bcm.edu	37	4	71346701	71346701	+	Missense_Mutation	SNP	C	C	G	rs6826961	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	124	66	186	0	0.532258	0	C|0.738;G|0.262	0.262	strong	.	MUC7	91	.	NM_001145007	exon4	c.C240G	p.N80K	TAATAACCCCCCC	.	PASS	Atlas-SNP
NOS1	4842	hgsc.bcm.edu	37	12	117669914	117669914	+	Silent	SNP	G	G	A	rs3741475	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	109	56	125	0	0.513761	0	G|0.747;A|0.253	0.253	strong	NOS1,colon,carcinoma,0,1	NOS1	240	1	NM_001204218	exon23	c.C3360T	p.D1120D	GAGCTCGTCTGTC	.	PASS	Atlas-SNP
RBP3	5949	hgsc.bcm.edu	37	10	48388508	48388508	+	Silent	SNP	G	G	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	144	60	153	0	0.416667	0	.	.	none	.	RBP3	152	.	NM_002900	exon1	c.C2370G	p.S790S	GGCCGTGGAGTAG	.	PASS	Atlas-SNP
NOTCH1	4851	hgsc.bcm.edu	37	9	139413908	139413908	+	Silent	SNP	C	C	T	rs2229975	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	38	97	0	0.447059	0	T|0.113;G|0.000;C|0.886	0.113	strong	.	NOTCH1	1980	.	NM_017617	exon5	c.G852A	p.P284P	CTCTGGCGGGCAG	.	PASS	Atlas-SNP
OR10H1	26539	hgsc.bcm.edu	37	19	15918647	15918647	+	Silent	SNP	G	G	T	rs77552342		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	73	212	1	0.973333	0.00471698	T|1.000;|0.000	1.000	weak	OR10H1,NS,malignant_melanoma,-1,1	OR10H1	59	1	NM_013940	exon1	c.C201A	p.S67S	GGAGACGGAGAGG	.	scavenged	Atlas-SNP
SPP1	6696	hgsc.bcm.edu	37	4	88903853	88903853	+	Silent	SNP	C	C	T	rs1126616	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	143	143	208	1	1	0.00480769	C|0.733;G|0.000;T|0.267	0.267	strong	SPP1,NS,carcinoma,0,1	SPP1	35	1	NM_001251830	exon8	c.C789T	p.A263A	GAAAGCCAATGAT	.	PASS	Atlas-SNP
ADORA3	140	hgsc.bcm.edu	37	1	112042787	112042787	+	Missense_Mutation	SNP	T	T	G	rs35511654	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	171	71	157	0	0.415205	0	T|0.898;G|0.102	0.102	strong	ADORA3,caecum,carcinoma,0,1	ADORA3	104	1	NM_000677	exon2	c.A742C	p.I248L	TGATGATAGATAA	.	PASS	Atlas-SNP
SF3B2	10992	hgsc.bcm.edu	37	11	65826704	65826704	+	Silent	SNP	G	G	A	rs1049872	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	81	65	80	0	0.802469	0	G|0.791;A|0.209	0.209	strong	.	SF3B2	85	.	NM_006842	exon11	c.G1215A	p.K405K	AGAGAAGGAGCCA	.	PASS	Atlas-SNP
GPR112	139378	hgsc.bcm.edu	37	X	135474420	135474420	+	Silent	SNP	C	C	A	rs1329546	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	210	208	388	0	0.990476	0	C|0.328;A|0.672	0.672	strong	.	GPR112	459	.	NM_153834	exon17	c.C7941A	p.T2647T	AACCACCTATGTT	.	PASS	Atlas-SNP
COL2A1	1280	hgsc.bcm.edu	37	12	48378380	48378380	+	Silent	SNP	A	A	G	rs41317939	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	38	15	64	0	0.394737	0	A|0.958;G|0.042	0.042	strong	.	COL2A1	368	.	NM_001844	exon28	c.T1836C	p.G612G	AGGCTCACCCTGA	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228524961	228524961	+	Silent	SNP	C	C	A	rs3795808	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	123	57	155	0	0.463415	0	A|0.286;C|0.714;G|0.000	0.286	strong	.	OBSCN	2142	.	NM_001271223	exon77	c.C19548A	p.P6516P	GGTGCCCGGAGGT	.	PASS	Atlas-SNP
FDXR	2232	hgsc.bcm.edu	37	17	72862593	72862593	+	Missense_Mutation	SNP	C	C	T	rs690514	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	158	72	132	0	0.455696	0	C|0.813;T|0.187	0.187	strong	FDXR_ENST00000581530,NS,carcinoma,0,4	FDXR	68	4	NM_001258012	exon4	c.G497A	p.R166Q	GCCTCCCGCAGCT	.	PASS	Atlas-SNP
KLHL29	114818	hgsc.bcm.edu	37	2	23926233	23926233	+	Silent	SNP	C	C	T	rs72796138	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	45	22	41	0	0.488889	0	C|0.912;T|0.088	0.088	strong	.	KLHL29	47	.	NM_052920	exon12	c.C2283T	p.I761I	CTTCATCGAGTCC	.	PASS	Atlas-SNP
MANEA	79694	hgsc.bcm.edu	37	6	96034612	96034612	+	Silent	SNP	G	G	A	rs62417813	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	44	19	61	0	0.431818	0	G|0.929;A|0.070	0.070	strong	.	MANEA	58	.	NM_024641	exon2	c.G297A	p.L99L	ACCTCTGAACAAT	.	PASS	Atlas-SNP
XRCC6BP1	91419	hgsc.bcm.edu	37	12	58350631	58350631	+	Silent	SNP	C	C	T	rs10122	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	105	62	116	0	0.590476	0	C|0.485;T|0.515	0.515	strong	.	XRCC6BP1	22	.	NM_033276	exon6	c.C699T	p.H233H	TGCTCACAGAGAC	.	PASS	Atlas-SNP
HIST1H2AM	8336	hgsc.bcm.edu	37	6	27860579	27860579	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	181	41	214	0	0.226519	0	.	.	none	.	HIST1H2AM	27	.	NM_003514	exon1	c.C349T	p.L117F	TGGGGAGCAGTAC	.	PASS	Atlas-SNP
MUC15	143662	hgsc.bcm.edu	37	11	26587133	26587133	+	Silent	SNP	T	T	C	rs293980	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	259	187	315	0	0.722008	0	T|0.311;C|0.689	0.689	strong	MUC15,NS,carcinoma,-1,1	MUC15	88	1	NM_001135092	exon3	c.A354G	p.S118S	TGCTGATGAGTTA	.	PASS	Atlas-SNP
RAB20	55647	hgsc.bcm.edu	37	13	111176519	111176519	+	Silent	SNP	G	G	T	rs375814	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	13	13	12	0	1	0	G|0.614;T|0.386	0.386	strong	RAB20_ENST00000267328,NS,carcinoma,0,2	RAB20	34	2	NM_017817	exon2	c.C198A	p.G66G	CATGGAGCCCAGG	.	PASS	Atlas-SNP
OR10H1	26539	hgsc.bcm.edu	37	19	15918802	15918802	+	Missense_Mutation	SNP	C	C	G	rs4808383	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	147	65	187	0	0.442177	0	C|0.832;G|0.168	0.168	strong	.	OR10H1	59	.	NM_013940	exon1	c.G46C	p.G16R	AGAAGCCGACGAG	.	PASS	Atlas-SNP
ETS2	2114	hgsc.bcm.edu	37	21	40191638	40191638	+	Silent	SNP	A	A	G	rs461155	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	57	57	63	0	1	0	A|0.297;G|0.703	0.703	strong	.	ETS2	87	.	NM_001256295	exon9	c.A1443G	p.P481P	TGACCCAGTGGAG	.	PASS	Atlas-SNP
C4BPB	725	hgsc.bcm.edu	37	1	207269919	207269919	+	Silent	SNP	C	C	T	rs8942	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	31	112	0	0.360465	0	C|0.623;T|0.377	0.377	strong	.	C4BPB	19	.	NM_001017365	exon5	c.C462T	p.N154N	AAATAACTTCACC	.	PASS	Atlas-SNP
VAPA	9218	hgsc.bcm.edu	37	18	9944960	9944960	+	Missense_Mutation	SNP	A	A	G	rs29132	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	47	144	0	0.51087	0	A|0.931;G|0.069	0.069	strong	.	VAPA	28	.	NM_003574	exon5	c.A457G	p.M153V	ACTTCAATGAGCA	.	PASS	Atlas-SNP
EFCAB2	84288	hgsc.bcm.edu	37	1	245245402	245245402	+	Silent	SNP	C	C	T	rs10927387	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	52	28	61	0	0.538462	0	C|0.661;T|0.339	0.339	strong	EFCAB2,NS,carcinoma,0,1	EFCAB2	19	1	NM_001143943	exon4	c.C201T	p.P67P	AGAACCCACTGGA	.	PASS	Atlas-SNP
RTL1	388015	hgsc.bcm.edu	37	14	101350274	101350274	+	Silent	SNP	C	C	T	rs61993320	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	49	22	69	0	0.44898	0	C|0.983;T|0.017	0.017	strong	.	RTL1	120	.	NM_001134888	exon1	c.G852A	p.L284L	CACACGCAGTGCC	.	PASS	Atlas-SNP
KRT40	125115	hgsc.bcm.edu	37	17	39135207	39135207	+	Missense_Mutation	SNP	A	A	G	rs150812789	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	126	52	124	0	0.412698	0	A|0.787;G|0.213	0.213	strong	KRT40,NS,carcinoma,+2,1	KRT40	27	1	NM_182497	exon8	c.T1045C	p.C349R	TCAGACACTGAAT	.	PASS	Atlas-SNP
TATDN1	83940	hgsc.bcm.edu	37	8	125528135	125528135	+	Silent	SNP	G	G	A	rs11542673	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	202	40	236	0	0.19802	0	G|0.918;A|0.082	0.082	strong	.	TATDN1	29	.	NM_032026	exon5	c.C339T	p.C113C	AAGTCCGCATTCT	.	PASS	Atlas-SNP
DND1	373863	hgsc.bcm.edu	37	5	140051086	140051086	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	256	43	446	1	0.167969	0.00224215	.	.	none	DND1,NS,haematopoietic_neoplasm,0,1	DND1	15	1	NM_194249	exon4	c.G854A	p.W285X	CGGTGCCAGCCAG	.	scavenged	Atlas-SNP
GPR180	160897	hgsc.bcm.edu	37	13	95273447	95273447	+	Silent	SNP	G	G	A	rs12429818	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	122	117	138	0	0.959016	0	G|0.877;A|0.123	0.123	strong	.	GPR180	24	.	NM_180989	exon6	c.G852A	p.T284T	TTCTACGCCTGCA	.	PASS	Atlas-SNP
RBL2	5934	hgsc.bcm.edu	37	16	53499374	53499374	+	Missense_Mutation	SNP	G	G	C	rs76818213	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	133	73	129	0	0.548872	0	G|0.984;C|0.016	0.016	strong	.	RBL2	115	.	NM_005611	exon13	c.G1723C	p.E575Q	AGAGCAGAAGATG	.	PASS	Atlas-SNP
RANBP2	5903	hgsc.bcm.edu	37	2	109371659	109371659	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	532	6	614	5	0.0112782	0.00814332	.	.	none	RANBP2_ENST00000283195,NS,carcinoma,0,2	RANBP2	488	2	NM_006267	exon17	c.G2410A	p.A804T	CGATGGGCAGAAG	.	scavenged	Atlas-SNP
AIFM3	150209	hgsc.bcm.edu	37	22	21330787	21330787	+	Silent	SNP	C	C	T	rs7285694	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	36	9	47	0	0.25	0	C|0.743;T|0.257	0.257	strong	.	AIFM3	49	.	NM_001146288	exon11	c.C1008T	p.A336A	GCTGGCCCGAGGC	.	PASS	Atlas-SNP
MGAT5B	146664	hgsc.bcm.edu	37	17	74936576	74936576	+	Silent	SNP	G	G	A	rs8081793	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	76	34	79	0	0.447368	0	G|0.734;A|0.266	0.266	strong	.	MGAT5B	98	.	NM_198955	exon12	c.G1704A	p.P568P	CAGCCCGCCCCAC	.	PASS	Atlas-SNP
PELI1	57162	hgsc.bcm.edu	37	2	64327592	64327592	+	Silent	SNP	T	T	C	rs329497	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	304	66	126	0	0.217105	0	T|0.705;C|0.295	0.295	strong	.	PELI1	34	.	NM_020651	exon4	c.A243G	p.L81L	CCGAGATAAAGTA	.	PASS	Atlas-SNP
ZFP106	64397	hgsc.bcm.edu	37	15	42743209	42743209	+	Missense_Mutation	SNP	G	G	A	rs201738274	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	187	37	158	0	0.197861	0	G|0.999;A|0.001	0.001	weak	.	ZFP106	117	.	NM_022473	exon2	c.C1192T	p.R398C	AATTACGTGTTTC	.	PASS	Atlas-SNP
KIRREL2	84063	hgsc.bcm.edu	37	19	36351935	36351935	+	Silent	SNP	G	G	T	rs35854130	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	25	14	38	0	0.56	0	G|0.811;T|0.189	0.189	strong	.	KIRREL2	170	.	NM_199180	exon8	c.G1053T	p.A351A	TGGCGCGCAGGTA	.	PASS	Atlas-SNP
TCP10L	140290	hgsc.bcm.edu	37	21	33956579	33956579	+	Silent	SNP	T	T	C	rs2017816	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	172	67	142	0	0.389535	0	T|0.582;C|0.418	0.418	strong	TCP10L,rectum,carcinoma,0,1	TCP10L	24	1	NM_144659	exon2	c.A36G	p.K12K	GCCCTCTTTGGGG	.	PASS	Atlas-SNP
WDR27	253769	hgsc.bcm.edu	37	6	170068086	170068086	+	Missense_Mutation	SNP	C	C	T	rs41265385	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	29	11	66	0	0.37931	0	C|0.840;T|0.160	0.160	strong	.	WDR27	129	.	NM_182552	exon5	c.G652A	p.G218S	TAAAGCCTCTGTC	.	PASS	Atlas-SNP
EXOC3L1	283849	hgsc.bcm.edu	37	16	67221737	67221737	+	Missense_Mutation	SNP	G	G	A	rs149684674	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	83	45	73	0	0.542169	0	G|0.999;A|0.001	0.001	strong	LOC283849,caecum,carcinoma,0,2	EXOC3L1	52	2	NM_178516	exon5	c.C431T	p.P144L	GCAGCCGGCACTA	.	PASS	Atlas-SNP
CTBP2	1488	hgsc.bcm.edu	37	10	126714966	126714966	+	Missense_Mutation	SNP	A	A	G	rs3012075	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	34	85	0	0.472222	0	A|0.547;G|0.453	0.453	strong	.	CTBP2	100	.	NM_022802	exon1	c.T1363C	p.Y455H	GGGGGTACGTGGG	.	PASS	Atlas-SNP
ZNF567	163081	hgsc.bcm.edu	37	19	37210529	37210529	+	Silent	SNP	A	A	G	rs3108200	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	94	41	87	0	0.43617	0	A|0.701;G|0.299	0.299	strong	.	ZNF567	61	.	NM_152603	exon4	c.A810G	p.R270R	TCAGAGAACTCAC	.	PASS	Atlas-SNP
PABPC4L	132430	hgsc.bcm.edu	37	4	135121368	135121368	+	Silent	SNP	G	G	T	rs2044116	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	70	72	0	1	0	G|0.347;T|0.653	0.653	strong	.	PABPC4L	60	.	NM_001114734	exon2	c.C981A	p.V327V	TCGCTCGACTTTC	.	PASS	Atlas-SNP
USP8	9101	hgsc.bcm.edu	37	15	50782703	50782703	+	Missense_Mutation	SNP	A	A	G	rs11638390	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	38	21	42	0	0.552632	0	A|0.874;G|0.126	0.126	strong	.	USP8	90	.	NM_001128610	exon14	c.A2215G	p.T739A	ACTCCAACAGTTA	.	PASS	Atlas-SNP
IFIT1	3434	hgsc.bcm.edu	37	10	91162182	91162182	+	Silent	SNP	C	C	T	rs41284944	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	128	65	140	0	0.507812	0	C|0.933;T|0.067	0.067	strong	.	IFIT1	30	.	NM_001270927	exon3	c.C150T	p.Y50Y	CAAATACAGTGTG	.	PASS	Atlas-SNP
DPP4	1803	hgsc.bcm.edu	37	2	162876789	162876789	+	Silent	SNP	T	T	C	rs200990780		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	35	85	0	0.479452	0	.	.	weak	.	DPP4	90	.	NM_001935	exon14	c.A1194G	p.T398T	GCCTTTTGTAATA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195506661	195506661	+	Silent	SNP	G	G	C	rs143659849	by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	95	89	203	0	0.936842	0	G|0.964;C|0.036	0.036	strong	.	MUC4	1505	.	NM_018406	exon2	c.C11790G	p.S3930S	TCCTGTGGATGCC	.	PASS	Atlas-SNP
TTLL1	25809	hgsc.bcm.edu	37	22	43455432	43455432	+	Silent	SNP	G	G	A	rs5759125	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	99	45	102	0	0.454545	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
MRPS2	51116	hgsc.bcm.edu	37	9	138395624	138395624	+	Missense_Mutation	SNP	C	C	T	rs34149047	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	44	21	57	0	0.477273	0	C|0.990;T|0.010	0.010	strong	.	MRPS2	17	.	NM_016034	exon4	c.C536T	p.A179V	CCAACGCGCGCCT	.	PASS	Atlas-SNP
RANBP6	26953	hgsc.bcm.edu	37	9	6012734	6012734	+	Silent	SNP	A	A	C	rs106033	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	55	130	0	0.597826	0	A|0.647;C|0.353	0.353	strong	.	RANBP6	127	.	NM_012416	exon1	c.T2874G	p.L958L	TACCAGAAGTGGA	.	PASS	Atlas-SNP
HTR3D	200909	hgsc.bcm.edu	37	3	183754294	183754294	+	Missense_Mutation	SNP	G	G	C	rs6443930	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	137	63	174	1	0.459854	0.00574713	G|0.481;C|0.519	0.519	strong	HTR3D,NS,carcinoma,0,1	HTR3D	65	1	NM_001145143	exon4	c.G329C	p.G110A	ACAGAGGTGAACG	.	scavenged	Atlas-SNP
HES7	84667	hgsc.bcm.edu	37	17	8025712	8025712	+	Silent	SNP	A	A	G	rs1348325	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	283	117	266	0	0.413428	0	A|0.823;G|0.177	0.177	strong	.	.	.	.	NM_001165967	exon3	c.T175C	p.L59L	ACTCCAATATCTC	.	PASS	Atlas-SNP
KLHDC7A	127707	hgsc.bcm.edu	37	1	18807938	18807938	+	Missense_Mutation	SNP	C	C	A	rs2992754	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	35	70	0	0.466667	0	C|0.770;A|0.230	0.230	strong	.	KLHDC7A	60	.	NM_152375	exon1	c.C463A	p.P155T	CCTGACCCTCCCC	.	PASS	Atlas-SNP
HERC2	8924	hgsc.bcm.edu	37	15	28517492	28517492	+	Missense_Mutation	SNP	C	C	A	rs77399744	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	94	17	99	0	0.180851	0	C|0.500;A|0.500	0.500	weak	.	HERC2	501	.	NM_004667	exon9	c.G952T	p.D318Y	CGCTGTCCCACAG	.	PASS	Atlas-SNP
WLS	79971	hgsc.bcm.edu	37	1	68624878	68624878	+	Silent	SNP	C	C	T	rs3748705	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	41	109	0	0.445652	0	C|0.664;T|0.336	0.336	strong	.	WLS	97	.	NM_024911	exon3	c.G432A	p.A144A	AGCAAACGCGTCA	.	PASS	Atlas-SNP
GANAB	23193	hgsc.bcm.edu	37	11	62397114	62397114	+	Missense_Mutation	SNP	T	T	C	rs76572368	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	151	29	193	0	0.192053	0	T|0.974;C|0.026	0.026	strong	.	GANAB	110	.	NM_198335	exon16	c.A1846G	p.M616V	GTTCCATGCCCCC	.	PASS	Atlas-SNP
IRAK2	3656	hgsc.bcm.edu	37	3	10264480	10264480	+	Missense_Mutation	SNP	C	C	G	rs3844283	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	114	60	137	0	0.526316	0	C|0.667;G|0.333	0.333	strong	IRAK2_ENST00000256458,caecum,carcinoma,-1,2	IRAK2	113	2	NM_001570	exon9	c.C1174G	p.L392V	GGGCAGCTGACAA	.	PASS	Atlas-SNP
USP35	57558	hgsc.bcm.edu	37	11	77911745	77911745	+	Missense_Mutation	SNP	C	C	T	rs147270370	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	100	20	109	0	0.2	0	C|0.996;T|0.004	0.004	strong	USP35_ENST00000263311,rectum,carcinoma,-1,2	USP35	179	2	NM_020798	exon6	c.C1088T	p.S363L	AGGACTCGAACTC	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	117	50	141	0	0.42735	0	C|0.526;T|0.474	0.474	strong	.	ANKRD35	96	.	NM_144698	exon10	c.C1282T	p.P428S	GGGCCACCCCAGA	.	PASS	Atlas-SNP
FAM171A1	221061	hgsc.bcm.edu	37	10	15256440	15256440	+	Missense_Mutation	SNP	C	C	T	rs150647132	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	34	71	0	0.465753	0	C|0.999;T|0.001	0.001	strong	.	FAM171A1	252	.	NM_001010924	exon8	c.G1147A	p.G383S	GGCGGCCGTGGCT	.	PASS	Atlas-SNP
ABCA7	10347	hgsc.bcm.edu	37	19	1049305	1049305	+	Silent	SNP	C	C	A	rs4147915	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	160	87	159	0	0.54375	0	C|0.843;A|0.157	0.157	strong	ABCA7,NS,carcinoma,0,1	ABCA7	174	1	NM_019112	exon18	c.C2421A	p.V807V	TGGCGTCTCCGTT	.	PASS	Atlas-SNP
TRIM6-TRIM34	445372	hgsc.bcm.edu	37	11	5653866	5653866	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	90	49	107	0	0.544444	0	.	.	none	.	TRIM6-TRIM34	68	.	NM_001003819	exon8	c.A1367G	p.E456G	ATGGAGAGAAACT	.	PASS	Atlas-SNP
CAMSAP1	157922	hgsc.bcm.edu	37	9	138742077	138742077	+	Silent	SNP	C	C	G	rs35981196	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	81	45	96	0	0.555556	0	C|0.836;G|0.164	0.164	strong	.	CAMSAP1	142	.	NM_015447	exon7	c.G951C	p.P317P	AACATTCGGCTAA	.	PASS	Atlas-SNP
ZNF169	169841	hgsc.bcm.edu	37	9	97062295	97062295	+	Missense_Mutation	SNP	C	C	T	rs34433105	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	74	36	82	0	0.486486	0	C|0.930;T|0.070	0.070	strong	.	ZNF169	60	.	NM_194320	exon5	c.C455T	p.S152L	ACAGCTCATTAAG	.	PASS	Atlas-SNP
ALPP	250	hgsc.bcm.edu	37	2	233243713	233243713	+	Missense_Mutation	SNP	G	G	C	rs113323105	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	74	38	92	0	0.513514	0	G|0.974;C|0.026	0.026	strong	.	ALPP	53	.	NM_001632	exon2	c.G109C	p.E37Q	AACCGCGAGGCAG	.	PASS	Atlas-SNP
LARS	51520	hgsc.bcm.edu	37	5	145506100	145506100	+	Silent	SNP	G	G	A	rs11540216	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	160	67	220	0	0.41875	0	G|0.767;T|0.009	.	strong	.	LARS	100	.	NM_020117	exon28	c.C2889T	p.N963N	TTTTCCGTTATTG	.	PASS	Atlas-SNP
GNL1	2794	hgsc.bcm.edu	37	6	30515043	30515043	+	Silent	SNP	T	T	C	rs3130247	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	96	46	121	0	0.479167	0	T|0.939;C|0.061	0.061	strong	.	GNL1	47	.	NM_005275	exon10	c.A1287G	p.A429A	GATCCCTGCCAGA	.	PASS	Atlas-SNP
ARHGAP9	64333	hgsc.bcm.edu	37	12	57870155	57870155	+	Missense_Mutation	SNP	A	A	C	rs11544238	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	47	20	46	0	0.425532	0	A|0.557;C|0.443	0.443	strong	.	ARHGAP9	79	.	NM_001080157	exon7	c.T1108G	p.S370A	AGCCTGAGGAGGG	.	PASS	Atlas-SNP
PLEKHA5	54477	hgsc.bcm.edu	37	12	19427766	19427766	+	Missense_Mutation	SNP	A	A	G	rs77598867	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	31	91	0	0.534483	0	A|0.989;G|0.011	0.011	strong	.	PLEKHA5	198	.	NM_001256470	exon11	c.A1162G	p.S388G	AATGTTAGCCTGG	.	PASS	Atlas-SNP
PLEKHG5	57449	hgsc.bcm.edu	37	1	6529443	6529443	+	Silent	SNP	A	A	G	rs730600	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	34	72	0	0.485714	0	A|0.720;G|0.280	0.280	strong	.	PLEKHG5	66	.	NM_001265592	exon19	c.T2238C	p.S746S	CTGGCCACTGGCC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195511959	195511959	+	Silent	SNP	G	G	A	rs369770584	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	66	15	113	1	0.227273	0.00884956	.	.	weak	MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	NM_018406	exon2	c.C6492T	p.T2164T	AGTGTCGGTGACA	.	scavenged	Atlas-SNP
CD44	960	hgsc.bcm.edu	37	11	35201842	35201842	+	Silent	SNP	C	C	T	rs1071695	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	158	121	180	0	0.765823	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
CRIPAK	285464	hgsc.bcm.edu	37	4	1388788	1388788	+	Silent	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	27	7	22	0	0.259259	0	.	.	none	CRIPAK,extremity,malignant_melanoma,+2,2	CRIPAK	185	2	NM_175918	exon1	c.C489T	p.D163D	TGCCGACGTGGAG	.	PASS	Atlas-SNP
GRK4	2868	hgsc.bcm.edu	37	4	3006043	3006043	+	Missense_Mutation	SNP	C	C	T	rs1024323	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	111	56	146	0	0.504505	0	C|0.576;T|0.424	0.424	strong	.	GRK4	72	.	NM_182982	exon5	c.C425T	p.A142V	AAAAAGCCTTTGA	.	PASS	Atlas-SNP
MYH9	4627	hgsc.bcm.edu	37	22	36684358	36684358	+	Silent	SNP	C	C	A	rs2269530	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	90	41	114	0	0.455556	0	C|0.785;A|0.215	0.215	strong	.	MYH9	225	.	NM_002473	exon34	c.G4872T	p.A1624A	GATGTGCGCCTCC	.	PASS	Atlas-SNP
GDF3	9573	hgsc.bcm.edu	37	12	7842932	7842932	+	Missense_Mutation	SNP	C	C	T	rs12819884	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	152	73	180	0	0.480263	0	C|0.752;T|0.248	0.248	strong	GDF3,NS,adenoma,0,2	GDF3	68	2	NM_020634	exon2	c.G637A	p.G213R	TCACCCCTGAGTC	.	PASS	Atlas-SNP
BEND2	139105	hgsc.bcm.edu	37	X	18230715	18230715	+	Missense_Mutation	SNP	A	A	C	rs17274127	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	93	92	151	0	0.989247	0	A|0.766;0|0.015	.	strong	.	BEND2	108	.	NM_001184767	exon4	c.T462G	p.F154L	TTTTGGAAAATCC	.	PASS	Atlas-SNP
MAGIX	79917	hgsc.bcm.edu	37	X	49021052	49021052	+	Silent	SNP	C	C	T	rs12843494	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	153	152	245	0	0.993464	0	C|0.926;0|0.013	.	strong	.	MAGIX	25	.	NM_001099681	exon3	c.C204T	p.S68S	TGTTAGCGTGCTG	.	PASS	Atlas-SNP
CCDC168	643677	hgsc.bcm.edu	37	13	103391605	103391605	+	Silent	SNP	T	T	C	rs17592480	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	42	145	0	0.482759	0	T|0.927;C|0.073	0.073	strong	.	.	.	.	NM_001146197	exon4	c.A11442G	p.K3814K	CTTTCCTTTCAAA	.	PASS	Atlas-SNP
ARHGAP5	394	hgsc.bcm.edu	37	14	32561296	32561296	+	Missense_Mutation	SNP	T	T	C	rs200111638		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	6	87	1	0.084507	0.0114943	T|0.999;C|0.001	0.001	weak	ARHGAP5,caecum,carcinoma,0,26	ARHGAP5	166	26	NM_001173	exon2	c.T1421C	p.V474A	AAGAGGTATATGG	.	scavenged	Atlas-SNP
TIAM2	26230	hgsc.bcm.edu	37	6	155561796	155561796	+	Missense_Mutation	SNP	C	C	T	rs11751128	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	32	14	58	0	0.4375	0	C|0.825;T|0.175	0.175	strong	.	TIAM2	161	.	NM_012454	exon15	c.C3301T	p.R1101C	CGCCTCCGCAAAG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195511364	195511364	+	Missense_Mutation	SNP	T	T	A	rs75187745	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	5	118	0	0.0704225	0	T|0.500;A|0.500	0.500	weak	MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	NM_018406	exon2	c.A7087T	p.T2363S	CACCTGTGGATAC	.	scavenged	Atlas-SNP
EXOSC8	11340	hgsc.bcm.edu	37	13	37577073	37577073	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	120	5	153	0	0.0416667	0	.	.	none	.	EXOSC8	16	.	NM_181503	exon4	c.T121C	p.S41P	TCAGGTTCAATTA	.	PASS	Atlas-SNP
ZDHHC4	55146	hgsc.bcm.edu	37	7	6621277	6621277	+	Missense_Mutation	SNP	G	G	A	rs11559146	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	174	38	243	0	0.218391	0	G|0.691;A|0.309	0.309	strong	.	ZDHHC4	36	.	NM_018106	exon4	c.G157A	p.V53M	AGAGCCGTGCATG	.	PASS	Atlas-SNP
BMS1	9790	hgsc.bcm.edu	37	10	43312807	43312807	+	Silent	SNP	C	C	T	rs79824313	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	41	22	52	0	0.536585	0	C|0.667;T|0.333	0.333	strong	BMS1,NS,carcinoma,0,1	BMS1	132	1	NM_014753	exon15	c.C2445T	p.P815P	TGACCCCGACGAA	.	PASS	Atlas-SNP
OR51F1	256892	hgsc.bcm.edu	37	11	4790396	4790396	+	Missense_Mutation	SNP	G	G	A	rs17324609	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	165	42	169	0	0.254545	0	G|0.915;A|0.085	0.085	strong	.	OR51F1	60	.	NM_001004752	exon1	c.C752T	p.A251V	AAGAAAGCAACTG	.	PASS	Atlas-SNP
UMOD	7369	hgsc.bcm.edu	37	16	20352618	20352618	+	Missense_Mutation	SNP	C	C	A	rs55772253	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	51	37	62	0	0.72549	0	C|0.983;A|0.017	0.017	strong	UMOD,right_upper_lobe,carcinoma,+2,1	UMOD	128	1	NM_003361	exon7	c.G1372T	p.V458L	TCCGCACGGTGAA	.	PASS	Atlas-SNP
BBS2	583	hgsc.bcm.edu	37	16	56545175	56545175	+	Missense_Mutation	SNP	T	T	C	rs11373	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	53	36	70	0	0.679245	0	T|0.778;C|0.222	0.222	strong	.	BBS2	67	.	NM_031885	exon3	c.A367G	p.I123V	GCACAATTGCATT	.	PASS	Atlas-SNP
SCIN	85477	hgsc.bcm.edu	37	7	12610594	12610594	+	Missense_Mutation	SNP	A	A	G	rs2240572	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	113	113	150	0	1	0	A|0.609;G|0.391	0.391	strong	SCIN_ENST00000297029,NS,carcinoma,0,6	SCIN	105	6	NM_001112706	exon1	c.A182G	p.H61R	CCTACCACCTGCA	.	PASS	Atlas-SNP
OR2K2	26248	hgsc.bcm.edu	37	9	114090279	114090279	+	Silent	SNP	A	A	G	rs314452	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	63	38	84	0	0.603175	0	A|0.465;G|0.535	0.535	strong	.	OR2K2	77	.	NM_205859	exon1	c.T435C	p.A145A	GACCGTAGCCATC	.	PASS	Atlas-SNP
WNK2	65268	hgsc.bcm.edu	37	9	95993326	95993326	+	Silent	SNP	T	T	C	rs11787888	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	199	98	231	0	0.492462	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
PPAN-P2RY11	692312	hgsc.bcm.edu	37	19	10225390	10225390	+	Silent	SNP	C	C	G	rs74462278	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	91	40	97	0	0.43956	0	C|0.997;G|0.003	0.003	strong	.	PPAN-P2RY11	81	.	NM_001040664	exon13	c.C2361G	p.P787P	AGAGCCCCAGTCC	.	PASS	Atlas-SNP
CROCC	9696	hgsc.bcm.edu	37	1	17265560	17265560	+	Missense_Mutation	SNP	C	C	T	rs9435793	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	11	7	2	1	0.636364	0.5	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
IL1RL1	9173	hgsc.bcm.edu	37	2	102955468	102955468	+	Missense_Mutation	SNP	C	C	A	rs1041973	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	140	62	158	0	0.442857	0	C|0.681;A|0.319	0.319	strong	.	IL1RL1	114	.	NM_016232	exon3	c.C233A	p.A78E	CAGCTGCAGTTGC	.	PASS	Atlas-SNP
ROS1	6098	hgsc.bcm.edu	37	6	117686840	117686840	+	Silent	SNP	T	T	C	rs2229078	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	125	66	127	0	0.528	0	T|0.968;C|0.032	0.032	strong	.	ROS1	728	.	NM_002944	exon19	c.A2877G	p.E959E	ATTTCCTTCAATC	.	PASS	Atlas-SNP
KIAA1683	80726	hgsc.bcm.edu	37	19	18375659	18375659	+	Silent	SNP	C	C	T	rs12608843	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	51	97	0	0.504951	0	C|0.805;T|0.195	0.195	strong	.	KIAA1683	190	.	NM_001145304	exon3	c.G2691A	p.L897L	GGCCAACAGAGTG	.	PASS	Atlas-SNP
MCCD1	401250	hgsc.bcm.edu	37	6	31496834	31496834	+	Missense_Mutation	SNP	C	C	T	rs146742941	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	46	25	68	0	0.543478	0	C|1.000;T|0.000	0.000	strong	MCCD1,NS,carcinoma,-1,1	MCCD1	3	1	NM_001011700	exon1	c.C43T	p.R15C	TTCCTTCGCCTCC	.	PASS	Atlas-SNP
GNAT3	346562	hgsc.bcm.edu	37	7	80117993	80117993	+	Splice_Site	SNP	C	C	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	61	13	76	0	0.213115	0	.	.	none	.	GNAT3	65	.	NM_001102386	exon4	c.162-1G>T	.	ATGATCCTATAAT	.	PASS	Atlas-SNP
TCHH	7062	hgsc.bcm.edu	37	1	152084213	152084213	+	Missense_Mutation	SNP	C	C	G	rs199978168	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	103	16	114	0	0.15534	0	C|0.978;G|0.023	0.023	strong	.	TCHH	275	.	NM_007113	exon3	c.G1480C	p.E494Q	TCTCCTCCTCCTC	.	PASS	Atlas-SNP
LILRB1	10859	hgsc.bcm.edu	37	19	55143452	55143452	+	Missense_Mutation	SNP	T	T	C	rs1061680	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	107	107	124	1	1	0.00806452	T|0.567;C|0.433	0.433	strong	LILRB1,NS,carcinoma,-1,1	LILRB1	140	1	NM_001081637	exon5	c.T425C	p.I142T	ATGTAATCCTCCA	.	PASS	Atlas-SNP
PLXNA4	91584	hgsc.bcm.edu	37	7	131883311	131883311	+	Missense_Mutation	SNP	C	C	T	rs62622406	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	45	21	42	0	0.466667	0	C|0.991;T|0.009	0.009	strong	.	PLXNA4	873	.	NM_020911	exon13	c.G2671A	p.A891T	GGGAGGCGATGTC	.	PASS	Atlas-SNP
PRAME	23532	hgsc.bcm.edu	37	22	22892449	22892449	+	Missense_Mutation	SNP	T	T	C	rs41277507	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	110	49	143	0	0.445455	0	T|0.971;C|0.029	0.029	strong	.	PRAME	78	.	NM_206954	exon5	c.A652G	p.M218V	TGGGCATTGCAAA	.	PASS	Atlas-SNP
ORAI1	84876	hgsc.bcm.edu	37	12	122079441	122079441	+	Silent	SNP	T	T	C	rs3825175	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	131	131	152	0	1	0	T|0.470;C|0.530	0.530	strong	.	ORAI1	66	.	NM_032790	exon2	c.T804C	p.T268T	TAAGACTGACCGA	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29910602	29910602	+	Missense_Mutation	SNP	G	G	T	rs41552219	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	108	12	77	0	0.111111	0	A|0.043;G|0.955;T|0.002	0.002	strong	HLA-A,NS,carcinoma,-2,4	HLA-A	89	4	NM_001242758	exon2	c.G142T	p.A48S	TTCATCGCCGTGG	.	scavenged	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	142	53	98	0	0.373239	0	A|0.733;G|0.267	0.267	strong	.	KIAA1024	146	.	NM_015206	exon3	c.A2494G	p.I832V	TGGACCATTGAGG	.	PASS	Atlas-SNP
PNPLA7	375775	hgsc.bcm.edu	37	9	140373607	140373607	+	Silent	SNP	C	C	T	rs61747526	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	74	49	48	0	0.662162	0	C|0.981;T|0.019	0.019	strong	.	PNPLA7	124	.	NM_001098537	exon24	c.G2664A	p.A888A	GGTGCGCGCTGGC	.	PASS	Atlas-SNP
VARS2	57176	hgsc.bcm.edu	37	6	30893941	30893941	+	Missense_Mutation	SNP	G	G	A	rs4678	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	209	108	160	0	0.516746	0	G|0.856;A|0.144	0.144	strong	.	VARS2	60	.	NM_001167734	exon30	c.G3236A	p.R1079Q	ACCTCCGGCAGCT	.	PASS	Atlas-SNP
TDRD9	122402	hgsc.bcm.edu	37	14	104394850	104394850	+	Silent	SNP	C	C	T	rs9324066	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	60	33	69	0	0.55	0	A|0.000;C|0.519;G|0.000;T|0.480	0.480	strong	TDRD9_ENST00000409874,colon,carcinoma,0,1	TDRD9	175	1	NM_153046	exon1	c.C4T	p.L2L	AGGATGCTGCGGA	.	PASS	Atlas-SNP
UTP20	27340	hgsc.bcm.edu	37	12	101776996	101776996	+	Missense_Mutation	SNP	G	G	C	rs1061436	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	55	27	55	0	0.490909	0	G|0.878;C|0.122	0.122	strong	.	UTP20	222	.	NM_014503	exon59	c.G7834C	p.E2612Q	AAGGAAGAGCTCG	.	PASS	Atlas-SNP
VPS52	6293	hgsc.bcm.edu	37	6	33236826	33236826	+	Silent	SNP	A	A	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	156	64	165	0	0.410256	0	.	.	none	.	VPS52	56	.	NM_022553	exon6	c.T513C	p.L171L	ATCAACAAGCTCC	.	PASS	Atlas-SNP
CCDC87	55231	hgsc.bcm.edu	37	11	66358126	66358126	+	Silent	SNP	C	C	T	rs486584	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	15	100	0	0.211268	0	C|0.597;T|0.402	0.402	strong	.	CCDC87	83	.	NM_018219	exon1	c.G2361A	p.L787L	CTCCTCCAGGAGG	.	PASS	Atlas-SNP
FUT10	84750	hgsc.bcm.edu	37	8	33246538	33246538	+	Silent	SNP	A	A	G	rs16880849	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	358	355	467	0	0.99162	0	A|0.769;G|0.231	0.231	strong	FUT10,NS,carcinoma,0,1	FUT10	62	1	NM_032664	exon4	c.T1155C	p.D385D	AAATGCATCGATG	.	PASS	Atlas-SNP
CCDC6	8030	hgsc.bcm.edu	37	10	61552763	61552763	+	Missense_Mutation	SNP	G	G	A	rs61740504	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	195	110	237	0	0.564103	0	G|0.992;A|0.008	0.008	strong	.	CCDC6	44	.	NM_005436	exon9	c.C1337T	p.P446L	GGTGGCGGAGGTG	.	PASS	Atlas-SNP
USP42	84132	hgsc.bcm.edu	37	7	6194274	6194274	+	Missense_Mutation	SNP	T	T	C	rs6463529	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	26	24	28	0	0.923077	0	T|0.533;C|0.467	0.467	strong	.	USP42	138	.	NM_032172	exon15	c.T3089C	p.L1030P	TGGAGCTGGACTG	.	PASS	Atlas-SNP
TH	7054	hgsc.bcm.edu	37	11	2191006	2191006	+	Silent	SNP	C	C	T	rs34510659	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	107	90	75	0	0.841121	0	C|0.971;T|0.029	0.029	strong	.	TH	43	.	NM_199292	exon3	c.G279A	p.S93S	GGGCTCCGAGGGG	.	PASS	Atlas-SNP
TMEM200A	114801	hgsc.bcm.edu	37	6	130761804	130761804	+	Silent	SNP	C	C	T	rs12200105	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	34	104	0	0.414634	0	C|0.743;T|0.257	0.257	strong	.	TMEM200A	108	.	NM_001258277	exon3	c.C237T	p.A79A	TATGGCCGTTCTT	.	PASS	Atlas-SNP
PIGG	54872	hgsc.bcm.edu	37	4	517461	517461	+	Missense_Mutation	SNP	T	T	C	rs7666425	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	130	73	191	0	0.561538	0	T|0.785;C|0.215	0.215	strong	.	PIGG	86	.	NM_001127178	exon9	c.T1828C	p.C610R	GGCCTCTGTGTGG	.	PASS	Atlas-SNP
CIITA	4261	hgsc.bcm.edu	37	16	11000848	11000848	+	Missense_Mutation	SNP	G	G	C	rs4774	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	48	43	58	0	0.895833	0	G|0.737;C|0.263	0.263	strong	CIITA_ENST00000324288,NS,carcinoma,0,1	CIITA	92	1	NM_000246	exon11	c.G1499C	p.G500A	TAGACGGCTTCGA	.	PASS	Atlas-SNP
SEC16A	9919	hgsc.bcm.edu	37	9	139369212	139369212	+	Silent	SNP	G	G	A	rs17567909	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	25	77	0	0.431034	0	G|0.926;A|0.074	0.074	strong	.	SEC16A	249	.	NM_014866	exon3	c.C2856T	p.P952P	AAATCCGGGAAGA	.	PASS	Atlas-SNP
ANKRD18B	441459	hgsc.bcm.edu	37	9	33548043	33548043	+	Silent	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	106	21	115	0	0.198113	0	.	.	none	.	ANKRD18B	46	.	NM_001244752	exon9	c.T1068C	p.S356S	TGACAGTCTCAGA	.	PASS	Atlas-SNP
SCN10A	6336	hgsc.bcm.edu	37	3	38739494	38739494	+	Silent	SNP	G	G	A	rs116353929	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	149	69	174	0	0.463087	0	G|0.979;A|0.021	0.021	strong	.	SCN10A	359	.	NM_006514	exon27	c.C5217T	p.D1739D	AAAGTCGTCCTCA	.	PASS	Atlas-SNP
KIAA0368	23392	hgsc.bcm.edu	37	9	114124354	114124354	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	128	28	161	0	0.21875	0	.	.	none	.	KIAA0368	144	.	NM_001080398	exon51	c.G6010T	p.E2004X	CTTTCTCCTGCAG	.	PASS	Atlas-SNP
CHAF1A	10036	hgsc.bcm.edu	37	19	4409756	4409756	+	Silent	SNP	A	A	G	rs2230636	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	34	19	46	0	0.558824	0	A|0.809;G|0.191	0.191	strong	.	CHAF1A	69	.	NM_005483	exon3	c.A960G	p.R320R	CCGCAGAGTGAGT	.	PASS	Atlas-SNP
FAM114A2	10827	hgsc.bcm.edu	37	5	153413390	153413390	+	Missense_Mutation	SNP	C	C	T	rs2578377	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	177	86	233	0	0.485876	0	C|0.344;T|0.656	0.656	strong	.	FAM114A2	51	.	NM_018691	exon4	c.G364A	p.G122S	TGGGACCAGGGAT	.	PASS	Atlas-SNP
MOB3A	126308	hgsc.bcm.edu	37	19	2078221	2078221	+	Silent	SNP	G	G	C	rs11541046	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	223	107	244	1	0.479821	0.00409836	G|0.848;C|0.152	0.152	strong	.	.	.	.	NM_130807	exon3	c.C339G	p.L113L	CGCGGAGAGTGCC	.	PASS	Atlas-SNP
HOMEZ	57594	hgsc.bcm.edu	37	14	23744932	23744932	+	Missense_Mutation	SNP	C	C	T	rs1055061	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	89	37	118	0	0.41573	0	C|0.894;T|0.106	0.106	strong	.	HOMEZ	80	.	NM_020834	exon2	c.G1505A	p.R502Q	GGTAATCGAGAGT	.	PASS	Atlas-SNP
C5	727	hgsc.bcm.edu	37	9	123783934	123783934	+	Silent	SNP	T	T	C	rs10985126	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	268	130	324	1	0.485075	0.00308642	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
TCEB3B	51224	hgsc.bcm.edu	37	18	44560875	44560875	+	Missense_Mutation	SNP	C	C	A	rs2010834	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	117	54	120	0	0.461538	0	C|0.518;A|0.482	0.482	strong	.	TCEB3B	141	.	NM_016427	exon1	c.G761T	p.C254F	GCCCCGCATGATT	.	PASS	Atlas-SNP
DGCR14	8220	hgsc.bcm.edu	37	22	19122665	19122665	+	Silent	SNP	C	C	T	rs2240111	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	131	69	164	0	0.526718	0	C|0.835;A|0.001	.	strong	.	DGCR14	43	.	NM_022719	exon9	c.G1059A	p.E353E	CAGCCGCTCCCTG	.	PASS	Atlas-SNP
DNAJC9	23234	hgsc.bcm.edu	37	10	75006868	75006868	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	88	42	79	0	0.477273	0	.	.	none	.	DNAJC9	19	.	NM_015190	exon1	c.C80T	p.S27F	CCGTCGGAGGCCT	.	PASS	Atlas-SNP
LILRA6	79168	hgsc.bcm.edu	37	19	54744799	54744799	+	Missense_Mutation	SNP	G	G	C	rs1052975	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	245	71	307	0	0.289796	0	G|0.816;C|0.184	0.184	strong	.	LILRA6	75	.	NM_024318	exon5	c.C863G	p.P288R	TGGGAGGGGCTCA	.	PASS	Atlas-SNP
NUSAP1	51203	hgsc.bcm.edu	37	15	41634587	41634587	+	Missense_Mutation	SNP	A	A	G	rs7178634	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	107	45	139	0	0.420561	0	A|0.684;G|0.316	0.316	strong	NUSAP1,NS,carcinoma,0,2	NUSAP1	32	2	NM_018454	exon2	c.A97G	p.T33A	CAGGCAACCAAGT	.	PASS	Atlas-SNP
ACAN	176	hgsc.bcm.edu	37	15	89402239	89402239	+	Silent	SNP	T	T	C	rs1042631	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	65	65	59	0	1	0	T|0.294;C|0.706	0.706	strong	ACAN,NS,carcinoma,0,1	ACAN	220	1	NM_001135	exon12	c.T6423C	p.L2141L	TAACCTTGAGAGA	.	PASS	Atlas-SNP
TROAP	10024	hgsc.bcm.edu	37	12	49722793	49722793	+	Silent	SNP	C	C	T	rs2230550	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	98	50	92	0	0.510204	0	C|0.969;T|0.031	0.031	strong	.	TROAP	80	.	NM_005480	exon9	c.C975T	p.P325P	ATCACCCTTTGGA	.	PASS	Atlas-SNP
MYLIP	29116	hgsc.bcm.edu	37	6	16145473	16145473	+	Silent	SNP	C	C	T	rs1060901	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	173	70	186	0	0.404624	0	C|0.950;T|0.050	0.050	strong	MYLIP,rectum,carcinoma,0,3	MYLIP	44	3	NM_013262	exon6	c.C1173T	p.C391C	GTGCTGCGAGGAG	.	PASS	Atlas-SNP
CCDC110	256309	hgsc.bcm.edu	37	4	186381115	186381115	+	Missense_Mutation	SNP	G	G	T	rs7699687	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	35	130	0	0.411765	0	G|0.564;T|0.436	0.436	strong	.	CCDC110	78	.	NM_152775	exon6	c.C626A	p.P209Q	ACATTTGGAGGTG	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	45	19	75	0	0.422222	0	C|0.710;T|0.290	0.290	strong	.	TRIM31	40	.	NM_007028	exon9	c.G1261A	p.E421K	GAACCTCACAAAA	.	PASS	Atlas-SNP
MAML1	9794	hgsc.bcm.edu	37	5	179201226	179201226	+	Missense_Mutation	SNP	A	A	C	rs148053500	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	39	25	46	0	0.641026	0	A|0.997;C|0.003	0.003	strong	.	MAML1	118	.	NM_014757	exon5	c.A2399C	p.N800T	GGCAGAACTCTCT	.	PASS	Atlas-SNP
FAT2	2196	hgsc.bcm.edu	37	5	150905398	150905398	+	Silent	SNP	C	C	T	rs3734051	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	36	76	1	0.461538	0.0131579	C|0.776;N|0.000	.	strong	FAT2,colon,carcinoma,-1,2	FAT2	465	2	NM_001447	exon17	c.G10437A	p.P3479P	TCCATCCGGGGTC	.	scavenged	Atlas-SNP
FAM83C	128876	hgsc.bcm.edu	37	20	33874720	33874720	+	Missense_Mutation	SNP	C	C	T	rs2425049	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	98	38	140	0	0.387755	0	C|0.647;T|0.353	0.353	strong	.	FAM83C	80	.	NM_178468	exon4	c.G1862A	p.R621Q	GGTGCCCGTCTGG	.	PASS	Atlas-SNP
BIN2	51411	hgsc.bcm.edu	37	12	51695839	51695839	+	Missense_Mutation	SNP	T	T	C	rs143984628	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	151	74	172	0	0.490066	0	T|1.000;C|0.000	0.000	strong	.	BIN2	58	.	NM_016293	exon5	c.A373G	p.M125V	TTTCCATGGTCCT	.	PASS	Atlas-SNP
FHL3	2275	hgsc.bcm.edu	37	1	38463504	38463504	+	Silent	SNP	C	C	T	rs7366048	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	119	119	150	0	1	0	C|0.477;T|0.523	0.523	strong	.	FHL3	9	.	NM_004468	exon5	c.G540A	p.P180P	ATGCCACGGCTGA	.	PASS	Atlas-SNP
TPST2	8459	hgsc.bcm.edu	37	22	26937321	26937321	+	Silent	SNP	G	G	A	rs17851532	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	33	16	27	0	0.484848	0	G|0.946;A|0.054	0.054	strong	.	TPST2	23	.	NM_001008566	exon3	c.C276T	p.P92P	CACCTCGGGGTGC	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	157	82	154	0	0.522293	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
SRP72	6731	hgsc.bcm.edu	37	4	57367891	57367891	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	198	43	243	0	0.217172	0	.	.	none	.	SRP72	59	.	NM_006947	exon19	c.G1880T	p.R627I	CCCCAAGACCTGG	.	PASS	Atlas-SNP
ACLY	47	hgsc.bcm.edu	37	17	40065774	40065774	+	Missense_Mutation	SNP	T	T	G	rs2304497	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	159	83	183	0	0.522013	0	T|0.896;G|0.104	0.104	strong	.	ACLY	85	.	NM_001096	exon5	c.A525C	p.E175D	CTTGTCTTCAGGG	.	PASS	Atlas-SNP
MUC20	200958	hgsc.bcm.edu	37	3	195453329	195453329	+	Silent	SNP	C	C	A	rs73203946	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	129	43	136	1	0.333333	0.00735294	C|0.967;A|0.033	0.033	strong	MUC20_ENST00000381954,NS,carcinoma,0,5	MUC20	84	5	NM_152673	exon3	c.C1342A	p.R448R	AGCAGCCGAGGGA	.	scavenged	Atlas-SNP
PRICKLE4	29964	hgsc.bcm.edu	37	6	41754576	41754576	+	Silent	SNP	C	C	T	rs9381093	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	55	33	68	0	0.6	0	C|0.588;T|0.412	0.412	strong	.	PRICKLE4	29	.	NM_013397	exon8	c.C864T	p.L288L	ACTCCTCGCTGCT	.	PASS	Atlas-SNP
INO80D	54891	hgsc.bcm.edu	37	2	206911228	206911228	+	Missense_Mutation	SNP	G	G	A	rs2909111	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	49	25	55	0	0.510204	0	G|0.629;A|0.371	0.371	strong	.	INO80D	134	.	NM_017759	exon5	c.C1073T	p.A358V	ACTTACGCATGTC	.	PASS	Atlas-SNP
EOGT	285203	hgsc.bcm.edu	37	3	69054341	69054341	+	Silent	SNP	T	T	C	rs6781612	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	57	24	74	0	0.421053	0	T|0.701;C|0.299	0.299	strong	.	.	.	.	NM_173654	exon7	c.A465G	p.R155R	GGTTGCTCTGCAG	.	PASS	Atlas-SNP
HSP90B1	7184	hgsc.bcm.edu	37	12	104341103	104341103	+	Silent	SNP	C	C	T	rs7645	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	186	101	195	0	0.543011	0	C|0.550;T|0.450	0.450	strong	.	HSP90B1	72	.	NM_003299	exon17	c.C2277T	p.P759P	AGAGCCCGAAGAA	.	PASS	Atlas-SNP
QPCTL	54814	hgsc.bcm.edu	37	19	46206262	46206262	+	Silent	SNP	G	G	A	rs17850756	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	228	125	201	0	0.548246	0	G|0.727;A|0.273	0.273	strong	QPCTL,NS,carcinoma,0,1	QPCTL	24	1	NM_017659	exon7	c.G1104A	p.L368L	CAACTTGTGCCGC	.	PASS	Atlas-SNP
CD96	10225	hgsc.bcm.edu	37	3	111286403	111286403	+	Missense_Mutation	SNP	T	T	C	rs147832650	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	43	92	0	0.597222	0	T|1.000;C|0.000	0.000	strong	.	CD96	75	.	NM_005816	exon3	c.T452C	p.I151T	ATACGATAGAAAT	.	PASS	Atlas-SNP
BIRC6	57448	hgsc.bcm.edu	37	2	32740138	32740138	+	Silent	SNP	T	T	C	rs34757266	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	39	91	0	0.402062	0	T|0.927;C|0.073	0.073	strong	.	BIRC6	838	.	NM_016252	exon55	c.T10650C	p.C3550C	AATGTGTCACGTA	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	55	23	79	0	0.418182	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
AIMP1	9255	hgsc.bcm.edu	37	4	107246190	107246190	+	Silent	SNP	G	G	C	rs11544777	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	279	149	354	0	0.53405	0	G|0.962;C|0.038	0.038	strong	.	AIMP1	20	.	NM_001142416	exon2	c.G96C	p.L32L	TGTTCTGAAGAGA	.	PASS	Atlas-SNP
FARSA	2193	hgsc.bcm.edu	37	19	13041558	13041558	+	Silent	SNP	G	G	A	rs373756496		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	14	9	23	0	0.642857	0	.	.	weak	.	FARSA	46	.	NM_004461	exon2	c.C153T	p.I51I	AGCCTCGATGACC	.	PASS	Atlas-SNP
FAM170B	170370	hgsc.bcm.edu	37	10	50339962	50339962	+	Missense_Mutation	SNP	A	A	T	rs75297145	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	41	20	56	0	0.487805	0	A|0.908;T|0.092	0.092	strong	.	FAM170B	20	.	NM_001164484	exon2	c.T548A	p.L183Q	CACTCCAGCAGGT	.	PASS	Atlas-SNP
SLC22A4	6583	hgsc.bcm.edu	37	5	131670546	131670546	+	Silent	SNP	C	C	G	rs272879	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	185	96	256	0	0.518919	0	C|0.395;G|0.605	0.605	strong	.	SLC22A4	45	.	NM_003059	exon7	c.C1182G	p.T394T	GCGAACCCTGCCC	.	PASS	Atlas-SNP
ANKRD6	22881	hgsc.bcm.edu	37	6	90340446	90340446	+	Missense_Mutation	SNP	C	C	T	rs61739327	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	42	18	49	0	0.428571	0	C|0.907;T|0.093	0.093	strong	.	ANKRD6	51	.	NM_001242809	exon16	c.C1907T	p.P636L	AGCAACCCGCAGC	.	PASS	Atlas-SNP
NRCAM	4897	hgsc.bcm.edu	37	7	107838464	107838464	+	Silent	SNP	G	G	T	rs381318	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	75	125	0	1	0	G|0.350;T|0.650	0.650	strong	.	NRCAM	267	.	NM_001037132	exon11	c.C1287A	p.V429V	CTGATAGACTGCA	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	105	49	137	0	0.466667	0	G|0.716;A|0.284	0.284	strong	.	MTOR	327	.	NM_004958	exon39	c.C5553T	p.S1851S	GGCCTCGCTCTCA	.	PASS	Atlas-SNP
WFDC9	259240	hgsc.bcm.edu	37	20	44238741	44238741	+	Missense_Mutation	SNP	T	T	G	rs2245898	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	52	78	0	0.666667	0	T|0.626;G|0.374	0.374	strong	WFDC9,NS,carcinoma,0,1	WFDC9	10	1	NM_147198	exon3	c.A80C	p.N27T	TCTTTGTTCCAGA	.	PASS	Atlas-SNP
ZNF749	388567	hgsc.bcm.edu	37	19	57955884	57955884	+	Silent	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	180	4	175	2	0.0222222	0.0114286	.	.	none	ZNF749,NS,carcinoma,0,2	ZNF749	75	2	NM_001023561	exon3	c.C1368T	p.H456H	TCAGCACCAGAAA	.	scavenged	Atlas-SNP
KRTAP12-2	353323	hgsc.bcm.edu	37	21	46086758	46086758	+	Missense_Mutation	SNP	C	C	T	rs13046903	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	113	110	85	0	0.973451	0	C|0.313;T|0.687	0.687	strong	.	KRTAP12-2	10	.	NM_181684	exon1	c.G46A	p.A16T	TGGGCGCGCAGCA	.	PASS	Atlas-SNP
WNK3	65267	hgsc.bcm.edu	37	X	54265469	54265469	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	50	34	63	0	0.68	0	.	.	none	.	WNK3	218	.	NM_001002838	exon18	c.G3715A	p.G1239S	CTCCACCGCTTGA	.	PASS	Atlas-SNP
OGDH	4967	hgsc.bcm.edu	37	7	44747578	44747578	+	Missense_Mutation	SNP	G	G	A	rs2070607	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	66	39	73	0	0.590909	0	G|0.955;A|0.045	0.045	strong	.	OGDH	145	.	NM_002541	exon23	c.G3052A	p.V1018I	CTGGACGTCTTCA	.	PASS	Atlas-SNP
BDKRB2	624	hgsc.bcm.edu	37	14	96703484	96703484	+	Missense_Mutation	SNP	C	C	T	rs1046248	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	149	74	125	0	0.496644	0	C|0.933;T|0.067	0.067	strong	.	BDKRB2	56	.	NM_000623	exon2	c.C40T	p.R14C	TCTGTTCGTGAGG	.	PASS	Atlas-SNP
AGAP6	414189	hgsc.bcm.edu	37	10	51748684	51748684	+	Missense_Mutation	SNP	G	G	A	rs77235195		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	5	5	7	0	1	0	A|1.000;|0.000	1.000	weak	AGAP6,NS,carcinoma,0,1	AGAP6	53	1	NM_001077665	exon1	c.G209A	p.R70Q	GTGACCGGGAGAT	.	scavenged	Atlas-SNP
MS4A6E	245802	hgsc.bcm.edu	37	11	60102396	60102396	+	Missense_Mutation	SNP	A	A	G	rs2304934	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	188	129	198	0	0.68617	0	A|0.691;G|0.309	0.309	strong	MS4A6E,NS,carcinoma,-2,1	MS4A6E	22	1	NM_139249	exon1	c.A28G	p.T10A	AATGAGACCATCA	.	PASS	Atlas-SNP
PNPO	55163	hgsc.bcm.edu	37	17	46020698	46020698	+	Silent	SNP	C	C	T	rs11079804	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	170	83	163	0	0.488235	0	C|0.855;T|0.145	0.145	strong	PNPO,NS,adenoma,0,1	PNPO	18	1	NM_018129	exon2	c.C165T	p.S55S	GACCTCCCTTGAC	.	PASS	Atlas-SNP
SIRPG	55423	hgsc.bcm.edu	37	20	1616892	1616892	+	Silent	SNP	A	A	G	rs2277760	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	266	126	250	0	0.473684	0	A|0.764;G|0.236	0.236	strong	.	SIRPG	61	.	NM_001039508	exon3	c.T690C	p.H230H	GGTGACATGGGCC	.	PASS	Atlas-SNP
OR8B3	390271	hgsc.bcm.edu	37	11	124266927	124266927	+	Silent	SNP	A	A	G	rs142812088		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	229	17	297	13	0.0742358	0.043771	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
OR8K1	390157	hgsc.bcm.edu	37	11	56113575	56113575	+	Missense_Mutation	SNP	A	A	G	rs10896271	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	88	19	132	0	0.215909	0	A|0.616;G|0.384	0.384	strong	.	OR8K1	93	.	NM_001002907	exon1	c.A61G	p.M21V	ATTCTCATGGGGA	.	PASS	Atlas-SNP
ANO2	57101	hgsc.bcm.edu	37	12	6030405	6030405	+	Missense_Mutation	SNP	A	A	G	rs3741903	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	43	104	0	0.467391	0	A|0.834;G|0.166	0.166	strong	.	ANO2	309	.	NM_020373	exon3	c.T323C	p.V108A	AGGTGCACCCCGC	.	PASS	Atlas-SNP
OXGR1	27199	hgsc.bcm.edu	37	13	97639827	97639827	+	Silent	SNP	T	T	G	rs9300380	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	145	71	173	0	0.489655	0	T|0.939;G|0.061	0.061	strong	.	OXGR1	46	.	NM_080818	exon4	c.A187C	p.R63R	AAGGTCTCATTTT	.	PASS	Atlas-SNP
PRR21	643905	hgsc.bcm.edu	37	2	240982116	240982116	+	Missense_Mutation	SNP	C	C	A	rs72993513	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	88	40	97	0	0.454545	0	C|0.741;A|0.259	0.259	strong	.	PRR21	53	.	NM_001080835	exon1	c.G284T	p.R95L	AAGGGCCGTGGGT	.	PASS	Atlas-SNP
GPR98	84059	hgsc.bcm.edu	37	5	90016778	90016778	+	Missense_Mutation	SNP	C	C	T	rs114137750	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	133	83	124	0	0.62406	0	C|0.989;T|0.011	0.011	strong	.	GPR98	605	.	NM_032119	exon45	c.C9650T	p.A3217V	AAGAAGCCAATAG	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228562350	228562350	+	Silent	SNP	T	T	C	rs72762068	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	139	60	190	0	0.431655	0	T|0.989;C|0.011	0.011	strong	.	OBSCN	2142	.	NM_001271223	exon108	c.T25431C	p.L8477L	CCAGCTTCTGACC	.	PASS	Atlas-SNP
UFL1	23376	hgsc.bcm.edu	37	6	96999725	96999725	+	Silent	SNP	C	C	T	rs1127175	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	152	150	242	1	0.986842	0.00413223	C|0.662;T|0.338	0.338	strong	KIAA0776,NS,carcinoma,0,2	.	.	2	NM_015323	exon17	c.C1911T	p.D637D	AGAAGACTTTATT	.	PASS	Atlas-SNP
GZMH	2999	hgsc.bcm.edu	37	14	25076906	25076906	+	Missense_Mutation	SNP	C	C	T	rs52812266		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	326	168	310	0	0.515337	0	.	.	weak	GZMH,colon,carcinoma,-1,1	GZMH	24	1	NM_033423	exon3	c.G251A	p.R84Q	TGGGTCCGCTCCT	.	PASS	Atlas-SNP
LACTB	114294	hgsc.bcm.edu	37	15	63433766	63433766	+	Missense_Mutation	SNP	G	G	A	rs2729835	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	150	147	184	0	0.98	0	G|0.329;A|0.671	0.671	strong	.	LACTB	29	.	NM_032857	exon6	c.G1406A	p.R469K	TGGAAAGGAAACA	.	PASS	Atlas-SNP
PDDC1	347862	hgsc.bcm.edu	37	11	771034	771034	+	Silent	SNP	A	A	G	rs7930569	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	102	22	95	0	0.215686	0	A|0.556;G|0.444	0.444	strong	.	PDDC1	16	.	NM_182612	exon7	c.T615C	p.T205T	CGGGACAGTGGAG	.	PASS	Atlas-SNP
COL6A5	256076	hgsc.bcm.edu	37	3	130110550	130110550	+	Missense_Mutation	SNP	A	A	G	rs11917356	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	44	97	0	0.637681	0	A|0.624;G|0.376	0.376	strong	.	COL6A5	205	.	NM_153264	exon7	c.A2945G	p.D982G	TGAAAGATGTTTT	.	PASS	Atlas-SNP
NQO2	4835	hgsc.bcm.edu	37	6	3015790	3015790	+	Silent	SNP	A	A	G	rs1049115	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	83	83	82	0	1	0	A|0.232;G|0.768	0.768	strong	.	NQO2	21	.	NM_000904	exon5	c.A330G	p.P110P	CGTGCCAGCCATC	.	PASS	Atlas-SNP
POLR2A	5430	hgsc.bcm.edu	37	17	7405937	7405937	+	Silent	SNP	C	C	T	rs2071504	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	80	36	89	0	0.45	0	C|0.849;T|0.151	0.151	strong	.	POLR2A	157	.	NM_000937	exon16	c.C2673T	p.Y891Y	GCGCTACGGCGAA	.	PASS	Atlas-SNP
MLL3	58508	hgsc.bcm.edu	37	7	151874498	151874498	+	Silent	SNP	C	C	T	rs10252263	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	156	71	176	0	0.455128	0	C|0.865;T|0.135	0.135	strong	.	MLL3	1564	.	NM_170606	exon38	c.G8040A	p.Q2680Q	AGAAGGCTGGGTG	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	47	20	60	0	0.425532	0	G|0.815;A|0.185	0.185	strong	.	FAM205A	45	.	NM_001141917	exon4	c.C713T	p.T238M	CTCTGCGTCATCT	.	PASS	Atlas-SNP
SMIM11	54065	hgsc.bcm.edu	37	21	35757915	35757915	+	Missense_Mutation	SNP	A	A	G	rs34016792	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	119	49	120	0	0.411765	0	A|0.979;G|0.021	0.021	strong	.	.	.	.	NM_058182	exon3	c.A152G	p.K51R	GGAAGAAGCAATC	.	PASS	Atlas-SNP
ARHGAP5	394	hgsc.bcm.edu	37	14	32561316	32561316	+	Nonsense_Mutation	SNP	G	G	T	rs200628183	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	79	10	84	1	0.126582	0.0119048	G|0.996;T|0.004	0.004	strong	ARHGAP5,uveal_tract,malignant_melanoma,0,1	ARHGAP5	166	1	NM_001173	exon2	c.G1441T	p.E481X	CAGCGAGAAATAG	.	scavenged	Atlas-SNP
CCDC67	159989	hgsc.bcm.edu	37	11	93141575	93141575	+	Missense_Mutation	SNP	T	T	C	rs371785641		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	84	19	110	1	0.22619	0.00909091	.	.	weak	CCDC67,NS,carcinoma,+1,1	CCDC67	57	1	NM_181645	exon12	c.T1505C	p.V502A	TAAAAGTGGAACA	.	scavenged	Atlas-SNP
DTNBP1	84062	hgsc.bcm.edu	37	6	15523448	15523448	+	Missense_Mutation	SNP	G	G	A	rs17470454	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	31	77	0	0.534483	0	G|0.970;A|0.030	0.030	strong	.	DTNBP1	56	.	NM_032122	exon10	c.C814T	p.P272S	ATTCAGGCCCTGC	.	PASS	Atlas-SNP
DOPEY2	9980	hgsc.bcm.edu	37	21	37617724	37617724	+	Missense_Mutation	SNP	C	C	A	rs3746866	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	35	60	0	0.603448	0	C|0.859;A|0.141	0.141	strong	DOPEY2,NS,carcinoma,0,1	DOPEY2	184	1	NM_005128	exon19	c.C3446A	p.P1149H	CCATCCCCATGGG	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	153	72	154	0	0.470588	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
DEFB127	140850	hgsc.bcm.edu	37	20	139576	139576	+	Missense_Mutation	SNP	C	C	A	rs16995685	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	165	69	232	0	0.418182	0	C|0.718;A|0.282	0.282	strong	.	DEFB127	15	.	NM_139074	exon2	c.C211A	p.R71S	CCACCTCGTCCAA	.	PASS	Atlas-SNP
SLC15A2	6565	hgsc.bcm.edu	37	3	121647286	121647286	+	Missense_Mutation	SNP	C	C	T	rs1143671	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	80	41	64	0	0.5125	0	C|0.523;T|0.477	0.477	strong	.	SLC15A2	92	.	NM_021082	exon15	c.C1225T	p.P409S	GCCCAGCCAGGTC	.	PASS	Atlas-SNP
IRF7	3665	hgsc.bcm.edu	37	11	613208	613208	+	Missense_Mutation	SNP	T	T	C	rs1131665	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	94	62	105	0	0.659574	0	T|0.719;C|0.281	0.281	strong	.	IRF7	23	.	NM_004031	exon7	c.A1274G	p.Q425R	TGACCTTGGAAGA	.	PASS	Atlas-SNP
GRIN2C	2905	hgsc.bcm.edu	37	17	72838649	72838649	+	Missense_Mutation	SNP	C	C	A	rs3744215	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	168	100	163	0	0.595238	0	C|0.689;A|0.311	0.311	strong	GRIN2C_ENST00000293190,NS,carcinoma,0,4	GRIN2C	144	4	NM_000835	exon13	c.G3627T	p.R1209S	GGCTACCCTGCTG	.	PASS	Atlas-SNP
SVEP1	79987	hgsc.bcm.edu	37	9	113168501	113168501	+	Missense_Mutation	SNP	A	A	G	rs41278435	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	120	60	147	0	0.5	0	A|0.964;G|0.036	0.036	strong	.	SVEP1	326	.	NM_153366	exon38	c.T9379C	p.S3127P	CGACAGACGGTGG	.	PASS	Atlas-SNP
TDRKH	11022	hgsc.bcm.edu	37	1	151751274	151751274	+	Missense_Mutation	SNP	C	C	G	rs17853082	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	43	138	0	0.505882	0	C|0.978;G|0.022	0.022	strong	.	TDRKH	45	.	NM_001083965	exon6	c.G770C	p.G257A	CCTCCTCCTTTGG	.	PASS	Atlas-SNP
PIM1	5292	hgsc.bcm.edu	37	6	37138412	37138412	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	39	11	18	0	0.282051	0	.	.	none	.	PIM1	71	.	NM_001243186	exon1	c.C334A	p.H112N	GACCTGCACGCCA	.	PASS	Atlas-SNP
TTLL3	26140	hgsc.bcm.edu	37	3	9876987	9876987	+	Silent	SNP	G	G	A	rs1057281	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	39	38	65	0	0.974359	0	G|0.873;A|0.127	0.127	strong	.	TTLL3	51	.	NM_001025930	exon13	c.G2562A	p.R854R	CCAGAGGCGCAGG	.	PASS	Atlas-SNP
SPATA21	374955	hgsc.bcm.edu	37	1	16736132	16736132	+	Missense_Mutation	SNP	T	T	C	rs4661746	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	35	21	52	0	0.6	0	T|0.794;C|0.206	0.206	strong	.	SPATA21	47	.	NM_198546	exon6	c.A551G	p.Q184R	CTGCTCTGGTGCA	.	PASS	Atlas-SNP
TNFRSF10A	8797	hgsc.bcm.edu	37	8	23060256	23060256	+	Missense_Mutation	SNP	T	T	C	rs17620	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	180	46	154	0	0.255556	0	T|0.514;C|0.486	0.486	strong	.	TNFRSF10A	40	.	NM_003844	exon3	c.A422G	p.H141R	CCAGGATGTTCTG	.	PASS	Atlas-SNP
POTEE	445582	hgsc.bcm.edu	37	2	132021766	132021766	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	144	7	157	5	0.0486111	0.0318471	.	.	none	ENSG00000188219,rectum,NS,0,1	.	.	1	NM_001083538	exon15	c.A2738C	p.K913T	ACATCAAAGAGAA	.	scavenged	Atlas-SNP
IQUB	154865	hgsc.bcm.edu	37	7	123119990	123119990	+	Silent	SNP	T	T	C	rs10500091	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	116	48	163	0	0.413793	0	T|0.782;C|0.218	0.218	strong	.	IQUB	117	.	NM_178827	exon8	c.A1269G	p.Q423Q	AAAAGATTGGTTA	.	PASS	Atlas-SNP
ST6GAL2	84620	hgsc.bcm.edu	37	2	107423188	107423188	+	Silent	SNP	G	G	A	rs1470591	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	99	44	126	0	0.444444	0	G|0.679;A|0.321	0.321	strong	ST6GAL2,NS,carcinoma,-1,1	ST6GAL2	159	1	NM_032528	exon6	c.C1536T	p.P512P	GAAGCCGGGAAGA	.	PASS	Atlas-SNP
HOMEZ	57594	hgsc.bcm.edu	37	14	23746340	23746340	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	63	29	71	0	0.460317	0	.	.	none	.	HOMEZ	80	.	NM_020834	exon2	c.G97A	p.G33S	TGAGACCGCTGGC	.	PASS	Atlas-SNP
HLA-DPB1	3115	hgsc.bcm.edu	37	6	33048600	33048600	+	Silent	SNP	T	T	G	rs9277351	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	49	24	57	1	0.489796	0.0175439	C|0.004;G|0.058;T|0.937	0.058	strong	HLA-DPB1,brain,glioma,+1,1	HLA-DPB1	28	1	NM_002121	exon2	c.T252G	p.A84A	GCCTGCTGCGGAG	.	scavenged	Atlas-SNP
HIVEP1	3096	hgsc.bcm.edu	37	6	12124257	12124257	+	Missense_Mutation	SNP	C	C	G	rs372404420		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	36	104	0	0.371134	0	.	.	weak	.	HIVEP1	242	.	NM_002114	exon4	c.C4229G	p.P1410R	CTTCACCTTCTCG	.	PASS	Atlas-SNP
EVA1C	59271	hgsc.bcm.edu	37	21	33840095	33840095	+	Silent	SNP	C	C	T	rs8130653	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	44	29	29	0	0.659091	0	C|0.917;T|0.083	0.083	strong	.	.	.	.	NM_058187	exon4	c.C573T	p.Y191Y	GACCTACGGCAGG	.	PASS	Atlas-SNP
OR51F1	256892	hgsc.bcm.edu	37	11	4790758	4790758	+	Silent	SNP	G	G	A	rs11033796	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	144	29	142	0	0.201389	0	G|0.690;A|0.310	0.310	strong	.	OR51F1	60	.	NM_001004752	exon1	c.C390T	p.D130D	CAGAGGGTCACAG	.	PASS	Atlas-SNP
RADIL	55698	hgsc.bcm.edu	37	7	4841313	4841313	+	Missense_Mutation	SNP	A	A	G	rs6966329	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	116	116	145	1	1	0.00689655	A|0.744;G|0.256	0.256	strong	.	RADIL	110	.	NM_018059	exon12	c.T2813C	p.L938P	CCGCTGAGTCCGT	.	PASS	Atlas-SNP
PLSCR1	5359	hgsc.bcm.edu	37	3	146234909	146234909	+	Missense_Mutation	SNP	G	G	A	rs343320	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	137	74	179	0	0.540146	0	G|0.948;A|0.052	0.052	strong	.	PLSCR1	35	.	NM_021105	exon8	c.C784T	p.H262Y	TCCAGTGCTTGGA	.	PASS	Atlas-SNP
OR5P2	120065	hgsc.bcm.edu	37	11	7817538	7817538	+	Missense_Mutation	SNP	T	T	C	rs7949771	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	79	65	84	0	0.822785	0	T|0.748;C|0.252	0.252	strong	.	OR5P2	68	.	NM_153444	exon1	c.A952G	p.N318D	CATTATTTGAAGT	.	PASS	Atlas-SNP
GRIN2B	2904	hgsc.bcm.edu	37	12	13764774	13764774	+	Silent	SNP	G	G	A	rs1805482	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	76	29	99	0	0.381579	0	G|0.753;A|0.247	0.247	strong	.	GRIN2B	303	.	NM_000834	exon8	c.C1665T	p.S555S	GTCAGCGCTGAAT	.	PASS	Atlas-SNP
IL1A	3552	hgsc.bcm.edu	37	2	113537223	113537223	+	Missense_Mutation	SNP	C	C	A	rs17561	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	124	62	164	0	0.5	0	C|0.765;A|0.235	0.235	strong	.	IL1A	19	.	NM_000575	exon5	c.G340T	p.A114S	AAGGTGCTGACCT	.	PASS	Atlas-SNP
FBXO40	51725	hgsc.bcm.edu	37	3	121340536	121340536	+	Missense_Mutation	SNP	T	T	C	rs4676684	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	88	42	80	0	0.477273	0	T|0.693;C|0.307	0.307	strong	.	FBXO40	108	.	NM_016298	exon3	c.T260C	p.V87A	TGCAGGTGTGCCC	.	PASS	Atlas-SNP
MKI67	4288	hgsc.bcm.edu	37	10	129903465	129903465	+	Silent	SNP	A	A	G	rs2857028	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	212	102	252	1	0.481132	0.00396825	T|0.007;G|0.212	0.212	strong	.	MKI67	363	.	NM_002417	exon13	c.T6639C	p.H2213H	TTTCTCATGAGTC	.	PASS	Atlas-SNP
C1orf68	100129271	hgsc.bcm.edu	37	1	152692512	152692512	+	Missense_Mutation	SNP	G	G	A	rs41268474	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	190	79	171	0	0.415789	0	G|0.900;A|0.100	0.100	strong	.	C1orf68	19	.	NM_001024679	exon1	c.G515A	p.C172Y	ACTGCTGTCTGGC	.	PASS	Atlas-SNP
ANKRD13A	88455	hgsc.bcm.edu	37	12	110449872	110449872	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	15	101	0	0.208333	0	.	.	none	.	ANKRD13A	39	.	NM_033121	exon2	c.T159A	p.H53Q	GGGACATTTGGAA	.	PASS	Atlas-SNP
TNFRSF6B	8771	hgsc.bcm.edu	37	20	62328453	62328453	+	Silent	SNP	T	T	C	rs2258056	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	52	18	53	0	0.346154	0	T|0.778;C|0.222	0.222	strong	TNFRSF6B,NS,carcinoma,0,1	TNFRSF6B	22	1	NM_003823	exon1	c.T333C	p.R111R	CAACCGTGCCTGC	.	PASS	Atlas-SNP
OR8U1	219417	hgsc.bcm.edu	37	11	56143424	56143424	+	Missense_Mutation	SNP	A	A	G	rs12788990	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	53	25	67	0	0.471698	0	A|0.893;G|0.107	0.107	strong	OR8U1,NS,carcinoma,0,1	OR8U1	59	1	NM_001005204	exon1	c.A325G	p.I109V	TTCATGATATCAG	.	PASS	Atlas-SNP
CPXCR1	53336	hgsc.bcm.edu	37	X	88008807	88008807	+	Missense_Mutation	SNP	G	G	A	rs5984611	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	82	167	0	1	0	0|0.003;A|0.269	0.269	strong	.	CPXCR1	83	.	NM_001184771	exon3	c.G392A	p.R131H	AAACTCGTTTTCG	.	PASS	Atlas-SNP
LRP2	4036	hgsc.bcm.edu	37	2	170099473	170099473	+	Silent	SNP	T	T	C	rs831042	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	135	70	213	0	0.518519	0	T|0.490;C|0.510	0.510	strong	.	LRP2	751	.	NM_004525	exon24	c.A3660G	p.A1220A	ACAGCCTGCTTCA	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100680521	100680521	+	Missense_Mutation	SNP	G	G	A	rs73712043	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	45	25	54	0	0.555556	0	G|0.963;A|0.037	0.037	strong	.	MUC17	804	.	NM_001040105	exon3	c.G5824A	p.E1942K	AGTTCTGAAATCA	.	PASS	Atlas-SNP
ALOX15	246	hgsc.bcm.edu	37	17	4535314	4535314	+	Missense_Mutation	SNP	G	G	A	rs34210653	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	63	32	61	0	0.507937	0	G|0.988;A|0.012	0.012	strong	.	ALOX15	70	.	NM_001140	exon13	c.C1679T	p.T560M	CGCATCGTGCAGG	.	PASS	Atlas-SNP
ZNF587	84914	hgsc.bcm.edu	37	19	58371259	58371259	+	Silent	SNP	A	A	G	rs75951435	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	339	56	232	0	0.165192	0	A|0.963;G|0.037	0.037	strong	ZNF587,NS,carcinoma,0,1	ZNF587	53	1	NM_032828	exon3	c.A1479G	p.E493E	GTATGAATGCAGT	.	scavenged	Atlas-SNP
GPR112	139378	hgsc.bcm.edu	37	X	135430044	135430044	+	Silent	SNP	T	T	C	rs877761	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	126	126	215	0	1	0	T|0.432;0|0.003	.	strong	.	GPR112	459	.	NM_153834	exon6	c.T4179C	p.T1393T	CAGGACTGTGGAA	.	PASS	Atlas-SNP
PTK2B	2185	hgsc.bcm.edu	37	8	27277537	27277537	+	Silent	SNP	G	G	A	rs1030526	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	163	40	165	0	0.245399	0	G|0.621;A|0.379	0.379	strong	.	PTK2B	304	.	NM_173174	exon8	c.G330A	p.T110T	GATGACGGTGGGT	.	PASS	Atlas-SNP
PCDHA10	56139	hgsc.bcm.edu	37	5	140235875	140235875	+	Missense_Mutation	SNP	G	G	A	rs143002904	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	31	31	91	0	1	0	G|0.995;A|0.005	0.005	strong	.	PCDHA10	358	.	NM_031859	exon1	c.G242A	p.G81D	AGAATGGCATTTT	.	PASS	Atlas-SNP
KANK3	256949	hgsc.bcm.edu	37	19	8399272	8399272	+	Silent	SNP	G	G	A	rs8106699	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	90	44	115	0	0.488889	0	G|0.859;A|0.141	0.141	strong	.	KANK3	35	.	NM_198471	exon4	c.C1359T	p.D453D	TGTGCCGTCTCTC	.	PASS	Atlas-SNP
SLC4A7	9497	hgsc.bcm.edu	37	3	27463229	27463229	+	Silent	SNP	C	C	T	rs79251239	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	124	124	126	0	1	0	C|0.855;T|0.145	0.145	strong	.	SLC4A7	119	.	NM_003615	exon9	c.G1281A	p.E427E	GGATGCCTCAGCA	.	PASS	Atlas-SNP
TMEM97	27346	hgsc.bcm.edu	37	17	26646320	26646320	+	Missense_Mutation	SNP	C	C	G	rs202198126	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	196	88	210	0	0.44898	0	C|0.999;G|0.001	0.001	weak	.	TMEM97	27	.	NM_014573	exon1	c.C55G	p.L19V	TACTTCCTCAGCC	.	PASS	Atlas-SNP
KRT27	342574	hgsc.bcm.edu	37	17	38938557	38938557	+	Silent	SNP	G	G	A	rs67771170	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	64	28	74	0	0.4375	0	G|0.899;A|0.101	0.101	strong	.	KRT27	41	.	NM_181537	exon1	c.C189T	p.G63G	TCCCCCGCCCAGA	.	PASS	Atlas-SNP
SLC1A5	6510	hgsc.bcm.edu	37	19	47291174	47291174	+	Missense_Mutation	SNP	G	G	C	rs3027956	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	30	46	0	0.422535	0	G|0.712;C|0.288	0.288	strong	.	SLC1A5	31	.	NM_005628	exon1	c.C49G	p.P17A	CGGTGGGCTCCGC	.	PASS	Atlas-SNP
STAT6	6778	hgsc.bcm.edu	37	12	57496654	57496654	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	120	14	114	0	0.116667	0	.	.	none	.	STAT6	69	.	NM_001178079	exon12	c.T1263A	p.N421K	TTTGGCATTGTTG	.	PASS	Atlas-SNP
PTPRB	5787	hgsc.bcm.edu	37	12	70990054	70990054	+	Missense_Mutation	SNP	T	T	C	rs2465811	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	38	82	0	0.506667	0	C|0.325;N|0.000	0.325	strong	.	PTPRB	676	.	NM_001109754	exon5	c.A1033G	p.S345G	GCAAGCTGGTTGA	.	PASS	Atlas-SNP
NOD1	10392	hgsc.bcm.edu	37	7	30491311	30491311	+	Silent	SNP	C	C	T	rs2075821	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	38	8	67	0	0.210526	0	C|0.707;T|0.293	0.293	strong	.	NOD1	79	.	NM_006092	exon6	c.G1722A	p.A574A	TTCCCGCGCCGGA	.	PASS	Atlas-SNP
OR5D18	219438	hgsc.bcm.edu	37	11	55587914	55587914	+	Missense_Mutation	SNP	A	A	G	rs55832853	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	26	94	0	0.298851	0	A|0.774;G|0.226	0.226	strong	OR5D18,NS,carcinoma,-1,1	OR5D18	121	1	NM_001001952	exon1	c.A809G	p.H270R	CCAGGCACACAGT	.	PASS	Atlas-SNP
LYPD5	284348	hgsc.bcm.edu	37	19	44303066	44303066	+	Missense_Mutation	SNP	C	C	G	rs11547806	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	174	82	186	0	0.471264	0	C|0.420;G|0.580	0.580	strong	LYPD5,NS,carcinoma,0,1	LYPD5	22	1	NM_001031749	exon3	c.G268C	p.A90P	CGTCCGCGTTCGA	.	PASS	Atlas-SNP
RRP12	23223	hgsc.bcm.edu	37	10	99141484	99141484	+	Silent	SNP	C	C	T	rs12218483	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	234	119	282	0	0.508547	0	C|0.769;T|0.231	0.231	strong	RRP12,colon,carcinoma,0,8	RRP12	97	8	NM_015179	exon11	c.G1308A	p.T436T	GCTCTGCGTAGCA	.	PASS	Atlas-SNP
UGT2B11	10720	hgsc.bcm.edu	37	4	70080233	70080233	+	Missense_Mutation	SNP	A	A	G	rs7697482	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	213	96	261	0	0.450704	0	A|0.500;G|0.500	0.500	weak	UGT2B11,NS,carcinoma,+1,1	UGT2B11	92	1	NM_001073	exon1	c.T208C	p.S70P	GAGTGGATGCATC	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179403750	179403750	+	Missense_Mutation	SNP	C	C	T	rs4894028	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	193	89	203	0	0.46114	0	C|0.965;G|0.000;T|0.035	0.035	strong	.	TTN	18412	.	NM_001267550	exon353	c.G98912A	p.R32971H	ATGATGCGGAACT	.	PASS	Atlas-SNP
IQGAP2	10788	hgsc.bcm.edu	37	5	75996909	75996909	+	Missense_Mutation	SNP	G	G	A	rs34592828	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	237	88	239	0	0.371308	0	A|0.027;G|0.973	0.027	strong	.	IQGAP2	186	.	NM_006633	exon34	c.G4376A	p.R1459Q	ATACTCGGAGATC	.	PASS	Atlas-SNP
CNOT4	4850	hgsc.bcm.edu	37	7	135047811	135047811	+	Missense_Mutation	SNP	G	G	C	rs200460078	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	139	75	110	0	0.539568	0	G|0.998;C|0.002	0.002	strong	CNOT4_ENST00000541284,NS,carcinoma,0,3	CNOT4	146	3	NM_001190850	exon12	c.C1968G	p.H656Q	GGCGCTGTGGTGG	.	PASS	Atlas-SNP
PCDHB4	56131	hgsc.bcm.edu	37	5	140503237	140503237	+	Missense_Mutation	SNP	A	A	G	rs78271884		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	77	28	98	0	0.363636	0	G|1.000;|0.000	1.000	weak	.	PCDHB4	177	.	NM_018938	exon1	c.A1657G	p.T553A	CTGGACACCAACG	.	PASS	Atlas-SNP
HN1	51155	hgsc.bcm.edu	37	17	73143748	73143748	+	Missense_Mutation	SNP	C	C	G	rs200749518		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	24	14	34	0	0.583333	0	C|0.999;G|0.001	0.001	weak	.	HN1	17	.	NM_016185	exon3	c.G200C	p.G67A	TTGGCACCTAAAA	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29911213	29911213	+	Nonsense_Mutation	SNP	G	G	A	rs199474545	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	132	32	293	0	0.242424	0	.	.	weak	.	HLA-A	89	.	NM_001242758	exon3	c.G512A	p.W171X	GCAAGTGGGAGGC	.	PASS	Atlas-SNP
WDR46	9277	hgsc.bcm.edu	37	6	33256397	33256397	+	Silent	SNP	G	G	A	rs9277965	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	147	80	166	0	0.544218	0	G|0.874;A|0.126	0.126	strong	.	WDR46	43	.	NM_005452	exon3	c.C354T	p.S118S	CTTTCGGGATTTG	.	PASS	Atlas-SNP
PDCD2L	84306	hgsc.bcm.edu	37	19	34895647	34895647	+	Missense_Mutation	SNP	G	G	A	rs141960904	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	76	37	68	0	0.486842	0	G|0.998;A|0.002	0.002	strong	.	PDCD2L	27	.	NM_032346	exon2	c.G202A	p.G68S	CTGGAAGGCTCCC	.	PASS	Atlas-SNP
ARSD	414	hgsc.bcm.edu	37	X	2836047	2836047	+	Missense_Mutation	SNP	C	C	T	rs67359049	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	93	8	103	0	0.0860215	0	C|0.938;T|0.062	0.062	strong	.	ARSD	47	.	NM_001669	exon5	c.G661A	p.G221S	AGAAACCGCAGGT	.	PASS	Atlas-SNP
PCNT	5116	hgsc.bcm.edu	37	21	47836078	47836078	+	Silent	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	158	2	168	0	0.0126582	0	.	.	none	PCNT,colon,carcinoma,+1,1	PCNT	283	1	NM_006031	exon30	c.T6246C	p.Y2082Y	GCTGTATTCCATG	.	scavenged	Atlas-SNP
SRRM4	84530	hgsc.bcm.edu	37	12	119588962	119588962	+	Missense_Mutation	SNP	G	G	A	rs2723880	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	45	23	76	0	0.511111	0	G|0.714;A|0.286	0.286	strong	.	SRRM4	131	.	NM_194286	exon10	c.G1217A	p.R406Q	CGTCCCGATCCCC	.	PASS	Atlas-SNP
RNASE9	390443	hgsc.bcm.edu	37	14	21024619	21024619	+	Missense_Mutation	SNP	A	A	G	rs1243647	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	114	59	141	0	0.517544	0	A|0.233;G|0.767	0.767	strong	.	RNASE9	30	.	NM_001110359	exon5	c.T625C	p.S209P	AGGGCGATATGAC	.	PASS	Atlas-SNP
ANKRD17	26057	hgsc.bcm.edu	37	4	73942678	73942678	+	Silent	SNP	C	C	T	rs2306058	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	136	71	165	0	0.522059	0	C|0.852;T|0.148	0.148	strong	.	ANKRD17	214	.	NM_032217	exon33	c.G7731A	p.T2577T	ATTTTCCGTGGAG	.	PASS	Atlas-SNP
SPTBN2	6712	hgsc.bcm.edu	37	11	66460527	66460527	+	Silent	SNP	C	C	T	rs639938	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	100	76	97	0	0.76	0	C|0.938;T|0.062	0.062	strong	.	SPTBN2	188	.	NM_006946	exon24	c.G4899A	p.L1633L	TTGCTCCAGCACC	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	166	85	200	0	0.512048	0	A|0.435;G|0.565	0.565	strong	.	WDR60	94	.	NM_018051	exon5	c.A818G	p.Q273R	GGCACCAAAGCAA	.	PASS	Atlas-SNP
SELPLG	6404	hgsc.bcm.edu	37	12	109017674	109017674	+	Missense_Mutation	SNP	A	A	G	rs201851784	byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	80	25	117	3	0.3125	0.025641	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
DNMT1	1786	hgsc.bcm.edu	37	19	10267077	10267077	+	Silent	SNP	T	T	C	rs2228611	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	104	103	100	0	0.990385	0	T|0.475;C|0.525	0.525	strong	.	DNMT1	148	.	NM_001130823	exon18	c.A1389G	p.P463P	AAGAGATGGGTCA	.	PASS	Atlas-SNP
RET	5979	hgsc.bcm.edu	37	10	43610119	43610119	+	Missense_Mutation	SNP	G	G	A	rs1799939	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	46	20	75	1	0.434783	0.0133333	G|0.839;A|0.161	0.161	strong	RET_ENST00000340058,adrenal_gland,pheochromocytoma,0,2	RET	916	2	NM_020630	exon11	c.G2071A	p.G691S	TCTTCCGGTGCCC	.	scavenged	Atlas-SNP
FOXS1	2307	hgsc.bcm.edu	37	20	30433139	30433139	+	Silent	SNP	G	G	A	rs6089096	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	114	56	103	0	0.491228	0	G|0.929;A|0.071	0.071	strong	.	FOXS1	29	.	NM_004118	exon1	c.C207T	p.N69N	TGACAGGTTGTGG	.	PASS	Atlas-SNP
STEAP1B	256227	hgsc.bcm.edu	37	7	22478207	22478207	+	Silent	SNP	G	G	T	rs2528843	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	61	12	68	0	0.196721	0	G|0.488;T|0.512	0.512	strong	.	STEAP1B	22	.	NM_001164460	exon5	c.C930A	p.A310A	AGGGCTGGCTGCT	.	PASS	Atlas-SNP
KRTAP9-1	728318	hgsc.bcm.edu	37	17	39346139	39346139	+	Missense_Mutation	SNP	A	A	G	rs61743546	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	34	13	51	0	0.382353	0	A|0.854;G|0.146	0.146	strong	.	KRTAP9-1	34	.	NM_001190460	exon1	c.A1G	p.M1V	GACACCATGACCC	.	PASS	Atlas-SNP
TMEM63B	55362	hgsc.bcm.edu	37	6	44115169	44115169	+	Missense_Mutation	SNP	G	G	A	rs4714759	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	138	59	139	0	0.427536	0	G|0.903;A|0.097	0.097	strong	TMEM63B,NS,carcinoma,0,1	TMEM63B	77	1	NM_018426	exon12	c.G919A	p.V307M	GAGAACGTGCCTA	.	PASS	Atlas-SNP
WDFY4	57705	hgsc.bcm.edu	37	10	50171949	50171949	+	Silent	SNP	C	C	T	rs41283297	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	162	72	150	0	0.444444	0	C|0.972;T|0.028	0.028	strong	WDFY4,colon,carcinoma,+1,1	WDFY4	205	1	NM_020945	exon54	c.C8286T	p.Y2762Y	TGGGTACAAGCAG	.	PASS	Atlas-SNP
ZC3HC1	51530	hgsc.bcm.edu	37	7	129664301	129664301	+	Silent	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	95	22	83	0	0.231579	0	.	.	none	.	ZC3HC1	45	.	NM_016478	exon7	c.A822G	p.Q274Q	CATACATTGCGAA	.	PASS	Atlas-SNP
CYP4V2	285440	hgsc.bcm.edu	37	4	187118114	187118114	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	55	16	66	0	0.290909	0	.	.	none	.	CYP4V2	49	.	NM_207352	exon4	c.C434T	p.S145F	GGCGCTCCAGGAG	.	PASS	Atlas-SNP
CBS	875	hgsc.bcm.edu	37	21	44488631	44488631	+	Missense_Mutation	SNP	T	T	G	rs34040148	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	137	51	101	0	0.372263	0	T|0.985;G|0.015	0.015	strong	.	CBS	85	.	NM_000071	exon4	c.A304C	p.K102Q	CACACTTCAGGCC	.	PASS	Atlas-SNP
TMEM71	137835	hgsc.bcm.edu	37	8	133764112	133764112	+	Missense_Mutation	SNP	T	T	C	rs117725783	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	145	27	161	0	0.186207	0	T|0.988;C|0.012	0.012	strong	.	TMEM71	55	.	NM_144649	exon4	c.A233G	p.D78G	AAGCTGTCTTCAG	.	PASS	Atlas-SNP
DARC	2532	hgsc.bcm.edu	37	1	159175465	159175465	+	Missense_Mutation	SNP	T	T	C	rs141404247		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	165	82	212	1	0.49697	0.00471698	T|1.000;C|0.000	0.000	weak	.	DARC	76	.	NM_001122951	exon1	c.T242C	p.V81A	GCACTGTCCTCTT	.	PASS	Atlas-SNP
OR6M1	390261	hgsc.bcm.edu	37	11	123676388	123676388	+	Missense_Mutation	SNP	G	G	A	rs76301014	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	59	13	74	0	0.220339	0	G|0.859;A|0.141	0.141	strong	.	OR6M1	60	.	NM_001005325	exon1	c.C670T	p.R224C	GGATACGCAGGAT	.	PASS	Atlas-SNP
ACSL5	51703	hgsc.bcm.edu	37	10	114154815	114154815	+	Silent	SNP	C	C	T	rs11195943	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	124	67	131	0	0.540323	0	C|0.918;T|0.082	0.082	strong	.	ACSL5	51	.	NM_016234	exon2	c.C279T	p.P93P	TCAACCCGTCTTA	.	PASS	Atlas-SNP
PSPH	5723	hgsc.bcm.edu	37	7	56088780	56088780	+	Silent	SNP	G	G	A	rs75497420	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	158	27	132	0	0.170886	0	G|0.957;A|0.044	0.044	strong	.	PSPH	23	.	NM_004577	exon4	c.C126T	p.D42D	CACCGCGTCCTCA	.	PASS	Atlas-SNP
ABCA13	154664	hgsc.bcm.edu	37	7	48311563	48311563	+	Missense_Mutation	SNP	T	T	G	rs17712293	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	80	28	139	0	0.35	0	T|0.817;G|0.183	0.183	strong	.	ABCA13	1192	.	NM_152701	exon17	c.T2300G	p.I767S	AGGATATTCTGAA	.	PASS	Atlas-SNP
ACAN	176	hgsc.bcm.edu	37	15	89398605	89398605	+	Missense_Mutation	SNP	G	G	T	rs938608	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	87	108	1	1	0.00925926	A|0.003;C|0.008	.	strong	AGC1,NS,carcinoma,-1,3	ACAN	220	3	NM_001135	exon12	c.G2789T	p.S930I	GGCCCAGCACTCC	.	PASS	Atlas-SNP
MARCH4	57574	hgsc.bcm.edu	37	2	217148417	217148417	+	Silent	SNP	C	C	A	rs876771	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	72	104	1	0.986301	0.00961538	C|0.576;A|0.424	0.424	strong	.	MARCH4	50	.	NM_020814	exon2	c.G552T	p.S184S	CTTGACCGAGCCA	.	PASS	Atlas-SNP
C1orf177	163747	hgsc.bcm.edu	37	1	55280637	55280637	+	Silent	SNP	C	C	T	rs200876449	by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	139	2	201	1	0.0143885	0.00497512	C|1.000;T|0.000	0.000	strong	C1orf177,NS,carcinoma,0,1	C1orf177	36	1	NM_001110533	exon8	c.C975T	p.P325P	CAAACCCGTCAAC	.	scavenged	Atlas-SNP
HIST1H3J	8356	hgsc.bcm.edu	37	6	27858421	27858421	+	Silent	SNP	A	A	G	rs200973	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	50	31	79	0	0.62	0	A|0.839;G|0.161	0.161	strong	.	HIST1H3J	16	.	NM_003535	exon1	c.T150C	p.R50R	GATCTCACGCAAG	.	PASS	Atlas-SNP
ZNF354C	30832	hgsc.bcm.edu	37	5	178506075	178506075	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	16	62	0	0.225352	0	.	.	none	.	ZNF354C	77	.	NM_014594	exon5	c.A642T	p.K214N	AGGAAAACCTCAC	.	PASS	Atlas-SNP
KIAA1551	55196	hgsc.bcm.edu	37	12	32134064	32134064	+	Missense_Mutation	SNP	A	A	G	rs7298803	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	174	94	232	0	0.54023	0	A|0.921;G|0.079	0.079	strong	.	.	.	.	NM_018169	exon4	c.A175G	p.I59V	AATCCAATTTCAC	.	PASS	Atlas-SNP
ZNF101	94039	hgsc.bcm.edu	37	19	19790159	19790159	+	Missense_Mutation	SNP	A	A	C	rs4808209	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	29	101	0	0.408451	0	A|0.947;C|0.053	0.053	strong	.	ZNF101	43	.	NM_033204	exon4	c.A361C	p.M121L	AGGCACATGAGAG	.	PASS	Atlas-SNP
ZNF563	147837	hgsc.bcm.edu	37	19	12429509	12429509	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	46	3	72	0	0.0652174	0	.	.	none	ZNF563,colon,carcinoma,+2,1	ZNF563	77	1	NM_145276	exon4	c.A1330G	p.T444A	CTCCCGTATGCAT	.	scavenged	Atlas-SNP
ZNF417	147687	hgsc.bcm.edu	37	19	58420699	58420699	+	Missense_Mutation	SNP	C	C	A	rs71354064		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	209	112	193	0	0.535885	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
PEPD	5184	hgsc.bcm.edu	37	19	33878837	33878837	+	Missense_Mutation	SNP	G	G	A	rs17570	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	114	59	100	0	0.517544	0	G|0.706;A|0.294	0.294	strong	.	PEPD	48	.	NM_000285	exon14	c.C1303T	p.L435F	GGTTAAGGAAGGA	.	PASS	Atlas-SNP
RLN2	6019	hgsc.bcm.edu	37	9	5300255	5300255	+	Missense_Mutation	SNP	C	C	A	rs61738986	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	179	49	198	0	0.273743	0	C|0.994;A|0.006	0.006	strong	RLN2,caecum,carcinoma,-1,2	RLN2	22	2	NM_134441	exon2	c.G401T	p.R134L	CTATTGCGAATAA	.	PASS	Atlas-SNP
DSPP	1834	hgsc.bcm.edu	37	4	88535868	88535868	+	Missense_Mutation	SNP	A	A	G	rs199719429	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	94	15	133	1	0.159574	0.0075188	.	.	weak	DSPP,NS,carcinoma,-1,2	DSPP	174	2	NM_014208	exon5	c.A2054G	p.N685S	GCAGCAACAGCAG	.	scavenged	Atlas-SNP
ZNF695	57116	hgsc.bcm.edu	37	1	247162688	247162688	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	107	29	124	0	0.271028	0	.	.	none	.	ZNF695	55	.	NM_001204221	exon3	c.C221A	p.P74H	TTCCAGGGCTCTT	.	PASS	Atlas-SNP
BIN1	274	hgsc.bcm.edu	37	2	127816632	127816632	+	Silent	SNP	G	G	A	rs2276579	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	43	25	49	0	0.581395	0	G|0.886;A|0.114	0.114	strong	.	BIN1	85	.	NM_139345	exon11	c.C957T	p.A319A	CCCGCCGGCCGGC	.	PASS	Atlas-SNP
TSNARE1	203062	hgsc.bcm.edu	37	8	143436034	143436034	+	Missense_Mutation	SNP	A	A	G	rs7814359	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	76	19	85	0	0.25	0	A|0.674;G|0.326	0.326	strong	.	TSNARE1	59	.	NM_145003	exon2	c.T52C	p.F18L	CCCCGAAAGGGCC	.	PASS	Atlas-SNP
PCDHGA8	9708	hgsc.bcm.edu	37	5	140772427	140772427	+	Missense_Mutation	SNP	T	T	G	rs726684	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	38	38	62	0	1	0	T|0.847;G|0.153	0.153	strong	.	PCDHGA8	146	.	NM_014004	exon1	c.T47G	p.L16R	TCCTGCTGTGCGC	.	PASS	Atlas-SNP
IL16	3603	hgsc.bcm.edu	37	15	81578139	81578139	+	Missense_Mutation	SNP	C	C	T	rs4072111	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	147	55	135	0	0.37415	0	C|0.870;T|0.130	0.130	strong	IL16,NS,carcinoma,0,1	IL16	254	1	NM_001172128	exon10	c.C1300T	p.P434S	CCAGTCCCCATCA	.	PASS	Atlas-SNP
RGS3	5998	hgsc.bcm.edu	37	9	116346236	116346236	+	Silent	SNP	G	G	A	rs41301525	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	56	25	83	0	0.446429	0	G|0.886;A|0.114	0.114	strong	.	RGS3	251	.	NM_144488	exon21	c.G2544A	p.A848A	ACCTGCGGCCCCC	.	PASS	Atlas-SNP
PTPRD	5789	hgsc.bcm.edu	37	9	8497250	8497250	+	Missense_Mutation	SNP	T	T	C	rs72694737	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	149	65	166	0	0.436242	0	T|0.979;C|0.021	0.021	strong	.	PTPRD	1348	.	NM_002839	exon26	c.A2341G	p.T781A	GTTCAGTAGTATC	.	PASS	Atlas-SNP
IGF2BP3	10643	hgsc.bcm.edu	37	7	23357321	23357321	+	Silent	SNP	C	C	T	rs156414	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	163	34	182	0	0.208589	0	T|0.301;G|0.001;C|0.698;N|0.000	0.301	strong	IGF2BP3,NS,carcinoma,0,1	IGF2BP3	71	1	NM_006547	exon12	c.G1332A	p.A444A	TGCTTCCGCTGGA	.	PASS	Atlas-SNP
MTMR7	9108	hgsc.bcm.edu	37	8	17157677	17157677	+	Missense_Mutation	SNP	T	T	G	rs3764796	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	130	27	135	0	0.207692	0	T|0.909;G|0.091	0.091	strong	.	MTMR7	75	.	NM_004686	exon14	c.A1677C	p.Q559H	CTCACTTTGCTTA	.	PASS	Atlas-SNP
AAK1	22848	hgsc.bcm.edu	37	2	69709919	69709919	+	Silent	SNP	A	A	G	rs6721259	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	68	28	81	0	0.411765	0	A|0.862;G|0.138	0.138	strong	.	AAK1	121	.	NM_014911	exon18	c.T2391C	p.S797S	GTCAGGAGATTTG	.	PASS	Atlas-SNP
PSMB6	5694	hgsc.bcm.edu	37	17	4701402	4701402	+	Silent	SNP	C	C	T	rs7468	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	125	125	146	0	1	0	C|0.958;T|0.042	0.042	strong	.	PSMB6	20	.	NM_002798	exon5	c.C531T	p.Y177Y	TACCTACCGGGAA	.	PASS	Atlas-SNP
MEFV	4210	hgsc.bcm.edu	37	16	3297181	3297181	+	Silent	SNP	C	C	T	rs224208	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	182	24	166	0	0.131868	0	C|0.414;T|0.586	0.586	strong	.	MEFV	170	.	NM_000243	exon5	c.G1422A	p.E474E	TTGCTGCTCCAGG	.	PASS	Atlas-SNP
TRPV4	59341	hgsc.bcm.edu	37	12	110238487	110238487	+	Silent	SNP	A	A	G	rs3742034	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	99	47	103	0	0.474747	0	A|0.872;G|0.128	0.128	strong	.	TRPV4	88	.	NM_147204	exon4	c.T789C	p.D263D	GTGGACATCAGCT	.	PASS	Atlas-SNP
C10orf71	118461	hgsc.bcm.edu	37	10	50531549	50531549	+	Missense_Mutation	SNP	G	G	T	rs56206226	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	60	23	58	0	0.383333	0	G|0.803;T|0.197	0.197	strong	.	C10orf71	179	.	NM_001135196	exon3	c.G959T	p.R320L	CTGAGCGCACAGT	.	PASS	Atlas-SNP
CPO	130749	hgsc.bcm.edu	37	2	207833983	207833983	+	Silent	SNP	A	A	G	rs7582305	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	128	69	171	0	0.539062	0	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	.	PASS	Atlas-SNP
NCEH1	57552	hgsc.bcm.edu	37	3	172365832	172365832	+	Missense_Mutation	SNP	T	T	G	rs2302815	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	117	65	130	0	0.555556	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
OR8D4	338662	hgsc.bcm.edu	37	11	123777502	123777502	+	Missense_Mutation	SNP	C	C	T	rs61907183	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	54	121	0	0.739726	0	C|0.930;T|0.070	0.070	strong	OR8D4,colon,carcinoma,-1,1	OR8D4	62	1	NM_001005197	exon1	c.C364T	p.R122C	TGCGATCGCTACG	.	PASS	Atlas-SNP
HS3ST6	64711	hgsc.bcm.edu	37	16	1962046	1962046	+	Missense_Mutation	SNP	C	C	T	rs1742399	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	48	36	55	0	0.75	0	C|0.646;T|0.354	0.354	strong	.	HS3ST6	26	.	NM_001009606	exon2	c.G481A	p.A161T	TCTGGGCGTAGTC	.	PASS	Atlas-SNP
KDM2B	84678	hgsc.bcm.edu	37	12	121881848	121881848	+	Silent	SNP	G	G	A	rs10849885	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	90	49	74	0	0.544444	0	G|0.666;A|0.334	0.334	strong	KDM2B_ENST00000377071,NS,carcinoma,0,2	KDM2B	218	2	NM_032590	exon16	c.C2418T	p.Y806Y	CTTCTCGTATTTC	.	PASS	Atlas-SNP
LMF1	64788	hgsc.bcm.edu	37	16	961051	961051	+	Silent	SNP	C	C	T	rs2277893	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	64	19	73	0	0.296875	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
ARHGAP42	143872	hgsc.bcm.edu	37	11	100665888	100665888	+	Silent	SNP	G	G	A	rs61999341	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	38	12	71	0	0.315789	0	G|0.975;A|0.025	0.025	strong	.	ARHGAP42	32	.	NM_152432	exon3	c.G303A	p.R101R	AGAAAGGCGAAGA	.	PASS	Atlas-SNP
FRG1	2483	hgsc.bcm.edu	37	4	190876283	190876283	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	162	9	136	0	0.0555556	0	.	.	none	.	FRG1	76	.	NM_004477	exon5	c.C409A	p.Q137K	AGAGAACAATGGG	.	PASS	Atlas-SNP
ACAN	176	hgsc.bcm.edu	37	15	89398825	89398825	+	Silent	SNP	C	C	T	rs4080952	bycluster;byfrequency;by2hit2allele;byhapmap	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	34	13	30	0	0.382353	0	C|0.250;T|0.750	0.750	strong	.	ACAN	220	.	NM_001135	exon12	c.C3009T	p.T1003T	AGAGACCACTGCC	.	PASS	Atlas-SNP
IQUB	154865	hgsc.bcm.edu	37	7	123152035	123152035	+	Silent	SNP	T	T	C	rs10270705	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	95	39	207	0	0.410526	0	T|0.667;C|0.333	0.333	strong	IQUB,middle_lobe,carcinoma,-2,2	IQUB	117	2	NM_178827	exon2	c.A360G	p.E120E	CAAAGATTCCTTT	.	PASS	Atlas-SNP
FAM114A1	92689	hgsc.bcm.edu	37	4	38879949	38879949	+	Missense_Mutation	SNP	G	G	A	rs11096964	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	112	47	118	0	0.419643	0	G|0.755;A|0.245	0.245	strong	.	FAM114A1	42	.	NM_138389	exon3	c.G250A	p.G84R	CTCAATGGAGACG	.	PASS	Atlas-SNP
PCNT	5116	hgsc.bcm.edu	37	21	47863757	47863757	+	Missense_Mutation	SNP	A	A	C	rs2073380	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	57	19	56	0	0.333333	0	A|0.810;C|0.190	0.190	strong	.	PCNT	283	.	NM_006031	exon45	c.A9735C	p.R3245S	ACCCAGAACCAGA	.	PASS	Atlas-SNP
MYCBPAP	84073	hgsc.bcm.edu	37	17	48595988	48595988	+	Missense_Mutation	SNP	G	G	C	rs8064455	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	88	37	119	0	0.420455	0	G|0.721;C|0.279	0.279	strong	.	MYCBPAP	135	.	NM_032133	exon5	c.G684C	p.E228D	AGAAGAGAAGAGA	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228548197	228548197	+	Missense_Mutation	SNP	G	G	A	rs10158354	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	34	15	57	0	0.441176	0	G|0.847;A|0.153	0.153	strong	.	OBSCN	2142	.	NM_052843	exon81	c.G19604A	p.R6535H	AGCCCCGTGGGGC	.	PASS	Atlas-SNP
ZNF836	162962	hgsc.bcm.edu	37	19	52658318	52658318	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	132	3	132	0	0.0227273	0	.	.	none	ZNF836_ENST00000322146,colon,carcinoma,-1,4	ZNF836	158	4	NM_001102657	exon5	c.G2618A	p.R873Q	GAAAACCGCCCAA	.	scavenged	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179582824	179582824	+	Silent	SNP	C	C	T	rs72648983	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	64	38	48	0	0.59375	0	C|0.981;T|0.019	0.019	strong	.	TTN	18412	.	NM_001267550	exon86	c.G24909A	p.K8303K	TCGTAGCTTTGTG	.	PASS	Atlas-SNP
GGT6	124975	hgsc.bcm.edu	37	17	4463713	4463713	+	Missense_Mutation	SNP	A	A	G	rs62066362	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	33	13	41	0	0.393939	0	A|0.986;G|0.014	0.014	strong	.	GGT6	22	.	NM_001122890	exon1	c.T104C	p.L35P	AGAACCAGCGCCT	.	PASS	Atlas-SNP
NUP88	4927	hgsc.bcm.edu	37	17	5290033	5290033	+	Silent	SNP	T	T	C	rs1071705	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	175	71	194	0	0.405714	0	T|0.566;C|0.434	0.434	strong	.	NUP88	47	.	NM_002532	exon16	c.A2157G	p.K719K	CTCCTCTTTCAGG	.	PASS	Atlas-SNP
MRPS5	64969	hgsc.bcm.edu	37	2	95775761	95775761	+	Silent	SNP	G	G	A	rs113259652	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	311	149	334	1	0.4791	0.00299401	G|0.968;A|0.032	0.032	strong	.	MRPS5	52	.	NM_031902	exon4	c.C303T	p.G101G	TAAAGCGCCTTTC	.	PASS	Atlas-SNP
KRTAP13-1	140258	hgsc.bcm.edu	37	21	31768539	31768539	+	Silent	SNP	G	G	C	rs9636833	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	107	42	122	0	0.392523	0	G|0.862;C|0.138	0.138	strong	.	KRTAP13-1	48	.	NM_181599	exon1	c.G135C	p.T45T	CAGCACGTGCCAG	.	PASS	Atlas-SNP
SYT15	83849	hgsc.bcm.edu	37	10	46968665	46968665	+	Silent	SNP	G	G	A	rs200814731	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	42	9	38	0	0.214286	0	G|0.911;A|0.089	0.089	strong	SYT15_ENST00000416127,colon,carcinoma,0,15	SYT15	165	15	NM_031912	exon3	c.C271T	p.L91L	TGTGCAGGGGCAC	.	PASS	Atlas-SNP
SLC25A15	10166	hgsc.bcm.edu	37	13	41373254	41373254	+	Silent	SNP	G	G	A	rs55943532	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	160	85	159	0	0.53125	0	G|0.923;A|0.077	0.077	strong	.	SLC25A15	30	.	NM_014252	exon3	c.G117A	p.T39T	GCAGACGTTCCCT	.	PASS	Atlas-SNP
REM1	28954	hgsc.bcm.edu	37	20	30064331	30064331	+	Missense_Mutation	SNP	A	A	G	rs1006459	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	95	46	114	0	0.484211	0	A|0.536;C|0.000;G|0.464	0.464	strong	REM1,right_upper_lobe,carcinoma,+1,1	REM1	54	1	NM_014012	exon2	c.A83G	p.H28R	GGGGCCACCAGCC	.	PASS	Atlas-SNP
LILRB1	10859	hgsc.bcm.edu	37	19	55142739	55142739	+	Silent	SNP	A	A	C	rs1985501	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	81	81	94	0	1	0	A|0.588;C|0.412	0.412	strong	.	LILRB1	140	.	NM_001081637	exon3	c.A52C	p.R18R	GGCCCCAGGACCC	.	PASS	Atlas-SNP
PCDHB8	56128	hgsc.bcm.edu	37	5	140559350	140559350	+	Missense_Mutation	SNP	C	C	T	rs17844499		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	15	7	5	0	0.466667	0	.	.	weak	PCDHB8,NS,carcinoma,-1,1	PCDHB8	199	1	NM_019120	exon1	c.C1735T	p.R579W	GTGCCCCGGGCGG	.	scavenged	Atlas-SNP
LMO7	4008	hgsc.bcm.edu	37	13	76423248	76423248	+	Missense_Mutation	SNP	T	T	C	rs7986131	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	31	75	0	0.534483	0	T|0.300;C|0.700	0.700	strong	LMO7_ENST00000465261,colon,carcinoma,0,3	LMO7	334	3	NM_015842	exon24	c.T3485C	p.M1162T	GGAACATGACCTC	.	PASS	Atlas-SNP
PZP	5858	hgsc.bcm.edu	37	12	9312951	9312951	+	Missense_Mutation	SNP	G	G	A	rs57006764	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	148	147	125	1	0.993243	0.008	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
TSC22D1	8848	hgsc.bcm.edu	37	13	45148708	45148708	+	Silent	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	142	6	143	2	0.0422535	0.013986	.	.	none	TSC22D1,NS,carcinoma,0,4	TSC22D1	88	4	NM_183422	exon1	c.G1503A	p.Q501Q	TTGTTGCTGCTGC	.	scavenged	Atlas-SNP
WFDC10B	280664	hgsc.bcm.edu	37	20	44314609	44314609	+	Missense_Mutation	SNP	A	A	G	rs232729	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	141	140	168	0	0.992908	0	A|0.257;G|0.743	0.743	strong	.	WFDC10B	15	.	NM_172006	exon3	c.T23C	p.L8P	AGGACAAGCAGCA	.	PASS	Atlas-SNP
PCDHB7	56129	hgsc.bcm.edu	37	5	140553917	140553917	+	Missense_Mutation	SNP	G	G	A	rs17844455	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	103	51	145	0	0.495146	0	G|0.825;A|0.175	0.175	strong	.	PCDHB7	231	.	NM_018940	exon1	c.G1501A	p.A501T	CCCCTCGCCTCCC	.	PASS	Atlas-SNP
TACC3	10460	hgsc.bcm.edu	37	4	1730215	1730215	+	Silent	SNP	C	C	G	rs798757	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	121	71	140	0	0.586777	0	C|0.830;G|0.170	0.170	strong	.	TACC3	69	.	NM_006342	exon4	c.C1086G	p.G362G	GTCCGGCCTCAAG	.	PASS	Atlas-SNP
ZNF560	147741	hgsc.bcm.edu	37	19	9580305	9580305	+	Splice_Site	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	89	4	80	0	0.0449438	0	.	.	none	.	ZNF560	162	.	NM_152476	exon9	c.529+1G>A	.	CACTCACCTTGGA	.	PASS	Atlas-SNP
BHLHE40	8553	hgsc.bcm.edu	37	3	5024771	5024771	+	Silent	SNP	T	T	C	rs908078	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	64	38	71	0	0.59375	0	T|0.855;C|0.145	0.145	strong	.	BHLHE40	35	.	NM_003670	exon5	c.T633C	p.G211G	CAAAGGTTCGGAA	.	PASS	Atlas-SNP
IPO4	79711	hgsc.bcm.edu	37	14	24653954	24653954	+	Missense_Mutation	SNP	G	G	A	rs7146310	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	224	109	190	0	0.486607	0	G|0.693;A|0.307	0.307	strong	IPO4,NS,carcinoma,+1,1	IPO4	74	1	NM_024658	exon16	c.C1538T	p.A513V	AGCGAGGCCTGGG	.	PASS	Atlas-SNP
ENGASE	64772	hgsc.bcm.edu	37	17	77076302	77076302	+	Silent	SNP	G	G	A	rs62063824	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	40	19	47	0	0.475	0	G|0.941;A|0.059	0.059	strong	.	ENGASE	55	.	NM_001042573	exon5	c.G579A	p.T193T	CATCACGGAGTGG	.	PASS	Atlas-SNP
KCNQ2	3785	hgsc.bcm.edu	37	20	62046278	62046278	+	Silent	SNP	G	G	C	rs1801545	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	122	59	113	0	0.483607	0	G|0.911;C|0.089;A|0.000	0.089	strong	.	KCNQ2	201	.	NM_172107	exon13	c.C1503G	p.A501A	TGACGCGGCACCC	.	PASS	Atlas-SNP
TEP1	7011	hgsc.bcm.edu	37	14	20850156	20850156	+	Missense_Mutation	SNP	C	C	G	rs1713457	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	96	46	102	0	0.479167	0	C|0.928;G|0.072	0.072	strong	.	TEP1	224	.	NM_007110	exon30	c.G4340C	p.S1447T	TCCCAGCTCTTAG	.	PASS	Atlas-SNP
OTOL1	131149	hgsc.bcm.edu	37	3	161221705	161221705	+	Missense_Mutation	SNP	A	A	C	rs3921595	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	91	38	108	0	0.417582	0	A|0.541;C|0.459	0.459	strong	.	OTOL1	63	.	NM_001080440	exon4	c.A1409C	p.E470A	ACCCAGAGGAAAC	.	PASS	Atlas-SNP
MYH7B	57644	hgsc.bcm.edu	37	20	33587596	33587596	+	Silent	SNP	G	G	A	rs80109502	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	24	43	0	0.413793	0	G|0.921;A|0.079	0.079	strong	.	MYH7B	145	.	NM_020884	exon38	c.G4794A	p.G1598G	ACAGGGGGCCCTG	.	PASS	Atlas-SNP
SLC38A7	55238	hgsc.bcm.edu	37	16	58713798	58713798	+	Missense_Mutation	SNP	G	G	A	rs7191331	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	63	25	49	0	0.396825	0	G|0.855;A|0.145	0.145	strong	SLC38A7,NS,carcinoma,0,1	SLC38A7	26	1	NM_018231	exon3	c.C233T	p.T78I	CCCGCAGTGCTGA	.	PASS	Atlas-SNP
ARHGAP35	2909	hgsc.bcm.edu	37	19	47424071	47424071	+	Silent	SNP	T	T	C	rs2228163	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	136	65	148	0	0.477941	0	T|0.985;C|0.015	0.015	strong	.	.	.	.	NM_004491	exon1	c.T2139C	p.T713T	AGAGACTCTGCAT	.	PASS	Atlas-SNP
CD207	50489	hgsc.bcm.edu	37	2	71060936	71060936	+	Missense_Mutation	SNP	G	G	C	rs17718987	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	155	155	192	0	1	0	G|0.841;C|0.159	0.159	strong	.	CD207	47	.	NM_015717	exon3	c.C406G	p.Q136E	GGATCTGTGCGTT	.	PASS	Atlas-SNP
CHGB	1114	hgsc.bcm.edu	37	20	5903323	5903323	+	Missense_Mutation	SNP	G	G	A	rs910122	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	65	34	95	0	0.523077	0	G|0.631;A|0.369	0.369	strong	CHGB,colon,carcinoma,+1,1	CHGB	112	1	NM_001819	exon4	c.G533A	p.R178Q	GGGAGCGAGGGGA	.	PASS	Atlas-SNP
SOGA2	23255	hgsc.bcm.edu	37	18	8784723	8784723	+	Missense_Mutation	SNP	A	A	G	rs3744979	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	60	30	63	0	0.5	0	A|0.838;G|0.162	0.162	strong	.	.	.	.	NM_015210	exon6	c.A1613G	p.D538G	TTGGGGATGGCCT	.	PASS	Atlas-SNP
KRT86	3892	hgsc.bcm.edu	37	12	52695754	52695754	+	Silent	SNP	C	C	T	rs74651927	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	66	37	39	0	0.560606	0	C|0.871;T|0.129	0.129	strong	.	KRT86	33	.	NM_002284	exon1	c.C54T	p.C18C	GGCCTGCGGGCCC	.	PASS	Atlas-SNP
ASIC4	55515	hgsc.bcm.edu	37	2	220402680	220402680	+	Missense_Mutation	SNP	T	T	C	rs11695248	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	66	40	62	0	0.606061	0	T|0.438;C|0.562	0.562	strong	.	.	.	.	NM_182847	exon9	c.T1856C	p.V619A	GCCGAGTGGAGGG	.	PASS	Atlas-SNP
FRYL	285527	hgsc.bcm.edu	37	4	48588742	48588742	+	Silent	SNP	C	C	T	rs34558821	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	51	21	68	0	0.411765	0	C|0.516;T|0.484	0.484	strong	.	FRYL	242	.	NM_015030	exon19	c.G1644A	p.G548G	TCTTTCCCCCCTG	.	PASS	Atlas-SNP
TMC3	342125	hgsc.bcm.edu	37	15	81625552	81625552	+	Silent	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	222	3	169	0	0.0135135	0	.	.	none	TMC3,NS,carcinoma,0,1	TMC3	112	1	NM_001080532	exon22	c.G2511A	p.S837S	TGTGCGCGATCTG	.	scavenged	Atlas-SNP
TCF20	6942	hgsc.bcm.edu	37	22	42606257	42606257	+	Silent	SNP	C	C	T	rs2070116	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	139	138	155	1	0.992806	0.00645161	C|0.788;T|0.212	0.212	strong	.	TCF20	164	.	NM_181492	exon1	c.G5055A	p.S1685S	AAAGGACGAGGCC	.	PASS	Atlas-SNP
WNK2	65268	hgsc.bcm.edu	37	9	96024182	96024182	+	Silent	SNP	G	G	C	rs12000967	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	76	36	52	0	0.473684	0	G|0.836;C|0.164	0.164	strong	.	WNK2	277	.	NM_006648	exon12	c.G3153C	p.S1051S	CCTCTCGCCGCCT	.	PASS	Atlas-SNP
PRHOXNB	646625	hgsc.bcm.edu	37	13	28562605	28562605	+	Missense_Mutation	SNP	T	T	G	rs3897926	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	74	40	83	0	0.540541	0	T|0.723;G|0.277	0.277	strong	PRHOXNB,NS,carcinoma,0,1	PRHOXNB	6	1	NM_001105577	exon1	c.A170C	p.Q57P	CCTGACTGTGCAA	.	PASS	Atlas-SNP
DYNC2LI1	51626	hgsc.bcm.edu	37	2	44004010	44004010	+	Missense_Mutation	SNP	T	T	C	rs2288709	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	357	357	197	0	1	0	T|0.516;C|0.483	0.483	strong	.	DYNC2LI1	46	.	NM_016008	exon2	c.T98C	p.F33S	AAAAATTTGTTTT	.	PASS	Atlas-SNP
GLTSCR2	29997	hgsc.bcm.edu	37	19	48248834	48248834	+	Silent	SNP	T	T	C	rs10404034	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	80	38	121	0	0.475	0	A|0.000;C|0.097;T|0.903	0.097	strong	.	GLTSCR2	45	.	NM_015710	exon1	c.T18C	p.S6S	AGGCAGTGGCGTT	.	PASS	Atlas-SNP
RNMTL1	55178	hgsc.bcm.edu	37	17	694847	694847	+	Silent	SNP	T	T	C	rs34081574	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	178	88	207	0	0.494382	0	T|0.992;C|0.008	0.008	strong	.	RNMTL1	25	.	NM_018146	exon4	c.T801C	p.N267N	TATCAATAATCTG	.	PASS	Atlas-SNP
PSMB9	5698	hgsc.bcm.edu	37	6	32825090	32825090	+	Missense_Mutation	SNP	G	G	A	rs17587	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	41	21	34	0	0.512195	0	G|0.760;A|0.240	0.240	strong	.	PSMB9	16	.	NM_002800	exon3	c.G179A	p.R60H	ACGAGCGCATCTA	.	PASS	Atlas-SNP
UBE3B	89910	hgsc.bcm.edu	37	12	109937534	109937534	+	Missense_Mutation	SNP	G	G	A	rs7298565	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	133	57	131	0	0.428571	0	G|0.446;A|0.554	0.554	strong	.	UBE3B	116	.	NM_130466	exon12	c.G1037A	p.R346Q	ACTGTCGGAAGTA	.	PASS	Atlas-SNP
LY9	4063	hgsc.bcm.edu	37	1	160793560	160793560	+	Missense_Mutation	SNP	A	A	G	rs509749	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	133	68	138	0	0.511278	0	A|0.404;G|0.596	0.596	strong	.	LY9	115	.	NM_002348	exon8	c.A1804G	p.M602V	AACACCATGTATG	.	PASS	Atlas-SNP
DAAM2	23500	hgsc.bcm.edu	37	6	39865047	39865047	+	Silent	SNP	T	T	C	rs3004067	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	123	64	152	0	0.520325	0	T|0.269;C|0.731	0.731	strong	.	DAAM2	101	.	NM_015345	exon21	c.T2607C	p.A869A	AGAAGCTGCCAAA	.	PASS	Atlas-SNP
HPSE	10855	hgsc.bcm.edu	37	4	84222157	84222157	+	Missense_Mutation	SNP	A	A	C	rs145560091	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	133	56	120	0	0.421053	0	A|0.999;C|0.001	0.001	strong	.	HPSE	55	.	NM_001098540	exon11	c.T1428G	p.D476E	GTATTTATCCACT	.	PASS	Atlas-SNP
PIEZO2	63895	hgsc.bcm.edu	37	18	10681711	10681711	+	Missense_Mutation	SNP	C	C	T	rs3748428	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	121	67	123	0	0.553719	0	C|0.882;T|0.118	0.118	strong	.	.	.	.	NM_022068	exon47	c.G7387A	p.V2463I	CCATAACTTTCAA	.	PASS	Atlas-SNP
LIG4	3981	hgsc.bcm.edu	37	13	108861913	108861913	+	Silent	SNP	A	A	G	rs1805386	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	112	112	168	0	1	0	A|0.870;G|0.130	0.130	strong	.	LIG4	91	.	NM_206937	exon3	c.T1704C	p.D568D	ATACATATCACTG	.	PASS	Atlas-SNP
ADPGK	83440	hgsc.bcm.edu	37	15	73044863	73044863	+	Missense_Mutation	SNP	G	G	A	rs34149613	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	177	87	171	0	0.491525	0	G|0.922;A|0.078	0.078	strong	.	ADPGK	19	.	NM_031284	exon7	c.C1310T	p.S437L	GCCTCCGAATGGG	.	PASS	Atlas-SNP
MYOZ1	58529	hgsc.bcm.edu	37	10	75394457	75394457	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	80	29	101	0	0.3625	0	.	.	none	.	MYOZ1	24	.	NM_021245	exon4	c.G287T	p.G96V	AGCTGTCCCCCCA	.	PASS	Atlas-SNP
OR2D3	120775	hgsc.bcm.edu	37	11	6942726	6942726	+	Missense_Mutation	SNP	G	G	C	rs10839659	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	342	67	322	0	0.195906	0	G|0.707;C|0.292	0.292	strong	.	OR2D3	51	.	NM_001004684	exon1	c.G494C	p.W165S	GGTCCTGGGCCAG	.	PASS	Atlas-SNP
RANBP2	5903	hgsc.bcm.edu	37	2	109368085	109368085	+	Silent	SNP	G	G	A	rs71306414	alternate_allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	162	5	181	0	0.0308642	0	ATGTAAACA|0.500;GTGTAAACG|0.500	.	alt	RANBP2_ENST00000283195,NS,carcinoma,0,2	RANBP2	488	2	NM_006267	exon11	c.G1557A	p.V519V	TCCTGTGTGTAAA	.	scavenged	Atlas-SNP
MATN2	4147	hgsc.bcm.edu	37	8	99033441	99033441	+	Missense_Mutation	SNP	G	G	A	rs61729731	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	112	85	152	1	0.758929	0.00657895	G|0.993;A|0.007	0.007	strong	.	MATN2	165	.	NM_002380	exon13	c.G1828A	p.V610I	AAGGATGTCTGCA	.	PASS	Atlas-SNP
MTTP	4547	hgsc.bcm.edu	37	4	100518224	100518224	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	33	11	35	0	0.333333	0	.	.	none	.	MTTP	127	.	NM_000253	exon9	c.C910T	p.L304F	TTGCAGCTCTCGG	.	PASS	Atlas-SNP
C10orf71	118461	hgsc.bcm.edu	37	10	50531972	50531972	+	Missense_Mutation	SNP	A	A	C	rs45554335	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	54	25	81	0	0.462963	0	A|0.802;C|0.198	0.198	strong	.	C10orf71	179	.	NM_001135196	exon3	c.A1382C	p.D461A	CAGCAGACAGCCA	.	PASS	Atlas-SNP
DROSHA	29102	hgsc.bcm.edu	37	5	31515657	31515657	+	Missense_Mutation	SNP	G	G	A	rs55656741	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	114	40	108	0	0.350877	0	G|0.675;A|0.325	0.325	strong	.	DROSHA	130	.	NM_013235	exon6	c.C962T	p.S321L	ACAACCGATAAAC	.	PASS	Atlas-SNP
CHD8	57680	hgsc.bcm.edu	37	14	21868678	21868678	+	Silent	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	54	15	70	0	0.277778	0	.	.	none	.	CHD8	339	.	NM_001170629	exon22	c.G4464A	p.V1488V	ACAGTACACGAGA	.	PASS	Atlas-SNP
LARP4	113251	hgsc.bcm.edu	37	12	50821551	50821551	+	Missense_Mutation	SNP	G	G	T	rs146142861	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	59	32	62	0	0.542373	0	G|0.983;T|0.017	0.017	strong	.	LARP4	58	.	NM_001170808	exon2	c.G25T	p.A9S	CAGGTAGCATCTA	.	PASS	Atlas-SNP
HERC4	26091	hgsc.bcm.edu	37	10	69695974	69695974	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	62	15	68	0	0.241935	0	.	.	none	.	HERC4	78	.	NM_022079	exon23	c.G2614A	p.G872S	TTGCACCAAAGTT	.	PASS	Atlas-SNP
LRGUK	136332	hgsc.bcm.edu	37	7	133906669	133906669	+	Missense_Mutation	SNP	C	C	T	rs35149449	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	30	17	48	0	0.566667	0	C|0.904;T|0.096	0.096	strong	.	LRGUK	113	.	NM_144648	exon16	c.C1982T	p.A661V	CACCAGCGGTAAG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195506555	195506555	+	Missense_Mutation	SNP	C	C	T	rs368695884		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	33	11	76	3	0.333333	0.0394737	.	.	weak	MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	NM_018406	exon2	c.G11896A	p.A3966T	AGGTGGCGTGACC	.	scavenged	Atlas-SNP
ZNF598	90850	hgsc.bcm.edu	37	16	2050192	2050192	+	Missense_Mutation	SNP	G	G	T	rs11556528	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	24	15	19	0	0.625	0	G|0.889;T|0.111	0.111	strong	.	ZNF598	55	.	NM_178167	exon11	c.C1358A	p.S453Y	GAGGAGGAAGTGG	.	PASS	Atlas-SNP
ZKSCAN2	342357	hgsc.bcm.edu	37	16	25258035	25258035	+	Silent	SNP	A	A	G	rs11649280	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	244	97	277	0	0.397541	0	A|0.696;G|0.304	0.304	strong	.	ZKSCAN2	90	.	NM_001012981	exon5	c.T1482C	p.N494N	ACTGAGATTCTGA	.	PASS	Atlas-SNP
TLR10	81793	hgsc.bcm.edu	37	4	38776303	38776303	+	Silent	SNP	T	T	C	rs11466652	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	159	78	166	0	0.490566	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
PM20D1	148811	hgsc.bcm.edu	37	1	205801872	205801872	+	Missense_Mutation	SNP	A	A	G	rs1361754	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	119	66	146	0	0.554622	0	A|0.603;G|0.397	0.397	strong	.	PM20D1	56	.	NM_152491	exon11	c.T1139C	p.I380T	GCCACAATGTTCT	.	PASS	Atlas-SNP
PCDHB15	56121	hgsc.bcm.edu	37	5	140626855	140626855	+	Missense_Mutation	SNP	C	C	T	rs56840646	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	11	5	3	0	0.454545	0	C|0.881;T|0.119	0.119	strong	PCDHB15,colon,carcinoma,-1,1	PCDHB15	138	1	NM_018935	exon1	c.C1709T	p.A570V	GCTCCGCGCCCTG	.	scavenged	Atlas-SNP
NTRK1	4914	hgsc.bcm.edu	37	1	156848918	156848918	+	Missense_Mutation	SNP	C	C	T	rs6336	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	143	59	143	0	0.412587	0	C|0.965;T|0.035	0.035	strong	.	NTRK1	287	.	NM_002529	exon15	c.C1810T	p.H604Y	AGATCCCATGGAC	.	PASS	Atlas-SNP
KIF1B	23095	hgsc.bcm.edu	37	1	10318652	10318652	+	Silent	SNP	C	C	G	rs12402052	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	39	83	1	0.52	0.0120482	C|0.760;G|0.240	0.240	strong	KIF1B_ENST00000377093,NS,carcinoma,0,2	KIF1B	242	2	NM_183416	exon4	c.C285G	p.A95A	TTTTGCCTATGGG	.	scavenged	Atlas-SNP
CYP7B1	9420	hgsc.bcm.edu	37	8	65527669	65527669	+	Missense_Mutation	SNP	C	C	T	rs59035258	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	190	139	242	0	0.731579	0	C|0.976;T|0.024	0.024	strong	CYP7B1,caecum,carcinoma,-1,3	CYP7B1	94	3	NM_004820	exon4	c.G971A	p.R324H	AGCAAACGGTCAA	.	PASS	Atlas-SNP
FAM46C	54855	hgsc.bcm.edu	37	1	118166096	118166096	+	Silent	SNP	C	C	T	rs2884587	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	227	104	240	0	0.45815	0	C|0.874;T|0.126	0.126	strong	.	FAM46C	25	.	NM_017709	exon2	c.C606T	p.I202I	TCCCATCTCTGAG	.	PASS	Atlas-SNP
GOLGA6C	653641	hgsc.bcm.edu	37	15	75562495	75562495	+	Silent	SNP	G	G	T	rs2636845		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	9	79	5	0.128571	0.0632911	.	.	weak	GOLGA6C_ENST00000300576,bladder,carcinoma,0,3	GOLGA6C	12	3	NM_001164404	exon18	c.G2037T	p.P679P	CCCCCCGGTACAG	.	scavenged	Atlas-SNP
MYH6	4624	hgsc.bcm.edu	37	14	23859610	23859610	+	Missense_Mutation	SNP	C	C	T	rs61741930	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	102	38	113	0	0.372549	0	C|0.931;T|0.069	0.069	strong	.	MYH6	274	.	NM_002471	exon26	c.G3388A	p.A1130T	CCCTGGCGGTGCG	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	47	86	1	0.652778	0.0116279	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
BOD1L1	259282	hgsc.bcm.edu	37	4	13601337	13601337	+	Missense_Mutation	SNP	G	G	A	rs3733557	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	33	89	1	0.471429	0.011236	G|0.894;A|0.106	0.106	strong	BOD1L,NS,carcinoma,0,1	.	.	1	NM_148894	exon10	c.C7187T	p.P2396L	GGACCCGGTTCTT	.	scavenged	Atlas-SNP
SSC5D	284297	hgsc.bcm.edu	37	19	56029188	56029188	+	Missense_Mutation	SNP	C	C	G	rs77400028	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	162	78	188	0	0.481481	0	C|0.838;G|0.162	0.162	strong	.	SSC5D	65	.	NM_001144950	exon14	c.C3545G	p.T1182S	ACCCCACCACGAC	.	PASS	Atlas-SNP
FAM214A	56204	hgsc.bcm.edu	37	15	52901283	52901283	+	Missense_Mutation	SNP	T	T	C	rs61731670	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	83	50	78	0	0.60241	0	T|0.697;C|0.303	0.303	strong	.	.	.	.	NM_019600	exon6	c.A1828G	p.T610A	AGGAAGTTGATAA	.	PASS	Atlas-SNP
UNC13D	201294	hgsc.bcm.edu	37	17	73824121	73824121	+	Silent	SNP	T	T	C	rs7210574	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	223	110	205	1	0.493274	0.00487805	T|0.444;C|0.556	0.556	strong	.	UNC13D	68	.	NM_199242	exon32	c.A3198G	p.E1066E	CTGGGCTTCTCGG	.	PASS	Atlas-SNP
CDHR4	389118	hgsc.bcm.edu	37	3	49832788	49832788	+	Missense_Mutation	SNP	G	G	A	rs73079003	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	83	30	121	0	0.361446	0	G|0.944;A|0.056	0.056	strong	CDHR4,NS,carcinoma,+1,1	CDHR4	37	1	NM_001007540	exon8	c.C872T	p.T291M	AGGGGCGTGGTGG	.	PASS	Atlas-SNP
KRTAP5-5	439915	hgsc.bcm.edu	37	11	1651555	1651555	+	Missense_Mutation	SNP	C	C	A	rs147101544	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	88	70	65	0	0.795455	0	C|0.928;A|0.072	0.072	strong	.	KRTAP5-5	86	.	NM_001001480	exon1	c.C485A	p.P162H	GCAAGCCCTGCTG	.	PASS	Atlas-SNP
PABPC4L	132430	hgsc.bcm.edu	37	4	135121066	135121066	+	Missense_Mutation	SNP	T	T	G	rs11099273	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	52	52	71	0	1	0	T|0.365;G|0.635	0.635	strong	.	PABPC4L	60	.	NM_001114734	exon2	c.A1283C	p.H428P	TCCTAGTGTCTCT	.	PASS	Atlas-SNP
GAS7	8522	hgsc.bcm.edu	37	17	9846521	9846521	+	Silent	SNP	G	G	C	rs17339499	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	46	76	0	0.534884	0	G|0.811;C|0.189	0.189	strong	.	GAS7	113	.	NM_201433	exon7	c.C648G	p.T216T	AGCCACGGTGCCG	.	PASS	Atlas-SNP
DST	667	hgsc.bcm.edu	37	6	56420158	56420158	+	Missense_Mutation	SNP	C	C	T	rs62621210	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	145	72	149	0	0.496552	0	C|0.959;T|0.041	0.041	strong	.	DST	1427	.	NM_015548	exon41	c.G7252A	p.V2418I	GTTCAACATCCTT	.	PASS	Atlas-SNP
SENP5	205564	hgsc.bcm.edu	37	3	196612959	196612959	+	Missense_Mutation	SNP	C	C	T	rs151102982	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	55	21	69	0	0.381818	0	C|0.993;T|0.007	0.007	strong	.	SENP5	68	.	NM_152699	exon2	c.C907T	p.H303Y	TGTCGGCATCAGC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195506303	195506303	+	Missense_Mutation	SNP	G	G	T	rs192584273	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	136	102	160	0	0.75	0	G|0.925;T|0.075	0.075	strong	MUC4_ENST00000463781,NS,carcinoma,0,4	MUC4	1505	4	NM_018406	exon2	c.C12148A	p.P4050T	TGACAGGAAGAGG	.	PASS	Atlas-SNP
KCNJ15	3772	hgsc.bcm.edu	37	21	39671476	39671476	+	Nonsense_Mutation	SNP	G	G	A	rs2230033	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	161	160	153	1	0.993789	0.00653595	G|0.642;A|0.358	0.358	strong	KCNJ15,colon,carcinoma,+1,1	KCNJ15	43	1	NM_170736	exon3	c.T293A	p.L98X	AACCCGGTGAGCC	.	PASS	Atlas-SNP
CRIPAK	285464	hgsc.bcm.edu	37	4	1389037	1389037	+	Missense_Mutation	SNP	G	G	A	rs76723438	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	55	23	79	0	0.418182	0	G|0.885;A|0.115	0.115	strong	.	CRIPAK	185	.	NM_175918	exon1	c.G738A	p.M246I	GCCCATGTGGAGT	.	PASS	Atlas-SNP
KRT32	3882	hgsc.bcm.edu	37	17	39620565	39620565	+	Missense_Mutation	SNP	C	C	T	rs72830046	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	127	64	121	0	0.503937	0	C|0.783;T|0.217	0.217	strong	.	KRT32	57	.	NM_002278	exon4	c.G839A	p.R280H	TCCCTGCGGTTGG	.	PASS	Atlas-SNP
FCHO2	115548	hgsc.bcm.edu	37	5	72351905	72351905	+	Silent	SNP	A	A	G	rs57213367	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	210	136	224	0	0.647619	0	A|0.828;G|0.172	0.172	strong	.	FCHO2	96	.	NM_138782	exon16	c.A1224G	p.T408T	GTTAACAAAATCA	.	PASS	Atlas-SNP
FCN2	2220	hgsc.bcm.edu	37	9	137779026	137779026	+	Missense_Mutation	SNP	C	C	T	rs17549193	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	109	109	158	0	1	0	C|0.716;T|0.284	0.284	strong	.	FCN2	55	.	NM_004108	exon8	c.C707T	p.T236M	CCCTGACGTTCCA	.	PASS	Atlas-SNP
USP17L7	392197	hgsc.bcm.edu	37	8	11990256	11990256	+	Silent	SNP	G	G	A	rs191378034	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	22	15	25	0	0.681818	0	G|0.968;A|0.032	0.032	strong	.	.	.	.	NM_001256869	exon1	c.C1263T	p.D421D	GTGCTCGTCCAAC	.	PASS	Atlas-SNP
NHSL1	57224	hgsc.bcm.edu	37	6	138745299	138745299	+	Silent	SNP	G	G	A	rs9495082	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	15	7	23	0	0.466667	0	G|0.893;A|0.107	0.107	strong	.	NHSL1	99	.	NM_020464	exon7	c.C4752T	p.P1584P	AGGGCCGGGGGCC	.	PASS	Atlas-SNP
TRPV4	59341	hgsc.bcm.edu	37	12	110252547	110252547	+	Missense_Mutation	SNP	G	G	A	rs3742030	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	30	13	22	0	0.433333	0	G|0.957;A|0.043	0.043	strong	.	TRPV4	88	.	NM_001177433	exon1	c.C55T	p.P19S	CCCCGGGGAGCTC	.	PASS	Atlas-SNP
LNPEP	4012	hgsc.bcm.edu	37	5	96350710	96350710	+	Missense_Mutation	SNP	G	G	A	rs2303138	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	139	76	118	0	0.546763	0	G|0.880;A|0.120	0.120	strong	.	LNPEP	80	.	NM_005575	exon13	c.G2287A	p.A763T	CATACTGCACCCA	.	PASS	Atlas-SNP
MAP2K2	5605	hgsc.bcm.edu	37	19	4117483	4117483	+	Silent	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	89	38	79	0	0.426966	0	.	.	none	.	MAP2K2	72	.	NM_030662	exon2	c.C237T	p.G79G	GCCCGCGCCCAGC	.	PASS	Atlas-SNP
TCEB3B	51224	hgsc.bcm.edu	37	18	44561100	44561100	+	Missense_Mutation	SNP	C	C	G	rs2571028	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	28	18	31	0	0.642857	0	C|0.467;G|0.533	0.533	strong	.	TCEB3B	141	.	NM_016427	exon1	c.G536C	p.R179P	GGCATCCGGAGGG	.	PASS	Atlas-SNP
PTPRN2	5799	hgsc.bcm.edu	37	7	157931144	157931144	+	Missense_Mutation	SNP	C	C	T	rs1130499	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	74	108	1	0.986667	0.00925926	C|0.623;T|0.377	0.377	strong	.	PTPRN2	243	.	NM_130843	exon7	c.G974A	p.S325N	AGGCCACTCAGGC	.	PASS	Atlas-SNP
TRIM65	201292	hgsc.bcm.edu	37	17	73888423	73888423	+	Silent	SNP	A	A	G	rs7222755	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	47	19	58	0	0.404255	0	A|0.591;G|0.409	0.409	strong	.	TRIM65	23	.	NM_001256124	exon3	c.T669C	p.H223H	CTCCAAATGGACC	.	PASS	Atlas-SNP
PKHD1L1	93035	hgsc.bcm.edu	37	8	110437384	110437384	+	Missense_Mutation	SNP	A	A	G	rs4735133	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	200	163	205	0	0.815	0	A|0.427;G|0.573	0.573	strong	PKHD1L1,NS,carcinoma,+1,1	PKHD1L1	522	1	NM_177531	exon24	c.A2768G	p.H923R	AAATTCATATTCA	.	PASS	Atlas-SNP
PLXNB2	23654	hgsc.bcm.edu	37	22	50726134	50726134	+	Missense_Mutation	SNP	C	C	T	rs375580670		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	37	11	21	0	0.297297	0	.	.	weak	.	PLXNB2	172	.	NM_012401	exon7	c.G1570A	p.A524T	GCTGGGCGCTGGT	.	PASS	Atlas-SNP
ADAM21	8747	hgsc.bcm.edu	37	14	70924697	70924697	+	Missense_Mutation	SNP	A	A	G	rs45545935	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	67	16	90	0	0.238806	0	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
KRT84	3890	hgsc.bcm.edu	37	12	52774158	52774158	+	Silent	SNP	G	G	A	rs951772	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	48	24	67	0	0.5	0	G|0.688;A|0.312	0.312	strong	.	KRT84	61	.	NM_033045	exon7	c.C1413T	p.G471G	CTCCTCGCCCTCC	.	PASS	Atlas-SNP
ARAP3	64411	hgsc.bcm.edu	37	5	141059868	141059868	+	Silent	SNP	T	T	C	rs11167756	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	190	96	216	1	0.505263	0.00462963	T|0.567;C|0.433	0.433	strong	.	ARAP3	139	.	NM_022481	exon2	c.A186G	p.L62L	TGTCTGTAGCAGG	.	PASS	Atlas-SNP
TMIGD2	126259	hgsc.bcm.edu	37	19	4294623	4294623	+	Missense_Mutation	SNP	C	C	A	rs58237134	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	65	31	63	0	0.476923	0	C|0.806;A|0.194	0.194	strong	.	TMIGD2	38	.	NM_144615	exon4	c.G503T	p.W168L	GCACCCCACACGA	.	PASS	Atlas-SNP
MYO3B	140469	hgsc.bcm.edu	37	2	171240249	171240249	+	Silent	SNP	C	C	T	rs11675394	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	94	57	118	0	0.606383	0	C|0.732;T|0.268	0.268	strong	MYO3B_ENST00000408978,rectum,carcinoma,0,6	MYO3B	320	6	NM_001083615	exon12	c.C1215T	p.R405R	GAAACGCGCCTCC	.	PASS	Atlas-SNP
FBXO2	26232	hgsc.bcm.edu	37	1	11710561	11710561	+	Missense_Mutation	SNP	T	T	G	rs9614	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	60	33	98	0	0.55	0	T|0.788;G|0.212	0.212	strong	.	FBXO2	25	.	NM_012168	exon2	c.A353C	p.K118T	CGCCGCTTGCTCA	.	PASS	Atlas-SNP
CDK5RAP2	55755	hgsc.bcm.edu	37	9	123220829	123220829	+	Silent	SNP	A	A	G	rs2501727	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	216	111	211	0	0.513889	0	A|0.802;G|0.198	0.198	strong	.	CDK5RAP2	157	.	NM_018249	exon20	c.T2274C	p.D758D	ATCACAATCTGAA	.	PASS	Atlas-SNP
ARSD	414	hgsc.bcm.edu	37	X	2836211	2836211	+	Missense_Mutation	SNP	A	A	T	rs73632977	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	136	18	135	0	0.132353	0	A|0.913;T|0.087	0.087	strong	.	ARSD	47	.	NM_001669	exon5	c.T497A	p.L166Q	TGGTTCAGGGGGT	.	PASS	Atlas-SNP
PCDHGC5	56097	hgsc.bcm.edu	37	5	140869003	140869003	+	Silent	SNP	T	T	C	rs1002519	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	50	50	75	0	1	0	T|0.810;C|0.190	0.190	strong	PCDHGC5_ENST00000252087,NS,carcinoma,-1,2	PCDHGC5	199	2	NM_018929	exon1	c.T196C	p.L66L	CTGCAATTGGGCT	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29913042	29913042	+	Silent	SNP	C	C	T	rs14288	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	125	125	208	1	1	0.00480769	C|0.102;T|0.898	0.898	strong	.	HLA-A	89	.	NM_001242758	exon7	c.C1077T	p.S359S	TGTGTCCCTCACA	.	PASS	Atlas-SNP
POM121C	100101267	hgsc.bcm.edu	37	7	75050958	75050958	+	Silent	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	409	125	397	1	0.305623	0.00251889	.	.	none	.	POM121C	46	.	NM_001099415	exon13	c.C2577T	p.S859S	GGTGGCGCTGGAG	.	PASS	Atlas-SNP
MLL3	58508	hgsc.bcm.edu	37	7	151878589	151878589	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	130	74	202	0	0.569231	0	.	.	none	.	MLL3	1564	.	NM_170606	exon36	c.C6356T	p.P2119L	GTTCCAGGCTGGG	.	PASS	Atlas-SNP
FREM2	341640	hgsc.bcm.edu	37	13	39343822	39343822	+	Missense_Mutation	SNP	C	C	T	rs9603422	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	200	108	235	0	0.54	0	C|0.848;T|0.152	0.152	strong	.	FREM2	385	.	NM_207361	exon4	c.C5518T	p.R1840W	CGAGTGCGGATCC	.	PASS	Atlas-SNP
PIEZO1	9780	hgsc.bcm.edu	37	16	88787704	88787704	+	Silent	SNP	G	G	C	rs8043924	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	83	82	118	1	0.987952	0.00847458	G|0.122;C|0.878	0.878	strong	PIEZO1,NS,carcinoma,0,2	PIEZO1	79	2	NM_001142864	exon39	c.C5538G	p.A1846A	GACCCTGGCTTCC	.	PASS	Atlas-SNP
BAIAP2	10458	hgsc.bcm.edu	37	17	79009061	79009061	+	Silent	SNP	C	C	T	rs8068528	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	79	38	54	0	0.481013	0	C|0.889;T|0.111	0.111	strong	BAIAP2_ENST00000321300,NS,carcinoma,0,2	BAIAP2	74	2	NM_001144888	exon1	c.C7T	p.L3L	ATGTCTCTGTCTC	.	PASS	Atlas-SNP
SLC22A15	55356	hgsc.bcm.edu	37	1	116609185	116609185	+	Silent	SNP	G	G	A	rs3748742	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	116	60	117	0	0.517241	0	G|0.891;A|0.109	0.109	strong	.	SLC22A15	65	.	NM_018420	exon11	c.G1410A	p.T470T	AGCCACGGGTCTG	.	PASS	Atlas-SNP
MROH7	374977	hgsc.bcm.edu	37	1	55166842	55166842	+	Silent	SNP	C	C	T	rs1065173	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	112	48	96	0	0.428571	0	C|0.744;T|0.256	0.256	strong	HEATR8_ENST00000421030,NS,carcinoma,0,2	.	.	2	NM_001039464	exon19	c.C3132T	p.P1044P	CCTGCCCTCCATG	.	PASS	Atlas-SNP
DST	667	hgsc.bcm.edu	37	6	56327856	56327856	+	Silent	SNP	C	C	T	rs144012429	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	141	78	167	0	0.553191	0	C|0.983;T|0.017	0.017	strong	.	DST	1427	.	NM_015548	exon82	c.G15117A	p.V5039V	AGATGGCACGGGA	.	PASS	Atlas-SNP
PLRG1	5356	hgsc.bcm.edu	37	4	155461113	155461113	+	Silent	SNP	T	T	C	rs7671792	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	88	88	140	0	1	0	T|0.738;C|0.262	0.262	strong	.	PLRG1	43	.	NM_002669	exon11	c.A1032G	p.Q344Q	AATAATTTGTGGT	.	PASS	Atlas-SNP
MICALL2	79778	hgsc.bcm.edu	37	7	1477844	1477844	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	129	103	132	0	0.79845	0	.	.	none	.	MICALL2	63	.	NM_182924	exon12	c.T2200C	p.Y734H	AGAGGTAGTCGGG	.	PASS	Atlas-SNP
ABCF2	10061	hgsc.bcm.edu	37	7	150915948	150915948	+	Silent	SNP	C	C	T	rs7782699	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	37	64	0	0.521127	0	C|0.909;T|0.091	0.091	strong	.	ABCF2	54	.	NM_007189	exon9	c.G1029A	p.A343A	AAACCTCGCAATG	.	PASS	Atlas-SNP
SDK2	54549	hgsc.bcm.edu	37	17	71426670	71426670	+	Silent	SNP	G	G	A	rs1105354	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	25	16	46	0	0.64	0	G|0.818;A|0.182	0.182	strong	.	SDK2	219	.	NM_001144952	exon12	c.C1563T	p.H521H	GGGGTCGTGGGTC	.	PASS	Atlas-SNP
PFKFB2	5208	hgsc.bcm.edu	37	1	207238419	207238419	+	Silent	SNP	C	C	T	rs72741390	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	115	43	148	0	0.373913	0	C|0.815;T|0.185	0.185	strong	.	PFKFB2	70	.	NM_001018053	exon8	c.C546T	p.N182N	AAGGAACAGAGAG	.	PASS	Atlas-SNP
TOX	9760	hgsc.bcm.edu	37	8	59739438	59739438	+	Silent	SNP	A	A	C	rs56215946	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	91	70	93	0	0.769231	0	A|0.950;C|0.050	0.050	strong	.	TOX	83	.	NM_014729	exon6	c.T948G	p.A316A	CTTCGCAGCCTCG	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	41	81	0	0.546667	0	A|0.697;G|0.303	0.303	strong	.	FAM71A	87	.	NM_153606	exon1	c.A758G	p.N253S	CCACTAATGTGCT	.	PASS	Atlas-SNP
DISC1	27185	hgsc.bcm.edu	37	1	232144598	232144598	+	Missense_Mutation	SNP	A	A	T	rs821616	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	79	45	108	0	0.56962	0	A|0.747;T|0.253	0.253	strong	.	DISC1	207	.	NM_001164537	exon12	c.A2206T	p.S736C	ATCCAGAGCCTAC	.	PASS	Atlas-SNP
CABIN1	23523	hgsc.bcm.edu	37	22	24487739	24487739	+	Missense_Mutation	SNP	G	G	A	rs117908385	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	120	60	115	0	0.5	0	G|0.987;A|0.013	0.013	strong	.	CABIN1	153	.	NM_001199281	exon24	c.G3728A	p.R1243H	CTGCCCGCTACCC	.	PASS	Atlas-SNP
HAVCR1	26762	hgsc.bcm.edu	37	5	156479426	156479426	+	Missense_Mutation	SNP	T	T	C	rs12522248	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	222	103	285	0	0.463964	0	T|0.756;C|0.244	0.244	strong	.	HAVCR1	84	.	NM_001099414	exon4	c.A619G	p.T207A	AGACAGTTGTTGT	.	PASS	Atlas-SNP
CD8A	925	hgsc.bcm.edu	37	2	87017575	87017575	+	Silent	SNP	C	C	T	rs2229240	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	103	63	110	0	0.61165	0	C|0.931;T|0.069	0.069	strong	.	CD8A	28	.	NM_001145873	exon5	c.G279A	p.R93R	CCCCAACCTCTTG	.	PASS	Atlas-SNP
TANC1	85461	hgsc.bcm.edu	37	2	160086692	160086692	+	Silent	SNP	A	A	G	rs3821296	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	109	48	124	0	0.440367	0	A|0.569;G|0.431	0.431	strong	.	TANC1	157	.	NM_033394	exon27	c.A4755G	p.T1585T	GGGAACAGGTACT	.	PASS	Atlas-SNP
ASB1	51665	hgsc.bcm.edu	37	2	239344412	239344412	+	Silent	SNP	C	C	T	rs3191996	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	80	39	82	0	0.4875	0	C|0.925;T|0.075	0.075	strong	ASB1,NS,carcinoma,0,1	ASB1	25	1	NM_001040445	exon3	c.C252T	p.I84I	GCGAATCGCGGCC	.	PASS	Atlas-SNP
CLDN18	51208	hgsc.bcm.edu	37	3	137749839	137749839	+	Silent	SNP	A	A	G	rs16847742	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	46	102	0	0.474227	0	A|0.879;G|0.121	0.121	strong	.	CLDN18	33	.	NM_016369	exon5	c.A642G	p.S214S	TGCCTCAGGCCAC	.	PASS	Atlas-SNP
C1orf65	164127	hgsc.bcm.edu	37	1	223567401	223567401	+	Missense_Mutation	SNP	T	T	C	rs6689850	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	181	80	181	0	0.441989	0	T|0.940;C|0.060	0.060	strong	.	C1orf65	71	.	NM_152610	exon1	c.T584C	p.V195A	CTTCTGTGCCCTC	.	PASS	Atlas-SNP
RCCD1	91433	hgsc.bcm.edu	37	15	91500554	91500554	+	Silent	SNP	C	C	T	rs146488462	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	36	19	8	0	0.527778	0	C|0.994;T|0.006	0.006	strong	.	RCCD1	9	.	NM_001017919	exon3	c.C378T	p.A126A	TCCGGCCGGTGAG	.	PASS	Atlas-SNP
PCDHB11	56125	hgsc.bcm.edu	37	5	140580941	140580941	+	Missense_Mutation	SNP	G	G	A	rs138686663	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	229	43	221	0	0.187773	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
BOC	91653	hgsc.bcm.edu	37	3	112997554	112997554	+	Silent	SNP	A	A	G	rs775228	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	87	115	0	1	0	A|0.404;G|0.596	0.596	strong	.	BOC	139	.	NM_033254	exon11	c.A1737G	p.K579K	CAGCAAAGAGCAG	.	PASS	Atlas-SNP
EXOC4	60412	hgsc.bcm.edu	37	7	133749164	133749164	+	Silent	SNP	G	G	A	rs6953296	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	52	27	66	0	0.519231	0	G|0.353;A|0.647	0.647	strong	.	EXOC4	118	.	NM_021807	exon18	c.G2808A	p.Q936Q	CAGCCAGACTGGG	.	PASS	Atlas-SNP
ZNF317	57693	hgsc.bcm.edu	37	19	9267319	9267319	+	Missense_Mutation	SNP	G	G	T	rs3752199	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	32	53	0	0.438356	0	G|0.865;T|0.135	0.135	strong	ZNF317,NS,carcinoma,0,1	ZNF317	61	1	NM_020933	exon3	c.G57T	p.Q19H	TCTCCAGGACTCA	.	PASS	Atlas-SNP
C1orf85	112770	hgsc.bcm.edu	37	1	156264000	156264000	+	Missense_Mutation	SNP	G	G	A	rs10908496	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	35	78	0	0.486111	0	G|0.796;A|0.204	0.204	strong	.	C1orf85	41	.	NM_001256608	exon4	c.C607T	p.P203S	GGGCTGGTCGGCT	.	PASS	Atlas-SNP
KRTAP4-8	728224	hgsc.bcm.edu	37	17	39253960	39253960	+	Missense_Mutation	SNP	C	C	T	rs80168553	byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	30	10	61	1	0.333333	0.0163934	C|0.500;T|0.500	0.500	strong	KRTAP4-8,right_lower_lobe,carcinoma,0,2	KRTAP4-8	57	2	NM_031960	exon1	c.G377A	p.R126H	CTGGGGCGGCAGC	.	scavenged	Atlas-SNP
ATAD5	79915	hgsc.bcm.edu	37	17	29159404	29159404	+	Silent	SNP	G	G	C	rs999796	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	48	25	59	0	0.520833	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
HIPK1	204851	hgsc.bcm.edu	37	1	114514543	114514543	+	Silent	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	182	94	222	1	0.516484	0.0045045	.	.	none	.	HIPK1	195	.	NM_198268	exon15	c.G3111A	p.G1037G	CGGGGGGACCAGT	.	PASS	Atlas-SNP
ZNF701	55762	hgsc.bcm.edu	37	19	53085659	53085659	+	Missense_Mutation	SNP	C	C	T	rs366793	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	101	181	0	1	0	C|0.309;T|0.691	0.691	strong	.	ZNF701	44	.	NM_001172655	exon5	c.C545T	p.T182I	CAAAAACCAAAAA	.	PASS	Atlas-SNP
DUSP4	1846	hgsc.bcm.edu	37	8	29197672	29197672	+	Silent	SNP	A	A	G	rs583034	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	35	23	33	0	0.657143	0	A|0.447;G|0.553	0.553	strong	.	DUSP4	58	.	NM_001394	exon2	c.T522C	p.S174S	TGTGGCACTGGGG	.	PASS	Atlas-SNP
C14orf39	317761	hgsc.bcm.edu	37	14	60903757	60903757	+	Missense_Mutation	SNP	G	G	A	rs1254319	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	141	72	158	0	0.510638	0	G|0.588;A|0.412	0.412	strong	.	C14orf39	79	.	NM_174978	exon18	c.C1570T	p.L524F	TCTCAAGTAAGTT	.	PASS	Atlas-SNP
C17orf97	400566	hgsc.bcm.edu	37	17	260299	260299	+	Missense_Mutation	SNP	G	G	A	rs4581766	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	14	9	6	0	0.642857	0	G|0.798;A|0.202	0.202	strong	C17orf97_ENST00000360127,NS,carcinoma,0,4	C17orf97	76	4	NM_001013672	exon1	c.G166A	p.E56K	GAGGAGGAGGAGC	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	126	61	138	0	0.484127	0	G|0.736;A|0.264	0.264	strong	.	CYP4B1	81	.	NM_001099772	exon8	c.G996A	p.M332I	CTGCATGGCCCTG	.	PASS	Atlas-SNP
PLIN4	729359	hgsc.bcm.edu	37	19	4512945	4512945	+	Missense_Mutation	SNP	C	C	T	rs75031432	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	153	21	267	1	0.137255	0.00374532	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
CBX2	84733	hgsc.bcm.edu	37	17	77758484	77758484	+	Silent	SNP	G	G	A	rs3751956	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	42	97	0	0.512195	0	G|0.744;A|0.256	0.256	strong	CBX2,NS,carcinoma,0,2	CBX2	50	2	NM_005189	exon5	c.G1242A	p.L414L	GAAGCTGGCTTCC	.	PASS	Atlas-SNP
COL24A1	255631	hgsc.bcm.edu	37	1	86512536	86512536	+	Missense_Mutation	SNP	C	C	T	rs60891279	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	128	126	198	0	0.984375	0	C|0.832;T|0.168	0.168	strong	COL24A1,NS,carcinoma,-1,1	COL24A1	202	1	NM_152890	exon12	c.G1922A	p.R641H	TTTCCACGGATCC	.	PASS	Atlas-SNP
ARHGEF10	9639	hgsc.bcm.edu	37	8	1833801	1833801	+	Missense_Mutation	SNP	G	G	C	rs9657362	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	44	15	45	0	0.340909	0	G|0.884;C|0.116	0.116	strong	ARHGEF10_ENST00000398564,NS,carcinoma,0,2	ARHGEF10	255	2	NM_014629	exon11	c.G1110C	p.L370F	GAATTTGTTCATT	.	PASS	Atlas-SNP
TTC3	7267	hgsc.bcm.edu	37	21	38534308	38534308	+	Missense_Mutation	SNP	C	C	G	rs377155188		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	145	79	165	0	0.544828	0	.	.	weak	.	TTC3	182	.	NM_001001894	exon31	c.C3113G	p.S1038C	TTGGGTCTGGAAC	.	PASS	Atlas-SNP
NKX1-2	390010	hgsc.bcm.edu	37	10	126136112	126136112	+	Silent	SNP	A	A	G	rs7075981	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	43	14	71	0	0.325581	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
KLHL33	123103	hgsc.bcm.edu	37	14	20897064	20897064	+	Missense_Mutation	SNP	C	C	T	rs7145318	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	136	135	140	0	0.992647	0	C|0.365;N|0.001	.	strong	.	KLHL33	37	.	NM_001109997	exon4	c.G1546A	p.A516T	GCACAGCGGGCAG	.	PASS	Atlas-SNP
CRLF3	51379	hgsc.bcm.edu	37	17	29113016	29113016	+	Silent	SNP	A	A	G	rs34756112	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	81	38	70	0	0.469136	0	A|0.868;G|0.132	0.132	strong	.	CRLF3	36	.	NM_015986	exon7	c.T993C	p.D331D	TATGCTATCTCTT	.	PASS	Atlas-SNP
DST	667	hgsc.bcm.edu	37	6	56481632	56481632	+	Silent	SNP	T	T	C	rs115542549	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	90	37	124	0	0.411111	0	T|0.974;C|0.026	0.026	strong	.	DST	1427	.	NM_001723	exon24	c.A6633G	p.A2211A	CTTCTCTGCCTCA	.	PASS	Atlas-SNP
DOCK5	80005	hgsc.bcm.edu	37	8	25265651	25265651	+	Missense_Mutation	SNP	C	C	A	rs34067851	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	68	108	0	0.8	0	C|0.986;A|0.014	0.014	strong	.	DOCK5	167	.	NM_024940	exon49	c.C5246A	p.A1749E	AGAAAGCACCAGA	.	PASS	Atlas-SNP
METTL20	254013	hgsc.bcm.edu	37	12	31815167	31815167	+	Missense_Mutation	SNP	G	G	T	rs61736289	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	48	23	60	0	0.479167	0	G|0.968;T|0.032	0.032	strong	.	METTL20	23	.	NM_173802	exon2	c.G280T	p.A94S	TACTGGGCAATCT	.	PASS	Atlas-SNP
AKNAD1	254268	hgsc.bcm.edu	37	1	109363232	109363232	+	Silent	SNP	T	T	C	rs1333130	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	60	60	67	0	1	0	T|0.694;C|0.306	0.306	strong	.	AKNAD1	83	.	NM_152763	exon14	c.A2184G	p.K728K	GATCCGTTTGGGT	.	PASS	Atlas-SNP
TTC21A	199223	hgsc.bcm.edu	37	3	39156124	39156124	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	128	19	141	0	0.148438	0	.	.	none	.	TTC21A	96	.	NM_145755	exon6	c.G607A	p.V203M	GAGGTGGTGAACC	.	PASS	Atlas-SNP
OR10H5	284433	hgsc.bcm.edu	37	19	15905206	15905206	+	Silent	SNP	T	T	C	rs61740798	byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	146	63	206	0	0.431507	0	T|0.250;C|0.750	0.750	strong	.	OR10H5	49	.	NM_001004466	exon1	c.T348C	p.T116T	GCTCACTGTCATG	.	PASS	Atlas-SNP
CD48	962	hgsc.bcm.edu	37	1	160654786	160654786	+	Silent	SNP	G	G	A	rs1980606	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	146	144	233	0	0.986301	0	G|0.772;A|0.228	0.228	strong	.	CD48	31	.	NM_001256030	exon2	c.C276T	p.G92G	CAGTGCGCCACTC	.	PASS	Atlas-SNP
PHF2	5253	hgsc.bcm.edu	37	9	96415482	96415482	+	Silent	SNP	A	A	T	rs56134753	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	54	24	48	0	0.444444	0	A|0.985;T|0.015	0.015	strong	.	PHF2	113	.	NM_005392	exon6	c.A624T	p.P208P	GGAGCCACCTGAC	.	PASS	Atlas-SNP
RABEP1	9135	hgsc.bcm.edu	37	17	5284719	5284719	+	Silent	SNP	T	T	C	rs1065482	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	35	92	0	0.507246	0	T|0.500;C|0.500	0.500	strong	.	RABEP1	59	.	NM_004703	exon17	c.T2406C	p.N802N	GAAGAATAAAGCT	.	PASS	Atlas-SNP
DSPP	1834	hgsc.bcm.edu	37	4	88536457	88536457	+	Silent	SNP	T	T	C	rs142031576	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	66	18	99	0	0.272727	0	.	.	weak	.	DSPP	174	.	NM_014208	exon5	c.T2643C	p.D881D	CAGTGATAGCAGT	.	PASS	Atlas-SNP
SRPX	8406	hgsc.bcm.edu	37	X	38009121	38009121	+	Missense_Mutation	SNP	G	G	A	rs35318931	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	72	119	0	0.986301	0	G|0.935;0|0.016	.	strong	.	SRPX	53	.	NM_006307	exon10	c.C1238T	p.S413F	CTGAAGGAGTAGA	.	PASS	Atlas-SNP
PTPRM	5797	hgsc.bcm.edu	37	18	8253407	8253407	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	19	104	0	0.22093	0	.	.	none	.	PTPRM	185	.	NM_001105244	exon19	c.T2749A	p.Y917N	GAGGAATACGAGG	.	PASS	Atlas-SNP
LAMB3	3914	hgsc.bcm.edu	37	1	209796329	209796329	+	Missense_Mutation	SNP	T	T	A	rs12748250	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	37	77	0	0.451219	0	T|0.890;A|0.110	0.110	strong	.	LAMB3	136	.	NM_000228	exon17	c.A2554T	p.M852L	TTACCATCTGCCT	.	PASS	Atlas-SNP
CYP2B6	1555	hgsc.bcm.edu	37	19	41512841	41512841	+	Missense_Mutation	SNP	G	G	T	rs56308434		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	149	76	160	0	0.510067	0	.	.	weak	.	CYP2B6	79	.	NM_000767	exon4	c.G516T	p.Q172H	CTTCCAGTCCATT	.	PASS	Atlas-SNP
TH	7054	hgsc.bcm.edu	37	11	2188238	2188238	+	Silent	SNP	C	C	T	rs6357	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	147	21	133	0	0.142857	0	C|0.798;T|0.202	0.202	strong	.	TH	43	.	NM_199292	exon8	c.G813A	p.K271K	GAGGCCCTTCAGC	.	PASS	Atlas-SNP
C2orf61	285051	hgsc.bcm.edu	37	2	47357129	47357129	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	186	27	93	0	0.145161	0	.	.	none	.	C2orf61	31	.	NM_173649	exon5	c.G470A	p.C157Y	AATACACAGCTCC	.	PASS	Atlas-SNP
MANEA	79694	hgsc.bcm.edu	37	6	96034560	96034560	+	Missense_Mutation	SNP	C	C	T	rs62417812	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	62	25	73	0	0.403226	0	C|0.917;T|0.083	0.083	strong	.	MANEA	58	.	NM_024641	exon2	c.C245T	p.T82I	AAATCACTATGAA	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1263687	1263687	+	Silent	SNP	C	C	T	rs55933911	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	142	115	129	0	0.809859	0	C|0.973;G|0.000;T|0.026	0.026	strong	.	MUC5B	473	.	NM_002458	exon31	c.C5577T	p.N1859N	CAAGAACGAAGAC	.	PASS	Atlas-SNP
ZNF627	199692	hgsc.bcm.edu	37	19	11725413	11725413	+	Silent	SNP	G	G	A	rs12151212	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	61	27	62	0	0.442623	0	G|0.865;A|0.135	0.135	strong	ZNF627,NS,carcinoma,0,1	ZNF627	43	1	NM_145295	exon2	c.G75A	p.Q25Q	TTCCCAGAAGAAT	.	PASS	Atlas-SNP
ERCC8	1161	hgsc.bcm.edu	37	5	60200665	60200665	+	Silent	SNP	A	A	G	rs4647100	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	216	124	237	1	0.574074	0.00421941	A|0.820;G|0.180	0.180	strong	.	ERCC8	31	.	NM_000082	exon5	c.T435C	p.Y145Y	ATGACTATAAACT	.	PASS	Atlas-SNP
TNNI2	7136	hgsc.bcm.edu	37	11	1861760	1861760	+	Silent	SNP	T	T	C	rs907610	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	76	75	72	0	0.986842	0	A|0.000;C|0.810;G|0.000;T|0.189	0.810	strong	.	TNNI2	24	.	NM_001145841	exon3	c.T60C	p.S20S	GCAGAGTGTGATG	.	PASS	Atlas-SNP
GGT6	124975	hgsc.bcm.edu	37	17	4463716	4463716	+	Missense_Mutation	SNP	G	G	A	rs62066363	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	36	13	39	0	0.361111	0	G|0.986;A|0.014	0.014	strong	.	GGT6	22	.	NM_001122890	exon1	c.C101T	p.A34V	ACCAGCGCCTCTG	.	PASS	Atlas-SNP
PIWIL3	440822	hgsc.bcm.edu	37	22	25145471	25145471	+	Missense_Mutation	SNP	A	A	G	rs1892722	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	59	35	90	0	0.59322	0	A|0.368;G|0.632	0.632	strong	.	PIWIL3	115	.	NM_001008496	exon11	c.T1234C	p.C412R	CTTTACATATTTC	.	PASS	Atlas-SNP
PRR21	643905	hgsc.bcm.edu	37	2	240981375	240981375	+	Missense_Mutation	SNP	T	T	A	rs6732185	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	60	24	94	0	0.4	0	T|0.277;A|0.723	0.723	strong	.	PRR21	53	.	NM_001080835	exon1	c.A1025T	p.K342M	AGAGACTTGGATG	.	PASS	Atlas-SNP
ZNF804A	91752	hgsc.bcm.edu	37	2	185803364	185803364	+	Missense_Mutation	SNP	C	C	G	rs3731834	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	123	121	128	0	0.98374	0	C|0.853;G|0.147	0.147	strong	.	ZNF804A	322	.	NM_194250	exon4	c.C3241G	p.L1081V	ACACCTCTGCAGC	.	PASS	Atlas-SNP
RUFY1	80230	hgsc.bcm.edu	37	5	179025789	179025789	+	Silent	SNP	G	G	A	rs72824522	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	229	125	211	0	0.545852	0	G|0.912;A|0.088	0.088	strong	.	RUFY1	101	.	NM_025158	exon14	c.G1728A	p.R576R	ACTCAGGATGGAG	.	PASS	Atlas-SNP
DPF3	8110	hgsc.bcm.edu	37	14	73220020	73220020	+	Silent	SNP	A	A	G	rs3742836	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	35	16	38	0	0.457143	0	A|0.773;G|0.227	0.227	strong	.	DPF3	117	.	NM_012074	exon3	c.T253C	p.L85L	GGTGCAATCGTCT	.	PASS	Atlas-SNP
OR1S2	219958	hgsc.bcm.edu	37	11	57971478	57971478	+	Missense_Mutation	SNP	A	A	G	rs11229281	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	239	46	293	0	0.192469	0	A|0.913;G|0.087	0.087	strong	.	OR1S2	119	.	NM_001004459	exon1	c.T176C	p.I59T	GCCACAATGATGA	.	PASS	Atlas-SNP
GMPR	2766	hgsc.bcm.edu	37	6	16290761	16290761	+	Missense_Mutation	SNP	T	T	A	rs1042391	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	137	62	159	0	0.452555	0	A|0.579;N|0.000	0.579	strong	.	GMPR	44	.	NM_006877	exon8	c.T766A	p.F256I	GAAGTGTTTGAGA	.	PASS	Atlas-SNP
DUOX2	50506	hgsc.bcm.edu	37	15	45400296	45400296	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	109	73	88	0	0.669725	0	.	.	none	.	DUOX2	137	.	NM_014080	exon13	c.T1523C	p.F508S	CGTACAAACTGGT	.	PASS	Atlas-SNP
MYO9B	4650	hgsc.bcm.edu	37	19	17306031	17306031	+	Silent	SNP	T	T	C	rs2279003	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	27	26	21	0	0.962963	0	T|0.284;C|0.716	0.716	strong	.	MYO9B	264	.	NM_001130065	exon22	c.T3795C	p.P1265P	GGCCCCTGGCAGC	.	PASS	Atlas-SNP
DSG1	1828	hgsc.bcm.edu	37	18	28919911	28919911	+	Missense_Mutation	SNP	A	A	G	rs61730306	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	102	45	120	0	0.441176	0	A|0.893;G|0.107	0.107	strong	.	DSG1	176	.	NM_001942	exon11	c.A1610G	p.K537R	GAGCCAAAGATTT	.	PASS	Atlas-SNP
IRAK1BP1	134728	hgsc.bcm.edu	37	6	79595097	79595097	+	Silent	SNP	A	A	G	rs6908105	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	151	151	224	1	1	0.00446429	A|0.684;G|0.316	0.316	strong	.	IRAK1BP1	18	.	NM_001010844	exon2	c.A318G	p.A106A	TCAGGCAGAAAAT	.	PASS	Atlas-SNP
C1orf189	388701	hgsc.bcm.edu	37	1	154178079	154178079	+	Silent	SNP	G	G	A	rs74957241	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	83	35	71	0	0.421687	0	G|0.926;A|0.074	0.074	strong	C1orf189,NS,carcinoma,-2,1	C1orf189	17	1	NM_001010979	exon2	c.C69T	p.V23V	CCTGTCGACCGTC	.	PASS	Atlas-SNP
DNAH9	1770	hgsc.bcm.edu	37	17	11543610	11543610	+	Missense_Mutation	SNP	A	A	G	rs61740059	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	66	28	73	0	0.424242	0	A|0.981;G|0.019	0.019	strong	.	DNAH9	695	.	NM_001372	exon10	c.A1810G	p.M604V	AAGAACATGCCCA	.	PASS	Atlas-SNP
SPICE1	152185	hgsc.bcm.edu	37	3	113187675	113187675	+	Missense_Mutation	SNP	G	G	C	rs16861032	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	193	93	199	0	0.481865	0	G|0.946;C|0.054	0.054	strong	.	SPICE1	130	.	NM_144718	exon9	c.C823G	p.L275V	AGTCTAGAGTCTC	.	PASS	Atlas-SNP
RXFP3	51289	hgsc.bcm.edu	37	5	33937601	33937601	+	Silent	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	209	3	209	0	0.0143541	0	.	.	none	RXFP3,NS,carcinoma,+2,1	RXFP3	114	1	NM_016568	exon1	c.G756A	p.P252P	TTTCCCGGACAAG	.	scavenged	Atlas-SNP
C1orf65	164127	hgsc.bcm.edu	37	1	223567531	223567531	+	Silent	SNP	G	G	A	rs2298063	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	180	82	184	0	0.455556	0	G|0.940;A|0.060	0.060	strong	C1orf65,colon,carcinoma,+1,1	C1orf65	71	1	NM_152610	exon1	c.G714A	p.P238P	GAGCCCGCACACC	.	PASS	Atlas-SNP
CAPN11	11131	hgsc.bcm.edu	37	6	44147821	44147821	+	Missense_Mutation	SNP	A	A	G	rs34710081	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	63	37	70	0	0.587302	0	A|0.815;G|0.185	0.185	strong	.	CAPN11	66	.	NM_007058	exon14	c.A1561G	p.I521V	TATATCATTATTC	.	PASS	Atlas-SNP
PABPN1L	390748	hgsc.bcm.edu	37	16	88931274	88931274	+	Missense_Mutation	SNP	C	C	T	rs76267236	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	222	85	206	1	0.382883	0.00485437	C|0.965;T|0.035	0.035	strong	PABPN1L_ENST00000419291,colon,carcinoma,0,2	PABPN1L	25	2	NM_001080487	exon5	c.G641A	p.G214D	ACCCGGCCCCGGA	.	scavenged	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29911218	29911218	+	Missense_Mutation	SNP	G	G	A	rs1059526	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	132	61	284	0	0.462121	0	A|0.067;G|0.933	0.067	strong	.	HLA-A	89	.	NM_001242758	exon3	c.G517A	p.A173T	TGGGAGGCGGCCC	.	PASS	Atlas-SNP
POM121C	100101267	hgsc.bcm.edu	37	7	75053499	75053499	+	Missense_Mutation	SNP	G	G	A	rs113744930	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	279	104	228	1	0.37276	0.00438596	G|0.881;A|0.119	0.119	strong	POM121C,NS,carcinoma,+1,1	POM121C	46	1	NM_001099415	exon12	c.C881T	p.S294L	GAGTTCGAGGCAG	.	scavenged	Atlas-SNP
UBR3	130507	hgsc.bcm.edu	37	2	170917648	170917648	+	Silent	SNP	A	A	G	rs10203212	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	105	46	105	0	0.438095	0	A|0.719;G|0.281	0.281	strong	.	UBR3	182	.	NM_172070	exon34	c.A4845G	p.L1615L	TGAACTATTTAAA	.	PASS	Atlas-SNP
ARSD	414	hgsc.bcm.edu	37	X	2833643	2833643	+	Missense_Mutation	SNP	C	C	A	rs115332247	by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	107	13	143	0	0.121495	0	.	.	strong	.	ARSD	47	.	NM_001669	exon6	c.G954T	p.Q318H	GCCATGCTGACTT	.	PASS	Atlas-SNP
FIGNL1	63979	hgsc.bcm.edu	37	7	50513721	50513721	+	Missense_Mutation	SNP	A	A	C	rs146680091	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	110	75	154	0	0.681818	0	A|0.997;C|0.003	0.003	strong	.	FIGNL1	73	.	NM_001042762	exon4	c.T1265G	p.L422W	GGCCTCAACATGG	.	PASS	Atlas-SNP
FOLH1B	219595	hgsc.bcm.edu	37	11	89420607	89420607	+	Splice_Site	SNP	G	G	A	rs61905507	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	270	65	301	0	0.240741	0	G|0.947;A|0.053	0.053	strong	.	FOLH1B	93	.	NM_153696	exon9	c.608+1G>A	.	GCCCAGGTAAATA	.	PASS	Atlas-SNP
GOLGA3	2802	hgsc.bcm.edu	37	12	133378440	133378440	+	Silent	SNP	C	C	T	rs2291258	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	44	43	39	0	0.977273	0	C|0.621;T|0.379	0.379	strong	.	GOLGA3	234	.	NM_001172557	exon8	c.G1713A	p.L571L	ACTCTGCAGGGAC	.	PASS	Atlas-SNP
LGR6	59352	hgsc.bcm.edu	37	1	202287537	202287537	+	Silent	SNP	G	G	A	rs788794	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	65	38	55	0	0.584615	0	G|0.538;A|0.462	0.462	strong	.	LGR6	102	.	NM_001017403	exon18	c.G2106A	p.A702A	CGCCGCGCTGCCC	.	PASS	Atlas-SNP
C19orf71	100128569	hgsc.bcm.edu	37	19	3543980	3543980	+	Missense_Mutation	SNP	C	C	T	rs190228213	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	160	77	174	0	0.48125	0	C|0.995;T|0.005	0.005	strong	.	C19orf71	12	.	NM_001135580	exon4	c.C602T	p.P201L	GGTCCCCGCCTTC	.	PASS	Atlas-SNP
CACNA1B	774	hgsc.bcm.edu	37	9	141008876	141008876	+	Silent	SNP	C	C	T	rs2229948	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	58	64	0	1	0	C|0.503;T|0.497	0.497	strong	.	CACNA1B	266	.	NM_001243812	exon40	c.C5583T	p.F1861F	GATATTCGACTTC	.	PASS	Atlas-SNP
SYNPO2	171024	hgsc.bcm.edu	37	4	119948046	119948046	+	Missense_Mutation	SNP	A	A	C	rs17263971	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	44	97	0	0.453608	0	A|0.774;C|0.226	0.226	strong	.	SYNPO2	353	.	NM_001128934	exon3	c.A522C	p.Q174H	CTCCCAAAGAGGA	.	PASS	Atlas-SNP
OR10H2	26538	hgsc.bcm.edu	37	19	15839081	15839081	+	Silent	SNP	C	C	T	rs2067083	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	250	66	208	0	0.264	0	C|0.708;T|0.292	0.292	strong	.	OR10H2	59	.	NM_013939	exon1	c.C228T	p.A76A	CGTGGCCATCATC	.	PASS	Atlas-SNP
ZNF136	7695	hgsc.bcm.edu	37	19	12298164	12298164	+	Missense_Mutation	SNP	G	G	A	rs200700405		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	39	22	36	0	0.564103	0	G|0.999;A|0.001	0.001	weak	ZNF136,colon,carcinoma,+1,1	ZNF136	57	1	NM_003437	exon4	c.G971A	p.R324Q	CCCTTCGACTACA	.	PASS	Atlas-SNP
SLC25A15	10166	hgsc.bcm.edu	37	13	41379272	41379272	+	Silent	SNP	C	C	T	rs9577152	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	37	88	0	0.513889	0	C|0.883;T|0.117	0.117	strong	SLC25A15,NS,carcinoma,0,1	SLC25A15	30	1	NM_014252	exon4	c.C333T	p.A111A	TGCAGCCGCCGGT	.	PASS	Atlas-SNP
CNKSR3	154043	hgsc.bcm.edu	37	6	154763401	154763401	+	Silent	SNP	G	G	A	rs6557351	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	41	31	90	0	0.756098	0	G|0.660;A|0.340	0.340	strong	CNKSR3,NS,carcinoma,0,1	CNKSR3	56	1	NM_173515	exon3	c.C240T	p.N80N	CTTCATGTTATCA	.	PASS	Atlas-SNP
CCDC8	83987	hgsc.bcm.edu	37	19	46914921	46914921	+	Missense_Mutation	SNP	G	G	A	rs34186470	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	84	46	116	0	0.547619	0	A|0.146;C|0.000;G|0.854	0.146	strong	.	CCDC8	56	.	NM_032040	exon1	c.C1147T	p.H383Y	CCCTGTGGTTATC	.	PASS	Atlas-SNP
PCNT	5116	hgsc.bcm.edu	37	21	47786524	47786524	+	Missense_Mutation	SNP	A	A	G	rs2839227	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	345	115	295	0	0.333333	0	A|0.704;C|0.002	.	strong	.	PCNT	283	.	NM_006031	exon15	c.A2635G	p.T879A	GAGATCACCGAGA	.	PASS	Atlas-SNP
RAD51AP2	729475	hgsc.bcm.edu	37	2	17696573	17696573	+	Missense_Mutation	SNP	C	C	T	rs834514	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	265	265	262	1	1	0.00381679	C|0.409;T|0.591	0.591	strong	.	RAD51AP2	134	.	NM_001099218	exon1	c.G3110A	p.G1037D	TTAGGACCTGCTA	.	PASS	Atlas-SNP
TNKS1BP1	85456	hgsc.bcm.edu	37	11	57080938	57080938	+	Silent	SNP	C	C	A	rs145901431	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	50	41	66	0	0.82	0	C|0.998;A|0.002	0.002	strong	.	TNKS1BP1	148	.	NM_033396	exon5	c.G1224T	p.G408G	CTCCTCCCCGCCA	.	PASS	Atlas-SNP
SERPIND1	3053	hgsc.bcm.edu	37	22	21133831	21133831	+	Missense_Mutation	SNP	C	C	A	rs5903	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	133	65	126	0	0.488722	0	A|0.004;C|0.984;T|0.013	0.004	strong	.	SERPIND1	92	.	NM_000185	exon2	c.C231A	p.D77E	GGACGACGACTAT	.	PASS	Atlas-SNP
FAM222B	55731	hgsc.bcm.edu	37	17	27085564	27085564	+	Silent	SNP	A	A	G	rs2043031	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	35	35	34	0	1	0	A|0.808;G|0.192	0.192	strong	.	.	.	.	NM_018182	exon4	c.T1413C	p.L471L	CATGGCAAGGTCC	.	PASS	Atlas-SNP
PSD4	23550	hgsc.bcm.edu	37	2	113940207	113940207	+	Silent	SNP	T	T	A	rs3738908	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	125	64	112	0	0.512	0	T|0.982;A|0.018	0.018	strong	.	PSD4	74	.	NM_012455	exon2	c.T174A	p.P58P	TGAACCTACCAGA	.	PASS	Atlas-SNP
FBXW10	10517	hgsc.bcm.edu	37	17	18671961	18671961	+	Missense_Mutation	SNP	C	C	T	rs79757327		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	169	74	158	0	0.43787	0	.	.	weak	.	FBXW10	82	.	NM_001267585	exon10	c.C1819T	p.R607C	TACGAGCGCTGCC	.	PASS	Atlas-SNP
NPAS2	4862	hgsc.bcm.edu	37	2	101587455	101587455	+	Silent	SNP	C	C	T	rs1562313	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	98	39	85	0	0.397959	0	C|0.766;T|0.234	0.234	strong	.	NPAS2	88	.	NM_002518	exon12	c.C1059T	p.Y353Y	CAGTTACGCAGAT	.	PASS	Atlas-SNP
SNX18	112574	hgsc.bcm.edu	37	5	53815219	53815219	+	Silent	SNP	G	G	A	rs35241631	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	59	24	57	0	0.40678	0	G|0.969;A|0.031	0.031	strong	.	SNX18	102	.	NM_052870	exon1	c.G1437A	p.E479E	CTTTGAGCTGGAC	.	PASS	Atlas-SNP
C9orf66	157983	hgsc.bcm.edu	37	9	214864	214864	+	Missense_Mutation	SNP	C	C	T	rs2236547	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	51	21	28	0	0.411765	0	C|0.737;T|0.263	0.263	strong	C9orf66,rectum,carcinoma,0,1	C9orf66	16	1	NM_152569	exon1	c.G533A	p.R178Q	GCCGACCGACAGA	.	PASS	Atlas-SNP
ULK3	25989	hgsc.bcm.edu	37	15	75131661	75131661	+	Silent	SNP	A	A	G	rs4886615	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	157	157	99	0	1	0	A|0.331;G|0.669	0.669	strong	ULK3_ENST00000440863,NS,carcinoma,0,1	ULK3	30	1	NM_001099436	exon8	c.T906C	p.A302A	TAAGGCAGCTGCT	.	PASS	Atlas-SNP
SKA3	221150	hgsc.bcm.edu	37	13	21742311	21742311	+	Missense_Mutation	SNP	C	C	T	rs61950353	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	471	88	563	0	0.186837	0	C|0.893;T|0.107	0.107	strong	.	SKA3	76	.	NM_145061	exon4	c.G559A	p.V187I	CAATTACGGGCTC	.	PASS	Atlas-SNP
C14orf39	317761	hgsc.bcm.edu	37	14	60945066	60945066	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	166	90	200	0	0.542169	0	.	.	none	.	C14orf39	79	.	NM_174978	exon5	c.A275G	p.Y92C	TGCATATAATCTT	.	PASS	Atlas-SNP
ZNF611	81856	hgsc.bcm.edu	37	19	53209553	53209553	+	Missense_Mutation	SNP	G	G	A	rs75841962		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	37	93	0	0.402174	0	.	.	weak	ZNF611,NS,carcinoma,0,1	ZNF611	72	1	NM_030972	exon7	c.C755T	p.P252L	AAATGGGGTATCT	.	PASS	Atlas-SNP
ZNF880	400713	hgsc.bcm.edu	37	19	52887904	52887904	+	Silent	SNP	T	T	C	rs2042913	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	25	24	36	0	0.96	0	T|0.637;C|0.363	0.363	strong	ZNF880,colon,carcinoma,0,1	ZNF880	45	1	NM_001145434	exon4	c.T1071C	p.C357C	TAAATGTGGCAAG	.	PASS	Atlas-SNP
OR11H12	440153	hgsc.bcm.edu	37	14	19378322	19378322	+	Missense_Mutation	SNP	G	G	A	rs201485834		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	433	12	518	4	0.0277136	0.00772201	.	.	weak	OR11H12,NS,malignant_melanoma,+1,1	OR11H12	58	1	NM_001013354	exon1	c.G729A	p.M243I	GGGTATGCCTTCA	.	scavenged	Atlas-SNP
CCDC148	130940	hgsc.bcm.edu	37	2	159195562	159195562	+	Silent	SNP	A	A	G	rs61746487	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	146	64	201	0	0.438356	0	A|0.948;G|0.052	0.052	strong	.	CCDC148	64	.	NM_138803	exon6	c.T522C	p.F174F	TCTTTCAAAGACA	.	PASS	Atlas-SNP
CRTC1	23373	hgsc.bcm.edu	37	19	18876309	18876309	+	Missense_Mutation	SNP	A	A	G	rs3746266	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	44	16	36	0	0.363636	0	A|0.865;G|0.135	0.135	strong	.	CRTC1	88	.	NM_001098482	exon10	c.A1030G	p.T344A	TCGCCCACCCTGT	.	PASS	Atlas-SNP
C3	718	hgsc.bcm.edu	37	19	6718146	6718146	+	Missense_Mutation	SNP	T	T	G	rs147859257	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	47	97	0	0.54023	0	T|0.998;G|0.002	0.002	strong	.	C3	192	.	NM_000064	exon4	c.A463C	p.K155Q	GCAGCTTGTGGTT	.	PASS	Atlas-SNP
OR7A17	26333	hgsc.bcm.edu	37	19	14991963	14991963	+	Missense_Mutation	SNP	C	C	A	rs10404119	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	50	20	93	0	0.4	0	C|0.711;A|0.289	0.289	strong	.	OR7A17	37	.	NM_030901	exon1	c.G205T	p.A69S	TGTCTGCAAAGGA	.	PASS	Atlas-SNP
FFAR3	2865	hgsc.bcm.edu	37	19	35850408	35850408	+	Missense_Mutation	SNP	C	C	T	rs138920343	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	405	113	417	0	0.279012	0	C|0.997;T|0.003	0.003	strong	.	FFAR3	40	.	NM_005304	exon2	c.C616T	p.R206C	TACAGCCGCCTGG	.	PASS	Atlas-SNP
PRG4	10216	hgsc.bcm.edu	37	1	186273994	186273994	+	Missense_Mutation	SNP	C	C	T	rs2273779	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	162	162	185	1	1	0.00540541	C|0.726;T|0.274	0.274	strong	.	PRG4	259	.	NM_005807	exon6	c.C538T	p.R180W	ACAATTCGGAAAA	.	PASS	Atlas-SNP
NEUROD6	63974	hgsc.bcm.edu	37	7	31378795	31378795	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	61	12	82	0	0.196721	0	.	.	none	.	NEUROD6	84	.	NM_022728	exon2	c.C88T	p.Q30X	TAATTTGCTTCTG	.	PASS	Atlas-SNP
ATP6V1B1	525	hgsc.bcm.edu	37	2	71170807	71170807	+	Silent	SNP	C	C	T	rs2266918	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	29	29	25	0	1	0	C|0.801;T|0.199	0.199	strong	.	ATP6V1B1	66	.	NM_001692	exon2	c.C138T	p.S46S	GTGCAGCGTGAAC	.	PASS	Atlas-SNP
FUCA2	2519	hgsc.bcm.edu	37	6	143816859	143816859	+	Silent	SNP	C	C	T	rs8161	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	75	129	0	1	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
MYOM1	8736	hgsc.bcm.edu	37	18	3067278	3067278	+	Silent	SNP	A	A	G	rs2230164	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	49	19	62	0	0.387755	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
SLC45A3	85414	hgsc.bcm.edu	37	1	205628616	205628616	+	Missense_Mutation	SNP	C	C	T	rs137949511	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	128	71	115	0	0.554688	0	C|0.994;T|0.006	0.006	strong	.	SLC45A3	54	.	NM_033102	exon5	c.G1408A	p.V470I	CACGTACGGAGAC	.	PASS	Atlas-SNP
TRAPPC12	51112	hgsc.bcm.edu	37	2	3469463	3469463	+	Silent	SNP	G	G	C	rs4971514	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	26	98	0	0.282609	0	G|0.566;C|0.434	0.434	strong	.	.	.	.	NM_016030	exon9	c.G1773C	p.L591L	TTCCCTGCAGGTA	.	PASS	Atlas-SNP
C9orf3	84909	hgsc.bcm.edu	37	9	97717527	97717527	+	Missense_Mutation	SNP	C	C	T	rs143555020	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	32	7	51	0	0.21875	0	C|1.000;T|0.000	0.000	strong	.	C9orf3	100	.	NM_001193329	exon7	c.C1730T	p.P577L	TTAATCCGGAGAA	.	PASS	Atlas-SNP
SF3B4	10262	hgsc.bcm.edu	37	1	149898292	149898292	+	Silent	SNP	A	A	G	rs115070660	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	43	110	0	0.597222	0	A|0.985;G|0.015	0.015	strong	.	SF3B4	37	.	NM_005850	exon3	c.T682C	p.L228L	ACCCCAATGATGA	.	PASS	Atlas-SNP
SH3BP4	23677	hgsc.bcm.edu	37	2	235949920	235949920	+	Silent	SNP	A	A	G	rs3731645	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	38	18	61	0	0.473684	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
SSC5D	284297	hgsc.bcm.edu	37	19	56029191	56029191	+	Missense_Mutation	SNP	C	C	T	rs76172483	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	162	77	190	0	0.475309	0	C|0.835;T|0.165	0.165	strong	.	SSC5D	65	.	NM_001144950	exon14	c.C3548T	p.T1183M	CCACCACGACCCC	.	PASS	Atlas-SNP
HSDL2	84263	hgsc.bcm.edu	37	9	115167994	115167994	+	Missense_Mutation	SNP	A	A	T	rs41280175	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	43	26	63	0	0.604651	0	A|0.995;T|0.005	0.005	strong	.	HSDL2	24	.	NM_032303	exon3	c.A272T	p.K91I	TCAAGAAATTTGG	.	PASS	Atlas-SNP
RBM27	54439	hgsc.bcm.edu	37	5	145650597	145650597	+	Silent	SNP	A	A	G	rs17104362	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	177	92	187	0	0.519774	0	A|0.836;G|0.164	0.164	strong	.	RBM27	119	.	NM_018989	exon18	c.A2772G	p.K924K	ACGGAAAAAACTC	.	PASS	Atlas-SNP
ZKSCAN8	7745	hgsc.bcm.edu	37	6	28120898	28120898	+	Silent	SNP	G	G	A	rs17774663	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	119	60	148	0	0.504202	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
NUP62CL	54830	hgsc.bcm.edu	37	X	106396402	106396402	+	Missense_Mutation	SNP	A	A	G	rs1298577	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	143	143	266	1	1	0.0037594	A|0.540;0|0.011	.	strong	.	NUP62CL	10	.	NM_017681	exon7	c.T530C	p.I177T	ACTTACATCTCCA	.	PASS	Atlas-SNP
SYCE1L	100130958	hgsc.bcm.edu	37	16	77245139	77245139	+	Missense_Mutation	SNP	T	T	C	rs61746433	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	156	101	176	0	0.647436	0	T|0.970;C|0.030	0.030	strong	.	SYCE1L	10	.	NM_001129979	exon7	c.T389C	p.L130P	AGGATCTGATGGG	.	PASS	Atlas-SNP
NIPSNAP1	8508	hgsc.bcm.edu	37	22	29957570	29957570	+	Silent	SNP	G	G	A	rs1058642	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	74	34	71	0	0.459459	0	G|0.757;A|0.243	0.243	strong	.	NIPSNAP1	17	.	NM_003634	exon6	c.C504T	p.L168L	GAACTCGAGGAGC	.	PASS	Atlas-SNP
LSP1	4046	hgsc.bcm.edu	37	11	1902771	1902771	+	Silent	SNP	T	T	C	rs147746785	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	190	37	135	0	0.194737	0	T|0.982;C|0.018	0.018	strong	.	LSP1	59	.	NM_001242932	exon4	c.T685C	p.L229L	GGCGCCTTGGACA	.	PASS	Atlas-SNP
KIAA1549	57670	hgsc.bcm.edu	37	7	138602916	138602916	+	Missense_Mutation	SNP	G	G	C	rs2718131	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	24	67	0	0.333333	0	G|0.756;C|0.244	0.244	strong	.	KIAA1549	314	.	NM_020910	exon2	c.C1456G	p.P486A	TGGAGGGGAAAAG	.	PASS	Atlas-SNP
UBR3	130507	hgsc.bcm.edu	37	2	170762566	170762566	+	Silent	SNP	A	A	T	rs10194785	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	38	106	0	0.463415	0	A|0.748;T|0.252	0.252	strong	.	UBR3	182	.	NM_172070	exon10	c.A1671T	p.L557L	AGAACTAAACGAG	.	PASS	Atlas-SNP
LIPM	340654	hgsc.bcm.edu	37	10	90580144	90580144	+	Silent	SNP	C	C	T	rs10788615	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	50	99	0	0.543478	0	C|0.705;N|0.000	.	strong	.	LIPM	17	.	NM_001128215	exon9	c.C1158T	p.H386H	GGCTCACGTGGAT	.	PASS	Atlas-SNP
GNRH2	2797	hgsc.bcm.edu	37	20	3025107	3025107	+	Missense_Mutation	SNP	C	C	T	rs6051545	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	95	52	109	0	0.547368	0	C|0.815;T|0.185	0.185	strong	.	GNRH2	15	.	NM_001501	exon2	c.C47T	p.A16V	TGACTGCCCACCT	.	PASS	Atlas-SNP
VAPA	9218	hgsc.bcm.edu	37	18	9944956	9944956	+	Silent	SNP	T	T	C	rs29133	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	48	138	0	0.521739	0	T|0.931;C|0.069	0.069	strong	.	VAPA	28	.	NM_003574	exon5	c.T453C	p.T151T	TGTCACTTCAATG	.	PASS	Atlas-SNP
MYO7B	4648	hgsc.bcm.edu	37	2	128388437	128388437	+	Missense_Mutation	SNP	A	A	C	rs138651379	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	254	128	297	1	0.503937	0.003367	A|0.987;C|0.013	0.013	strong	MYO7B_ENST00000428314,NS,haematopoietic_neoplasm,0,2	MYO7B	359	2	NM_001080527	exon35	c.A4813C	p.K1605Q	CCACCCAAGGAAA	.	PASS	Atlas-SNP
PCDHA8	56140	hgsc.bcm.edu	37	5	140222138	140222138	+	Missense_Mutation	SNP	G	G	C	rs144906391	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	134	3	299	0	0.0223881	0	.	.	weak	PCDHA8_ENST00000531613,middle_lobe,carcinoma,-1,2	PCDHA8	366	2	NM_031856	exon1	c.G1232C	p.S411T	TGGACAGCGCCCT	.	scavenged	Atlas-SNP
SNTB2	6645	hgsc.bcm.edu	37	16	69318149	69318149	+	Splice_Site	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	88	4	85	0	0.0454545	0	.	.	none	.	SNTB2	22	.	NM_006750	exon5	c.1345+2T>C	.	TCTAGGTAGAGAT	.	PASS	Atlas-SNP
VCX2	51480	hgsc.bcm.edu	37	X	8138182	8138182	+	Missense_Mutation	SNP	A	A	G	rs41305169	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	95	85	233	2	0.894737	0.00858369	A|0.518;G|0.482	0.482	strong	.	VCX2	16	.	NM_016378	exon3	c.T311C	p.L104P	TGACTCAGGGGGT	.	PASS	Atlas-SNP
DOK7	285489	hgsc.bcm.edu	37	4	3491504	3491504	+	Missense_Mutation	SNP	G	G	A	rs59932476	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	40	99	0	0.45977	0	G|0.946;A|0.054	0.054	strong	.	DOK7	44	.	NM_001164673	exon6	c.G742A	p.G248R	ACATGCGGGCAGG	.	PASS	Atlas-SNP
MKNK1	8569	hgsc.bcm.edu	37	1	47028362	47028362	+	Missense_Mutation	SNP	C	C	T	rs55791614	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	171	104	181	0	0.608187	0	C|0.996;T|0.004	0.004	strong	.	MKNK1	36	.	NM_003684	exon11	c.G922A	p.D308N	CACAGTCGGCCCC	.	PASS	Atlas-SNP
RNF111	54778	hgsc.bcm.edu	37	15	59323048	59323048	+	Missense_Mutation	SNP	C	C	G	rs2899642	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	159	65	148	0	0.408805	0	C|0.704;G|0.296	0.296	strong	.	RNF111	179	.	NM_017610	exon2	c.C27G	p.N9K	ATATAACGAGCTC	.	PASS	Atlas-SNP
CRIPAK	285464	hgsc.bcm.edu	37	4	1388379	1388379	+	Missense_Mutation	SNP	G	G	A	rs56109734	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	90	20	129	2	0.222222	0.0155039	G|0.996;A|0.004	0.004	strong	CRIPAK,NS,carcinoma,0,1	CRIPAK	185	1	NM_175918	exon1	c.G80A	p.C27Y	GCTCATGTGCCCA	.	scavenged	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29912333	29912333	+	Missense_Mutation	SNP	C	C	T	rs3179982	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	149	58	207	0	0.389262	0	C|0.487;T|0.513	0.513	strong	.	HLA-A	89	.	NM_001242758	exon5	c.C952T	p.L318F	GTTCTCCTTGGAG	.	PASS	Atlas-SNP
ATF4	468	hgsc.bcm.edu	37	22	39917515	39917515	+	Missense_Mutation	SNP	A	A	C	rs4894	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	111	110	125	0	0.990991	0	A|0.706;C|0.294	0.294	strong	.	ATF4	27	.	NM_001675	exon1	c.A65C	p.Q22P	TCGACCAGTCGGG	.	PASS	Atlas-SNP
DHRS9	10170	hgsc.bcm.edu	37	2	169952233	169952233	+	Silent	SNP	T	T	C	rs1059261	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	144	68	155	0	0.472222	0	T|0.732;C|0.268	0.268	strong	.	DHRS9	29	.	NM_005771	exon8	c.T916C	p.L306L	TTTTTATTGTTGA	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	77	38	94	0	0.493506	0	G|0.800;A|0.200	0.200	strong	.	EGFL7	11	.	NM_016215	exon8	c.G457A	p.V153I	CGCTGCGTCAACA	.	PASS	Atlas-SNP
STRC	161497	hgsc.bcm.edu	37	15	43892847	43892847	+	Silent	SNP	G	G	C	rs12438025	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	219	69	235	0	0.315068	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
OR5T2	219464	hgsc.bcm.edu	37	11	56000600	56000600	+	Missense_Mutation	SNP	G	G	T	rs3919907	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	20	92	0	0.28169	0	G|0.810;T|0.190	0.190	strong	OR5T2,NS,carcinoma,+1,1	OR5T2	107	1	NM_001004746	exon1	c.C62A	p.S21Y	CAAAAAGAATGAA	.	PASS	Atlas-SNP
MSH3	4437	hgsc.bcm.edu	37	5	79966029	79966029	+	Silent	SNP	G	G	A	rs1805355	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	202	100	204	0	0.49505	0	G|0.817;A|0.183	0.183	strong	.	MSH3	129	.	NM_002439	exon4	c.G693A	p.P231P	TACGCCGCTAGAA	.	PASS	Atlas-SNP
TOP2A	7153	hgsc.bcm.edu	37	17	38548586	38548586	+	Silent	SNP	T	T	G	rs34270904	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	232	108	321	0	0.465517	0	T|0.966;G|0.034	0.034	strong	.	TOP2A	124	.	NM_001067	exon31	c.A3972C	p.T1324T	GAATTTTGTTTTT	.	PASS	Atlas-SNP
CDC20B	166979	hgsc.bcm.edu	37	5	54424381	54424381	+	Silent	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	184	64	199	0	0.347826	0	.	.	none	.	CDC20B	61	.	NM_001170402	exon7	c.C762T	p.Y254Y	CCAGATGTATACA	.	PASS	Atlas-SNP
EPHB4	2050	hgsc.bcm.edu	37	7	100410597	100410597	+	Silent	SNP	G	G	A	rs2230585	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	84	45	113	0	0.535714	0	G|0.683;A|0.317	0.317	strong	.	EPHB4	106	.	NM_004444	exon12	c.C1890T	p.C630C	CCCCCGGCACACC	.	PASS	Atlas-SNP
PPP6R3	55291	hgsc.bcm.edu	37	11	68377475	68377475	+	Missense_Mutation	SNP	A	A	G	rs79540432	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	41	57	0	0.706897	0	A|0.992;G|0.008	0.008	strong	.	PPP6R3	159	.	NM_001164160	exon24	c.A2572G	p.S858G	CCCAGCAGCAGTC	.	PASS	Atlas-SNP
SLC9C1	285335	hgsc.bcm.edu	37	3	111981924	111981924	+	Missense_Mutation	SNP	T	T	C	rs9809404	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	184	182	261	0	0.98913	0	T|0.395;C|0.605	0.605	strong	.	.	.	.	NM_183061	exon10	c.A1044G	p.I348M	AGGGCTTATTAAA	.	PASS	Atlas-SNP
C1QC	714	hgsc.bcm.edu	37	1	22970642	22970642	+	Silent	SNP	C	C	T	rs15940	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	160	78	188	0	0.4875	0	C|0.703;T|0.297	0.297	strong	.	C1QC	35	.	NM_001114101	exon2	c.C126T	p.P42P	CCTGCCCGGGGCA	.	PASS	Atlas-SNP
LRRFIP1	9208	hgsc.bcm.edu	37	2	238668802	238668802	+	Silent	SNP	A	A	G	rs3213868	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	74	48	102	0	0.648649	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
CACNB4	785	hgsc.bcm.edu	37	2	152955482	152955482	+	Missense_Mutation	SNP	G	G	C	rs200662010	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	124	61	117	0	0.491935	0	G|1.000;C|0.000	0.000	strong	.	CACNB4	108	.	NM_001145798	exon1	c.C44G	p.P15R	GAGTGCGGCCCGT	.	PASS	Atlas-SNP
KIAA1549	57670	hgsc.bcm.edu	37	7	138602417	138602417	+	Missense_Mutation	SNP	G	G	A	rs2774960	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	49	24	66	0	0.489796	0	G|0.595;A|0.405	0.405	strong	KIAA1549_ENST00000422774,NS,carcinoma,+1,3	KIAA1549	314	3	NM_020910	exon2	c.C1955T	p.P652L	TCACTCGGCATCA	.	PASS	Atlas-SNP
ZNF431	170959	hgsc.bcm.edu	37	19	21326358	21326358	+	Missense_Mutation	SNP	A	A	G	rs17445374	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	30	73	0	0.428571	0	A|0.836;G|0.164	0.164	strong	.	ZNF431	71	.	NM_133473	exon2	c.A8G	p.D3G	AGGACGACTTGAA	.	PASS	Atlas-SNP
CCL4	6351	hgsc.bcm.edu	37	17	34432663	34432663	+	Silent	SNP	A	A	G	rs1049807	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	389	209	413	0	0.537275	0	A|0.816;G|0.184	0.184	strong	.	CCL4	14	.	NM_002984	exon3	c.A237G	p.E79E	CAGTGAATCCTGG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195515413	195515413	+	Missense_Mutation	SNP	C	C	T	rs55868431	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	41	61	0	0.569444	0	C|0.963;T|0.037	0.037	strong	MUC4_ENST00000463781,NS,carcinoma,-1,2	MUC4	1505	2	NM_018406	exon2	c.G3038A	p.S1013N	GAAGGGCTGGTGA	.	PASS	Atlas-SNP
SDC4	6385	hgsc.bcm.edu	37	20	43976991	43976991	+	Missense_Mutation	SNP	A	A	G	rs2228384	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	54	54	62	0	1	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
WBSCR27	155368	hgsc.bcm.edu	37	7	73254812	73254812	+	Missense_Mutation	SNP	T	T	C	rs13241921	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	119	119	132	1	1	0.00757576	T|0.385;C|0.615	0.615	strong	WBSCR27,colon,carcinoma,0,2	WBSCR27	21	2	NM_152559	exon4	c.A320G	p.Q107R	GGGGCCTGGGCCT	.	PASS	Atlas-SNP
SATL1	340562	hgsc.bcm.edu	37	X	84363140	84363140	+	Missense_Mutation	SNP	A	A	G	rs10126146	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	393	388	595	1	0.987277	0.00168067	A|0.262;0|0.014	.	strong	.	SATL1	70	.	NM_001012980	exon1	c.T835C	p.W279R	CACTCCATTGGTT	.	PASS	Atlas-SNP
SCIN	85477	hgsc.bcm.edu	37	7	12620804	12620804	+	Silent	SNP	C	C	T	rs17283717	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	73	96	0	1	0	C|0.733;T|0.267	0.267	strong	.	SCIN	105	.	NM_001112706	exon3	c.C474T	p.D158D	CTGGGACAGTTTC	.	PASS	Atlas-SNP
ZNF260	339324	hgsc.bcm.edu	37	19	37005298	37005298	+	Silent	SNP	A	A	G	rs76808668	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	59	25	90	0	0.423729	0	A|0.915;G|0.085	0.085	strong	.	ZNF260	34	.	NM_001166038	exon3	c.T843C	p.C281C	TGTTCCACATTCA	.	PASS	Atlas-SNP
ARHGAP23	57636	hgsc.bcm.edu	37	17	36636008	36636008	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	382	35	345	0	0.091623	0	.	.	none	ARHGAP23,NS,carcinoma,0,5	ARHGAP23	48	5	NM_001199417	exon14	c.C2513T	p.P838L	CTGGGCCCAAAGC	.	scavenged	Atlas-SNP
ITIH1	3697	hgsc.bcm.edu	37	3	52825912	52825912	+	Silent	SNP	C	C	A	rs7549	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	195	87	178	0	0.446154	0	C|0.941;A|0.059	0.059	strong	.	ITIH1	108	.	NM_002215	exon22	c.C2721A	p.V907V	TATCGTCCCCGAC	.	PASS	Atlas-SNP
ACHE	43	hgsc.bcm.edu	37	7	100488658	100488658	+	Missense_Mutation	SNP	G	G	C	rs1799806	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	122	52	147	2	0.42623	0.0136054	G|0.724;C|0.276	0.276	strong	ACHE,NS,carcinoma,0,1	ACHE	80	1	NM_015831	exon5	c.C1775G	p.P592R	GGCCTCGGAGCAG	.	scavenged	Atlas-SNP
ECE1	1889	hgsc.bcm.edu	37	1	21573722	21573722	+	Silent	SNP	G	G	A	rs2229450	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	123	64	149	0	0.520325	0	G|0.817;N|0.000;A|0.183	0.183	strong	.	ECE1	76	.	NM_001397	exon9	c.C1155T	p.T385T	TCTGTCGGTGGTG	.	PASS	Atlas-SNP
BUB1B	701	hgsc.bcm.edu	37	15	40488851	40488851	+	Silent	SNP	G	G	A	rs1047130	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	126	65	129	0	0.515873	0	G|0.793;A|0.207	0.207	strong	.	BUB1B	71	.	NM_001211	exon9	c.G1164A	p.A388A	GCAAGCGTCTGAG	.	PASS	Atlas-SNP
SIGLEC9	27180	hgsc.bcm.edu	37	19	51630482	51630482	+	Missense_Mutation	SNP	C	C	A	rs2258983	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	99	37	71	0	0.373737	0	C|0.349;A|0.651	0.651	strong	.	SIGLEC9	85	.	NM_001198558	exon4	c.C944A	p.A315E	GGGATGCAGCTGA	.	PASS	Atlas-SNP
DIP2A	23181	hgsc.bcm.edu	37	21	47961711	47961711	+	Silent	SNP	G	G	A	rs2070435	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	77	27	79	0	0.350649	0	G|0.580;A|0.420	0.420	strong	.	DIP2A	332	.	NM_206891	exon18	c.G2079A	p.L693L	AGTCCTGTCGATG	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	46	46	72	0	1	0	T|0.829;G|0.171	0.171	strong	.	NCOA7	92	.	NM_001199619	exon17	c.T2826G	p.D942E	ATTTGATTGAAAT	.	PASS	Atlas-SNP
HAUS4	54930	hgsc.bcm.edu	37	14	23421593	23421593	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	183	97	206	0	0.530055	0	.	.	none	.	HAUS4	34	.	NM_001166270	exon4	c.C274T	p.L92F	CCACAAGCAACTC	.	PASS	Atlas-SNP
KRTAP10-4	386672	hgsc.bcm.edu	37	21	45994302	45994302	+	Missense_Mutation	SNP	T	T	C	rs201123486	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	234	20	202	17	0.0854701	0.0841584	.	.	weak	KRTAP10-4,NS,carcinoma,0,1	KRTAP10-4	44	1	NM_198687	exon1	c.T667C	p.S223P	TCCTCCTCCTGCC	.	scavenged	Atlas-SNP
ENG	2022	hgsc.bcm.edu	37	9	130605385	130605385	+	Silent	SNP	C	C	T	rs11545664	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	26	10	47	0	0.384615	0	C|0.852;T|0.148	0.148	strong	.	ENG	44	.	NM_001114753	exon2	c.G207A	p.L69L	GAACTCCAGGAAG	.	PASS	Atlas-SNP
ODF2L	57489	hgsc.bcm.edu	37	1	86818572	86818572	+	Silent	SNP	T	T	C	rs272496	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	379	177	434	0	0.467018	0	T|0.315;C|0.685	0.685	strong	.	ODF2L	53	.	NM_001007022	exon17	c.A1863G	p.E621E	ATTTTGTTCTTCA	.	PASS	Atlas-SNP
SCIN	85477	hgsc.bcm.edu	37	7	12617727	12617727	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	148	64	144	0	0.432432	0	.	.	none	.	SCIN	105	.	NM_001112706	exon2	c.A238C	p.I80L	GCTGCCATCTTCA	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105415433	105415433	+	Missense_Mutation	SNP	T	T	C	rs199970974	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	95	22	0	0	0.231579	.	T|0.962;C|0.038	0.038	strong	AHNAK2_ENST00000333244,NS,carcinoma,0,2	AHNAK2	719	2	NM_138420	exon7	c.A6355G	p.M2119V	CCTCCATGCTGGG	.	scavenged	Atlas-SNP
C3orf30	152405	hgsc.bcm.edu	37	3	118867047	118867047	+	Missense_Mutation	SNP	C	C	G	rs9289122	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	234	232	288	0	0.991453	0	C|0.521;G|0.479	0.479	strong	.	C3orf30	64	.	NM_152539	exon2	c.C1419G	p.D473E	AATTGACCAAGGA	.	PASS	Atlas-SNP
PPFIA3	8541	hgsc.bcm.edu	37	19	49641651	49641651	+	Silent	SNP	C	C	T	rs117880896	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	53	27	74	0	0.509434	0	C|0.974;T|0.026	0.026	strong	.	PPFIA3	71	.	NM_003660	exon16	c.C2043T	p.P681P	GGCACCCCCTAGC	.	PASS	Atlas-SNP
ARAP3	64411	hgsc.bcm.edu	37	5	141036337	141036337	+	Silent	SNP	A	A	G	rs7703648	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	33	104	0	0.383721	0	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
RPTOR	57521	hgsc.bcm.edu	37	17	78935197	78935197	+	Silent	SNP	C	C	T	rs9899178	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	34	33	19	0	0.970588	0	C|0.703;T|0.297	0.297	strong	.	RPTOR	122	.	NM_020761	exon31	c.C3609T	p.R1203R	CAGCCGCGTCATG	.	PASS	Atlas-SNP
SYNGAP1	8831	hgsc.bcm.edu	37	6	33405994	33405994	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	285	149	276	2	0.522807	0.00724638	.	.	none	SYNGAP1_ENST00000293748,right_lower_lobe,carcinoma,0,2	SYNGAP1	202	2	NM_006772	exon8	c.G1312A	p.A438T	GAGCCCGCCCTGA	.	scavenged	Atlas-SNP
PER3	8863	hgsc.bcm.edu	37	1	7890024	7890024	+	Missense_Mutation	SNP	T	T	G	rs201662971	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	14	161	0	0.164706	0	.	.	weak	PER3,NS,carcinoma,0,3	PER3	95	3	NM_016831	exon18	c.T2990G	p.M997R	CTCCCATGAAGAA	.	PASS	Atlas-SNP
ZC3H4	23211	hgsc.bcm.edu	37	19	47571039	47571039	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	33	6	46	0	0.181818	0	.	.	none	.	ZC3H4	96	.	NM_015168	exon15	c.C2486T	p.S829F	CGGCTGGACGTCT	.	PASS	Atlas-SNP
SLCO1C1	53919	hgsc.bcm.edu	37	12	20876168	20876168	+	Missense_Mutation	SNP	C	C	T	rs144285413	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	213	111	296	0	0.521127	0	C|0.994;T|0.006	0.006	strong	.	SLCO1C1	216	.	NM_017435	exon9	c.C1166T	p.S389F	CATCCTCCAGGGC	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179643775	179643775	+	Missense_Mutation	SNP	C	C	T	rs36021856	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	144	76	174	0	0.527778	0	C|0.993;T|0.007	0.007	strong	.	TTN	18412	.	NM_001267550	exon24	c.G4034A	p.G1345D	GCTCTGCCATCTT	.	PASS	Atlas-SNP
SPATA22	84690	hgsc.bcm.edu	37	17	3352294	3352294	+	Missense_Mutation	SNP	A	A	G	rs1488689	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	247	128	321	1	0.518219	0.00311526	A|0.769;G|0.231	0.231	strong	.	SPATA22	49	.	NM_032598	exon6	c.T479C	p.I160T	TCAGGTATTCTTA	.	PASS	Atlas-SNP
DOCK1	1793	hgsc.bcm.edu	37	10	129216658	129216658	+	Silent	SNP	T	T	C	rs2229600	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	56	27	41	0	0.482143	0	A|0.000;C|0.325;G|0.000;T|0.674	0.325	strong	.	DOCK1	188	.	NM_001380	exon45	c.T4482C	p.I1494I	TGCCATTGAGACC	.	PASS	Atlas-SNP
KRTAP10-3	386682	hgsc.bcm.edu	37	21	45978592	45978592	+	Missense_Mutation	SNP	T	T	C	rs452472	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	116	48	93	0	0.413793	0	T|0.735;C|0.265	0.265	strong	KRTAP10-3,rectum,carcinoma,0,1	KRTAP10-3	17	1	NM_198696	exon1	c.A7G	p.T3A	TAGACGTGGCCAT	.	PASS	Atlas-SNP
RPH3A	22895	hgsc.bcm.edu	37	12	113325629	113325629	+	Silent	SNP	T	T	C	rs4141253	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	68	35	73	0	0.514706	0	T|0.535;C|0.465	0.465	strong	.	RPH3A	98	.	NM_001143854	exon17	c.T1464C	p.F488F	CAAATTTGGCCAC	.	PASS	Atlas-SNP
PPP6R1	22870	hgsc.bcm.edu	37	19	55756980	55756980	+	Silent	SNP	A	A	G	rs3745920	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	71	41	0	0.986111	0	A|0.789;G|0.211	0.211	strong	PPP6R1_ENST00000412770,NS,carcinoma,0,2	PPP6R1	63	2	NM_014931	exon3	c.T294C	p.A98A	CTCATCAGCACCC	.	PASS	Atlas-SNP
CES1	1066	hgsc.bcm.edu	37	16	55862720	55862720	+	Silent	SNP	T	T	C	rs74019278	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	107	25	149	0	0.233645	0	T|0.634;C|0.366	0.366	strong	CES1_ENST00000360526,caecum,carcinoma,0,2	CES1	78	2	NM_001025195	exon2	c.A219G	p.E73E	CCATGGTTCTGCA	.	PASS	Atlas-SNP
PASK	23178	hgsc.bcm.edu	37	2	242063448	242063448	+	Silent	SNP	G	G	A	rs2302052	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	25	125	0	0.347222	0	G|0.898;A|0.102	0.102	strong	.	PASK	230	.	NM_015148	exon11	c.C2820T	p.A940A	CCTGGCGGCTGAG	.	PASS	Atlas-SNP
MUC20	200958	hgsc.bcm.edu	37	3	195452689	195452689	+	Silent	SNP	C	C	T	rs2688541	bycluster;by2hit2allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	814	443	829	1	0.544226	0.00120627	T|1.000;|0.000	1.000	weak	MUC20,NS,carcinoma,0,1	MUC20	84	1	NM_152673	exon3	c.C702T	p.D234D	ATCTGACGTCACT	.	scavenged	Atlas-SNP
CAMKK2	10645	hgsc.bcm.edu	37	12	121691088	121691088	+	Silent	SNP	G	G	T	rs3815990	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	174	97	184	0	0.557471	0	G|0.958;T|0.042	0.042	strong	.	CAMKK2	87	.	NM_153500	exon10	c.C1095A	p.I365I	AGAGAAGATCTTG	.	PASS	Atlas-SNP
PRG4	10216	hgsc.bcm.edu	37	1	186276661	186276661	+	Missense_Mutation	SNP	A	A	G	rs61831150	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	54	50	73	0	0.925926	0	A|0.713;G|0.287	0.287	strong	PRG4,brain,glioma,0,1	PRG4	259	1	NM_005807	exon7	c.A1810G	p.T604A	CCCACCACTCCCA	.	PASS	Atlas-SNP
LILRB2	10288	hgsc.bcm.edu	37	19	54783836	54783836	+	Silent	SNP	G	G	A	rs111453734	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	84	49	92	0	0.583333	0	G|0.997;A|0.003	0.003	strong	.	LILRB2	94	.	NM_005874	exon4	c.C165T	p.A55A	CTCCTGGGCTTCA	.	PASS	Atlas-SNP
CAPS	828	hgsc.bcm.edu	37	19	5915300	5915300	+	Missense_Mutation	SNP	C	C	A	rs147363394	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	111	57	97	0	0.513514	0	C|0.999;A|0.001	0.001	strong	.	CAPS	14	.	NM_004058	exon5	c.C537A	p.F179L	GGAGTTCGTGGCC	.	PASS	Atlas-SNP
MFF	56947	hgsc.bcm.edu	37	2	228197238	228197238	+	Silent	SNP	G	G	A	rs11557342	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	211	91	243	0	0.43128	0	G|0.922;A|0.078	0.078	strong	MFF,NS,carcinoma,0,1	MFF	48	1	NM_020194	exon5	c.G363A	p.T121T	ACTTACGCTGAGT	.	PASS	Atlas-SNP
PLA2G7	7941	hgsc.bcm.edu	37	6	46672943	46672943	+	Missense_Mutation	SNP	A	A	G	rs1051931	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	85	119	1	0.977012	0.00840336	A|0.223;G|0.777	0.777	strong	.	PLA2G7	49	.	NM_005084	exon11	c.T1136C	p.V379A	ATAGCTACATTTG	.	PASS	Atlas-SNP
PDE1C	5137	hgsc.bcm.edu	37	7	31855569	31855569	+	Silent	SNP	G	G	A	rs2302450	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	209	156	269	0	0.746412	0	G|0.761;A|0.239	0.239	strong	PDE1C_ENST00000396191,NS,carcinoma,0,2	PDE1C	465	2	NM_001191058	exon16	c.C1962T	p.A654A	CTTCTCGGCTTTG	.	PASS	Atlas-SNP
WNT9A	7483	hgsc.bcm.edu	37	1	228113046	228113046	+	Silent	SNP	C	C	T	rs8192629	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	124	60	81	0	0.483871	0	C|0.927;T|0.073	0.073	strong	.	WNT9A	39	.	NM_003395	exon2	c.G270A	p.A90A	CTCGAGCGCACTC	.	PASS	Atlas-SNP
DDX11	1663	hgsc.bcm.edu	37	12	31244716	31244716	+	Silent	SNP	C	C	T	rs77924271	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	414	126	454	0	0.304348	0	T|1.000;|0.000	1.000	weak	.	DDX11	188	.	NM_030653	exon10	c.C1153T	p.L385L	ATCCGGCTGCAGG	.	PASS	Atlas-SNP
HHLA2	11148	hgsc.bcm.edu	37	3	108081247	108081247	+	Silent	SNP	G	G	A	rs16854512	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	27	80	0	0.465517	0	G|0.836;A|0.164	0.164	strong	.	HHLA2	95	.	NM_007072	exon7	c.G1062A	p.A354A	CTCTGCGATTTTG	.	PASS	Atlas-SNP
BCAS3	54828	hgsc.bcm.edu	37	17	58952044	58952044	+	Silent	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	49	25	48	0	0.510204	0	.	.	none	.	BCAS3	90	.	NM_001099432	exon9	c.G606A	p.Q202Q	CTTGCAGGAGAAA	.	PASS	Atlas-SNP
CASZ1	54897	hgsc.bcm.edu	37	1	10703243	10703243	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	51	16	59	0	0.313726	0	.	.	none	.	CASZ1	150	.	NM_001079843	exon19	c.A3994T	p.N1332Y	CGAAGTTCTTCCC	.	PASS	Atlas-SNP
AGRN	375790	hgsc.bcm.edu	37	1	986732	986732	+	Missense_Mutation	SNP	G	G	A	rs144245019	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	74	56	66	0	0.756757	0	G|0.993;A|0.007	0.007	strong	.	AGRN	110	.	NM_198576	exon31	c.G5353A	p.D1785N	GGCTTCGACGGTG	.	PASS	Atlas-SNP
KRTAP10-2	386679	hgsc.bcm.edu	37	21	45971299	45971299	+	Missense_Mutation	SNP	T	T	C	rs233240	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	109	33	100	0	0.302752	0	T|0.767;C|0.233	0.233	strong	KRTAP10-2,bladder,carcinoma,0,3	KRTAP10-2	21	3	NM_198693	exon1	c.A43G	p.N15D	AGGAGTTGGTGCA	.	PASS	Atlas-SNP
KIFC3	3801	hgsc.bcm.edu	37	16	57795343	57795343	+	Silent	SNP	G	G	A	rs12920931	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	223	127	173	0	0.569507	0	G|0.970;A|0.030	0.030	strong	.	KIFC3	55	.	NM_001130100	exon14	c.C1854T	p.S618S	GTCCACGCTCTGC	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	161	159	171	0	0.987578	0	C|0.624;T|0.376	0.376	strong	.	TTN	18412	.	NM_001267550	exon123	c.G31864A	p.G10622R	CAACTCCCTTCTG	.	PASS	Atlas-SNP
BTBD16	118663	hgsc.bcm.edu	37	10	124089075	124089075	+	Missense_Mutation	SNP	G	G	A	rs986178	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	48	21	29	0	0.4375	0	G|0.902;A|0.098	0.098	strong	BTBD16,NS,carcinoma,0,1	BTBD16	44	1	NM_144587	exon11	c.G992A	p.G331D	TGCACGGCATCAC	.	PASS	Atlas-SNP
SHPRH	257218	hgsc.bcm.edu	37	6	146267376	146267376	+	Silent	SNP	T	T	C	rs201477770	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	20	10	57	0	0.5	0	T|1.000;C|0.000	0.000	strong	.	SHPRH	169	.	NM_173082	exon7	c.A1314G	p.Q438Q	AGGGCATTGAACT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195511526	195511526	+	Missense_Mutation	SNP	C	C	T	rs200787582	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	20	9	57	2	0.45	0.0350877	C|0.823;T|0.177	0.177	strong	MUC4_ENST00000463781,NS,carcinoma,+1,5	MUC4	1505	5	NM_018406	exon2	c.G6925A	p.D2309N	AAGCGTCGGTGAC	.	scavenged	Atlas-SNP
APH1B	83464	hgsc.bcm.edu	37	15	63594660	63594660	+	Missense_Mutation	SNP	G	G	T	rs61751105	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	166	67	129	0	0.403614	0	G|0.990;T|0.010	0.010	strong	.	APH1B	27	.	NM_031301	exon5	c.G595T	p.V199L	CTGCTGGTGTCAG	.	PASS	Atlas-SNP
ZFP69	339559	hgsc.bcm.edu	37	1	40961449	40961449	+	Silent	SNP	T	T	C	rs3795348	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	66	37	109	0	0.560606	0	T|0.960;C|0.040	0.040	strong	.	.	.	.	NM_198494	exon6	c.T1299C	p.H433H	AATCCATACTGGG	.	PASS	Atlas-SNP
ALCAM	214	hgsc.bcm.edu	37	3	105266331	105266331	+	Silent	SNP	A	A	G	rs9855810	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	183	99	180	0	0.540984	0	A|0.924;G|0.076	0.076	strong	.	ALCAM	71	.	NM_001627	exon11	c.A1338G	p.Q446Q	CATTCAATGGACA	.	PASS	Atlas-SNP
ANO7	50636	hgsc.bcm.edu	37	2	242147054	242147054	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	49	11	50	0	0.22449	0	.	.	none	.	ANO7	136	.	NM_001001891	exon11	c.G1208A	p.W403X	CTTTCTGGCTGCT	.	PASS	Atlas-SNP
ARL10	285598	hgsc.bcm.edu	37	5	175793532	175793532	+	Silent	SNP	C	C	T	rs2303666	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	100	44	87	0	0.44	0	C|0.894;T|0.106	0.106	strong	.	ARL10	19	.	NM_173664	exon2	c.C333T	p.G111G	CTGGGGCTTCAAC	.	PASS	Atlas-SNP
JSRP1	126306	hgsc.bcm.edu	37	19	2253687	2253687	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	20	9	15	0	0.45	0	.	.	none	.	JSRP1	18	.	NM_144616	exon5	c.C368T	p.S123L	TTGAGCGACAGGT	.	PASS	Atlas-SNP
KRTAP4-3	85290	hgsc.bcm.edu	37	17	39324104	39324104	+	Silent	SNP	A	A	G	rs368619075		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	192	2	247	4	0.0104167	0.0161943	.	.	weak	KRTAP4-3,colon,carcinoma,0,1	KRTAP4-3	40	1	NM_033187	exon1	c.T321C	p.S107S	GCAACTAGAAATG	.	scavenged	Atlas-SNP
ZNF880	400713	hgsc.bcm.edu	37	19	52888050	52888050	+	Missense_Mutation	SNP	A	A	G	rs76053634	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	7	7	33	0	1	0	A|0.867;G|0.133	0.133	strong	ZNF880,colon,carcinoma,0,2	ZNF880	45	2	NM_001145434	exon4	c.A1217G	p.Q406R	GAGAGCAACCTTA	.	PASS	Atlas-SNP
C5orf52	100190949	hgsc.bcm.edu	37	5	157102159	157102159	+	Missense_Mutation	SNP	G	G	A	rs10051838	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	102	44	102	0	0.431373	0	G|0.823;A|0.177	0.177	strong	C5orf52,NS,carcinoma,+1,1	C5orf52	17	1	NM_001145132	exon2	c.G272A	p.R91Q	TATCTCGGGTGAT	.	PASS	Atlas-SNP
NSA2	10412	hgsc.bcm.edu	37	5	74069863	74069863	+	Silent	SNP	A	A	G	rs6874609	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	95	62	72	0	0.652632	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
OR56B1	387748	hgsc.bcm.edu	37	11	5757785	5757785	+	Silent	SNP	C	C	T	rs12792180	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	122	101	138	0	0.827869	0	C|0.895;T|0.105	0.105	strong	.	OR56B1	38	.	NM_001005180	exon1	c.C39T	p.S13S	CAATAGCTCCAAA	.	PASS	Atlas-SNP
IGSF10	285313	hgsc.bcm.edu	37	3	151162998	151162998	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	149	2	178	1	0.0134228	0.00561798	.	.	none	IGSF10,NS,carcinoma,+2,1	IGSF10	279	1	NM_178822	exon4	c.G4771A	p.E1591K	TTACTTCTGGCTT	.	scavenged	Atlas-SNP
UGT2B7	7364	hgsc.bcm.edu	37	4	69972952	69972952	+	Silent	SNP	C	C	T	rs4348159	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	108	43	153	0	0.398148	0	C|0.845;T|0.155	0.155	strong	.	UGT2B7	79	.	NM_001074	exon4	c.C1062T	p.Y354Y	GCTCTACAAGTGG	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	179	72	191	0	0.402235	0	C|0.631;T|0.368	0.368	strong	.	MEP1B	54	.	NM_005925	exon14	c.C2084T	p.P695L	TGACTCCGCAAAA	.	PASS	Atlas-SNP
SGK494	0	hgsc.bcm.edu	37	17	26938651	26938651	+	Missense_Mutation	SNP	C	C	T	rs34026109	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	67	36	76	0	0.537313	0	C|0.980;T|0.020	0.020	strong	.	.	.	.	NM_001174103	exon9	c.G745A	p.G249S	ACAGACCAAAGTC	.	PASS	Atlas-SNP
TMEM151A	256472	hgsc.bcm.edu	37	11	66062014	66062014	+	Silent	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	68	38	52	0	0.558824	0	.	.	none	.	TMEM151A	39	.	NM_153266	exon2	c.G297A	p.L99L	CTACCTGTACATC	.	PASS	Atlas-SNP
SLC7A13	157724	hgsc.bcm.edu	37	8	87235273	87235273	+	Missense_Mutation	SNP	C	C	T	rs2976189	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	113	112	121	0	0.99115	0	C|0.874;T|0.126	0.126	strong	.	SLC7A13	97	.	NM_138817	exon2	c.G745A	p.V249M	CAGTCACCAGAGG	.	PASS	Atlas-SNP
MYO10	4651	hgsc.bcm.edu	37	5	16794780	16794780	+	Missense_Mutation	SNP	G	G	A	rs7737765	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	130	56	91	0	0.430769	0	G|0.839;A|0.161	0.161	strong	.	MYO10	198	.	NM_012334	exon4	c.C442T	p.H148Y	TGTCGTGGCGCTT	.	PASS	Atlas-SNP
SIRT3	23410	hgsc.bcm.edu	37	11	233067	233067	+	Missense_Mutation	SNP	C	C	T	rs11246020	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	289	229	278	0	0.792388	0	T|0.146;C|0.854	0.146	strong	.	SIRT3	28	.	NM_012239	exon3	c.G622A	p.V208I	GAGTGACGTTGGG	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105418638	105418638	+	Silent	SNP	A	A	G	rs78353106	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	178	67	106	0	0.376404	0	A|0.849;G|0.151	0.151	strong	.	AHNAK2	719	.	NM_138420	exon7	c.T3150C	p.P1050P	AGAAGCAGGCTGA	.	PASS	Atlas-SNP
AGO2	27161	hgsc.bcm.edu	37	8	141566311	141566311	+	Silent	SNP	C	C	T	rs2271738	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	125	104	168	0	0.832	0	C|0.623;T|0.377	0.377	strong	.	.	.	.	NM_012154	exon9	c.G1101A	p.A367A	AGCAGTCGCTCTG	.	PASS	Atlas-SNP
DDX60L	91351	hgsc.bcm.edu	37	4	169369862	169369862	+	Missense_Mutation	SNP	A	A	T	rs10029536	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	255	116	338	0	0.454902	0	A|0.918;T|0.082	0.082	strong	.	DDX60L	116	.	NM_001012967	exon9	c.T1065A	p.N355K	AACATGATTTAAA	.	PASS	Atlas-SNP
CDH5	1003	hgsc.bcm.edu	37	16	66432424	66432424	+	Silent	SNP	C	C	T	rs3826229	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	105	105	112	0	1	0	A|0.000;C|0.632;G|0.000;T|0.368	0.368	strong	CDH5,NS,carcinoma,+1,2	CDH5	111	2	NM_001795	exon10	c.C1551T	p.I517I	ATTCATCTTGAAT	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179477717	179477717	+	Silent	SNP	A	A	G	rs2115558	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	136	58	120	0	0.426471	0	A|0.929;G|0.071	0.071	strong	.	TTN	18412	.	NM_001267550	exon265	c.T49731C	p.H16577H	TCCATCATGTTCT	.	PASS	Atlas-SNP
TNN	63923	hgsc.bcm.edu	37	1	175087885	175087885	+	Missense_Mutation	SNP	A	A	G	rs6694078	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	155	77	159	1	0.496774	0.00628931	A|0.852;G|0.148	0.148	strong	TNN,NS,carcinoma,0,1	TNN	297	1	NM_022093	exon11	c.A2575G	p.M859V	CCGGGCATGGAGT	.	scavenged	Atlas-SNP
GRK7	131890	hgsc.bcm.edu	37	3	141497368	141497368	+	Missense_Mutation	SNP	G	G	A	rs34429284	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	108	46	120	0	0.425926	0	G|0.998;A|0.002	0.002	strong	.	GRK7	65	.	NM_139209	exon1	c.G242A	p.R81H	CGTTCCGCAAGGC	.	PASS	Atlas-SNP
CTAGE15	441294	hgsc.bcm.edu	37	7	143270172	143270172	+	Missense_Mutation	SNP	A	A	G	rs72611576	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	210	183	25	0	0.871429	0	A|0.440;G|0.560	0.560	strong	.	.	.	.	NM_001008747	exon1	c.A1262G	p.E421G	TGGAAGAAAAGCT	.	PASS	Atlas-SNP
SLC25A27	9481	hgsc.bcm.edu	37	6	46623698	46623698	+	Silent	SNP	T	T	C	rs3757241	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	106	106	140	0	1	0	T|0.141;C|0.859	0.859	strong	.	SLC25A27	22	.	NM_001204051	exon2	c.T225C	p.A75A	CACAGCTCTAGGG	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	20	100	0	0.25641	0	C|0.742;T|0.258	0.258	strong	.	KRTAP10-2	21	.	NM_198693	exon1	c.G624A	p.P208P	GCAGCACGGAGAG	.	PASS	Atlas-SNP
CCDC158	339965	hgsc.bcm.edu	37	4	77305346	77305346	+	Silent	SNP	A	A	G	rs17001890	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	91	41	126	0	0.450549	0	A|0.776;G|0.224	0.224	strong	.	CCDC158	114	.	NM_001042784	exon5	c.T621C	p.H207H	GCTGTCATGTTCA	.	PASS	Atlas-SNP
SPATA19	219938	hgsc.bcm.edu	37	11	133714522	133714522	+	Missense_Mutation	SNP	G	G	A	rs2282602	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	68	50	107	0	0.735294	0	G|0.673;A|0.327	0.327	strong	.	SPATA19	36	.	NM_174927	exon3	c.C149T	p.A50V	CGAGAAGCCTCTT	.	PASS	Atlas-SNP
MON1A	84315	hgsc.bcm.edu	37	3	49949071	49949071	+	Silent	SNP	A	A	G	rs868891	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	79	50	107	0	0.632911	0	A|0.671;G|0.329	0.329	strong	MON1A,NS,carcinoma,0,1	MON1A	41	1	NM_032355	exon3	c.T792C	p.P264P	GTACACAGGCTTC	.	PASS	Atlas-SNP
INHBA	3624	hgsc.bcm.edu	37	7	41729843	41729843	+	Missense_Mutation	SNP	C	C	T	rs138819536	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	54	43	82	0	0.796296	0	C|0.998;T|0.002	0.002	strong	INHBA,NS,carcinoma,0,1	INHBA	118	1	NM_002192	exon3	c.G686A	p.R229Q	AGCAACCGCTGGA	.	PASS	Atlas-SNP
GPR149	344758	hgsc.bcm.edu	37	3	154147336	154147336	+	Silent	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	146	33	167	0	0.226027	0	.	.	none	GPR149,NS,carcinoma,-1,1	GPR149	134	1	NM_001038705	exon1	c.G69A	p.T23T	AAGGTCCGTAGAA	.	PASS	Atlas-SNP
CCDC169	728591	hgsc.bcm.edu	37	13	36801415	36801415	+	Missense_Mutation	SNP	C	C	T	rs9546785	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	180	176	265	0	0.977778	0	C|0.624;T|0.376	0.376	strong	.	CCDC169	20	.	NM_001198908	exon8	c.G649A	p.G217R	TTTGTCCGAGGCA	.	PASS	Atlas-SNP
ADAMTSL3	57188	hgsc.bcm.edu	37	15	84651185	84651185	+	Silent	SNP	C	C	A	rs8031704	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	197	196	165	0	0.994924	0	C|0.593;A|0.407	0.407	strong	ADAMTSL3,NS,adenoma,0,2	ADAMTSL3	290	2	NM_207517	exon21	c.C2805A	p.P935P	GTGCCCCGTGCGA	.	PASS	Atlas-SNP
TMEM9B	56674	hgsc.bcm.edu	37	11	8977830	8977830	+	Silent	SNP	A	A	G	rs2568068	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	54	6	48	0	0.111111	0	T|0.006;G|0.283	0.283	strong	.	TMEM9B	6	.	NM_020644	exon3	c.T213C	p.V71V	CTCCACAACATGA	.	PASS	Atlas-SNP
RADIL	55698	hgsc.bcm.edu	37	7	4856904	4856904	+	Missense_Mutation	SNP	T	T	C	rs201312293	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	100	65	124	0	0.65	0	T|0.997;C|0.003	0.003	strong	RADIL,right_upper_lobe,carcinoma,0,1	RADIL	110	1	NM_018059	exon7	c.A1694G	p.Y565C	AAGGCGTACAGCA	.	PASS	Atlas-SNP
AMPD2	271	hgsc.bcm.edu	37	1	110170896	110170896	+	Silent	SNP	T	T	C	rs863978	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	69	92	0	0.985714	0	T|0.265;C|0.735	0.735	strong	.	AMPD2	75	.	NM_004037	exon10	c.T1434C	p.H478H	TGTGCATGCGGTC	.	PASS	Atlas-SNP
ABCA7	10347	hgsc.bcm.edu	37	19	1047161	1047161	+	Silent	SNP	A	A	G	rs3752237	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	55	28	50	0	0.509091	0	A|0.347;G|0.653	0.653	strong	.	ABCA7	174	.	NM_019112	exon15	c.A1851G	p.G617G	GCTGGGAGACATC	.	PASS	Atlas-SNP
CCDC148	130940	hgsc.bcm.edu	37	2	159201754	159201754	+	Missense_Mutation	SNP	T	T	C	rs4664950	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	240	117	269	0	0.4875	0	C|0.020;G|0.000;T|0.980	0.020	strong	.	CCDC148	64	.	NM_138803	exon3	c.A224G	p.Q75R	TATTCCTGCCACC	.	PASS	Atlas-SNP
C19orf45	374877	hgsc.bcm.edu	37	19	7573301	7573301	+	Silent	SNP	C	C	T	rs3087602		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	99	34	107	0	0.343434	0	.	.	weak	.	C19orf45	36	.	NM_198534	exon9	c.C1503T	p.C501C	CCTGTGCCCCAGC	.	PASS	Atlas-SNP
POF1B	79983	hgsc.bcm.edu	37	X	84563135	84563135	+	Missense_Mutation	SNP	T	T	A	rs363774	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	151	150	246	0	0.993378	0	T|0.137;0|0.004	.	strong	.	POF1B	77	.	NM_024921	exon10	c.A1045T	p.M349L	CTGTCATATCATT	.	PASS	Atlas-SNP
KIF21B	23046	hgsc.bcm.edu	37	1	200978027	200978027	+	Missense_Mutation	SNP	G	G	A	rs140589352	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	51	26	42	0	0.509804	0	G|0.987;A|0.013	0.013	strong	.	KIF21B	208	.	NM_017596	exon3	c.C317T	p.S106L	TCCTCCGACGTTG	.	PASS	Atlas-SNP
TNKS1BP1	85456	hgsc.bcm.edu	37	11	57081197	57081197	+	Missense_Mutation	SNP	G	G	C	rs4939134	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	168	168	211	1	1	0.00473934	G|0.586;C|0.414	0.414	strong	.	TNKS1BP1	148	.	NM_033396	exon5	c.C965G	p.T322S	TCAGGAGTCTGGG	.	PASS	Atlas-SNP
DNAH14	127602	hgsc.bcm.edu	37	1	225555512	225555512	+	Silent	SNP	C	C	T	rs11578981	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	43	21	52	0	0.488372	0	C|0.637;T|0.363	0.363	strong	.	DNAH14	300	.	NM_001373	exon75	c.C11817T	p.A3939A	GATTGCCGTGGAA	.	PASS	Atlas-SNP
KCNJ2	3759	hgsc.bcm.edu	37	17	68172326	68172326	+	Silent	SNP	C	C	T	rs173135	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	49	23	81	0	0.469388	0	C|0.867;T|0.133	0.133	strong	.	KCNJ2	74	.	NM_000891	exon2	c.C1146T	p.L382L	TGCCCTCACAAGC	.	PASS	Atlas-SNP
SHROOM3	57619	hgsc.bcm.edu	37	4	77661017	77661017	+	Missense_Mutation	SNP	A	A	C	rs76656494	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	50	26	79	0	0.52	0	A|0.988;C|0.012	0.012	strong	.	SHROOM3	134	.	NM_020859	exon5	c.A1691C	p.E564A	TGCCTGAAAATGA	.	PASS	Atlas-SNP
TTLL3	26140	hgsc.bcm.edu	37	3	9876919	9876919	+	Missense_Mutation	SNP	G	G	A	rs1057278	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	48	48	60	0	1	0	G|0.859;A|0.141	0.141	strong	.	TTLL3	51	.	NM_001025930	exon13	c.G2494A	p.A832T	CCCAGGGCTGAGG	.	PASS	Atlas-SNP
CES1	1066	hgsc.bcm.edu	37	16	55862883	55862883	+	Missense_Mutation	SNP	C	C	A	rs3826190	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	44	6	82	0	0.136364	0	C|0.632;A|0.368	0.368	strong	CES1_ENST00000360526,NS,carcinoma,0,1	CES1	78	1	NM_001025195	exon2	c.G56T	p.G19V	GGATGCCCTGCTG	.	scavenged	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195511780	195511780	+	Missense_Mutation	SNP	G	G	A	rs391928	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	83	17	104	0	0.204819	0	G|0.789;A|0.211	0.211	strong	MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	NM_018406	exon2	c.C6671T	p.P2224L	AGAAGAGGGATGG	.	PASS	Atlas-SNP
ARSD	414	hgsc.bcm.edu	37	X	2836181	2836181	+	Missense_Mutation	SNP	A	A	T	rs73632975	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	133	17	141	0	0.12782	0	A|0.913;T|0.087	0.087	strong	.	ARSD	47	.	NM_001669	exon5	c.T527A	p.M176K	AAGGGCATGCCGT	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179435337	179435337	+	Silent	SNP	T	T	G	rs6732060	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	159	74	163	0	0.465409	0	T|0.892;G|0.108	0.108	strong	.	TTN	18412	.	NM_001267550	exon326	c.A75522C	p.A25174A	ACGTACTGCATCT	.	PASS	Atlas-SNP
KRT84	3890	hgsc.bcm.edu	37	12	52778829	52778829	+	Missense_Mutation	SNP	C	C	A	rs140632920	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	98	55	111	0	0.561224	0	C|0.998;A|0.002	0.002	strong	.	KRT84	61	.	NM_033045	exon1	c.G541T	p.D181Y	CCTTGTCAATGAA	.	PASS	Atlas-SNP
SLC25A39	51629	hgsc.bcm.edu	37	17	42398052	42398052	+	Missense_Mutation	SNP	A	A	G	rs2011951	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	94	45	80	0	0.478723	0	A|0.426;G|0.574	0.574	strong	.	SLC25A39	24	.	NM_001143780	exon9	c.T739C	p.F247L	GCCTGAACCCATT	.	PASS	Atlas-SNP
AP5Z1	9907	hgsc.bcm.edu	37	7	4830971	4830971	+	Silent	SNP	G	G	T	rs77393809	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	153	39	142	0	0.254902	0	G|0.985;T|0.015	0.015	strong	.	.	.	.	NM_014855	exon17	c.G2379T	p.T793T	GCGCACGGTCAGC	.	PASS	Atlas-SNP
PDLIM5	10611	hgsc.bcm.edu	37	4	95496940	95496940	+	Silent	SNP	G	G	A	rs115743950	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	205	115	203	0	0.560976	0	G|0.991;A|0.009	0.009	strong	PDLIM5,NS,carcinoma,+1,2	PDLIM5	76	2	NM_006457	exon5	c.G465A	p.A155A	CCATGCGACCACC	.	PASS	Atlas-SNP
AMPD1	270	hgsc.bcm.edu	37	1	115236057	115236057	+	Nonsense_Mutation	SNP	G	G	A	rs17602729	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	162	79	216	1	0.487654	0.00462963	G|0.923;A|0.077	0.077	strong	AMPD1_ENST00000520113,NS,carcinoma,0,2	AMPD1	223	2	NM_000036	exon2	c.C133T	p.Q45X	ACTCACGTTTCTC	.	PASS	Atlas-SNP
DHX9	1660	hgsc.bcm.edu	37	1	182845346	182845346	+	Silent	SNP	C	C	T	rs35533583	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	195	95	235	0	0.487179	0	C|0.976;T|0.024	0.024	strong	.	DHX9	114	.	NM_001357	exon17	c.C1977T	p.G659G	GCCTGGCTGGAAT	.	PASS	Atlas-SNP
HIST1H3G	8355	hgsc.bcm.edu	37	6	26271208	26271208	+	Silent	SNP	T	T	C	rs141036055	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	50	22	84	0	0.44	0	T|0.999;C|0.001	0.001	strong	.	HIST1H3G	20	.	NM_003534	exon1	c.A405G	p.R135R	CTACGCTCTCTCC	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	141	75	142	0	0.531915	0	G|0.380;A|0.620	0.620	strong	.	.	.	.	NM_178466	exon4	c.G406A	p.V136I	AACATCGTAAAGA	.	PASS	Atlas-SNP
DENND5A	23258	hgsc.bcm.edu	37	11	9225486	9225486	+	Missense_Mutation	SNP	C	C	G	rs952374	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	81	97	0	0.80198	0	C|0.715;G|0.285	0.285	strong	.	DENND5A	84	.	NM_015213	exon4	c.G670C	p.E224Q	GTTGCTCCAGCAC	.	PASS	Atlas-SNP
ZNF804A	91752	hgsc.bcm.edu	37	2	185801871	185801871	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	60	20	69	0	0.333333	0	.	.	none	.	ZNF804A	322	.	NM_194250	exon4	c.A1748T	p.K583I	GGTTGAAAGAGAC	.	PASS	Atlas-SNP
UGT1A5	54579	hgsc.bcm.edu	37	2	234621661	234621661	+	Silent	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	150	2	177	0	0.0133333	0	.	.	none	UGT1A5,NS,malignant_melanoma,+2,1	UGT1A5	66	1	NM_019078	exon1	c.C24T	p.P8P	GGTTCCCCTGCCG	.	scavenged	Atlas-SNP
NSMAF	8439	hgsc.bcm.edu	37	8	59508166	59508166	+	Silent	SNP	A	A	G	rs149564750	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	185	41	270	0	0.221622	0	A|0.994;G|0.006	0.006	strong	.	NSMAF	156	.	NM_001144772	exon22	c.T1938C	p.N646N	GATGTTATTCCAG	.	PASS	Atlas-SNP
LPP	4026	hgsc.bcm.edu	37	3	188590446	188590446	+	Silent	SNP	A	A	G	rs1136644	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	183	95	212	0	0.519126	0	A|0.579;G|0.421	0.421	strong	LPP_ENST00000312675,NS,carcinoma,+1,1	LPP	72	1	NM_005578	exon10	c.A1605G	p.R535R	CCCGCGATGTTCT	.	PASS	Atlas-SNP
ARHGAP6	395	hgsc.bcm.edu	37	X	11682921	11682921	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	110	37	114	0	0.336364	0	.	.	none	.	ARHGAP6	130	.	NM_006125	exon1	c.G28T	p.V10F	AGAAGACGCTGTG	.	PASS	Atlas-SNP
ALOXE3	59344	hgsc.bcm.edu	37	17	8021608	8021608	+	Missense_Mutation	SNP	G	G	C	rs3027229	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	65	31	89	0	0.476923	0	G|0.877;C|0.123	0.123	strong	.	ALOXE3	145	.	NM_001165960	exon2	c.C97G	p.P33A	TATCAGGAGCCTG	.	PASS	Atlas-SNP
TMPRSS13	84000	hgsc.bcm.edu	37	11	117779305	117779305	+	Missense_Mutation	SNP	C	C	A	rs80264810	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	32	8	57	0	0.25	0	C|0.971;A|0.029	0.029	strong	.	TMPRSS13	75	.	NM_001206790	exon9	c.G1304T	p.R435L	GGAGAGCGGGGAG	.	PASS	Atlas-SNP
HIST1H1E	3008	hgsc.bcm.edu	37	6	26156817	26156817	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	10	90	0	0.138889	0	.	.	none	.	HIST1H1E	69	.	NM_005321	exon1	c.G199A	p.A67T	GCGCTGGCAGCCG	.	PASS	Atlas-SNP
SIGLEC1	6614	hgsc.bcm.edu	37	20	3672836	3672836	+	Silent	SNP	G	G	A	rs910653	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	22	10	19	0	0.454545	0	G|0.663;A|0.337	0.337	strong	.	SIGLEC1	210	.	NM_023068	exon16	c.C4044T	p.D1348D	GACAGCGTCCTGA	.	PASS	Atlas-SNP
ADAMTS7	11173	hgsc.bcm.edu	37	15	79067099	79067099	+	Silent	SNP	G	G	C	rs142017909	byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	113	13	102	0	0.115044	0	G|0.970;C|0.030	0.030	strong	ADAMTS7,NS,carcinoma,0,3	ADAMTS7	142	3	NM_014272	exon12	c.C1743G	p.R581R	GCGCTTGCGCTCA	.	PASS	Atlas-SNP
DAAM2	23500	hgsc.bcm.edu	37	6	39851818	39851818	+	Silent	SNP	G	G	A	rs3003929	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	99	40	127	0	0.40404	0	G|0.407;A|0.593	0.593	strong	.	DAAM2	101	.	NM_015345	exon15	c.G1926A	p.K642K	TGAAAAGATGTTT	.	PASS	Atlas-SNP
BRWD1	54014	hgsc.bcm.edu	37	21	40608530	40608530	+	Silent	SNP	A	A	C	rs143020455	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	115	56	107	0	0.486957	0	A|0.999;C|0.001	0.001	strong	.	BRWD1	325	.	NM_018963	exon23	c.T2757G	p.P919P	CTTCTTAGGCTTA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195477791	195477791	+	Silent	SNP	G	G	A	rs2291652	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	34	15	62	0	0.441176	0	G|0.628;A|0.372	0.372	strong	.	MUC4	1505	.	NM_018406	exon23	c.C15840T	p.I5280I	CCCGGAGATGGGC	.	PASS	Atlas-SNP
ADAMTSL4	54507	hgsc.bcm.edu	37	1	150526406	150526406	+	Silent	SNP	C	C	T	rs6681639	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	67	40	85	0	0.597015	0	C|0.647;T|0.353	0.353	strong	ADAMTSL4,NS,carcinoma,0,1	ADAMTSL4	101	1	NM_019032	exon6	c.C939T	p.G313G	GCAGGGCCAAGGG	.	PASS	Atlas-SNP
SNPH	9751	hgsc.bcm.edu	37	20	1285549	1285549	+	Silent	SNP	G	G	A	rs35467629	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	33	77	0	0.452055	0	G|0.965;A|0.035	0.035	strong	.	SNPH	89	.	NM_014723	exon6	c.G336A	p.T112T	GAAGACGCAGCTG	.	PASS	Atlas-SNP
KRT15	3866	hgsc.bcm.edu	37	17	39671724	39671724	+	Missense_Mutation	SNP	T	T	C	rs2305556	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	34	16	38	0	0.470588	0	T|0.806;C|0.194	0.194	strong	.	KRT15	60	.	NM_002275	exon6	c.A1247G	p.K416R	GCCTACTTGGCAT	.	PASS	Atlas-SNP
TBL3	10607	hgsc.bcm.edu	37	16	2025604	2025604	+	Missense_Mutation	SNP	G	G	C	rs8052713	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	8	6	15	0	0.75	0	G|0.921;C|0.079	0.079	strong	TBL3,NS,carcinoma,0,1	TBL3	54	1	NM_006453	exon10	c.G880C	p.E294Q	GGGCAGGAGCTGA	.	PASS	Atlas-SNP
ACSS1	84532	hgsc.bcm.edu	37	20	25038484	25038484	+	Silent	SNP	G	G	T	rs66817095	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	131	57	126	0	0.435115	0	G|0.845;T|0.155	0.155	strong	.	ACSS1	46	.	NM_001252677	exon1	c.C255A	p.T85T	GTAGGGGGTGTCC	.	PASS	Atlas-SNP
NBPF10	100132406	hgsc.bcm.edu	37	1	145368461	145368461	+	Missense_Mutation	SNP	A	A	C	rs12128680	bycluster;byfrequency;byhapmap	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	197	36	204	0	0.182741	0	A|0.899;C|0.101	0.101	strong	.	NBPF10	221	.	NM_001039703	exon84	c.A10439C	p.E3480A	TGATGGAAGTGGA	.	PASS	Atlas-SNP
SNRNP48	154007	hgsc.bcm.edu	37	6	7601720	7601720	+	Silent	SNP	C	C	T	rs3734586	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	40	93	0	0.39604	0	C|0.776;T|0.224	0.224	strong	.	SNRNP48	32	.	NM_152551	exon5	c.C558T	p.S186S	TGACAGCGATCTC	.	PASS	Atlas-SNP
XPC	7508	hgsc.bcm.edu	37	3	14199908	14199908	+	Missense_Mutation	SNP	C	C	T	rs2227999	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	45	25	62	0	0.555556	0	C|0.969;T|0.031	0.031	strong	.	XPC	60	.	NM_004628	exon9	c.G1475A	p.R492H	TCCTTACGATGGC	.	PASS	Atlas-SNP
POM121L12	285877	hgsc.bcm.edu	37	7	53103946	53103946	+	Silent	SNP	G	G	C	rs12113170	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	41	12	41	0	0.292683	0	G|0.631;C|0.369	0.369	strong	.	POM121L12	146	.	NM_182595	exon1	c.G582C	p.G194G	CGACGGGCCGTTG	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105415333	105415333	+	Missense_Mutation	SNP	T	T	C	rs201240658	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	9	2	0	0.0891089	0	T|0.965;C|0.035	0.035	strong	AHNAK2_ENST00000333244,NS,carcinoma,0,1	AHNAK2	719	1	NM_138420	exon7	c.A6455G	p.K2152R	TTGAACTTGCTGT	.	scavenged	Atlas-SNP
HMCN1	83872	hgsc.bcm.edu	37	1	186121996	186121996	+	Missense_Mutation	SNP	C	C	T	rs114629728	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	170	88	215	0	0.517647	0	C|0.996;T|0.004	0.004	strong	.	HMCN1	797	.	NM_031935	exon96	c.C15011T	p.T5004I	AAGTCACTGTAAA	.	PASS	Atlas-SNP
ZNF85	7639	hgsc.bcm.edu	37	19	21132453	21132453	+	Missense_Mutation	SNP	C	C	G	rs146063134	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	18	8	41	0	0.444444	0	C|0.999;G|0.001	0.001	strong	.	ZNF85	72	.	NM_001256171	exon5	c.C1223G	p.A408G	GAAAAGCCTTTAA	.	PASS	Atlas-SNP
FHL5	9457	hgsc.bcm.edu	37	6	97063522	97063522	+	Missense_Mutation	SNP	C	C	G	rs9373985	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	116	115	130	0	0.991379	0	C|0.612;G|0.388	0.388	strong	.	FHL5	73	.	NM_020482	exon7	c.C729G	p.S243R	AGACAGCCAGTGG	.	PASS	Atlas-SNP
NELL1	4745	hgsc.bcm.edu	37	11	20805286	20805286	+	Missense_Mutation	SNP	G	G	A	rs8176785	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	64	50	112	0	0.78125	0	G|0.367;A|0.633	0.633	strong	.	NELL1	179	.	NM_006157	exon3	c.G245A	p.R82Q	TGTTCCGGAACAA	.	PASS	Atlas-SNP
CRIPAK	285464	hgsc.bcm.edu	37	4	1388786	1388786	+	Missense_Mutation	SNP	G	G	C	rs146249377		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	25	4	21	0	0.16	0	.	.	weak	CRIPAK,extremity,malignant_melanoma,0,2	CRIPAK	185	2	NM_175918	exon1	c.G487C	p.D163H	CGTGCCGACGTGG	.	PASS	Atlas-SNP
R3HDM1	23518	hgsc.bcm.edu	37	2	136467084	136467084	+	Silent	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	307	149	425	1	0.485342	0.00235294	.	.	none	.	R3HDM1	84	.	NM_015361	exon21	c.G2436A	p.Q812Q	CCAGCAGCTTCAA	.	PASS	Atlas-SNP
LIMS1	3987	hgsc.bcm.edu	37	2	109276110	109276110	+	Missense_Mutation	SNP	G	G	A	rs146149508	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	859	303	630	0	0.352736	0	G|0.994;A|0.006	0.006	strong	.	LIMS1	38	.	NM_001193485	exon2	c.G232A	p.G78S	AAGGGCGGCTTTG	.	PASS	Atlas-SNP
PELI3	246330	hgsc.bcm.edu	37	11	66240882	66240882	+	Silent	SNP	T	T	C	rs2277302	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	51	39	52	0	0.764706	0	T|0.739;C|0.261	0.261	strong	.	PELI3	36	.	NM_145065	exon6	c.T627C	p.D209D	CTTCGATGCCTCT	.	PASS	Atlas-SNP
UGT1A10	54575	hgsc.bcm.edu	37	2	234545861	234545861	+	Silent	SNP	C	C	T	rs17854828	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	176	108	164	0	0.613636	0	C|0.868;T|0.132	0.132	strong	.	UGT1A10	71	.	NM_019075	exon1	c.C693T	p.A231A	AATAGCCTCTGAA	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1265987	1265987	+	Missense_Mutation	SNP	C	C	G	rs3021158	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	253	44	256	0	0.173913	0	C|0.873;G|0.127	0.127	strong	MUC5AC,brain,glioma,0,1	MUC5B	473	1	NM_002458	exon31	c.C7877G	p.T2626R	CAGGGACGGCACG	.	PASS	Atlas-SNP
CAMKK2	10645	hgsc.bcm.edu	37	12	121701681	121701681	+	Silent	SNP	G	G	A	rs2230776	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	84	39	77	0	0.464286	0	G|0.911;A|0.089	0.089	strong	.	CAMKK2	87	.	NM_153500	exon6	c.C687T	p.P229P	CTCAATGGGGCCC	.	PASS	Atlas-SNP
P2RX3	5024	hgsc.bcm.edu	37	11	57137371	57137371	+	Silent	SNP	G	G	A	rs2276039	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	128	128	151	0	1	0	G|0.664;A|0.336	0.336	strong	P2RX3,NS,adenoma,0,1	P2RX3	55	1	NM_002559	exon12	c.G1095A	p.T365T	GACTACGCTGAAA	.	PASS	Atlas-SNP
CRIPAK	285464	hgsc.bcm.edu	37	4	1388508	1388508	+	Missense_Mutation	SNP	T	T	C	rs55703801	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	122	27	125	2	0.221311	0.016	.	.	weak	CRIPAK,rectum,carcinoma,0,1	CRIPAK	185	1	NM_175918	exon1	c.T209C	p.V70A	CACGTGTCCATGT	.	scavenged	Atlas-SNP
MYO18B	84700	hgsc.bcm.edu	37	22	26247456	26247456	+	Silent	SNP	G	G	A	rs5996988	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	56	30	51	0	0.535714	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
SORCS1	114815	hgsc.bcm.edu	37	10	108380256	108380256	+	Missense_Mutation	SNP	G	G	A	rs144056795	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	112	25	98	0	0.223214	0	G|0.999;A|0.001	0.001	strong	SORCS1_ENST00000344440,right_upper_lobe,carcinoma,+1,3	SORCS1	534	3	NM_001206572	exon20	c.C2726T	p.A909V	GCCGTCGCATTGA	.	PASS	Atlas-SNP
TTLL6	284076	hgsc.bcm.edu	37	17	46847364	46847364	+	Missense_Mutation	SNP	C	C	A	rs2032844	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	218	104	275	0	0.477064	0	C|0.755;A|0.245	0.245	strong	.	TTLL6	113	.	NM_001130918	exon14	c.G2136T	p.E712D	ACTGTACTCAGAG	.	PASS	Atlas-SNP
IL2RA	3559	hgsc.bcm.edu	37	10	6067969	6067969	+	Silent	SNP	C	C	T	rs2228150	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	158	73	220	1	0.462025	0.00454545	T|0.080;G|0.006	0.080	strong	.	IL2RA	37	.	NM_000417	exon2	c.G84A	p.P28P	CTCTGGCGGGTCA	.	PASS	Atlas-SNP
TTBK1	84630	hgsc.bcm.edu	37	6	43251880	43251880	+	Silent	SNP	C	C	G	rs45564136	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	11	6	14	0	0.545455	0	C|0.952;G|0.048	0.048	strong	.	TTBK1	124	.	NM_032538	exon14	c.C3402G	p.P1134P	CACGCCCGCCTCT	.	PASS	Atlas-SNP
PRB3	5544	hgsc.bcm.edu	37	12	11420563	11420563	+	Missense_Mutation	SNP	G	G	T	rs200902635	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	94	3	69	0	0.0319149	0	.	.	weak	PRB3_ENST00000538488,NS,carcinoma,0,1	PRB3	84	1	NM_006249	exon3	c.C620A	p.P207Q	GGGGGTGGTCCTT	.	scavenged	Atlas-SNP
SCNN1G	6340	hgsc.bcm.edu	37	16	23226787	23226787	+	Silent	SNP	C	C	G	rs5723	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	16	9	13	0	0.5625	0	C|0.788;G|0.212	0.212	strong	.	SCNN1G	82	.	NM_001039	exon13	c.C1947G	p.L649L	TGAGCTCTGAGGC	.	PASS	Atlas-SNP
ATAD5	79915	hgsc.bcm.edu	37	17	29162173	29162173	+	Silent	SNP	T	T	C	rs11655623	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	146	64	207	0	0.438356	0	T|0.859;C|0.141	0.141	strong	.	ATAD5	150	.	NM_024857	exon2	c.T1074C	p.P358P	TGATCCTGAGAAT	.	PASS	Atlas-SNP
WNK2	65268	hgsc.bcm.edu	37	9	96026243	96026243	+	Silent	SNP	G	G	A	rs55981123	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	36	74	0	0.461538	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
TRPC1	7220	hgsc.bcm.edu	37	3	142524858	142524858	+	Silent	SNP	G	G	A	rs1132030	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	169	73	203	0	0.431953	0	A|0.353;G|0.647;T|0.000	0.353	strong	.	TRPC1	82	.	NM_001251845	exon13	c.G2163A	p.R721R	ATGGAGGAATTTG	.	PASS	Atlas-SNP
AMBN	258	hgsc.bcm.edu	37	4	71469006	71469006	+	Silent	SNP	C	C	T	rs113360877	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	149	65	186	0	0.436242	0	C|0.987;T|0.013	0.013	strong	.	AMBN	73	.	NM_016519	exon10	c.C678T	p.H226H	TTCTCACGGACCA	.	PASS	Atlas-SNP
GSG2	83903	hgsc.bcm.edu	37	17	3628362	3628362	+	Missense_Mutation	SNP	T	T	C	rs3809806	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	81	43	109	0	0.530864	0	T|0.447;C|0.553	0.553	strong	GSG2_ENST00000325418,NS,carcinoma,0,1	GSG2	48	1	NM_031965	exon1	c.T1133C	p.V378A	AGAATGTCTGCTT	.	PASS	Atlas-SNP
LRRC37A3	374819	hgsc.bcm.edu	37	17	62856646	62856646	+	Silent	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	38	21	38	0	0.552632	0	.	.	none	.	LRRC37A3	75	.	NM_199340	exon11	c.C3618T	p.L1206L	ACTTCCGAGCCTT	.	PASS	Atlas-SNP
FAM102A	399665	hgsc.bcm.edu	37	9	130742271	130742271	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	17	68	0	0.236111	0	.	.	none	.	FAM102A	32	.	NM_001035254	exon1	c.G146A	p.R49K	TCCTACCTTGACG	.	PASS	Atlas-SNP
SH3BGR	6450	hgsc.bcm.edu	37	21	40871810	40871810	+	Missense_Mutation	SNP	T	T	C	rs9974333	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	97	104	0	1	0	T|0.476;C|0.524	0.524	strong	SH3BGR,NS,carcinoma,-1,2	SH3BGR	29	2	NM_007341	exon4	c.T563C	p.V188A	AAGATGTGGGCAA	.	PASS	Atlas-SNP
OR4C16	219428	hgsc.bcm.edu	37	11	55339798	55339798	+	Silent	SNP	C	C	T	rs557667	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	176	39	191	0	0.221591	0	C|0.755;T|0.245	0.245	strong	.	OR4C16	104	.	NM_001004701	exon1	c.C195T	p.S65S	CTTATCCTTATCT	.	PASS	Atlas-SNP
ASB10	136371	hgsc.bcm.edu	37	7	150878260	150878260	+	Silent	SNP	C	C	G	rs2253592	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	169	79	157	0	0.467456	0	C|0.485;G|0.515	0.515	strong	.	ASB10	99	.	NM_001142459	exon3	c.G870C	p.A290A	CTGGTCCGCAGCA	.	PASS	Atlas-SNP
GCNT1	2650	hgsc.bcm.edu	37	9	79117751	79117751	+	Missense_Mutation	SNP	A	A	G	rs2282683	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	98	52	99	0	0.530612	0	A|0.773;G|0.227	0.227	strong	.	GCNT1	52	.	NM_001490	exon4	c.A454G	p.I152V	TATTGCATTCATG	.	PASS	Atlas-SNP
C5	727	hgsc.bcm.edu	37	9	123716103	123716103	+	Silent	SNP	T	T	C	rs41258306	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	170	84	177	0	0.494118	0	T|0.939;C|0.061	0.061	strong	.	C5	124	.	NM_001735	exon40	c.A4806G	p.K1602K	TACCTTTTTAATG	.	PASS	Atlas-SNP
ETFB	2109	hgsc.bcm.edu	37	19	51857774	51857774	+	Missense_Mutation	SNP	T	T	G	rs143144671	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	94	65	106	0	0.691489	0	T|0.998;G|0.002	0.002	strong	.	ETFB	46	.	NM_001014763	exon1	c.A119C	p.E40A	AGCCATTCCTGGG	.	PASS	Atlas-SNP
ALCAM	214	hgsc.bcm.edu	37	3	105260520	105260520	+	Missense_Mutation	SNP	C	C	T	rs1044243	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	37	83	0	0.513889	0	C|0.920;T|0.080	0.080	strong	.	ALCAM	71	.	NM_001627	exon8	c.C902T	p.T301M	CACTGACGGATGT	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1092948	1092948	+	Silent	SNP	C	C	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	56	4	37	0	0.0714286	0	.	.	none	MUC2_ENST00000441003,NS,carcinoma,+1,12	MUC2	614	12	NM_002457	exon30	c.C4767G	p.T1589T	CACCACCACTACG	.	scavenged	Atlas-SNP
OR4C15	81309	hgsc.bcm.edu	37	11	55322211	55322211	+	Silent	SNP	A	A	G	rs9804659	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	59	19	56	0	0.322034	0	A|0.760;G|0.240	0.240	strong	.	OR4C15	145	.	NM_001001920	exon1	c.A429G	p.K143K	GACAAAAACCATC	.	PASS	Atlas-SNP
BCAR1	9564	hgsc.bcm.edu	37	16	75269477	75269477	+	Silent	SNP	A	A	C	rs61729595	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	19	53	0	0.223529	0	A|0.962;C|0.038	0.038	strong	BCAR1_ENST00000393420,NS,carcinoma,0,2	BCAR1	184	2	NM_001170714	exon6	c.T1458G	p.S486S	GGACGCAGACTGG	.	PASS	Atlas-SNP
PSPH	5723	hgsc.bcm.edu	37	7	56088902	56088902	+	Missense_Mutation	SNP	C	C	T	rs77329757	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	131	17	145	0	0.129771	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	.	scavenged	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105415431	105415431	+	Missense_Mutation	SNP	C	C	G	rs199873247	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	96	22	0	0	0.229167	.	C|0.965;G|0.036	0.036	strong	AHNAK2_ENST00000333244,NS,carcinoma,-2,2	AHNAK2	719	2	NM_138420	exon7	c.G6357C	p.M2119I	CACCTCCATGCTG	.	scavenged	Atlas-SNP
ZNF675	171392	hgsc.bcm.edu	37	19	23837195	23837195	+	Silent	SNP	T	T	C	rs77385655	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	98	49	102	0	0.5	0	T|0.900;C|0.100	0.100	strong	.	ZNF675	88	.	NM_138330	exon4	c.A540G	p.S180S	GCAAAATGATCTG	.	PASS	Atlas-SNP
KANK4	163782	hgsc.bcm.edu	37	1	62739198	62739198	+	Silent	SNP	G	G	A	rs17855078	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	126	55	118	0	0.436508	0	G|0.724;A|0.276	0.276	strong	.	KANK4	135	.	NM_181712	exon3	c.C1578T	p.S526S	TCTGTCGCTGCCC	.	PASS	Atlas-SNP
OR5B3	441608	hgsc.bcm.edu	37	11	58170469	58170469	+	Silent	SNP	C	C	A	rs11229412	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	107	80	103	0	0.747664	0	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	.	PASS	Atlas-SNP
UMODL1	89766	hgsc.bcm.edu	37	21	43531345	43531345	+	Silent	SNP	G	G	A	rs76618631	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	35	14	27	0	0.4	0	G|0.983;A|0.017	0.017	strong	.	UMODL1	186	.	NM_173568	exon11	c.G2013A	p.A671A	CCAGGCGAGCCCC	.	PASS	Atlas-SNP
PABPC1	26986	hgsc.bcm.edu	37	8	101721785	101721785	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	220	73	256	0	0.331818	0	.	.	none	.	PABPC1	76	.	NM_002568	exon8	c.A1147T	p.M383L	TCTGCATATACTG	.	PASS	Atlas-SNP
TSSK1B	83942	hgsc.bcm.edu	37	5	112770027	112770027	+	Silent	SNP	T	T	G	rs26980	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	30	81	0	0.517241	0	T|0.931;G|0.069	0.069	strong	.	TSSK1B	89	.	NM_032028	exon1	c.A510C	p.A170A	GCTTAATGCCATT	.	PASS	Atlas-SNP
TRIOBP	11078	hgsc.bcm.edu	37	22	38121152	38121152	+	Missense_Mutation	SNP	C	C	A	rs9610841	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	151	71	176	0	0.470199	0	C|0.623;A|0.377	0.377	strong	TRIOBP_ENST00000344404,NS,carcinoma,+1,1	TRIOBP	262	1	NM_001039141	exon7	c.C2589A	p.N863K	AGACAACCCTGGA	.	PASS	Atlas-SNP
NBAS	51594	hgsc.bcm.edu	37	2	15607853	15607853	+	Silent	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	246	136	211	1	0.552846	0.00473934	.	.	none	.	NBAS	246	.	NM_015909	exon18	c.C1953T	p.A651A	ATTCTTGGCAGGC	.	PASS	Atlas-SNP
MMP14	4323	hgsc.bcm.edu	37	14	23312923	23312923	+	Silent	SNP	T	T	C	rs2236307	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	28	94	0	0.4	0	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
TMEM132A	54972	hgsc.bcm.edu	37	11	60698054	60698054	+	Silent	SNP	G	G	A	rs2074416	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	45	45	49	0	1	0	G|0.692;A|0.308	0.308	strong	.	TMEM132A	135	.	NM_178031	exon5	c.G939A	p.L313L	CAAGCTGGACCGC	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	93	91	106	1	0.978495	0.00943396	G|0.152;C|0.848	0.848	strong	.	ADAMTS10	132	.	NM_030957	exon4	c.C401G	p.T134S	TGGGAGGTGCTGG	.	PASS	Atlas-SNP
SERPINA5	5104	hgsc.bcm.edu	37	14	95053891	95053891	+	Silent	SNP	C	C	T	rs6111	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	41	16	73	0	0.390244	0	C|0.783;T|0.217	0.217	strong	.	SERPINA5	69	.	NM_000624	exon3	c.C192T	p.S64S	CCAGAGCATCTTC	.	PASS	Atlas-SNP
NOLC1	9221	hgsc.bcm.edu	37	10	103920475	103920475	+	Missense_Mutation	SNP	T	T	C	rs1049455	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	118	53	142	0	0.449153	0	T|0.797;C|0.203	0.203	strong	.	NOLC1	61	.	NM_004741	exon10	c.T1366C	p.S456P	GCTCTATCTCTGC	.	PASS	Atlas-SNP
PDIA4	9601	hgsc.bcm.edu	37	7	148709061	148709061	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	60	10	70	0	0.166667	0	.	.	none	.	PDIA4	57	.	NM_004911	exon6	c.C856T	p.P286S	TGGAGGGAGGCCC	.	PASS	Atlas-SNP
KIF25	3834	hgsc.bcm.edu	37	6	168442765	168442765	+	Missense_Mutation	SNP	G	G	A	rs2073634	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	104	28	122	0	0.269231	0	G|0.927;A|0.073	0.073	strong	.	KIF25	75	.	NM_030615	exon7	c.G763A	p.A255T	AACCCCGCAGGGC	.	PASS	Atlas-SNP
IDUA	3425	hgsc.bcm.edu	37	4	994414	994414	+	Missense_Mutation	SNP	G	G	A	rs3755955	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	185	97	193	1	0.524324	0.00518135	G|0.859;A|0.141	0.141	strong	.	IDUA	33	.	NM_000203	exon3	c.G314A	p.R105Q	CTGGACGGGGCCT	.	PASS	Atlas-SNP
UMODL1	89766	hgsc.bcm.edu	37	21	43510514	43510514	+	Silent	SNP	C	C	G	rs2839464	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	50	89	0	0.515464	0	C|0.733;G|0.267	0.267	strong	.	UMODL1	186	.	NM_173568	exon6	c.C897G	p.A299A	TCCAGCCACGTCT	.	PASS	Atlas-SNP
BTN3A1	11119	hgsc.bcm.edu	37	6	26409890	26409890	+	Missense_Mutation	SNP	G	G	C	rs41266839	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	26	8	58	0	0.307692	0	G|0.951;C|0.049	0.049	strong	.	BTN3A1	80	.	NM_007048	exon5	c.G845C	p.R282T	AGTTCAGAAAGAA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195511358	195511358	+	Missense_Mutation	SNP	C	C	G	rs77614482	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	8	114	0	0.115942	0	C|0.991;G|0.009	0.009	weak	.	MUC4	1505	.	NM_018406	exon2	c.G7093C	p.D2365H	TGGTGTCACCTGT	.	PASS	Atlas-SNP
CLCF1	23529	hgsc.bcm.edu	37	11	67132804	67132804	+	Missense_Mutation	SNP	G	G	A	rs78755659	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	81	20	86	0	0.246914	0	G|0.992;A|0.008	0.008	strong	.	CLCF1	15	.	NM_013246	exon3	c.C481T	p.P161S	GCAGCGGCTGGGG	.	PASS	Atlas-SNP
ST3GAL1	6482	hgsc.bcm.edu	37	8	134488007	134488007	+	Silent	SNP	G	G	A	rs2230542	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	80	15	132	0	0.1875	0	G|0.495;A|0.505	0.505	strong	ST3GAL1,NS,carcinoma,0,1	ST3GAL1	39	1	NM_173344	exon5	c.C261T	p.T87T	CTGGGCGGTCAGC	.	PASS	Atlas-SNP
KIF18A	81930	hgsc.bcm.edu	37	11	28045367	28045367	+	Silent	SNP	G	G	A	rs35440657	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	115	20	143	0	0.173913	0	G|0.995;A|0.005	0.005	strong	KIF18A,caecum,carcinoma,0,1	KIF18A	92	1	NM_031217	exon16	c.C2535T	p.D845D	ATTTACGTCTGCA	.	PASS	Atlas-SNP
HEG1	57493	hgsc.bcm.edu	37	3	124731485	124731485	+	Missense_Mutation	SNP	C	C	G	rs10804567	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	152	75	159	0	0.493421	0	C|0.293;G|0.707	0.707	strong	.	HEG1	109	.	NM_020733	exon6	c.G2938C	p.V980L	AGGACACTGTTGT	.	PASS	Atlas-SNP
BMS1	9790	hgsc.bcm.edu	37	10	43281089	43281089	+	Silent	SNP	T	T	C	rs7074877	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	44	133	0	0.511628	0	T|0.503;C|0.497	0.497	strong	.	BMS1	132	.	NM_014753	exon3	c.T336C	p.T112T	GTTGACTGAGATC	.	PASS	Atlas-SNP
ANGPTL2	23452	hgsc.bcm.edu	37	9	129870763	129870763	+	Missense_Mutation	SNP	C	C	T	rs370920897		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	63	14	52	0	0.222222	0	.	.	weak	ANGPTL2,colon,carcinoma,-1,1	ANGPTL2	46	1	NM_012098	exon2	c.G248A	p.R83Q	TGCACTCGGTTCT	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	128	45	126	0	0.351562	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
TAS2R14	50840	hgsc.bcm.edu	37	12	11091693	11091693	+	Silent	SNP	T	T	A	rs7138535	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	39	91	0	0.534247	0	T|0.766;A|0.234	0.234	strong	.	TAS2R14	26	.	NM_023922	exon1	c.A114T	p.G38G	CTTTCTTCCCTTG	.	PASS	Atlas-SNP
HERC3	8916	hgsc.bcm.edu	37	4	89625427	89625427	+	Missense_Mutation	SNP	G	G	C	rs1804080	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	126	52	185	0	0.412698	0	G|0.801;C|0.199	0.199	strong	.	HERC3	82	.	NM_014606	exon24	c.G2836C	p.E946Q	GAACTGGAAGAGG	.	PASS	Atlas-SNP
CGN	57530	hgsc.bcm.edu	37	1	151501841	151501841	+	Missense_Mutation	SNP	C	C	G	rs12044926	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	63	36	75	0	0.571429	0	C|0.943;G|0.057	0.057	strong	.	CGN	106	.	NM_020770	exon11	c.C1912G	p.Q638E	CGGACACAGGAGG	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	36	177	0	0.413793	0	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
PLEKHA8	84725	hgsc.bcm.edu	37	7	30113706	30113706	+	Silent	SNP	A	A	G	rs11977829	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	261	64	329	1	0.245211	0.00303951	A|0.748;G|0.252	0.252	strong	PLEKHA8_ENST00000449726,NS,carcinoma,0,2	PLEKHA8	68	2	NM_001197027	exon13	c.A1320G	p.T440T	TAAAACATTGCGG	.	scavenged	Atlas-SNP
SPNS1	83985	hgsc.bcm.edu	37	16	28995211	28995211	+	Silent	SNP	C	C	T	rs113165798	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	65	33	56	0	0.507692	0	C|0.995;T|0.005	0.005	strong	.	SPNS1	47	.	NM_001142448	exon12	c.C1425T	p.G475G	GGGCGGCGCAGCC	.	PASS	Atlas-SNP
MYO1F	4542	hgsc.bcm.edu	37	19	8616999	8616999	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	102	23	121	0	0.22549	0	.	.	none	.	MYO1F	128	.	NM_012335	exon7	c.G554A	p.G185D	ATCTTGCCCCCAT	.	PASS	Atlas-SNP
PDE1C	5137	hgsc.bcm.edu	37	7	31855577	31855577	+	Missense_Mutation	SNP	A	A	C	rs2230175	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	207	52	267	0	0.251208	0	A|0.990;C|0.010	0.010	strong	.	PDE1C	465	.	NM_001191058	exon16	c.T1954G	p.S652A	CTTTGGAGTTTTT	.	PASS	Atlas-SNP
RFX6	222546	hgsc.bcm.edu	37	6	117246719	117246719	+	Silent	SNP	C	C	T	rs4946206	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	93	35	122	0	0.376344	0	C|0.744;T|0.256	0.256	strong	.	RFX6	141	.	NM_173560	exon16	c.C1782T	p.H594H	AAGCCACGTGGAG	.	PASS	Atlas-SNP
GOLGB1	2804	hgsc.bcm.edu	37	3	121413362	121413362	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	41	123	0	0.471264	0	.	.	none	.	GOLGB1	319	.	NM_001256486	exon13	c.A6008G	p.Q2003R	TCTTTCTGAGCAC	.	PASS	Atlas-SNP
SHISA9	729993	hgsc.bcm.edu	37	16	13297254	13297254	+	Missense_Mutation	SNP	C	C	G	rs112510263	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	33	28	26	0	0.848485	0	C|0.987;G|0.013	0.013	strong	.	SHISA9	33	.	NM_001145204	exon3	c.C695G	p.A232G	CAGATGCCACCCA	.	PASS	Atlas-SNP
SPECC1	92521	hgsc.bcm.edu	37	17	20108184	20108184	+	Missense_Mutation	SNP	C	C	G	rs9908032	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	31	76	0	0.534483	0	C|0.883;G|0.117	0.117	strong	.	SPECC1	100	.	NM_001033553	exon4	c.C822G	p.S274R	CAGCAGCTGCCCA	.	PASS	Atlas-SNP
ZNF169	169841	hgsc.bcm.edu	37	9	97055310	97055310	+	Missense_Mutation	SNP	C	C	T	rs1536690	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	171	84	204	0	0.491228	0	C|0.805;T|0.195	0.195	strong	ZNF169,NS,carcinoma,+1,1	ZNF169	60	1	NM_194320	exon4	c.C215T	p.P72L	ACGAACCTTGGAG	.	PASS	Atlas-SNP
LRP3	4037	hgsc.bcm.edu	37	19	33696621	33696621	+	Silent	SNP	C	C	T	rs3745975	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	54	37	51	0	0.685185	0	C|0.956;T|0.044	0.044	strong	.	LRP3	46	.	NM_002333	exon5	c.C945T	p.G315G	CCTGGGCGAGCGC	.	PASS	Atlas-SNP
MTUS1	57509	hgsc.bcm.edu	37	8	17611916	17611916	+	Silent	SNP	C	C	T	rs61740538	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	145	26	214	0	0.17931	0	C|0.982;T|0.018	0.018	strong	.	MTUS1	144	.	NM_001001924	exon2	c.G1401A	p.S467S	CTCCTTCGAGTCT	.	PASS	Atlas-SNP
RBPJL	11317	hgsc.bcm.edu	37	20	43944958	43944958	+	Silent	SNP	G	G	T	rs2741500	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	100	48	112	0	0.48	0	G|0.853;T|0.147	0.147	strong	.	RBPJL	67	.	NM_014276	exon10	c.G1152T	p.P384P	CACTCCGGTGCCT	.	PASS	Atlas-SNP
IFITM3	10410	hgsc.bcm.edu	37	11	320649	320649	+	Silent	SNP	G	G	A	rs11553885	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	83	9	67	1	0.108434	0.0149254	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
FAM153B	202134	hgsc.bcm.edu	37	5	175528119	175528119	+	Missense_Mutation	SNP	T	T	C	rs2006825		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	554	7	551	1	0.0126354	0.00181488	T|0.500;C|0.500	0.500	weak	FAM153B,NS,carcinoma,0,4	FAM153B	28	4	NM_001265615	exon10	c.T401C	p.M134T	TTCACATGGTAAA	.	scavenged	Atlas-SNP
PRRC2B	84726	hgsc.bcm.edu	37	9	134371165	134371165	+	Silent	SNP	C	C	T	rs41296113	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	22	4	34	0	0.181818	0	C|0.936;T|0.064	0.064	strong	.	PRRC2B	266	.	NM_013318	exon31	c.C6594T	p.A2198A	GGGAGCCGTGAAG	.	PASS	Atlas-SNP
QRSL1	55278	hgsc.bcm.edu	37	6	107113715	107113715	+	Silent	SNP	G	G	A	rs2015205	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	107	55	155	0	0.514019	0	G|0.595;A|0.405	0.405	strong	.	QRSL1	30	.	NM_018292	exon11	c.G1425A	p.L475L	AGGACTGCAGTTT	.	PASS	Atlas-SNP
NDOR1	27158	hgsc.bcm.edu	37	9	140110555	140110555	+	Missense_Mutation	SNP	G	G	A	rs62587579	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	26	86	0	0.371429	0	G|0.962;A|0.038	0.038	strong	.	NDOR1	71	.	NM_001144026	exon13	c.G1591A	p.V531I	CAGAAAGTATATG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195507062	195507062	+	Missense_Mutation	SNP	C	C	T	rs199822551	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	43	27	3	0.52439	0.111111	.	.	weak	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.G11389A	p.D3797N	AAGTGTCGGTGAC	.	scavenged	Atlas-SNP
SLC2A9	56606	hgsc.bcm.edu	37	4	9922130	9922130	+	Missense_Mutation	SNP	C	C	T	rs3733591	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	154	76	160	0	0.493506	0	C|0.781;T|0.219	0.219	strong	.	SLC2A9	158	.	NM_020041	exon7	c.G881A	p.R294H	TGCACGCGGCTCT	.	PASS	Atlas-SNP
EPPK1	83481	hgsc.bcm.edu	37	8	144940290	144940290	+	Missense_Mutation	SNP	C	C	G	rs201976887	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	118	22	78	0	0.186441	0	.	.	weak	EPPK1,NS,carcinoma,0,5	EPPK1	199	5	NM_031308	exon1	c.G7132C	p.D2378H	TGGGGTCGGCCAG	.	PASS	Atlas-SNP
APMAP	57136	hgsc.bcm.edu	37	20	24954303	24954303	+	Silent	SNP	G	G	C	rs148400044	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	116	62	131	0	0.534483	0	G|0.998;C|0.002	0.002	strong	.	APMAP	3	.	NM_020531	exon4	c.C399G	p.A133A	AAACCGGGCAATG	.	PASS	Atlas-SNP
CDH8	1006	hgsc.bcm.edu	37	16	61689493	61689493	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	220	5	150	1	0.0227273	0.00666667	.	.	none	CDH8,rectum,carcinoma,+1,1	CDH8	273	1	NM_001796	exon11	c.T1787C	p.V596A	CCACAGACCCTGA	.	scavenged	Atlas-SNP
VWA5A	4013	hgsc.bcm.edu	37	11	124015994	124015994	+	Silent	SNP	C	C	T	rs1056615	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	24	90	0	0.32	0	C|0.391;T|0.609	0.609	strong	VWA5A,colon,carcinoma,+1,1	VWA5A	102	1	NM_014622	exon17	c.C2205T	p.H735H	GCTGCACAGCAAT	.	PASS	Atlas-SNP
ESPL1	9700	hgsc.bcm.edu	37	12	53680011	53680011	+	Missense_Mutation	SNP	T	T	G	rs111320105	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	48	23	63	0	0.479167	0	T|0.983;G|0.017	0.017	strong	.	ESPL1	158	.	NM_012291	exon18	c.T3491G	p.V1164G	GCTGGGTATTGGT	.	PASS	Atlas-SNP
PCDH18	54510	hgsc.bcm.edu	37	4	138452706	138452706	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	119	31	167	0	0.260504	0	.	.	none	.	PCDH18	229	.	NM_019035	exon1	c.T537A	p.N179K	AAAATCATTGGCA	.	PASS	Atlas-SNP
ZNF598	90850	hgsc.bcm.edu	37	16	2048796	2048796	+	Silent	SNP	C	C	T	rs1058474	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	107	82	97	0	0.766355	0	C|0.885;T|0.115	0.115	strong	.	ZNF598	55	.	NM_178167	exon13	c.G2268A	p.R756R	AAGGTTCCTCTCC	.	PASS	Atlas-SNP
GAD1	2571	hgsc.bcm.edu	37	2	171716266	171716266	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	90	19	99	0	0.211111	0	.	.	none	.	GAD1	79	.	NM_000817	exon17	c.G1659C	p.M553I	GACCATGGTTGGC	.	PASS	Atlas-SNP
TNS1	7145	hgsc.bcm.edu	37	2	218713282	218713282	+	Missense_Mutation	SNP	G	G	A	rs3796033	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	150	61	147	0	0.406667	0	G|0.602;A|0.398	0.398	strong	.	TNS1	251	.	NM_022648	exon17	c.C1583T	p.T528I	TCACTGGTGTTGG	.	PASS	Atlas-SNP
TYW1	55253	hgsc.bcm.edu	37	7	66660242	66660242	+	Missense_Mutation	SNP	A	A	G	rs71563185		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	135	32	198	1	0.237037	0.00505051	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	.	scavenged	Atlas-SNP
CUBN	8029	hgsc.bcm.edu	37	10	17147521	17147521	+	Missense_Mutation	SNP	G	G	T	rs1801224	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	152	71	196	0	0.467105	0	T|0.469;G|0.343;C|0.092;A|0.097	0.469	strong	.	CUBN	515	.	NM_001081	exon11	c.C1165A	p.P389T	CATTTGGCCCATA	.	PASS	Atlas-SNP
XRCC6	2547	hgsc.bcm.edu	37	22	42059768	42059768	+	Silent	SNP	G	G	T	rs56558005		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	164	72	173	0	0.439024	0	.	.	weak	.	XRCC6	64	.	NM_001469	exon13	c.G1779T	p.G593G	GAGTGGGCTGAAG	.	PASS	Atlas-SNP
ARHGEF1	9138	hgsc.bcm.edu	37	19	42409189	42409189	+	Splice_Site	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	16	78	0	0.205128	0	.	.	none	ARHGEF1,NS,carcinoma,+1,1	ARHGEF1	95	1	NM_004706	exon23	c.2249+1G>A	.	GAAAAAGTGAGGG	.	PASS	Atlas-SNP
OR10H5	284433	hgsc.bcm.edu	37	19	15905431	15905431	+	Silent	SNP	T	T	C	rs4808381	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	206	103	279	0	0.5	0	T|0.623;C|0.377	0.377	strong	.	OR10H5	49	.	NM_001004466	exon1	c.T573C	p.D191D	TGGAGATGATGTG	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	55	167	2	0.544554	0.011976	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	.	scavenged	Atlas-SNP
TTC22	55001	hgsc.bcm.edu	37	1	55266797	55266797	+	Missense_Mutation	SNP	G	G	C	rs671108	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	118	53	83	0	0.449153	0	G|0.830;C|0.170	0.170	strong	.	TTC22	40	.	NM_001114108	exon1	c.C40G	p.L14V	CGATGAGGGCGTC	.	PASS	Atlas-SNP
RRN3	54700	hgsc.bcm.edu	37	16	15165103	15165103	+	Silent	SNP	G	G	A	rs73491931	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	331	71	359	0	0.214502	0	G|0.945;A|0.055	0.055	strong	.	RRN3	36	.	NM_018427	exon13	c.C1134T	p.F378F	CTCTGCGAATCCC	.	PASS	Atlas-SNP
COBL	23242	hgsc.bcm.edu	37	7	51097216	51097216	+	Missense_Mutation	SNP	G	G	A	rs17656599	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	79	21	85	0	0.265823	0	G|0.919;A|0.081	0.081	strong	.	COBL	167	.	NM_015198	exon10	c.C1577T	p.P526L	TCCTGTGGGCAGT	.	PASS	Atlas-SNP
PPP1R18	170954	hgsc.bcm.edu	37	6	30652781	30652781	+	Missense_Mutation	SNP	C	C	T	rs9262143	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	53	109	0	0.546392	0	C|0.942;T|0.058	0.058	strong	.	.	.	.	NM_001134870	exon2	c.G1015A	p.G339R	CCTTCCCGGAGTT	.	PASS	Atlas-SNP
PRR5-ARHGAP8	553158	hgsc.bcm.edu	37	22	45221423	45221423	+	Silent	SNP	A	A	T	rs3209476	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	163	79	169	0	0.484663	0	A|0.825;T|0.175	0.175	strong	PRR5-ARHGAP8,colon,carcinoma,+1,2	PRR5-ARHGAP8	53	2	NM_181334	exon10	c.A912T	p.P304P	GACACCACCGCCG	.	PASS	Atlas-SNP
CNTNAP4	85445	hgsc.bcm.edu	37	16	76461498	76461498	+	Splice_Site	SNP	T	T	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	168	74	134	0	0.440476	0	.	.	none	.	CNTNAP4	600	.	NM_033401	exon4	c.537+2T>G	.	ATACAGTAAGTGT	.	PASS	Atlas-SNP
CDHR3	222256	hgsc.bcm.edu	37	7	105615406	105615406	+	Missense_Mutation	SNP	G	G	A	rs35008315	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	221	104	254	0	0.470588	0	G|0.824;A|0.176	0.176	strong	.	CDHR3	153	.	NM_152750	exon2	c.G163A	p.V55M	TCACCTGTGATCC	.	PASS	Atlas-SNP
AGBL1	123624	hgsc.bcm.edu	37	15	86702241	86702241	+	Missense_Mutation	SNP	C	C	T	rs79814209	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	98	48	130	0	0.489796	0	C|0.980;T|0.020	0.020	strong	.	AGBL1	151	.	NM_152336	exon4	c.C334T	p.R112C	CGAAAGCGCACCC	.	PASS	Atlas-SNP
ZCWPW2	152098	hgsc.bcm.edu	37	3	28454627	28454627	+	Missense_Mutation	SNP	A	A	G	rs148504648	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	83	28	131	0	0.337349	0	A|0.998;G|0.002	0.002	strong	.	ZCWPW2	49	.	NM_001040432	exon2	c.A68G	p.N23S	TGGAAAACATGTA	.	PASS	Atlas-SNP
OR10H5	284433	hgsc.bcm.edu	37	19	15905639	15905639	+	Silent	SNP	C	C	T	rs3746151	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	144	63	153	0	0.4375	0	C|0.841;T|0.159	0.159	strong	.	OR10H5	49	.	NM_001004466	exon1	c.C781T	p.L261L	ATTTACCTGAAGC	.	PASS	Atlas-SNP
PGAP1	80055	hgsc.bcm.edu	37	2	197711870	197711870	+	Silent	SNP	G	G	A	rs149815494	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	147	59	204	0	0.401361	0	G|0.993;A|0.007	0.007	strong	.	PGAP1	84	.	NM_024989	exon22	c.C2007T	p.A669A	AATGACGGCATCT	.	PASS	Atlas-SNP
LRP2	4036	hgsc.bcm.edu	37	2	170103336	170103336	+	Silent	SNP	T	T	C	rs831043	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	191	92	205	0	0.481675	0	T|0.456;C|0.544	0.544	strong	.	LRP2	751	.	NM_004525	exon21	c.A3069G	p.T1023T	CTGCTCTGTGGGT	.	PASS	Atlas-SNP
C17orf97	400566	hgsc.bcm.edu	37	17	263643	263643	+	Missense_Mutation	SNP	C	C	A	rs199668575	byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	114	2	207	3	0.0175439	0.0144928	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
NHLRC2	374354	hgsc.bcm.edu	37	10	115644040	115644040	+	Missense_Mutation	SNP	G	G	A	rs7913176	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	105	57	111	0	0.542857	0	G|0.771;A|0.229	0.229	strong	NHLRC2,NS,carcinoma,0,1	NHLRC2	56	1	NM_198514	exon5	c.G940A	p.V314I	AGCACTGTAGCTG	.	PASS	Atlas-SNP
CCDC168	643677	hgsc.bcm.edu	37	13	103385534	103385534	+	Missense_Mutation	SNP	C	C	T	rs17592438	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	172	72	223	0	0.418605	0	C|0.926;T|0.074	0.074	strong	.	.	.	.	NM_001146197	exon4	c.G17513A	p.R5838Q	CACCGTCGGATCA	.	PASS	Atlas-SNP
B4GALT4	8702	hgsc.bcm.edu	37	3	118945796	118945796	+	Missense_Mutation	SNP	G	G	C	rs3764779	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	156	96	150	0	0.615385	0	G|0.722;C|0.278	0.278	strong	B4GALT4,NS,carcinoma,0,1	B4GALT4	30	1	NM_212543	exon5	c.C346G	p.Q116E	ATTCCTGAGGGCG	.	PASS	Atlas-SNP
FBN3	84467	hgsc.bcm.edu	37	19	8203328	8203328	+	Missense_Mutation	SNP	G	G	A	rs7246376	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	114	114	106	0	1	0	G|0.739;A|0.260	0.260	strong	FBN3,NS,carcinoma,+1,1	FBN3	300	1	NM_032447	exon8	c.C986T	p.P329L	GGGACCGGGCCAG	.	PASS	Atlas-SNP
KIF26B	55083	hgsc.bcm.edu	37	1	245850095	245850095	+	Silent	SNP	C	C	T	rs871840	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	79	47	79	0	0.594937	0	C|0.808;T|0.192	0.192	strong	.	KIF26B	343	.	NM_018012	exon12	c.C3810T	p.D1270D	CCAGGACGCAGGG	.	PASS	Atlas-SNP
GNRHR	2798	hgsc.bcm.edu	37	4	68619601	68619601	+	Silent	SNP	G	G	A	rs4986942	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	132	50	149	0	0.378788	0	G|0.914;A|0.086	0.086	strong	.	GNRHR	31	.	NM_000406	exon1	c.C453T	p.S151S	GCTGTTGCTTTTC	.	PASS	Atlas-SNP
FAM170B	170370	hgsc.bcm.edu	37	10	50339925	50339925	+	Silent	SNP	G	G	A	rs12765281	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	37	20	46	0	0.540541	0	G|0.768;A|0.232	0.232	strong	.	FAM170B	20	.	NM_001164484	exon2	c.C585T	p.D195D	CAGCCAGTCCGGC	.	PASS	Atlas-SNP
B3GNTL1	146712	hgsc.bcm.edu	37	17	80923536	80923536	+	Silent	SNP	C	C	T	rs4986144	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	57	27	46	0	0.473684	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
RRP1	8568	hgsc.bcm.edu	37	21	45219524	45219524	+	Silent	SNP	T	T	C	rs4566449	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	102	34	98	0	0.333333	0	T|0.688;C|0.312	0.312	strong	.	RRP1	23	.	NM_003683	exon9	c.T885C	p.V295V	CCCCGTTCTCCAG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195509331	195509331	+	Silent	SNP	C	C	A	rs369416005		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	89	12	47	3	0.134831	0.0638298	.	.	weak	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.G9120T	p.P3040P	AGGAAGCGGGGTG	.	scavenged	Atlas-SNP
C14orf37	145407	hgsc.bcm.edu	37	14	58605043	58605043	+	Missense_Mutation	SNP	G	G	A	rs61741199	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	112	112	139	0	1	0	G|0.928;A|0.072	0.072	strong	.	C14orf37	87	.	NM_001001872	exon2	c.C1034T	p.T345I	TGTGCTGTCTGAG	.	PASS	Atlas-SNP
PNPLA1	285848	hgsc.bcm.edu	37	6	36260858	36260858	+	Silent	SNP	C	C	T	rs2239795	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	63	33	57	0	0.52381	0	C|0.568;T|0.432	0.432	strong	PNPLA1_ENST00000394571,NS,carcinoma,+2,2	PNPLA1	92	2	NM_001145717	exon3	c.C459T	p.F153F	CTGCTTCGTCCCG	.	PASS	Atlas-SNP
TNFRSF19	55504	hgsc.bcm.edu	37	13	24167505	24167505	+	Missense_Mutation	SNP	T	T	A	rs9550987	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	48	27	66	0	0.5625	0	A|0.272;N|0.000	0.272	strong	.	TNFRSF19	52	.	NM_018647	exon3	c.T91A	p.S31T	TGTGAATCAGGAG	.	PASS	Atlas-SNP
TNK1	8711	hgsc.bcm.edu	37	17	7286326	7286326	+	Silent	SNP	T	T	A	rs1554948	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	98	98	74	0	1	0	T|0.623;A|0.377	0.377	strong	.	TNK1	31	.	NM_003985	exon2	c.T81A	p.L27L	CATCCTTGAGGAG	.	PASS	Atlas-SNP
FAM154B	283726	hgsc.bcm.edu	37	15	82563991	82563991	+	Missense_Mutation	SNP	C	C	T	rs16973457	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	288	113	243	0	0.392361	0	C|0.582;T|0.418	0.418	strong	.	FAM154B	50	.	NM_001008226	exon2	c.C101T	p.P34L	ATGTGCCAGAAGA	.	PASS	Atlas-SNP
ZNF304	57343	hgsc.bcm.edu	37	19	57868483	57868483	+	Missense_Mutation	SNP	G	G	A	rs45612632	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	50	67	0	0.684932	0	G|0.981;A|0.019	0.019	strong	.	ZNF304	74	.	NM_020657	exon3	c.G1246A	p.A416T	ACCGGGGCAAGGC	.	PASS	Atlas-SNP
HMBS	3145	hgsc.bcm.edu	37	11	118962230	118962230	+	Silent	SNP	G	G	T	rs1131488	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	111	76	131	0	0.684685	0	G|0.792;T|0.208	0.208	strong	.	HMBS	27	.	NM_000190	exon9	c.G606T	p.V202V	CCGGGTGGGGCAG	.	PASS	Atlas-SNP
ELP2	55250	hgsc.bcm.edu	37	18	33750046	33750046	+	Silent	SNP	C	C	T	rs8299	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	143	70	144	0	0.48951	0	C|0.645;T|0.355	0.355	strong	ELP2,colon,carcinoma,0,2	ELP2	70	2	NM_001242875	exon21	c.C2292T	p.C764C	TGAGTGCGACTCC	.	PASS	Atlas-SNP
WDR93	56964	hgsc.bcm.edu	37	15	90260145	90260145	+	Missense_Mutation	SNP	T	T	A	rs7163367	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	35	80	0	0.492958	0	A|0.415;N|0.000	0.415	strong	WDR93,NS,carcinoma,-1,2	WDR93	63	2	NM_020212	exon7	c.T760A	p.S254T	CAGAACTCCCTTG	.	PASS	Atlas-SNP
PLIN4	729359	hgsc.bcm.edu	37	19	4512890	4512890	+	Missense_Mutation	SNP	G	G	A	rs199944112	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	127	13	241	0	0.102362	0	G|0.996;A|0.004	0.004	weak	.	PLIN4	191	.	NM_001080400	exon3	c.C1040T	p.T347I	AGGACAGTCTTGG	.	PASS	Atlas-SNP
ICAM3	3385	hgsc.bcm.edu	37	19	10445806	10445806	+	Silent	SNP	C	C	T	rs3181047	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	90	47	93	0	0.522222	0	C|0.995;T|0.005	0.005	strong	.	ICAM3	29	.	NM_002162	exon4	c.G873A	p.E291E	GACGATCTCCCGG	.	PASS	Atlas-SNP
OTOP3	347741	hgsc.bcm.edu	37	17	72937851	72937851	+	Missense_Mutation	SNP	G	G	A	rs9890664	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	76	30	110	0	0.394737	0	G|0.360;A|0.640	0.640	strong	.	OTOP3	64	.	NM_178233	exon2	c.G437A	p.R146Q	CCCGCCGACCACA	.	PASS	Atlas-SNP
CD207	50489	hgsc.bcm.edu	37	2	71062648	71062648	+	Missense_Mutation	SNP	G	G	A	rs10489990	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	91	35	128	0	0.384615	0	G|0.716;A|0.284	0.284	strong	CD207,NS,carcinoma,0,1	CD207	47	1	NM_015717	exon2	c.C164T	p.A55V	ACGGAGGCGACCA	.	PASS	Atlas-SNP
HCN4	10021	hgsc.bcm.edu	37	15	73621946	73621946	+	Silent	SNP	G	G	A	rs12909882	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	122	47	112	0	0.385246	0	G|0.929;A|0.071	0.071	strong	.	HCN4	150	.	NM_005477	exon4	c.C1558T	p.L520L	AGTCCAGGGACTG	.	PASS	Atlas-SNP
KRT81	3887	hgsc.bcm.edu	37	12	52681080	52681080	+	Silent	SNP	G	G	A	rs4761784	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	114	44	121	0	0.385965	0	G|0.744;A|0.256	0.256	strong	.	KRT81	46	.	NM_002281	exon7	c.C1053T	p.A351A	AGACTGGGCCACC	.	PASS	Atlas-SNP
TSEN54	283989	hgsc.bcm.edu	37	17	73518328	73518328	+	Missense_Mutation	SNP	A	A	C	rs77247739	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	23	9	35	0	0.391304	0	A|0.926;C|0.074	0.074	strong	.	TSEN54	27	.	NM_207346	exon8	c.A1166C	p.Q389P	GGCGGCAGGTGCA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195507349	195507349	+	Missense_Mutation	SNP	A	A	C	rs200575589	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	67	10	70	0	0.149254	0	.	.	weak	.	MUC4	1505	.	NM_018406	exon2	c.T11102G	p.I3701S	GAAGGGATGGTGA	.	PASS	Atlas-SNP
TRPT1	83707	hgsc.bcm.edu	37	11	63993287	63993287	+	Missense_Mutation	SNP	C	C	T	rs11549691	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	42	35	36	0	0.833333	0	C|0.947;T|0.053	0.053	strong	.	TRPT1	14	.	NM_001033678	exon2	c.G46A	p.G16S	TTCTACCCCTGGA	.	PASS	Atlas-SNP
DPP6	1804	hgsc.bcm.edu	37	7	154667643	154667643	+	Silent	SNP	G	G	A	rs2230064	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	31	90	0	0.378049	0	G|0.805;A|0.195	0.195	strong	.	DPP6	383	.	NM_130797	exon20	c.G1911A	p.V637V	GAGTGTGGCTGAG	.	PASS	Atlas-SNP
KRTAP4-2	85291	hgsc.bcm.edu	37	17	39334241	39334241	+	Missense_Mutation	SNP	G	G	C	rs62067292	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	43	23	61	0	0.534884	0	G|0.941;C|0.059	0.059	strong	.	KRTAP4-2	93	.	NM_033062	exon1	c.C176G	p.T59S	CAGCAGGTGGGCT	.	PASS	Atlas-SNP
SART1	9092	hgsc.bcm.edu	37	11	65732651	65732651	+	Silent	SNP	G	G	A	rs550435	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	92	85	0	1	0	G|0.565;A|0.435	0.435	strong	.	SART1	41	.	NM_005146	exon4	c.G516A	p.A172A	GCTGGCGGCTGCC	.	PASS	Atlas-SNP
ACTN1	87	hgsc.bcm.edu	37	14	69341653	69341653	+	Missense_Mutation	SNP	T	T	A	rs11557769	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	42	15	76	0	0.357143	0	T|0.988;A|0.012	0.012	strong	ACTN1,NS,carcinoma,+2,1	ACTN1	77	1	NM_001130004	exon22	c.A2668T	p.T890S	GGCCGGTGTAGGG	.	PASS	Atlas-SNP
TAS2R20	259295	hgsc.bcm.edu	37	12	11150240	11150240	+	Missense_Mutation	SNP	T	T	C	rs7135018	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	84	44	89	0	0.52381	0	T|0.779;C|0.221	0.221	strong	.	TAS2R20	17	.	NM_176889	exon1	c.A235G	p.K79E	TTACTTTTAAATT	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	112	51	126	0	0.455357	0	A|0.517;G|0.483	0.483	strong	.	GPATCH1	79	.	NM_018025	exon15	c.A2171G	p.H724R	AAGAGCATGCACC	.	PASS	Atlas-SNP
ZNF320	162967	hgsc.bcm.edu	37	19	53384197	53384197	+	Silent	SNP	A	A	G	rs61745485	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	47	18	72	0	0.382979	0	A|0.933;G|0.067	0.067	strong	.	ZNF320	67	.	NM_207333	exon4	c.T1182C	p.F394F	TGTACTAAAAACC	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	126	91	178	1	0.722222	0.00561798	A|0.839;G|0.161	0.161	strong	.	.	.	.	NM_001163560	exon10	c.T782C	p.I261T	TCTGGTATATCTT	.	PASS	Atlas-SNP
MYCBP2	23077	hgsc.bcm.edu	37	13	77632470	77632470	+	Silent	SNP	C	C	T	rs2285386	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	164	71	201	0	0.432927	0	C|0.903;T|0.097	0.097	strong	.	MYCBP2	1029	.	NM_015057	exon78	c.G13212A	p.E4404E	ACAGTGCTCTTCG	.	PASS	Atlas-SNP
DSC1	1823	hgsc.bcm.edu	37	18	28710615	28710615	+	Silent	SNP	C	C	A	rs1816634	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	201	85	246	0	0.422886	0	C|0.914;A|0.086	0.086	strong	.	DSC1	240	.	NM_024421	exon16	c.G2547T	p.S849S	GTTATACGAACAA	.	PASS	Atlas-SNP
SSTR5	6755	hgsc.bcm.edu	37	16	1129872	1129872	+	Missense_Mutation	SNP	C	C	T	rs169068	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	33	9	23	0	0.272727	0	C|0.484;T|0.516	0.516	strong	.	SSTR5	36	.	NM_001172560	exon2	c.C1004T	p.P335L	CGGAGCCGCGTCC	.	PASS	Atlas-SNP
OR8K1	390157	hgsc.bcm.edu	37	11	56113593	56113593	+	Missense_Mutation	SNP	C	C	A	rs10896272	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	100	24	143	0	0.24	0	C|0.621;A|0.379	0.379	strong	.	OR8K1	93	.	NM_001002907	exon1	c.C79A	p.P27T	GACAACCCTGGGC	.	PASS	Atlas-SNP
CCDC102A	92922	hgsc.bcm.edu	37	16	57555076	57555076	+	Silent	SNP	C	C	T	rs28446687	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	122	72	122	0	0.590164	0	C|0.768;T|0.232	0.232	strong	.	CCDC102A	22	.	NM_033212	exon4	c.G825A	p.A275A	GCTCAACGCCAGT	.	PASS	Atlas-SNP
OR5R1	219479	hgsc.bcm.edu	37	11	56184888	56184888	+	Missense_Mutation	SNP	G	G	A	rs998544	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	168	28	177	0	0.166667	0	G|0.630;N|0.000	.	strong	.	OR5R1	83	.	NM_001004744	exon1	c.C821T	p.A274V	ACAGAAGCCATCT	.	PASS	Atlas-SNP
AKR1C1	1645	hgsc.bcm.edu	37	10	5014935	5014935	+	Missense_Mutation	SNP	C	C	A	rs142200840	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	329	131	358	0	0.398176	0	C|0.990;A|0.010	0.010	strong	.	AKR1C1	39	.	NM_001353	exon7	c.C840A	p.N280K	ACAGAACGTGCAG	.	PASS	Atlas-SNP
SLC38A10	124565	hgsc.bcm.edu	37	17	79225330	79225330	+	Missense_Mutation	SNP	C	C	A	rs55872261	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	41	27	21	0	0.658537	0	C|0.955;A|0.045	0.045	strong	.	SLC38A10	133	.	NM_001037984	exon14	c.G2028T	p.E676D	CGCTCGCTCCACG	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	325	324	314	1	0.996923	0.00318471	C|0.365;A|0.635	0.635	strong	.	C2orf16	357	.	NM_032266	exon1	c.C1979A	p.A660E	AGTCTGCAGAATT	.	PASS	Atlas-SNP
MORC3	23515	hgsc.bcm.edu	37	21	37736413	37736413	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	381	5	269	0	0.0131234	0	.	.	none	MORC3,NS,carcinoma,0,1	MORC3	78	1	NM_015358	exon14	c.G1475A	p.R492Q	TGTTTCGGCCAAC	.	scavenged	Atlas-SNP
MDGA1	266727	hgsc.bcm.edu	37	6	37631768	37631768	+	Missense_Mutation	SNP	A	A	G	rs10947690	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	84	34	100	0	0.404762	0	A|0.894;G|0.106	0.106	strong	.	MDGA1	104	.	NM_153487	exon2	c.T182C	p.L61P	GTTACAAGGCACT	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1270647	1270647	+	Missense_Mutation	SNP	G	G	C	rs185838223	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	732	153	731	0	0.209016	0	G|0.952;C|0.048	0.048	strong	.	MUC5B	473	.	NM_002458	exon31	c.G12537C	p.Q4179H	GGCCCAGCCTGGT	.	PASS	Atlas-SNP
FGF6	2251	hgsc.bcm.edu	37	12	4554630	4554630	+	Missense_Mutation	SNP	A	A	G	rs11613495	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	46	22	55	0	0.478261	0	A|0.879;G|0.121	0.121	strong	.	FGF6	40	.	NM_020996	exon1	c.T107C	p.V36A	GAGGGCACCACCA	.	PASS	Atlas-SNP
ADAMTS7	11173	hgsc.bcm.edu	37	15	79092750	79092750	+	Silent	SNP	G	G	C	rs7173267	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	68	29	40	0	0.426471	0	G|0.752;C|0.248	0.248	strong	.	ADAMTS7	142	.	NM_014272	exon2	c.C240G	p.A80A	GTAGAAGGCGGGC	.	PASS	Atlas-SNP
ADAMTS19	171019	hgsc.bcm.edu	37	5	128796860	128796860	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	14	13	8	0	0.928571	0	.	.	none	.	ADAMTS19	216	.	NM_133638	exon2	c.C139A	p.P47T	CGGGAGCCGGTGG	.	PASS	Atlas-SNP
OR10H3	26532	hgsc.bcm.edu	37	19	15853080	15853080	+	Missense_Mutation	SNP	G	G	A	rs2240229	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	63	30	100	0	0.47619	0	G|0.833;A|0.167	0.167	strong	.	OR10H3	53	.	NM_013938	exon1	c.G878A	p.S293N	TTTTCAGTCTAAG	.	PASS	Atlas-SNP
PCDHB4	56131	hgsc.bcm.edu	37	5	140503017	140503017	+	Silent	SNP	G	G	A	rs61741162	byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	84	4	113	0	0.047619	0	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
ZNF717	100131827	hgsc.bcm.edu	37	3	75786440	75786440	+	Silent	SNP	C	C	T	rs6790146	bycluster;byfrequency;by2hit2allele;byhapmap	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	23	21	21	1	0.913043	0.047619	C|0.603;T|0.397	0.397	strong	ZNF717,NS,carcinoma,0,1	ZNF717	160	1	NM_001128223	exon5	c.G2334A	p.G778G	GTGAGTCCCCTGA	.	scavenged	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195510062	195510062	+	Missense_Mutation	SNP	G	G	C	rs200366897	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	90	8	58	0	0.0888889	0	.	.	weak	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.C8389G	p.H2797D	TGGTGTGACCTGT	.	scavenged	Atlas-SNP
SYK	6850	hgsc.bcm.edu	37	9	93606309	93606309	+	Silent	SNP	G	G	A	rs35758162	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	77	40	70	0	0.519481	0	G|0.847;A|0.153	0.153	strong	.	SYK	132	.	NM_003177	exon2	c.G129A	p.Q43Q	GCGCCAGAGCCGC	.	PASS	Atlas-SNP
HRNR	388697	hgsc.bcm.edu	37	1	152192327	152192327	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	162	2	192	0	0.0123457	0	.	.	none	HRNR,bladder,carcinoma,0,1	HRNR	403	1	NM_001009931	exon3	c.A1778T	p.Q593L	GAGGACTGTCCTG	.	scavenged	Atlas-SNP
LRIT3	345193	hgsc.bcm.edu	37	4	110791273	110791273	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	37	110	0	0.506849	0	.	.	none	.	LRIT3	107	.	NM_198506	exon4	c.G1368T	p.K456N	GGCAAAGAATGGA	.	PASS	Atlas-SNP
C7orf26	79034	hgsc.bcm.edu	37	7	6639953	6639953	+	Silent	SNP	G	G	A	rs34300529	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	40	12	58	0	0.3	0	G|0.883;A|0.117	0.117	strong	C7orf26,NS,carcinoma,0,1	C7orf26	33	1	NM_024067	exon4	c.G1074A	p.V358V	GCAGGTGGCCATG	.	PASS	Atlas-SNP
CDON	50937	hgsc.bcm.edu	37	11	125871721	125871721	+	Missense_Mutation	SNP	G	G	C	rs145983470	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	77	138	0	0.762376	0	G|0.994;C|0.006	0.006	strong	CDON,right_lower_lobe,carcinoma,0,1	CDON	137	1	NM_016952	exon11	c.C2051G	p.T684S	GCCTGGGTGTTTT	.	PASS	Atlas-SNP
GJA8	2703	hgsc.bcm.edu	37	1	147380460	147380460	+	Silent	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	42	11	63	0	0.261905	0	.	.	none	GJA8,NS,carcinoma,+2,1	GJA8	108	1	NM_005267	exon2	c.G378A	p.Q126Q	GGACCAGGGCAGC	.	PASS	Atlas-SNP
SLAMF1	6504	hgsc.bcm.edu	37	1	160580549	160580549	+	Missense_Mutation	SNP	G	G	T	rs3796504	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	181	57	278	0	0.314917	0	G|0.945;T|0.055	0.055	strong	.	SLAMF1	74	.	NM_003037	exon7	c.C997A	p.P333T	TCTCTGGAAGTGT	.	PASS	Atlas-SNP
MUC15	143662	hgsc.bcm.edu	37	11	26586801	26586801	+	Missense_Mutation	SNP	G	G	A	rs15783	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	102	79	157	0	0.77451	0	G|0.424;A|0.576	0.576	strong	MUC15,colon,carcinoma,0,1	MUC15	88	1	NM_001135092	exon3	c.C686T	p.T229I	TAAGGGGTAAACC	.	PASS	Atlas-SNP
KXD1	79036	hgsc.bcm.edu	37	19	18679379	18679379	+	Missense_Mutation	SNP	C	C	G	rs7648	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	37	17	51	0	0.459459	0	C|0.536;G|0.464	0.464	strong	.	.	.	.	NM_001171948	exon6	c.C469G	p.P157A	GTCCAGCCTGGCT	.	PASS	Atlas-SNP
NBPF10	100132406	hgsc.bcm.edu	37	1	145293469	145293469	+	Missense_Mutation	SNP	G	G	C	rs6671324	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	8	69	0	0.106667	0	.	.	weak	.	NBPF10	221	.	NM_001039703	exon1	c.G64C	p.E22Q	ATCAACGAGACAT	.	PASS	Atlas-SNP
ADAMTSL4	54507	hgsc.bcm.edu	37	1	150531905	150531905	+	Missense_Mutation	SNP	C	C	A	rs150225445	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	42	119	0	0.415842	0	C|0.993;A|0.007	0.007	strong	.	ADAMTSL4	101	.	NM_019032	exon17	c.C2906A	p.A969D	GGCAGGCCTGCCA	.	PASS	Atlas-SNP
CWF19L1	55280	hgsc.bcm.edu	37	10	101995477	101995477	+	Silent	SNP	T	T	G	rs139693285	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	38	16	51	0	0.421053	0	T|0.999;G|0.001	0.001	strong	.	CWF19L1	39	.	NM_018294	exon13	c.A1419C	p.T473T	TTCTCCTGTGTCA	.	PASS	Atlas-SNP
MLC1	23209	hgsc.bcm.edu	37	22	50515270	50515270	+	Silent	SNP	T	T	C	rs6010164	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	51	23	64	0	0.45098	0	T|0.887;C|0.113	0.113	strong	.	MLC1	48	.	NM_015166	exon7	c.A597G	p.S199S	TCTTACTGAGTAA	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29912087	29912087	+	Missense_Mutation	SNP	G	G	T	rs2231093	byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	125	41	146	0	0.328	0	G|0.860;T|0.140	0.140	strong	.	HLA-A	89	.	NM_001242758	exon4	c.G808T	p.A270S	TGGGCGGCTGTGG	.	PASS	Atlas-SNP
SBSPON	157869	hgsc.bcm.edu	37	8	74005131	74005131	+	Missense_Mutation	SNP	A	A	G	rs59331088	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	156	122	137	0	0.782051	0	A|0.660;G|0.340	0.340	strong	.	.	.	.	NM_153225	exon1	c.T172C	p.F58L	CGGTGAAGCGACA	.	PASS	Atlas-SNP
IGFBP3	3486	hgsc.bcm.edu	37	7	45956969	45956969	+	Missense_Mutation	SNP	T	T	G	rs9282734	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	68	25	109	0	0.367647	0	T|0.974;G|0.026	0.026	strong	.	IGFBP3	40	.	NM_001013398	exon2	c.A491C	p.H164P	ACCCGGTGCGTGC	.	PASS	Atlas-SNP
CES1	1066	hgsc.bcm.edu	37	16	55862762	55862762	+	Silent	SNP	C	C	G	rs3826194	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	95	15	152	1	0.157895	0.00657895	C|0.766;G|0.234	0.234	strong	CES1_ENST00000360526,caecum,carcinoma,0,2	CES1	78	2	NM_001025195	exon2	c.G177C	p.P59P	AAGAGGCGGCTTG	.	scavenged	Atlas-SNP
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33036977	33036977	+	Silent	SNP	G	G	A	rs2308927	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	49	19	68	0	0.387755	0	G|0.903;A|0.097	0.097	strong	.	HLA-DPA1	20	.	NM_033554	exon3	c.C447T	p.N149N	CGTGACGTTGAGC	.	PASS	Atlas-SNP
ZNF628	89887	hgsc.bcm.edu	37	19	55995272	55995272	+	Silent	SNP	G	G	A	rs11550705	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	67	67	86	0	1	0	G|0.723;A|0.277	0.277	strong	.	ZNF628	75	.	NM_033113	exon3	c.G2712A	p.P904P	TGGCCCGGGCCCC	.	PASS	Atlas-SNP
REST	5978	hgsc.bcm.edu	37	4	57798174	57798174	+	Silent	SNP	C	C	G	rs3796528	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	135	67	139	0	0.496296	0	C|0.914;G|0.086	0.086	strong	REST,NS,carcinoma,0,1	REST	104	1	NM_001193508	exon4	c.C3150G	p.A1050A	GGAAGCCTTGGCA	.	PASS	Atlas-SNP
RRN3	54700	hgsc.bcm.edu	37	16	15178499	15178499	+	Missense_Mutation	SNP	G	G	A	rs76732059	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	335	90	300	0	0.268657	0	G|0.960;A|0.040	0.040	strong	.	RRN3	36	.	NM_018427	exon7	c.C596T	p.S199L	ACTCACGATGGTA	.	PASS	Atlas-SNP
THSD7A	221981	hgsc.bcm.edu	37	7	11675855	11675855	+	Silent	SNP	C	C	T	rs61996273	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	217	216	226	1	0.995392	0.00442478	C|0.880;T|0.120	0.120	strong	.	THSD7A	219	.	NM_015204	exon2	c.G924A	p.R308R	GTTCTGCCTGTTT	.	PASS	Atlas-SNP
CNPY3	10695	hgsc.bcm.edu	37	6	42906384	42906384	+	Missense_Mutation	SNP	G	G	T	rs9471969	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	103	46	146	0	0.446602	0	G|0.754;T|0.246	0.246	strong	.	CNPY3	25	.	NM_006586	exon6	c.G692T	p.S231I	AGAGCAGCAGGGC	.	PASS	Atlas-SNP
WBSCR28	135886	hgsc.bcm.edu	37	7	73280020	73280020	+	Silent	SNP	C	C	T	rs1136647	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	162	160	207	1	0.987654	0.00483092	C|0.529;T|0.471	0.471	strong	WBSCR28,NS,carcinoma,+1,1	WBSCR28	24	1	NM_182504	exon3	c.C615T	p.T205T	CATCACCTGGACC	.	PASS	Atlas-SNP
PDLIM7	9260	hgsc.bcm.edu	37	5	176917897	176917897	+	Silent	SNP	C	C	T	rs1132445	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	313	132	288	0	0.421725	0	T|0.049;G|0.000;C|0.951	0.049	strong	.	PDLIM7	32	.	NM_213636	exon7	c.G546A	p.P182P	CTCATCCGGGTCT	.	PASS	Atlas-SNP
ZNF831	128611	hgsc.bcm.edu	37	20	57768399	57768399	+	Silent	SNP	T	T	C	rs442091	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	74	32	71	0	0.432432	0	T|0.666;C|0.334	0.334	strong	ZNF831,NS,carcinoma,+2,1	ZNF831	287	1	NM_178457	exon1	c.T2325C	p.A775A	AGAGGCTCCCAGG	.	PASS	Atlas-SNP
SELPLG	6404	hgsc.bcm.edu	37	12	109017673	109017673	+	Silent	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	25	117	4	0.294118	0.034188	.	.	none	SELPLG_ENST00000550948,NS,carcinoma,-1,7	SELPLG	138	7	NM_001206609	exon2	c.G459A	p.V153V	CGTGGGCACTGGT	.	scavenged	Atlas-SNP
GREB1	9687	hgsc.bcm.edu	37	2	11727507	11727507	+	Splice_Site	SNP	G	G	A	rs13394619	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	65	26	76	0	0.4	0	G|0.377;A|0.623	0.623	strong	GREB1_ENST00000263834,NS,carcinoma,0,1	GREB1	308	1	NM_148903	exon10	c.1160-1G>A	.	ACTGCAGTATTTG	.	PASS	Atlas-SNP
RPAP1	26015	hgsc.bcm.edu	37	15	41813279	41813279	+	Silent	SNP	C	C	T	rs3743031	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	158	64	198	0	0.405063	0	C|0.680;T|0.320	0.320	strong	RPAP1,NS,carcinoma,0,1	RPAP1	111	1	NM_015540	exon22	c.G3105A	p.R1035R	AGGGACCCTGCTG	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	40	24	70	0	0.6	0	G|0.679;A|0.321	0.321	strong	.	PCSK5	329	.	NM_001190482	exon30	c.G3824A	p.G1275D	AAGACGGCATATG	.	PASS	Atlas-SNP
MYO9B	4650	hgsc.bcm.edu	37	19	17317955	17317955	+	Silent	SNP	A	A	G	rs8110964	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	188	102	221	0	0.542553	0	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	.	PASS	Atlas-SNP
TMEM63B	55362	hgsc.bcm.edu	37	6	44119676	44119676	+	Silent	SNP	A	A	G	rs3734697	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	132	62	108	0	0.469697	0	A|0.910;G|0.090	0.090	strong	TMEM63B,NS,carcinoma,0,1	TMEM63B	77	1	NM_018426	exon19	c.A1767G	p.P589P	CATCCCAGGCCTG	.	PASS	Atlas-SNP
DDX52	11056	hgsc.bcm.edu	37	17	35984410	35984410	+	Missense_Mutation	SNP	T	T	C	rs7216445	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	55	24	81	0	0.436364	0	C|0.654;T|0.346	0.654	strong	.	DDX52	40	.	NM_007010	exon9	c.A1207G	p.M403V	CTCTCATGGCCAG	.	PASS	Atlas-SNP
BTN3A2	11118	hgsc.bcm.edu	37	6	26373507	26373507	+	Missense_Mutation	SNP	G	G	A	rs13216828	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	56	55	79	0	0.982143	0	G|0.922;A|0.078	0.078	strong	.	BTN3A2	44	.	NM_001197246	exon5	c.G920A	p.S307N	CAGAGAGCCTCCA	.	PASS	Atlas-SNP
ANKRD18B	441459	hgsc.bcm.edu	37	9	33566234	33566234	+	Silent	SNP	C	C	T	rs79153255		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	91	91	100	0	1	0	T|1.000;|0.000	1.000	weak	.	ANKRD18B	46	.	NM_001244752	exon13	c.C2289T	p.A763A	TATGGCCGAGAAG	.	PASS	Atlas-SNP
CYYR1	116159	hgsc.bcm.edu	37	21	27852724	27852724	+	Silent	SNP	A	A	G	rs966410	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	64	41	55	0	0.640625	0	A|0.549;G|0.451	0.451	strong	.	CYYR1	38	.	NM_052954	exon3	c.T201C	p.V67V	TCCAAAAACAATG	.	PASS	Atlas-SNP
SMARCA2	6595	hgsc.bcm.edu	37	9	2191309	2191309	+	Missense_Mutation	SNP	C	C	G	rs2296212	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	143	88	125	0	0.615385	0	C|0.831;G|0.169	0.169	strong	.	SMARCA2	313	.	NM_003070	exon33	c.C4638G	p.D1546E	AGATGACAAAGGC	.	PASS	Atlas-SNP
LRIG1	26018	hgsc.bcm.edu	37	3	66434643	66434643	+	Missense_Mutation	SNP	T	T	C	rs2306272	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	234	94	256	1	0.401709	0.00390625	T|0.707;C|0.293	0.293	strong	.	LRIG1	138	.	NM_015541	exon14	c.A1843G	p.M615V	GGGCCATGGTGGT	.	PASS	Atlas-SNP
SVIL	6840	hgsc.bcm.edu	37	10	29747417	29747417	+	Silent	SNP	C	C	T	rs1887465	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	66	34	79	0	0.515152	0	C|0.733;T|0.267	0.267	strong	.	SVIL	226	.	NM_021738	exon37	c.G6504A	p.P2168P	CCCCTCCGGGAGT	.	PASS	Atlas-SNP
MTTP	4547	hgsc.bcm.edu	37	4	100504664	100504664	+	Missense_Mutation	SNP	T	T	C	rs3816873	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	259	123	311	3	0.474903	0.0096463	T|0.748;C|0.252	0.252	strong	MTTP,NS,carcinoma,0,1	MTTP	127	1	NM_000253	exon4	c.T383C	p.I128T	ATCTAATCCATGG	.	scavenged	Atlas-SNP
CDH1	999	hgsc.bcm.edu	37	16	68862165	68862165	+	Silent	SNP	C	C	T	rs33964119	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	84	34	85	0	0.404762	0	A|0.000;C|0.956;G|0.000;T|0.043	0.043	strong	CDH1,colon,carcinoma,0,3	CDH1	535	3	NM_004360	exon14	c.C2253T	p.N751N	GGACAACGTTTAT	.	PASS	Atlas-SNP
MTAP	4507	hgsc.bcm.edu	37	9	21816758	21816758	+	Missense_Mutation	SNP	G	G	A	rs7023954	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	33	82	0	0.458333	0	G|0.589;A|0.411	0.411	strong	.	MTAP	23	.	NM_002451	exon3	c.G166A	p.V56I	GATTGCGTCCTCC	.	PASS	Atlas-SNP
CDHR3	222256	hgsc.bcm.edu	37	7	105621512	105621512	+	Silent	SNP	G	G	T	rs193795	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	121	120	130	0	0.991736	0	G|0.578;T|0.422	0.422	strong	.	CDHR3	153	.	NM_152750	exon3	c.G348T	p.L116L	AGACCTGCAAGTC	.	PASS	Atlas-SNP
OR3A2	4995	hgsc.bcm.edu	37	17	3181384	3181384	+	Silent	SNP	C	C	T	rs769434	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	41	106	0	0.405941	0	C|0.838;T|0.162	0.162	strong	.	OR3A2	36	.	NM_002551	exon1	c.G846A	p.G282G	TCCAACCCCTTTA	.	PASS	Atlas-SNP
HAUS8	93323	hgsc.bcm.edu	37	19	17170885	17170885	+	Missense_Mutation	SNP	C	C	T	rs1130222	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	30	14	53	0	0.466667	0	T|0.368;G|0.076;C|0.484;A|0.072	0.368	strong	.	HAUS8	31	.	NM_033417	exon5	c.G247A	p.G83R	CCTTTCCGACCCC	.	PASS	Atlas-SNP
RIF1	55183	hgsc.bcm.edu	37	2	152311612	152311612	+	Missense_Mutation	SNP	A	A	G	rs61750444	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	143	76	179	1	0.531469	0.00558659	A|0.976;G|0.024	0.024	strong	RIF1,NS,carcinoma,-2,1	RIF1	244	1	NM_018151	exon22	c.A2548G	p.M850V	CCTTCTATGATCC	.	scavenged	Atlas-SNP
ARHGEF12	23365	hgsc.bcm.edu	37	11	120317168	120317168	+	Missense_Mutation	SNP	A	A	G	rs201670344	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	59	12	72	0	0.20339	0	A|1.000;C|0.000	.	strong	.	ARHGEF12	133	.	NM_015313	exon17	c.A1402G	p.M468V	CAAACTATGCAAG	.	PASS	Atlas-SNP
COG4	25839	hgsc.bcm.edu	37	16	70515355	70515355	+	Silent	SNP	C	C	T	rs11054	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	51	29	51	0	0.568627	0	C|0.538;A|0.002	.	strong	.	COG4	64	.	NM_015386	exon18	c.G2142A	p.S714S	AATGAGCGACCTC	.	PASS	Atlas-SNP
PSPH	5723	hgsc.bcm.edu	37	7	56088825	56088825	+	Missense_Mutation	SNP	T	T	A	rs74445297	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	197	29	195	0	0.147208	0	T|0.752;A|0.248	0.248	strong	.	PSPH	23	.	NM_004577	exon4	c.A81T	p.R27S	TTCTTCTCTGATG	.	PASS	Atlas-SNP
MRPL28	10573	hgsc.bcm.edu	37	16	419092	419092	+	Silent	SNP	A	A	G	rs3830160	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	100	99	140	0	0.99	0	A|0.346;G|0.654	0.654	strong	.	MRPL28	15	.	NM_006428	exon3	c.T417C	p.Y139Y	GAGCCCATAAGCC	.	PASS	Atlas-SNP
SH3TC1	54436	hgsc.bcm.edu	37	4	8238151	8238151	+	Silent	SNP	C	C	T	rs11603	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	265	129	306	0	0.486792	0	C|0.684;T|0.316	0.316	strong	.	SH3TC1	105	.	NM_018986	exon16	c.C3552T	p.T1184T	CATCACCCTGGGT	.	PASS	Atlas-SNP
EXOC3	11336	hgsc.bcm.edu	37	5	453567	453567	+	Silent	SNP	G	G	A	rs2672722	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	139	138	145	0	0.992806	0	G|0.438;A|0.562	0.562	strong	.	EXOC3	54	.	NM_007277	exon4	c.G447A	p.E149E	CCTGGAGTGCTCC	.	PASS	Atlas-SNP
RADIL	55698	hgsc.bcm.edu	37	7	4839882	4839882	+	Missense_Mutation	SNP	T	T	C	rs3816854	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	110	87	119	0	0.790909	0	T|0.926;C|0.074	0.074	strong	.	RADIL	110	.	NM_018059	exon13	c.A2902G	p.T968A	CCTCGGTGCTGGA	.	PASS	Atlas-SNP
SERPINA11	256394	hgsc.bcm.edu	37	14	94912799	94912799	+	Silent	SNP	G	G	A	rs12888805	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	179	75	193	0	0.418994	0	G|0.707;A|0.293	0.293	strong	SERPINA11,right_lower_lobe,carcinoma,-1,1	SERPINA11	53	1	NM_001080451	exon3	c.C786T	p.T262T	GAGGACGGTGCAA	.	PASS	Atlas-SNP
TG	7038	hgsc.bcm.edu	37	8	133980076	133980076	+	Silent	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	43	100	0	0.551282	0	.	.	none	TG,colon,carcinoma,0,1	TG	416	1	NM_003235	exon31	c.G5724A	p.E1908E	CGCAGAGATAACA	.	PASS	Atlas-SNP
HJURP	55355	hgsc.bcm.edu	37	2	234761225	234761225	+	Missense_Mutation	SNP	C	C	T	rs2286430	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	67	67	120	0	1	0	C|0.621;T|0.379	0.379	strong	.	HJURP	72	.	NM_018410	exon3	c.G226A	p.E76K	CTCCTTCGTTTCT	.	PASS	Atlas-SNP
LMF1	64788	hgsc.bcm.edu	37	16	1004554	1004554	+	Silent	SNP	C	C	T	rs3751667	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	17	99	0	0.2	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
CHGB	1114	hgsc.bcm.edu	37	20	5904040	5904040	+	Missense_Mutation	SNP	G	G	A	rs742711	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	43	19	44	0	0.44186	0	G|0.775;A|0.225	0.225	strong	CHGB,NS,carcinoma,0,1	CHGB	112	1	NM_001819	exon4	c.G1250A	p.R417H	AGGGACGCCATCA	.	PASS	Atlas-SNP
SPP1	6696	hgsc.bcm.edu	37	4	88902692	88902692	+	Silent	SNP	T	T	C	rs4754	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	174	174	200	0	1	0	T|0.713;C|0.287	0.287	strong	SPP1,NS,carcinoma,0,1	SPP1	35	1	NM_001251830	exon7	c.T321C	p.D107D	TGATGATGACCAT	.	PASS	Atlas-SNP
ZNF83	55769	hgsc.bcm.edu	37	19	53117531	53117531	+	Missense_Mutation	SNP	C	C	T	rs1056185	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	126	124	152	0	0.984127	0	C|0.299;T|0.700	0.700	strong	.	ZNF83	73	.	NM_018300	exon3	c.G287A	p.S96N	CGCTCACTACATT	.	PASS	Atlas-SNP
SSX7	280658	hgsc.bcm.edu	37	X	52674514	52674514	+	Missense_Mutation	SNP	G	G	T	rs140796367	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	647	434	926	1	0.670788	0.00107991	G|0.933;T|0.067	0.067	strong	.	SSX7	34	.	NM_173358	exon7	c.C546A	p.D182E	TTCAGGGTCGCTG	.	PASS	Atlas-SNP
CEP192	55125	hgsc.bcm.edu	37	18	13116432	13116432	+	Missense_Mutation	SNP	G	G	T	rs1786263	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	93	42	101	0	0.451613	0	G|0.251;T|0.749	0.749	strong	.	CEP192	340	.	NM_032142	exon43	c.G7346T	p.R2449L	GGTTCCGGCCGAC	.	PASS	Atlas-SNP
DAOA	267012	hgsc.bcm.edu	37	13	106142235	106142235	+	Silent	SNP	C	C	T	rs778294	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	31	79	0	0.430556	0	C|0.763;T|0.237	0.237	strong	.	DAOA	26	.	NM_001161812	exon4	c.C183T	p.T61T	TGAGACCGGATCT	.	PASS	Atlas-SNP
DYNC2LI1	51626	hgsc.bcm.edu	37	2	44028013	44028013	+	Missense_Mutation	SNP	A	A	T	rs11556157	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	138	40	84	0	0.289855	0	A|0.758;T|0.242	0.242	strong	.	DYNC2LI1	46	.	NM_001193464	exon9	c.A691T	p.I231L	CTAAAAATACGTG	.	PASS	Atlas-SNP
PDE10A	10846	hgsc.bcm.edu	37	6	165832227	165832227	+	Silent	SNP	C	C	T	rs220740	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	21	9	65	0	0.428571	0	C|0.710;T|0.290	0.290	strong	.	PDE10A	154	.	NM_001130690	exon11	c.G894A	p.A298A	GAAAAGCGCACAA	.	PASS	Atlas-SNP
ESPN	83715	hgsc.bcm.edu	37	1	6500762	6500762	+	Missense_Mutation	SNP	G	G	A	rs200602012	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	35	13	12	0	0.371429	0	G|0.991;A|0.010	0.010	weak	.	ESPN	32	.	NM_031475	exon4	c.G752A	p.G251D	GCCGCGGCCACAC	.	PASS	Atlas-SNP
TLR10	81793	hgsc.bcm.edu	37	4	38775794	38775794	+	Missense_Mutation	SNP	A	A	G	rs11466657	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	90	41	95	0	0.455556	0	A|0.970;G|0.030	0.030	strong	.	TLR10	87	.	NM_001017388	exon2	c.T1418C	p.I473T	AATGCAATATTTA	.	PASS	Atlas-SNP
ENDOD1	23052	hgsc.bcm.edu	37	11	94862577	94862577	+	Missense_Mutation	SNP	G	G	T	rs3740861	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	322	239	424	2	0.742236	0.00471698	G|0.794;T|0.206	0.206	strong	ENDOD1,NS,carcinoma,-1,1	ENDOD1	26	1	NM_015036	exon2	c.G1337T	p.G446V	CCATGGGCGCTAT	.	PASS	Atlas-SNP
SERPINE2	5270	hgsc.bcm.edu	37	2	224862842	224862842	+	Silent	SNP	A	A	G	rs12457	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	93	35	112	0	0.376344	0	A|0.718;G|0.282	0.282	strong	.	SERPINE2	103	.	NM_001136530	exon3	c.T513C	p.N171N	GGTTTCATTTTTA	.	PASS	Atlas-SNP
KIF1B	23095	hgsc.bcm.edu	37	1	10435324	10435324	+	Silent	SNP	C	C	A	rs11121552	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	44	127	0	0.536585	0	C|0.759;A|0.241	0.241	strong	KIF1B,NS,carcinoma,0,1	KIF1B	242	1	NM_015074	exon46	c.C5163A	p.T1721T	AAACACCTTTGCT	.	PASS	Atlas-SNP
CHRNA5	1138	hgsc.bcm.edu	37	15	78882925	78882925	+	Missense_Mutation	SNP	G	G	A	rs16969968	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	131	131	109	0	1	0	G|0.771;A|0.229	0.229	strong	.	CHRNA5	48	.	NM_000745	exon5	c.G1192A	p.D398N	GCGCTCGATTCTA	.	PASS	Atlas-SNP
KCNJ18	100134444	hgsc.bcm.edu	37	17	21318773	21318773	+	Missense_Mutation	SNP	G	G	A	rs3752034	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	117	27	108	0	0.230769	0	G|0.744;A|0.256	0.256	strong	KCNJ12,NS,carcinoma,+1,1	.	.	1	NM_001194958	exon3	c.G119A	p.R40H	CGCGGCGCAGGTG	.	PASS	Atlas-SNP
PODXL	5420	hgsc.bcm.edu	37	7	131196062	131196062	+	Silent	SNP	C	C	T	rs17744792	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	40	123	0	0.39604	0	C|0.871;T|0.129	0.129	strong	.	PODXL	53	.	NM_001018111	exon2	c.G231A	p.S77S	CTTGACCGAGGCC	.	PASS	Atlas-SNP
EXOSC6	118460	hgsc.bcm.edu	37	16	70285780	70285780	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	18	9	5	0	0.5	0	.	.	none	.	EXOSC6	1	.	NM_058219	exon1	c.C24G	p.I8M	GCCGCGGATGCGG	.	PASS	Atlas-SNP
BCL10	8915	hgsc.bcm.edu	37	1	85742012	85742012	+	Silent	SNP	G	G	C	rs11576939	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	108	53	133	0	0.490741	0	G|0.735;C|0.265	0.265	strong	.	BCL10	39	.	NM_003921	exon1	c.C24G	p.L8L	CTCGGTGAGGGAC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195513515	195513515	+	Missense_Mutation	SNP	C	C	T	rs201194776	byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	253	42	190	3	0.166008	0.0157895	C|0.965;T|0.036	0.036	strong	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.G4936A	p.A1646T	GGGTGGCGTGACC	.	scavenged	Atlas-SNP
REEP4	80346	hgsc.bcm.edu	37	8	21997738	21997738	+	Silent	SNP	A	A	T	rs35574275	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	102	78	122	0	0.764706	0	A|0.923;T|0.077	0.077	strong	REEP4,NS,carcinoma,0,1	REEP4	13	1	NM_025232	exon3	c.T129A	p.I43I	AAAAACAATCCAG	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	55	29	103	0	0.527273	0	T|0.884;C|0.116	0.116	strong	.	LBP	60	.	NM_004139	exon13	c.T1306C	p.F436L	AACACCTTCTACC	.	PASS	Atlas-SNP
INCENP	3619	hgsc.bcm.edu	37	11	61895741	61895741	+	Silent	SNP	A	A	G	rs1675131	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	49	75	0	0.710145	0	A|0.521;G|0.478	0.478	strong	.	INCENP	122	.	NM_001040694	exon2	c.A108G	p.E36E	TGAGGAAATCCAA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195511412	195511412	+	Missense_Mutation	SNP	T	T	A	rs199878638		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	51	22	96	0	0.431373	0	.	.	weak	.	MUC4	1505	.	NM_018406	exon2	c.A7039T	p.T2347S	GACCTGTGGATGC	.	PASS	Atlas-SNP
COL6A6	131873	hgsc.bcm.edu	37	3	130361856	130361856	+	Missense_Mutation	SNP	G	G	A	rs16830494	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	219	117	272	0	0.534247	0	G|0.887;A|0.113	0.113	strong	COL6A6_ENST00000358511,colon,carcinoma,+1,2	COL6A6	497	2	NM_001102608	exon30	c.G5216A	p.R1739Q	ATGTGCGAGACCG	.	PASS	Atlas-SNP
TMCO3	55002	hgsc.bcm.edu	37	13	114156093	114156093	+	Silent	SNP	C	C	T	rs2260080	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	47	122	0	0.465347	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
UBXN11	91544	hgsc.bcm.edu	37	1	26608879	26608879	+	Missense_Mutation	SNP	C	C	T	rs1134581	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	25	10	29	3	0.4	0.103448	C|1.000;|0.000	.	weak	UBXN11,NS,carcinoma,+2,2	UBXN11	54	2	NM_183008	exon16	c.G1474A	p.G492S	TGGGGCCGGGACC	.	scavenged	Atlas-SNP
PCYOX1	51449	hgsc.bcm.edu	37	2	70488470	70488470	+	Missense_Mutation	SNP	C	C	T	rs2706762	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	150	72	166	0	0.48	0	C|0.912;T|0.088	0.088	strong	.	PCYOX1	34	.	NM_016297	exon3	c.C446T	p.S149F	TTCAATCCCTCCG	.	PASS	Atlas-SNP
DNAH1	25981	hgsc.bcm.edu	37	3	52428988	52428988	+	Silent	SNP	C	C	A	rs11708581	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	233	101	268	1	0.433476	0.00373134	C|0.940;A|0.060	0.060	strong	DNAH1_ENST00000420323,NS,carcinoma,0,2	DNAH1	534	2	NM_015512	exon68	c.C10881A	p.V3627V	GCTAGTCCTCCGC	.	PASS	Atlas-SNP
PIGG	54872	hgsc.bcm.edu	37	4	520853	520853	+	Missense_Mutation	SNP	G	G	A	rs13114026	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	226	107	215	0	0.473451	0	G|0.827;A|0.173	0.173	strong	.	PIGG	86	.	NM_001127178	exon10	c.G2095A	p.V699I	CTCTCTGTCCTGG	.	PASS	Atlas-SNP
RAD51AP1	10635	hgsc.bcm.edu	37	12	4662210	4662210	+	Silent	SNP	T	T	C	rs17850028	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	110	47	141	0	0.427273	0	T|0.944;C|0.056	0.056	strong	.	RAD51AP1	30	.	NM_001130862	exon8	c.T669C	p.S223S	CTTCTCTATGAGA	.	PASS	Atlas-SNP
CYP4F2	8529	hgsc.bcm.edu	37	19	15990431	15990431	+	Missense_Mutation	SNP	C	C	T	rs2108622	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	26	83	0	0.376812	0	C|0.779;T|0.221	0.221	strong	.	CYP4F2	97	.	NM_001082	exon11	c.G1297A	p.V433M	GCCACACAGCTGG	.	PASS	Atlas-SNP
SLC9C1	285335	hgsc.bcm.edu	37	3	111921116	111921116	+	Missense_Mutation	SNP	C	C	A	rs9288938	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	158	155	182	1	0.981013	0.00549451	C|0.676;A|0.324	0.324	strong	.	.	.	.	NM_183061	exon18	c.G2303T	p.S768I	TTAGAACTTGTAA	.	PASS	Atlas-SNP
GTPBP10	85865	hgsc.bcm.edu	37	7	90001496	90001496	+	Missense_Mutation	SNP	G	G	C	rs35001814	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	68	25	86	0	0.367647	0	G|0.908;C|0.092	0.092	strong	.	GTPBP10	31	.	NM_033107	exon5	c.G492C	p.L164F	CTCTTTGCTAAGT	.	PASS	Atlas-SNP
CSNK1G2	1455	hgsc.bcm.edu	37	19	1979386	1979386	+	Silent	SNP	C	C	T	rs11550450	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	47	24	50	0	0.510638	0	C|0.820;T|0.180	0.180	strong	.	CSNK1G2	28	.	NM_001319	exon8	c.C837T	p.L279L	GGTGCTCTGCGAG	.	PASS	Atlas-SNP
WDR65	149465	hgsc.bcm.edu	37	1	43675499	43675499	+	Missense_Mutation	SNP	C	C	T	rs41301054	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	115	65	188	0	0.565217	0	C|0.972;T|0.028	0.028	strong	.	WDR65	76	.	NM_152498	exon11	c.C1841T	p.S614L	GCACCTCGGTGGG	.	PASS	Atlas-SNP
NRXN1	9378	hgsc.bcm.edu	37	2	50779939	50779939	+	Silent	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	261	55	134	0	0.210728	0	.	.	none	NRXN1_ENST00000536085,rectum,carcinoma,0,6	NRXN1	1118	6	NM_001135659	exon10	c.C1665T	p.G555G	GATGAGGCCATTT	.	PASS	Atlas-SNP
TNR	7143	hgsc.bcm.edu	37	1	175375469	175375469	+	Missense_Mutation	SNP	C	C	A	rs2239819	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	190	92	195	0	0.484211	0	C|0.755;N|0.000	.	strong	TNR,NS,carcinoma,0,1	TNR	399	1	NM_003285	exon3	c.G382T	p.A128S	AACTGGCACATGG	.	PASS	Atlas-SNP
E4F1	1877	hgsc.bcm.edu	37	16	2278509	2278509	+	Silent	SNP	G	G	A	rs2241070	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	207	42	213	0	0.202899	0	G|0.959;A|0.041	0.041	strong	.	E4F1	53	.	NM_004424	exon2	c.G294A	p.A98A	CACAGCGTTGCTG	.	PASS	Atlas-SNP
PCED1A	64773	hgsc.bcm.edu	37	20	2816821	2816821	+	Silent	SNP	C	C	T	rs2274669	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	123	114	134	0	0.926829	0	C|0.833;G|0.000;T|0.167	0.167	strong	FAM113A,colon,carcinoma,0,1	.	.	1	NM_022760	exon7	c.G981A	p.P327P	AGGAAGCGGGTAG	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	52	137	0	0.536082	0	C|0.845;G|0.155	0.155	strong	.	ANKIB1	92	.	NM_019004	exon20	c.C2544G	p.S848S	GAGTTCCTTGGAT	.	PASS	Atlas-SNP
CNTNAP3	79937	hgsc.bcm.edu	37	9	39085764	39085764	+	Silent	SNP	G	G	A	rs2150942	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	99	94	889	3	0.949495	0.00337458	.	.	weak	CNTNAP3,NS,carcinoma,-1,1	CNTNAP3	82	1	NM_033655	exon21	c.C3411T	p.A1137A	TTTGACGGCGTTG	.	scavenged	Atlas-SNP
OR1J2	26740	hgsc.bcm.edu	37	9	125273574	125273574	+	Missense_Mutation	SNP	G	G	A	rs4836891	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	176	84	202	0	0.477273	0	G|0.918;A|0.082	0.082	strong	OR1J2,NS,carcinoma,-1,2	OR1J2	64	2	NM_054107	exon1	c.G494A	p.R165Q	TGACCCGGCTGTC	.	PASS	Atlas-SNP
OR10G2	26534	hgsc.bcm.edu	37	14	22102293	22102293	+	Missense_Mutation	SNP	C	C	T	rs56451138		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	143	8	379	3	0.0559441	0.00791557	C|0.750;T|0.250	0.250	weak	OR10G2,NS,carcinoma,0,1	OR10G2	35	1	NM_001005466	exon1	c.G706A	p.A236T	CATCAGCGGTGCG	.	scavenged	Atlas-SNP
OPA3	80207	hgsc.bcm.edu	37	19	46057081	46057081	+	Silent	SNP	A	A	G	rs3826860	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	50	49	46	0	0.98	0	A|0.295;G|0.705	0.705	strong	OPA3_ENST00000263275,NS,carcinoma,0,1	OPA3	19	1	NM_025136	exon2	c.T231C	p.A77A	CAGCTCAGCTGCC	.	PASS	Atlas-SNP
SHROOM1	134549	hgsc.bcm.edu	37	5	132159393	132159393	+	Silent	SNP	G	G	A	rs33935150	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	65	30	91	0	0.461538	0	G|0.939;A|0.061	0.061	strong	.	SHROOM1	35	.	NM_133456	exon5	c.C1875T	p.N625N	GGCAGGGTTTTCA	.	PASS	Atlas-SNP
MURC	347273	hgsc.bcm.edu	37	9	103348634	103348634	+	Silent	SNP	G	G	A	rs2780956	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	33	17	35	0	0.515152	0	G|0.649;A|0.351	0.351	strong	.	MURC	43	.	NM_001018116	exon2	c.G996A	p.R332R	AGGAAGGGAAATC	.	PASS	Atlas-SNP
SUMF1	285362	hgsc.bcm.edu	37	3	4403837	4403837	+	Silent	SNP	A	A	G	rs2633852	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	63	63	92	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
ABCA13	154664	hgsc.bcm.edu	37	7	48313949	48313949	+	Silent	SNP	C	C	T	rs6583483	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	24	4	82	0	0.166667	0	C|0.878;T|0.122	0.122	strong	.	ABCA13	1192	.	NM_152701	exon17	c.C4686T	p.Y1562Y	TATTTACTTTAAC	.	PASS	Atlas-SNP
ZFYVE27	118813	hgsc.bcm.edu	37	10	99504630	99504630	+	Missense_Mutation	SNP	G	G	T	rs10882993	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	36	36	38	0	1	0	G|0.267;N|0.000	.	strong	.	ZFYVE27	31	.	NM_001002261	exon3	c.G413T	p.G138V	AGAGAGGTCGCCT	.	PASS	Atlas-SNP
TGM4	7047	hgsc.bcm.edu	37	3	44943389	44943389	+	Missense_Mutation	SNP	G	G	A	rs1995641	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	77	44	119	0	0.571429	0	G|0.521;A|0.479	0.479	strong	.	TGM4	82	.	NM_003241	exon8	c.G937A	p.E313K	AATGGCGAGAAAA	.	PASS	Atlas-SNP
SLC38A10	124565	hgsc.bcm.edu	37	17	79226264	79226264	+	Missense_Mutation	SNP	T	T	C	rs35546507	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	34	95	0	0.465753	0	T|0.957;C|0.043	0.043	strong	.	SLC38A10	133	.	NM_001037984	exon13	c.A1676G	p.K559R	GGCCTCTTCCCAA	.	PASS	Atlas-SNP
INO80	54617	hgsc.bcm.edu	37	15	41277551	41277551	+	Silent	SNP	T	T	C	rs61757083	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	99	50	159	0	0.50505	0	T|0.992;C|0.008	0.008	strong	.	INO80	122	.	NM_017553	exon32	c.A3906G	p.E1302E	ATACTTTTCCCGC	.	PASS	Atlas-SNP
HLA-C	3107	hgsc.bcm.edu	37	6	31239613	31239613	+	Missense_Mutation	SNP	C	C	T	rs2308538	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	55	11	61	0	0.2	0	T|0.155;C|0.845	0.155	strong	HLA-C_ENST00000383329,NS,carcinoma,0,2	HLA-C	92	2	NM_002117	exon2	c.G106A	p.V36M	GGGACACGGCGGT	.	scavenged	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105415264	105415264	+	Missense_Mutation	SNP	G	G	A	rs201041268	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	114	20	30	0	0.175439	0	G|0.980;A|0.019	0.019	strong	AHNAK2_ENST00000333244,NS,carcinoma,0,1	AHNAK2	719	1	NM_138420	exon7	c.C6524T	p.S2175L	TCCACCGAGGCCT	.	scavenged	Atlas-SNP
PSMA4	5685	hgsc.bcm.edu	37	15	78841220	78841220	+	Silent	SNP	T	T	C	rs8053	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	170	168	175	0	0.988235	0	T|0.307;C|0.693	0.693	strong	.	PSMA4	17	.	NM_001102667	exon9	c.T720C	p.H240H	AAAACATGAGGAA	.	PASS	Atlas-SNP
DYNC1H1	1778	hgsc.bcm.edu	37	14	102446161	102446161	+	Silent	SNP	G	G	A	rs3818188	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	137	72	159	0	0.525547	0	G|0.812;A|0.188	0.188	strong	.	DYNC1H1	395	.	NM_001376	exon4	c.G624A	p.P208P	CCTGCCGATTCAT	.	PASS	Atlas-SNP
OR51B5	282763	hgsc.bcm.edu	37	11	5364742	5364742	+	Missense_Mutation	SNP	C	C	T	rs11036913	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	20	17	20	0	0.85	0	C|0.671;T|0.329	0.329	strong	.	OR51B5	60	.	NM_001005567	exon5	c.G13A	p.G5S	AGCTGCCGCTGGA	.	PASS	Atlas-SNP
RP1L1	94137	hgsc.bcm.edu	37	8	10468172	10468172	+	Missense_Mutation	SNP	G	G	A	rs4840502	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	122	122	163	0	1	0	G|0.311;A|0.689	0.689	strong	RP1L1,colon,carcinoma,0,1	RP1L1	453	1	NM_178857	exon4	c.C3436T	p.R1146W	GGTACCGAGGGGA	.	PASS	Atlas-SNP
KANK4	163782	hgsc.bcm.edu	37	1	62740065	62740065	+	Silent	SNP	A	A	G	rs12127930	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	171	78	220	0	0.45614	0	A|0.524;G|0.476	0.476	strong	.	KANK4	135	.	NM_181712	exon3	c.T711C	p.G237G	CACCACACCCTCT	.	PASS	Atlas-SNP
OR52L1	338751	hgsc.bcm.edu	37	11	6007899	6007899	+	Missense_Mutation	SNP	C	C	T	rs4501959	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	94	93	101	0	0.989362	0	C|0.822;T|0.178	0.178	strong	.	OR52L1	100	.	NM_001005173	exon1	c.G262A	p.D88N	CCAGGTCGATGGC	.	PASS	Atlas-SNP
SDC3	9672	hgsc.bcm.edu	37	1	31351513	31351513	+	Silent	SNP	G	G	A	rs1891419	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	39	108	0	0.47561	0	G|0.818;A|0.182	0.182	strong	.	SDC3	45	.	NM_014654	exon2	c.C213T	p.P71P	ATCATCGGGAAAG	.	PASS	Atlas-SNP
FAM170B	170370	hgsc.bcm.edu	37	10	50340304	50340304	+	Missense_Mutation	SNP	C	C	A	rs17773851	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	30	86	0	0.422535	0	C|0.765;A|0.235	0.235	strong	.	FAM170B	20	.	NM_001164484	exon2	c.G206T	p.R69L	CAGTCCCGCATCC	.	PASS	Atlas-SNP
MCTP1	79772	hgsc.bcm.edu	37	5	94278129	94278129	+	Silent	SNP	T	T	C	rs293035	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	34	70	0	0.435897	0	T|0.746;C|0.254	0.254	strong	.	MCTP1	110	.	NM_024717	exon4	c.A984G	p.V328V	GTCAAATACCTGA	.	PASS	Atlas-SNP
SPTBN4	57731	hgsc.bcm.edu	37	19	41012190	41012190	+	Silent	SNP	C	C	T	rs7258094	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	190	96	224	0	0.505263	0	C|0.772;T|0.228	0.228	strong	.	SPTBN4	213	.	NM_020971	exon13	c.C1713T	p.D571D	GGCAGACGACCTG	.	PASS	Atlas-SNP
ZFP42	132625	hgsc.bcm.edu	37	4	188924523	188924523	+	Missense_Mutation	SNP	A	A	G	rs138176771	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	46	89	0	0.528736	0	A|0.999;G|0.001	0.001	strong	ZFP42,NS,carcinoma,-2,1	ZFP42	87	1	NM_174900	exon4	c.A562G	p.I188V	AGCGCAATCGCTT	.	PASS	Atlas-SNP
TM4SF20	79853	hgsc.bcm.edu	37	2	228230945	228230945	+	Missense_Mutation	SNP	G	G	A	rs76547437	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	176	95	206	0	0.539773	0	G|0.895;A|0.105	0.105	strong	TM4SF20,NS,carcinoma,0,1	TM4SF20	24	1	NM_024795	exon3	c.C265T	p.L89F	TGAAAAGTGATGA	.	PASS	Atlas-SNP
MYBPC1	4604	hgsc.bcm.edu	37	12	102045163	102045163	+	Missense_Mutation	SNP	C	C	G	rs3817552	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	96	44	133	0	0.458333	0	C|0.844;G|0.156	0.156	strong	.	MYBPC1	235	.	NM_206819	exon16	c.C1518G	p.H506Q	GGTTCACAAGGGA	.	PASS	Atlas-SNP
C7orf71	285941	hgsc.bcm.edu	37	7	26678856	26678856	+	Silent	SNP	A	A	G	rs57000259	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	18	13	10	0	0.722222	0	A|0.601;G|0.399	0.399	strong	.	C7orf71	6	.	NM_001145531	exon2	c.A93G	p.R31R	GACAAGACACATG	.	PASS	Atlas-SNP
RAI1	10743	hgsc.bcm.edu	37	17	17698901	17698901	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	2	80	0	0.0232558	0	.	.	none	RAI1,NS,carcinoma,0,1	RAI1	121	1	NM_030665	exon3	c.G2639A	p.S880N	TGGGCAGCCCCGA	.	scavenged	Atlas-SNP
TRIT1	54802	hgsc.bcm.edu	37	1	40349131	40349131	+	Silent	SNP	G	G	A	rs3845570	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	71	79	0	1	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
FGFRL1	53834	hgsc.bcm.edu	37	4	1006333	1006333	+	Silent	SNP	G	G	A	rs4647942	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	9	9	1	0	1	0	G|0.475;A|0.525	0.525	strong	.	FGFRL1	77	.	NM_001004356	exon2	c.G60A	p.P20P	CTTCCCGCCGGCC	.	PASS	Atlas-SNP
ABP1	26	hgsc.bcm.edu	37	7	150557665	150557665	+	Missense_Mutation	SNP	C	C	G	rs1049793	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	55	29	110	0	0.527273	0	C|0.600;G|0.400	0.400	strong	ABP1,NS,carcinoma,0,1	ABP1	92	1	NM_001272072	exon4	c.C1990G	p.H664D	CCCTGGCACCCGC	.	PASS	Atlas-SNP
PKHD1	5314	hgsc.bcm.edu	37	6	51768466	51768466	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	98	34	114	0	0.346939	0	.	.	none	PKHD1,colon,carcinoma,0,1	PKHD1	927	1	NM_170724	exon43	c.G6925A	p.E2309K	GTCCCTCGGCACC	.	PASS	Atlas-SNP
KIF24	347240	hgsc.bcm.edu	37	9	34310927	34310927	+	Missense_Mutation	SNP	T	T	C	rs10972048	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	335	138	382	1	0.41194	0.0026178	T|0.590;C|0.410	0.410	strong	.	KIF24	64	.	NM_194313	exon2	c.A418G	p.M140V	GTAGCATGTGTTC	.	PASS	Atlas-SNP
FCHSD1	89848	hgsc.bcm.edu	37	5	141030640	141030640	+	Silent	SNP	C	C	T	rs17287002	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	74	32	70	0	0.432432	0	C|0.962;T|0.038	0.038	strong	.	FCHSD1	51	.	NM_033449	exon2	c.G66A	p.L22L	GATGCTCAGCTGT	.	PASS	Atlas-SNP
ZNF536	9745	hgsc.bcm.edu	37	19	31039939	31039939	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	93	4	107	0	0.0430108	0	.	.	none	.	ZNF536	424	.	NM_014717	exon4	c.A3413G	p.K1138R	ATGGAAAGGCCCA	.	PASS	Atlas-SNP
ZNF469	84627	hgsc.bcm.edu	37	16	88501034	88501034	+	Missense_Mutation	SNP	G	G	C	rs12598474	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	77	35	69	0	0.454545	0	G|0.685;C|0.315	0.315	strong	ZNF469,NS,carcinoma,0,1	ZNF469	121	1	NM_001127464	exon2	c.G7072C	p.G2358R	GAGACCGGGCGCT	.	PASS	Atlas-SNP
PCSK9	255738	hgsc.bcm.edu	37	1	55505647	55505647	+	Missense_Mutation	SNP	G	G	T	rs11591147	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	46	87	0	0.474227	0	G|0.990;T|0.010	0.010	strong	.	PCSK9	76	.	NM_174936	exon1	c.G137T	p.R46L	CCTTGCGTTCCGA	.	PASS	Atlas-SNP
GRM3	2913	hgsc.bcm.edu	37	7	86415987	86415987	+	Silent	SNP	C	C	T	rs2228595	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	35	19	32	0	0.542857	0	C|0.946;T|0.054	0.054	strong	.	GRM3	237	.	NM_000840	exon3	c.C879T	p.A293A	CAATGCCTCCTTC	.	PASS	Atlas-SNP
ACOT11	26027	hgsc.bcm.edu	37	1	55064980	55064980	+	Missense_Mutation	SNP	G	G	A	rs2304303	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	124	63	137	0	0.508065	0	G|0.956;A|0.044	0.044	strong	ACOT11_ENST00000371316,caecum,carcinoma,0,2	ACOT11	105	2	NM_147161	exon8	c.G776A	p.R259H	TCTGCCGTGCCCA	.	PASS	Atlas-SNP
ZNF100	163227	hgsc.bcm.edu	37	19	21909948	21909948	+	Missense_Mutation	SNP	G	G	A	rs7246400	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	19	19	22	0	1	0	G|0.451;A|0.549	0.549	strong	.	ZNF100	62	.	NM_173531	exon5	c.C1166T	p.T389I	TGTTTAGTAAGGT	.	PASS	Atlas-SNP
TMPRSS15	5651	hgsc.bcm.edu	37	21	19713821	19713821	+	Silent	SNP	C	C	T	rs2824751	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	102	102	149	0	1	0	C|0.811;T|0.189	0.189	strong	TMPRSS15,NS,carcinoma,-1,1	TMPRSS15	189	1	NM_002772	exon13	c.G1473A	p.A491A	ATCCAACGCAATA	.	PASS	Atlas-SNP
LY9	4063	hgsc.bcm.edu	37	1	160793442	160793442	+	Silent	SNP	A	A	G	rs474131	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	164	96	173	0	0.585366	0	A|0.447;G|0.553	0.553	strong	.	LY9	115	.	NM_002348	exon8	c.A1686G	p.V562V	TGAGGTATTTGAC	.	PASS	Atlas-SNP
C2orf81	388963	hgsc.bcm.edu	37	2	74641624	74641624	+	Silent	SNP	G	G	C	rs2240444	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	130	54	154	0	0.415385	0	G|0.496;C|0.504	0.504	strong	.	C2orf81	23	.	NM_001145054	exon4	c.C1599G	p.P533P	CAACACGGGCTTC	.	PASS	Atlas-SNP
MLLT6	4302	hgsc.bcm.edu	37	17	36873149	36873149	+	Silent	SNP	C	C	T	rs9892493	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	100	45	100	0	0.45	0	C|0.869;T|0.131	0.131	strong	.	MLLT6	80	.	NM_005937	exon10	c.C1566T	p.S522S	CAGCTCCGGCCTG	.	PASS	Atlas-SNP
TMEM8A	58986	hgsc.bcm.edu	37	16	426432	426432	+	Missense_Mutation	SNP	T	T	C	rs2071915	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	54	54	66	0	1	0	C|0.542;N|0.001	0.542	strong	.	TMEM8A	49	.	NM_021259	exon6	c.A928G	p.I310V	GCTGGATGGTCAC	.	PASS	Atlas-SNP
PCDH18	54510	hgsc.bcm.edu	37	4	138449683	138449683	+	Silent	SNP	A	A	G	rs10018837	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	152	62	205	0	0.407895	0	A|0.443;G|0.557	0.557	strong	.	PCDH18	229	.	NM_019035	exon3	c.T2689C	p.L897L	CACCCAACAGCCT	.	PASS	Atlas-SNP
UTP18	51096	hgsc.bcm.edu	37	17	49338257	49338257	+	Silent	SNP	C	C	T	rs14180	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	48	48	27	0	1	0	C|0.927;T|0.073	0.073	strong	.	UTP18	28	.	NM_016001	exon1	c.C312T	p.D104D	CGAGGACGCGTTG	.	PASS	Atlas-SNP
PCDHGC5	56097	hgsc.bcm.edu	37	5	140871425	140871425	+	Missense_Mutation	SNP	A	A	G	rs17208425	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	103	103	104	0	1	0	A|0.821;G|0.179	0.179	strong	.	PCDHGC5	199	.	NM_032407	exon1	c.A2618G	p.E873G	TGCGCGAAACCAG	.	PASS	Atlas-SNP
NUP210	23225	hgsc.bcm.edu	37	3	13399786	13399786	+	Missense_Mutation	SNP	G	G	A	rs6795271	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	119	51	126	0	0.428571	0	G|0.734;A|0.266	0.266	strong	.	NUP210	182	.	NM_024923	exon16	c.C2264T	p.A755V	ACAGGCGCGAGGG	.	PASS	Atlas-SNP
WBSCR27	155368	hgsc.bcm.edu	37	7	73249165	73249165	+	Missense_Mutation	SNP	T	T	A	rs13246460	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	77	75	77	0	0.974026	0	T|0.351;A|0.649	0.649	strong	.	WBSCR27	21	.	NM_152559	exon6	c.A646T	p.R216W	ACCACCTCCAGCT	.	PASS	Atlas-SNP
NEGR1	257194	hgsc.bcm.edu	37	1	72748169	72748169	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	273	76	295	0	0.278388	0	.	.	none	.	NEGR1	60	.	NM_173808	exon1	c.G9C	p.M3I	CAGCATCATGTCC	.	PASS	Atlas-SNP
WDR88	126248	hgsc.bcm.edu	37	19	33635761	33635761	+	Silent	SNP	C	C	T	rs3848596	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	165	81	179	0	0.490909	0	C|0.574;N|0.000	.	strong	.	WDR88	50	.	NM_173479	exon3	c.C399T	p.D133D	GGTGGACGGTTCT	.	PASS	Atlas-SNP
ARHGEF37	389337	hgsc.bcm.edu	37	5	149001551	149001551	+	Missense_Mutation	SNP	A	A	C	rs4629585	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	203	91	226	1	0.448276	0.00442478	A|0.596;C|0.404	0.404	strong	.	ARHGEF37	45	.	NM_001001669	exon9	c.A1261C	p.M421L	CAGATCATGTGCA	.	PASS	Atlas-SNP
OR51A2	401667	hgsc.bcm.edu	37	11	4976447	4976447	+	Missense_Mutation	SNP	C	C	G	rs77497717	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	623	621	37	0	0.99679	0	C|0.897;G|0.103	0.103	strong	.	OR51A2	40	.	NM_001004748	exon1	c.G497C	p.R166T	AAGCTTCTTAAAG	.	PASS	Atlas-SNP
ACTR3B	57180	hgsc.bcm.edu	37	7	152520490	152520490	+	Missense_Mutation	SNP	C	C	T	rs78661149		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	232	60	197	0	0.258621	0	C|0.500;T|0.500	0.500	weak	ACTR3B,NS,haematopoietic_neoplasm,0,1	ACTR3B	50	1	NM_020445	exon8	c.C748T	p.R250W	GATCCCCGGAAGT	.	scavenged	Atlas-SNP
BMP6	654	hgsc.bcm.edu	37	6	7862631	7862631	+	Silent	SNP	G	G	C	rs17557	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	33	81	0	0.37931	0	G|0.489;C|0.511	0.511	strong	.	BMP6	67	.	NM_001718	exon4	c.G1104C	p.V368V	TGAGGTGCACGTG	.	PASS	Atlas-SNP
MFHAS1	9258	hgsc.bcm.edu	37	8	8748148	8748148	+	Silent	SNP	A	A	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	61	35	82	0	0.57377	0	.	.	none	.	MFHAS1	58	.	NM_004225	exon1	c.T2421G	p.L807L	AGGCTTAAGCAGC	.	PASS	Atlas-SNP
SPON2	10417	hgsc.bcm.edu	37	4	1165748	1165748	+	Missense_Mutation	SNP	T	T	C	rs6836335	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	151	67	128	0	0.443709	0	T|0.847;C|0.153	0.153	strong	.	SPON2	22	.	NM_012445	exon2	c.A112G	p.R38G	GGGCTCTGGCGGA	.	PASS	Atlas-SNP
GLI3	2737	hgsc.bcm.edu	37	7	42007201	42007201	+	Missense_Mutation	SNP	T	T	C	rs62622373	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	182	132	226	1	0.725275	0.00442478	T|0.999;C|0.001	0.001	strong	.	GLI3	312	.	NM_000168	exon14	c.A2424G	p.I808M	ATTTCCTATGAGA	.	PASS	Atlas-SNP
BTN3A2	11118	hgsc.bcm.edu	37	6	26370707	26370707	+	Silent	SNP	T	T	C	rs9379862	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	127	126	160	0	0.992126	0	T|0.752;C|0.248	0.248	strong	.	BTN3A2	44	.	NM_001197246	exon3	c.T591C	p.D197D	TGCAGATGGAGTG	.	PASS	Atlas-SNP
PPWD1	23398	hgsc.bcm.edu	37	5	64881936	64881936	+	Silent	SNP	A	A	G	rs27141	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	186	185	169	0	0.994624	0	A|0.396;G|0.604	0.604	strong	.	PPWD1	47	.	NM_015342	exon10	c.A1725G	p.P575P	CAGGCCATACACA	.	PASS	Atlas-SNP
ZNF417	147687	hgsc.bcm.edu	37	19	58421128	58421128	+	Missense_Mutation	SNP	C	C	T	rs3826671	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	492	345	396	1	0.701219	0.00252525	C|0.500;T|0.500	0.500	weak	ZNF417,NS,carcinoma,+1,1	ZNF417	44	1	NM_152475	exon3	c.G518A	p.R173H	AACTCGCGGAAGA	.	scavenged	Atlas-SNP
FRMD3	257019	hgsc.bcm.edu	37	9	85863091	85863091	+	Silent	SNP	A	A	G	rs10114696	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	29	108	0	0.386667	0	A|0.685;G|0.315	0.315	strong	.	FRMD3	96	.	NM_174938	exon14	c.T1536C	p.Y512Y	AATGTCATAGCTC	.	PASS	Atlas-SNP
OR52H1	390067	hgsc.bcm.edu	37	11	5566076	5566076	+	Silent	SNP	G	G	A	rs139835065	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	123	108	108	0	0.878049	0	G|0.998;A|0.002	0.002	strong	.	OR52H1	46	.	NM_001005289	exon1	c.C678T	p.Y226Y	GTGTGCGTAGGAA	.	PASS	Atlas-SNP
ACACB	32	hgsc.bcm.edu	37	12	109644616	109644616	+	Silent	SNP	C	C	T	rs17848814	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	114	46	136	0	0.403509	0	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	.	PASS	Atlas-SNP
GPATCH1	55094	hgsc.bcm.edu	37	19	33602757	33602757	+	Silent	SNP	C	C	T	rs10420258	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	98	42	145	0	0.428571	0	C|0.829;T|0.171	0.171	strong	.	GPATCH1	79	.	NM_018025	exon12	c.C1713T	p.H571H	CACTCACGCCAAG	.	PASS	Atlas-SNP
PDE4DIP	9659	hgsc.bcm.edu	37	1	145021150	145021150	+	Missense_Mutation	SNP	T	T	C	rs11538401	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	224	26	234	0	0.116071	0	T|0.979;C|0.021	0.021	strong	PDE4DIP_ENST00000369348,NS,carcinoma,0,1	PDE4DIP	817	1	NM_022359	exon2	c.A251G	p.D84G	CCATCATCCTCTG	.	PASS	Atlas-SNP
TJP2	9414	hgsc.bcm.edu	37	9	71862975	71862975	+	Silent	SNP	C	C	T	rs2282336	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	55	33	74	0	0.6	0	C|0.770;T|0.230	0.230	strong	.	TJP2	120	.	NM_001170416	exon19	c.C2808T	p.T936T	CTTAACCGCCATG	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1268955	1268955	+	Silent	SNP	C	C	T	rs2943523		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	830	135	471	0	0.162651	0	.	.	weak	MUC5AC,colon,carcinoma,+1,1	MUC5B	473	1	NM_002458	exon31	c.C10845T	p.L3615L	GGGCCTCGAGTGC	.	scavenged	Atlas-SNP
OR6K3	391114	hgsc.bcm.edu	37	1	158687896	158687896	+	Missense_Mutation	SNP	C	C	T	rs857705	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	94	47	108	0	0.5	0	C|0.776;T|0.224	0.224	strong	.	OR6K3	101	.	NM_001005327	exon1	c.G10A	p.G4R	GGTTTCCGCTCTC	.	PASS	Atlas-SNP
PKD1L2	114780	hgsc.bcm.edu	37	16	81253917	81253917	+	Missense_Mutation	SNP	A	A	G	rs9924530	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	188	188	119	0	1	0	A|0.429;G|0.571	0.571	strong	.	PKD1L2	361	.	NM_001076780	exon1	c.T59C	p.V20A	GGCTTAACAGTGG	.	PASS	Atlas-SNP
NAV2	89797	hgsc.bcm.edu	37	11	19901632	19901632	+	Silent	SNP	G	G	A	rs11025310	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	64	83	0	0.752941	0	G|0.645;A|0.355	0.355	strong	NAV2,caecum,carcinoma,+1,1	NAV2	255	1	NM_145117	exon5	c.G729A	p.A243A	GCCAGCGCCACAT	.	PASS	Atlas-SNP
FCGBP	8857	hgsc.bcm.edu	37	19	40363020	40363020	+	Missense_Mutation	SNP	G	G	A	rs741143	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	37	19	39	0	0.513514	0	G|0.749;A|0.251	0.251	strong	FCGBP,NS,carcinoma,-1,1	FCGBP	416	1	NM_003890	exon32	c.C15050T	p.A5017V	CCGGGCGCCCGCC	.	PASS	Atlas-SNP
SASS6	163786	hgsc.bcm.edu	37	1	100575933	100575933	+	Missense_Mutation	SNP	G	G	A	rs13375867	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	227	105	240	0	0.462555	0	G|0.659;A|0.341	0.341	strong	.	SASS6	61	.	NM_194292	exon8	c.C776T	p.A259V	TTAGCCGCTTCTA	.	PASS	Atlas-SNP
DNAH6	1768	hgsc.bcm.edu	37	2	84924823	84924823	+	Missense_Mutation	SNP	T	T	C	rs78190897	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	66	32	81	0	0.484848	0	T|0.868;C|0.132	0.132	strong	.	DNAH6	194	.	NM_001370	exon47	c.T7649C	p.V2550A	AAGAAGTAGGAAT	.	PASS	Atlas-SNP
ARHGEF19	128272	hgsc.bcm.edu	37	1	16534646	16534646	+	Missense_Mutation	SNP	C	C	G	rs221058	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	196	82	232	0	0.418367	0	C|0.794;G|0.206	0.206	strong	ARHGEF19,colon,carcinoma,0,1	ARHGEF19	49	1	NM_153213	exon3	c.G487C	p.G163R	CCTGGCCAGGCTC	.	PASS	Atlas-SNP
CMYA5	202333	hgsc.bcm.edu	37	5	79095417	79095417	+	Missense_Mutation	SNP	C	C	T	rs10043986	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	124	62	141	0	0.5	0	C|0.938;T|0.062	0.062	strong	.	CMYA5	643	.	NM_153610	exon13	c.C12188T	p.P4063L	AGCCCCCGGATTC	.	PASS	Atlas-SNP
ATP4A	495	hgsc.bcm.edu	37	19	36048741	36048741	+	Silent	SNP	G	G	T	rs2230181	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	96	48	92	0	0.5	0	G|0.705;T|0.295	0.295	strong	.	ATP4A	123	.	NM_000704	exon11	c.C1509A	p.I503I	CGTATGGATGGAC	.	PASS	Atlas-SNP
PPAN-P2RY11	692312	hgsc.bcm.edu	37	19	10225060	10225060	+	Silent	SNP	C	C	T	rs77496977	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	55	32	39	0	0.581818	0	C|0.997;T|0.003	0.003	strong	.	PPAN-P2RY11	81	.	NM_001040664	exon13	c.C2031T	p.Y677Y	CCTCTACGCCAGC	.	PASS	Atlas-SNP
LDLR	3949	hgsc.bcm.edu	37	19	11227602	11227602	+	Silent	SNP	C	C	T	rs688	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	137	69	111	0	0.50365	0	C|0.717;N|0.000	.	strong	.	LDLR	72	.	NM_001195798	exon12	c.C1773T	p.N591N	TGTCAACGGGGGC	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	79	79	118	0	1	0	A|0.625;G|0.375	0.375	strong	.	ABCB5	357	.	NM_001163941	exon14	c.A1678G	p.K560E	GAAAGCAAGTCAG	.	PASS	Atlas-SNP
RUNDC3B	154661	hgsc.bcm.edu	37	7	87445520	87445520	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	233	3	267	0	0.0128755	0	.	.	none	RUNDC3B,NS,carcinoma,-1,1	RUNDC3B	63	1	NM_138290	exon11	c.C1219T	p.P407S	CTAGATCCAGGCC	.	scavenged	Atlas-SNP
DMXL2	23312	hgsc.bcm.edu	37	15	51748564	51748564	+	Silent	SNP	A	A	G	rs76659258	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	146	58	155	0	0.39726	0	A|0.975;G|0.025	0.025	strong	DMXL2,NS,carcinoma,0,1	DMXL2	262	1	NM_001174116	exon37	c.T8277C	p.L2759L	TTTCATAAGCTTT	.	PASS	Atlas-SNP
TNS1	7145	hgsc.bcm.edu	37	2	218712306	218712306	+	Silent	SNP	C	C	T	rs1004814	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	66	31	96	0	0.469697	0	C|0.594;T|0.406	0.406	strong	.	TNS1	251	.	NM_022648	exon17	c.G2559A	p.A853A	TGAAGTCGCTTCC	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	36	87	0	0.514286	0	G|0.614;C|0.386	0.386	strong	.	KRTAP16-1	12	.	NM_001146182	exon1	c.C1019G	p.P340R	ACAGAAGGACAGC	.	PASS	Atlas-SNP
C10orf71	118461	hgsc.bcm.edu	37	10	50533386	50533386	+	Silent	SNP	C	C	T	rs41306409	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	94	48	80	0	0.510638	0	C|0.988;T|0.012	0.012	strong	.	C10orf71	179	.	NM_001135196	exon3	c.C2796T	p.N932N	GGCCAACGAGGTC	.	PASS	Atlas-SNP
DFNB31	25861	hgsc.bcm.edu	37	9	117166311	117166311	+	Silent	SNP	G	G	A	rs34963246	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	67	23	38	0	0.343284	0	A|0.112;G|0.887;T|0.000	0.112	strong	.	DFNB31	100	.	NM_015404	exon10	c.C2283T	p.S761S	GTCCTCGCTTAGA	.	PASS	Atlas-SNP
MYH4	4622	hgsc.bcm.edu	37	17	10360854	10360854	+	Missense_Mutation	SNP	C	C	T	rs12949680	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	112	52	117	0	0.464286	0	C|0.945;T|0.055	0.055	strong	.	MYH4	349	.	NM_017533	exon16	c.G1780A	p.A594T	AGCCGGCGATGTT	.	PASS	Atlas-SNP
RFFL	117584	hgsc.bcm.edu	37	17	33348541	33348541	+	Missense_Mutation	SNP	C	C	T	rs34747500	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	91	4	109	0	0.043956	0	C|0.986;T|0.014	0.014	strong	.	RFFL	27	.	NM_001017368	exon3	c.G440A	p.R147H	GAGGCACGAGTCC	.	PASS	Atlas-SNP
BTN3A2	11118	hgsc.bcm.edu	37	6	26370657	26370657	+	Missense_Mutation	SNP	A	A	G	rs9358936	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	110	110	132	0	1	0	A|0.926;G|0.074	0.074	strong	.	BTN3A2	44	.	NM_001197246	exon3	c.A541G	p.N181D	TGGAGCAACGCCA	.	PASS	Atlas-SNP
AKAP7	9465	hgsc.bcm.edu	37	6	131520655	131520655	+	Missense_Mutation	SNP	G	G	A	rs1190788	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	94	22	113	0	0.234043	0	G|0.752;A|0.248	0.248	strong	.	AKAP7	61	.	NM_016377	exon6	c.G644A	p.S215N	GCAGAAGTTTTAA	.	PASS	Atlas-SNP
DCDC2	51473	hgsc.bcm.edu	37	6	24291203	24291203	+	Missense_Mutation	SNP	T	T	C	rs2274305	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	104	40	95	0	0.384615	0	T|0.493;C|0.507	0.507	strong	.	DCDC2	53	.	NM_001195610	exon6	c.A661G	p.S221G	ACTCACTGTAAGG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195508343	195508343	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	154	24	111	0	0.155844	0	.	.	none	MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	NM_018406	exon2	c.T10108A	p.S3370T	CTGTGGAAGCTGA	.	scavenged	Atlas-SNP
SHCBP1	79801	hgsc.bcm.edu	37	16	46642286	46642286	+	Silent	SNP	G	G	A	rs34559393	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	31	79	0	0.336957	0	G|0.955;A|0.045	0.045	strong	.	SHCBP1	54	.	NM_024745	exon5	c.C612T	p.N204N	CCAAATGTTTTGG	.	PASS	Atlas-SNP
OR2D3	120775	hgsc.bcm.edu	37	11	6942952	6942952	+	Silent	SNP	T	T	C	rs2035844	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	261	208	295	1	0.796935	0.00338983	T|0.667;C|0.333	0.333	strong	.	OR2D3	51	.	NM_001004684	exon1	c.T720C	p.T240T	CTCCACTGTTATC	.	PASS	Atlas-SNP
PHRF1	57661	hgsc.bcm.edu	37	11	609068	609068	+	Silent	SNP	G	G	A	rs7928902	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	41	34	37	1	0.829268	0.027027	G|0.799;A|0.201	0.201	strong	PHRF1_ENST00000264555,rectum,carcinoma,0,4	PHRF1	188	4	NM_020901	exon14	c.G3609A	p.A1203A	CCCAGCGCCCCTT	.	scavenged	Atlas-SNP
GRID1	2894	hgsc.bcm.edu	37	10	88126072	88126072	+	Silent	SNP	G	G	A	rs61856638	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	21	9	8	0	0.428571	0	G|0.654;A|0.346	0.346	strong	.	GRID1	204	.	NM_017551	exon1	c.C78T	p.I26I	CTTACCGATGTGG	.	PASS	Atlas-SNP
TTC40	54777	hgsc.bcm.edu	37	10	134726272	134726272	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	63	34	76	0	0.539683	0	.	.	none	.	TTC40	100	.	NM_001200049	exon19	c.A2386G	p.I796V	AGCTGATGATCAG	.	PASS	Atlas-SNP
FKBP9	11328	hgsc.bcm.edu	37	7	33028165	33028165	+	Missense_Mutation	SNP	G	G	A	rs150348129	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	63	37	80	0	0.587302	0	G|0.988;A|0.012	0.012	strong	FKBP9_ENST00000490776,NS,carcinoma,0,2	FKBP9	335	2	NM_007270	exon6	c.G940A	p.V314M	GGCTACGTGATTC	.	PASS	Atlas-SNP
GRIA1	2890	hgsc.bcm.edu	37	5	153078582	153078582	+	Silent	SNP	A	A	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	104	25	126	0	0.240385	0	.	.	none	GRIA1_ENST00000544403,NS,carcinoma,+1,2	GRIA1	321	2	NM_001258021	exon10	c.A1431C	p.R477R	AGCCCGAGACCCT	.	PASS	Atlas-SNP
TNRC6A	27327	hgsc.bcm.edu	37	16	24801979	24801979	+	Silent	SNP	C	C	T	rs13336754	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	153	108	118	0	0.705882	0	C|0.763;T|0.237	0.237	strong	.	TNRC6A	171	.	NM_014494	exon6	c.C2016T	p.S672S	GGAGAGCGATGGT	.	PASS	Atlas-SNP
CYP4F2	8529	hgsc.bcm.edu	37	19	16008388	16008388	+	Missense_Mutation	SNP	A	A	C	rs3093105	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	26	53	0	0.448276	0	A|0.824;C|0.176	0.176	strong	.	CYP4F2	97	.	NM_001082	exon2	c.T34G	p.W12G	CTGGCCAGAGGCC	.	PASS	Atlas-SNP
PIK3IP1	113791	hgsc.bcm.edu	37	22	31679110	31679110	+	Missense_Mutation	SNP	G	G	C	rs2040533	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	68	36	93	0	0.529412	0	G|0.183;C|0.817	0.817	strong	.	PIK3IP1	20	.	NM_052880	exon6	c.C752G	p.T251S	GGGGTGGTGCCCT	.	PASS	Atlas-SNP
LAMA2	3908	hgsc.bcm.edu	37	6	129635800	129635800	+	Missense_Mutation	SNP	G	G	A	rs2306942	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	41	14	65	0	0.341463	0	G|0.896;A|0.104	0.104	strong	.	LAMA2	481	.	NM_000426	exon24	c.G3412A	p.V1138M	CCTCAGGTGAATG	.	PASS	Atlas-SNP
KRTAP10-11	386678	hgsc.bcm.edu	37	21	46067194	46067194	+	Silent	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	108	5	88	1	0.0462963	0.0113636	.	.	none	KRTAP10-11,NS,carcinoma,0,1	KRTAP10-11	36	1	NM_198692	exon1	c.C819T	p.C273C	CTCCTGCGTGTCC	.	scavenged	Atlas-SNP
CCDC27	148870	hgsc.bcm.edu	37	1	3679775	3679775	+	Missense_Mutation	SNP	C	C	T	rs10910024	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	36	21	60	0	0.583333	0	C|0.836;T|0.164	0.164	strong	.	CCDC27	79	.	NM_152492	exon7	c.C1058T	p.T353M	AGGACACGGGTGC	.	PASS	Atlas-SNP
CEACAM6	4680	hgsc.bcm.edu	37	19	42265889	42265889	+	Missense_Mutation	SNP	G	G	T	rs11548735	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	31	83	0	0.43662	0	G|0.489;T|0.511	0.511	strong	.	CEACAM6	52	.	NM_002483	exon4	c.G716T	p.G239V	CAGATGGCCCCAC	.	PASS	Atlas-SNP
TPX2	22974	hgsc.bcm.edu	37	20	30381758	30381758	+	Silent	SNP	G	G	C	rs1062794	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	150	61	191	0	0.406667	0	G|0.637;C|0.363	0.363	strong	.	TPX2	61	.	NM_012112	exon14	c.G1617C	p.S539S	TTTCTCGTTTGAT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195509443	195509443	+	Missense_Mutation	SNP	A	A	G	rs74585045		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	51	13	33	0	0.254902	0	A|0.250;G|0.750	0.750	weak	.	MUC4	1505	.	NM_018406	exon2	c.T9008C	p.I3003T	TGACCTATGGATG	.	PASS	Atlas-SNP
HPS1	3257	hgsc.bcm.edu	37	10	100190920	100190920	+	Silent	SNP	G	G	A	rs1801287	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	163	79	171	0	0.484663	0	G|0.745;A|0.255	0.255	strong	HPS1,NS,carcinoma,0,1	HPS1	65	1	NM_000195	exon7	c.C636T	p.L212L	GTGCACGAGCAGG	.	PASS	Atlas-SNP
ABCA4	24	hgsc.bcm.edu	37	1	94466659	94466659	+	Silent	SNP	A	A	G	rs1801555	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	51	24	47	0	0.470588	0	A|0.712;G|0.288	0.288	strong	.	ABCA4	275	.	NM_000350	exon46	c.T6285C	p.D2095D	GGGCTCATCCTGG	.	PASS	Atlas-SNP
ORM1	5004	hgsc.bcm.edu	37	9	117087412	117087412	+	Missense_Mutation	SNP	G	G	A	rs1126801	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	128	67	150	0	0.523438	0	G|0.972;A|0.028	0.028	strong	.	ORM1	20	.	NM_000607	exon5	c.G520A	p.V174M	GATGTCGTGTACA	.	PASS	Atlas-SNP
PROCR	10544	hgsc.bcm.edu	37	20	33764554	33764554	+	Missense_Mutation	SNP	A	A	G	rs867186	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	182	91	211	0	0.5	0	A|0.909;G|0.091	0.091	strong	.	PROCR	26	.	NM_006404	exon4	c.A655G	p.S219G	GTGGGCAGTTTCA	.	PASS	Atlas-SNP
RBBP6	5930	hgsc.bcm.edu	37	16	24583406	24583406	+	Silent	SNP	A	A	G	rs7593	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	131	131	163	0	1	0	A|0.650;G|0.350	0.350	strong	.	RBBP6	158	.	NM_006910	exon18	c.A5019G	p.A1673A	GAAAGCAAAAGAG	.	PASS	Atlas-SNP
FAM207A	85395	hgsc.bcm.edu	37	21	46387078	46387078	+	Missense_Mutation	SNP	G	G	T	rs2294168	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	34	24	41	0	0.705882	0	G|0.887;T|0.113	0.113	strong	C21orf70,NS,carcinoma,-1,1	.	.	1	NM_058190	exon4	c.G482T	p.S161I	CTGGCAGCCGGCG	.	PASS	Atlas-SNP
KIF26A	26153	hgsc.bcm.edu	37	14	104643650	104643650	+	Missense_Mutation	SNP	C	C	T	rs372336742		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	58	62	0	0.597938	0	.	.	weak	KIF26A,NS,carcinoma,0,1	KIF26A	84	1	NM_015656	exon12	c.C4525T	p.R1509W	GGGTCGCGGGCTC	.	PASS	Atlas-SNP
CCDC33	80125	hgsc.bcm.edu	37	15	74625175	74625175	+	Missense_Mutation	SNP	C	C	A	rs200735867	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	66	36	59	0	0.545455	0	.	.	weak	.	CCDC33	160	.	NM_025055	exon16	c.C1927A	p.Q643K	CAGCAACAGGCCC	.	PASS	Atlas-SNP
IMPACT	55364	hgsc.bcm.edu	37	18	22020467	22020467	+	Missense_Mutation	SNP	T	T	A	rs582234	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	99	51	101	0	0.515152	0	T|0.899;A|0.101	0.101	strong	.	IMPACT	37	.	NM_018439	exon6	c.T375A	p.D125E	CCCAGATGTAAAG	.	PASS	Atlas-SNP
EIF2AK3	9451	hgsc.bcm.edu	37	2	88926536	88926536	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	55	19	44	0	0.345455	0	.	.	none	.	EIF2AK3	160	.	NM_004836	exon1	c.A257G	p.E86G	CGAGGCTCCTGCT	.	PASS	Atlas-SNP
MST1R	4486	hgsc.bcm.edu	37	3	49924940	49924940	+	Missense_Mutation	SNP	T	T	C	rs1062633	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	66	42	135	0	0.636364	0	T|0.500;C|0.499	0.499	strong	.	MST1R	205	.	NM_002447	exon20	c.A4003G	p.R1335G	GTACTCTGAAGGT	.	PASS	Atlas-SNP
FLT3LG	2323	hgsc.bcm.edu	37	19	49983673	49983673	+	Silent	SNP	C	C	T	rs1042120	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	46	30	40	0	0.652174	0	C|0.820;T|0.180	0.180	strong	.	FLT3LG	22	.	NM_001204503	exon6	c.C600T	p.A200A	GCTGGCCGCTGCC	.	PASS	Atlas-SNP
RNF213	57674	hgsc.bcm.edu	37	17	78293189	78293189	+	Missense_Mutation	SNP	A	A	T	rs55996424	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	42	112	0	0.482759	0	A|0.768;T|0.232	0.232	strong	.	RNF213	766	.	NM_020954	exon17	c.A3101T	p.K1034M	CTATGAAGCACCC	.	PASS	Atlas-SNP
HECA	51696	hgsc.bcm.edu	37	6	139487836	139487836	+	Silent	SNP	T	T	C	rs3173082	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	50	28	88	0	0.56	0	T|0.328;C|0.672	0.672	strong	.	HECA	45	.	NM_016217	exon2	c.T687C	p.N229N	CCCAAATAAGCCC	.	PASS	Atlas-SNP
GAA	2548	hgsc.bcm.edu	37	17	78083791	78083791	+	Silent	SNP	C	C	T	rs1800305	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	117	66	133	0	0.564103	0	C|0.902;T|0.098	0.098	strong	.	GAA	66	.	NM_001079803	exon10	c.C1374T	p.Y458Y	GCCCTACGACGAG	.	PASS	Atlas-SNP
EFHC2	80258	hgsc.bcm.edu	37	X	44094685	44094685	+	Missense_Mutation	SNP	G	G	T	rs2208592	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	120	117	131	1	0.975	0.00763359	G|0.910;0|0.026	.	strong	.	EFHC2	81	.	NM_025184	exon9	c.C1289A	p.S430Y	CTTTTGGAGCCAT	.	PASS	Atlas-SNP
ZDHHC11	79844	hgsc.bcm.edu	37	5	825297	825297	+	Silent	SNP	A	A	G	rs1808545	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	120	20	139	0	0.166667	0	A|0.977;G|0.023	0.023	strong	.	ZDHHC11	97	.	NM_024786	exon8	c.T1005C	p.D335D	ATCCCCATCCTGG	.	PASS	Atlas-SNP
XIRP1	165904	hgsc.bcm.edu	37	3	39228043	39228043	+	Missense_Mutation	SNP	T	T	G	rs11711871	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	83	40	97	2	0.481928	0.0206186	T|0.872;G|0.128	0.128	strong	XIRP1,NS,carcinoma,+1,1	XIRP1	173	1	NM_001198621	exon2	c.A2894C	p.H965P	GTTGGGTGCAGGC	.	scavenged	Atlas-SNP
FOXA3	3171	hgsc.bcm.edu	37	19	46376217	46376217	+	Silent	SNP	C	C	A	rs3810327	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	111	57	159	0	0.513514	0	C|0.927;A|0.073	0.073	strong	.	FOXA3	19	.	NM_004497	exon2	c.C954A	p.P318P	ACCTCCCAAACTG	.	PASS	Atlas-SNP
ZNF679	168417	hgsc.bcm.edu	37	7	63726645	63726645	+	Missense_Mutation	SNP	T	T	C	rs1830035	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	38	13	50	0	0.342105	0	T|0.900;C|0.100	0.100	strong	.	ZNF679	80	.	NM_153363	exon5	c.T634C	p.Y212H	AATTCCTACCAAT	.	PASS	Atlas-SNP
ZPLD1	131368	hgsc.bcm.edu	37	3	102157417	102157417	+	Missense_Mutation	SNP	A	A	G	rs6784389	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	120	50	140	0	0.416667	0	A|0.882;G|0.118	0.118	strong	.	ZPLD1	82	.	NM_175056	exon2	c.A134G	p.N45S	ATGCCAACCTCCA	.	PASS	Atlas-SNP
EPHA3	2042	hgsc.bcm.edu	37	3	89391215	89391215	+	Silent	SNP	G	G	A	rs56112995	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	31	81	0	0.430556	0	G|0.995;A|0.005	0.005	strong	EPHA3_ENST00000452448,caecum,carcinoma,0,4	EPHA3	501	4	NM_005233	exon5	c.G1281A	p.A427A	TGCTGCGGTCAGC	.	PASS	Atlas-SNP
VEGFB	7423	hgsc.bcm.edu	37	11	64004692	64004692	+	Silent	SNP	C	C	T	rs12366035	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	116	18	147	0	0.155172	0	C|0.792;T|0.208	0.208	strong	VEGFB,NS,carcinoma,0,1	VEGFB	18	1	NM_003377	exon5	c.C408T	p.D136D	GCCAGACAGGTGA	.	PASS	Atlas-SNP
VWF	7450	hgsc.bcm.edu	37	12	6173433	6173433	+	Missense_Mutation	SNP	C	C	T	rs1800377	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	147	147	157	0	1	0	C|0.886;T|0.114	0.114	strong	.	VWF	338	.	NM_000552	exon12	c.G1411A	p.V471I	GCTGGACGTCCTG	.	PASS	Atlas-SNP
PTPRD	5789	hgsc.bcm.edu	37	9	8485834	8485834	+	Missense_Mutation	SNP	G	G	A	rs35929428	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	116	54	154	0	0.465517	0	G|0.929;A|0.071	0.071	strong	.	PTPRD	1348	.	NM_002839	exon28	c.C2983T	p.R995C	GAGCACGTACTTT	.	PASS	Atlas-SNP
GPR112	139378	hgsc.bcm.edu	37	X	135480126	135480126	+	Silent	SNP	T	T	C	rs5974595	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	105	105	138	0	1	0	T|0.287;C|0.713	0.713	strong	.	GPR112	459	.	NM_153834	exon20	c.T8271C	p.F2757F	CATTTTTCTGGGA	.	PASS	Atlas-SNP
GJD3	125111	hgsc.bcm.edu	37	17	38519831	38519831	+	Silent	SNP	G	G	T	rs141158879	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	26	67	0	0.448276	0	G|0.992;T|0.008	0.008	strong	.	GJD3	2	.	NM_152219	exon1	c.C237A	p.L79L	GTGGAAGAGCCAG	.	PASS	Atlas-SNP
NLRP5	126206	hgsc.bcm.edu	37	19	56572832	56572832	+	Missense_Mutation	SNP	G	G	A	rs10409555	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	165	69	209	0	0.418182	0	G|0.645;A|0.355	0.355	strong	.	NLRP5	217	.	NM_153447	exon15	c.G3541A	p.V1181I	CCCCGAGTCGTAA	.	PASS	Atlas-SNP
IGLL5	100423062	hgsc.bcm.edu	37	22	23230348	23230348	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	143	28	149	0	0.195804	0	.	.	none	.	IGLL5	26	.	NM_001178126	exon1	c.C115G	p.L39V	GGCCTGCTGCGCC	.	PASS	Atlas-SNP
COL28A1	340267	hgsc.bcm.edu	37	7	7514293	7514293	+	Missense_Mutation	SNP	T	T	C	rs199518824	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	81	63	81	0	0.777778	0	.	.	weak	.	COL28A1	113	.	NM_001037763	exon15	c.A1241G	p.K414R	GAACCTTTTTCAC	.	PASS	Atlas-SNP
MED24	9862	hgsc.bcm.edu	37	17	38189328	38189328	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	48	10	75	0	0.208333	0	.	.	none	.	MED24	89	.	NM_014815	exon8	c.C803T	p.T268M	ACCATCGTCAGCT	.	PASS	Atlas-SNP
FHAD1	114827	hgsc.bcm.edu	37	1	15599025	15599025	+	Silent	SNP	G	G	A	rs75432354	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	38	71	0	0.436782	0	G|0.874;A|0.126	0.126	strong	.	FHAD1	78	.	NM_052929	exon3	c.G300A	p.P100P	ACCTCCGGTGAGT	.	PASS	Atlas-SNP
PXDNL	137902	hgsc.bcm.edu	37	8	52321238	52321238	+	Silent	SNP	G	G	A	rs141024159	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	67	46	75	0	0.686567	0	G|0.989;A|0.011	0.011	strong	.	PXDNL	414	.	NM_144651	exon17	c.C2946T	p.A982A	CTCCGTGGCCATC	.	PASS	Atlas-SNP
LY75	4065	hgsc.bcm.edu	37	2	160746800	160746800	+	Silent	SNP	T	T	C	rs34592866	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	127	58	103	0	0.456693	0	T|0.962;C|0.038	0.038	strong	.	LY75	151	.	NM_002349	exon4	c.A726G	p.E242E	ATAAGCTTCTTTC	.	PASS	Atlas-SNP
OLFM2	93145	hgsc.bcm.edu	37	19	9964946	9964946	+	Silent	SNP	G	G	A	rs11556088	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	113	54	140	0	0.477876	0	G|0.905;A|0.095	0.095	strong	.	OLFM2	42	.	NM_058164	exon6	c.C1281T	p.R427R	GAGGGCGCGCTCC	.	PASS	Atlas-SNP
PCDHB6	56130	hgsc.bcm.edu	37	5	140530852	140530852	+	Silent	SNP	G	G	C	rs246708	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	192	93	224	1	0.484375	0.00446429	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
NPHS1	4868	hgsc.bcm.edu	37	19	36340009	36340009	+	Missense_Mutation	SNP	G	G	A	rs113825926	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	48	19	58	0	0.395833	0	G|0.992;A|0.008	0.008	strong	.	NPHS1	165	.	NM_004646	exon8	c.C881T	p.T294I	GCCTGGGTGTGCT	.	PASS	Atlas-SNP
PCDHGB4	8641	hgsc.bcm.edu	37	5	140769334	140769334	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	36	11	38	0	0.305556	0	.	.	none	.	PCDHGB4	125	.	NM_032098	exon1	c.G1883C	p.R628P	CAGCGCGTGCCTT	.	PASS	Atlas-SNP
ZNRD1	30834	hgsc.bcm.edu	37	6	30030057	30030057	+	Silent	SNP	G	G	A	rs10745	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	25	86	0	0.352113	0	G|0.942;A|0.058	0.058	strong	.	.	.	.	NM_170783	exon3	c.G303A	p.Q101Q	CAGACAGATGCGT	.	PASS	Atlas-SNP
ARMC4	55130	hgsc.bcm.edu	37	10	28250610	28250610	+	Missense_Mutation	SNP	C	C	A	rs80260946		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	165	19	216	1	0.115152	0.00462963	.	.	weak	ARMC4,NS,malignant_melanoma,0,3	ARMC4	177	3	NM_018076	exon10	c.G1273T	p.D425Y	AGCTATCGCTAAC	.	scavenged	Atlas-SNP
LSS	4047	hgsc.bcm.edu	37	21	47614443	47614443	+	Silent	SNP	A	A	G	rs2254522	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	30	75	0	0.344828	0	A|0.712;C|0.002	.	strong	.	LSS	50	.	NM_001001438	exon20	c.T1950C	p.H650H	TGTGTTATGGATC	.	PASS	Atlas-SNP
PCNXL3	399909	hgsc.bcm.edu	37	11	65387378	65387378	+	Silent	SNP	T	T	A	rs61744384	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	18	96	0	0.257143	0	T|0.604;A|0.396	0.396	strong	.	PCNXL3	140	.	NM_032223	exon8	c.T1983A	p.A661A	GGGTGCTGTGCAC	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1268481	1268481	+	Silent	SNP	G	G	A	rs186744090	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	436	29	454	0	0.0665138	0	G|0.973;A|0.027	0.027	strong	MUC5B,NS,haematopoietic_neoplasm,0,4	MUC5B	473	4	NM_002458	exon31	c.G10371A	p.R3457R	CGGGCGGTCCCTG	.	scavenged	Atlas-SNP
ANXA9	8416	hgsc.bcm.edu	37	1	150958836	150958836	+	Missense_Mutation	SNP	A	A	G	rs267733	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	100	103	0	0.990099	0	A|0.906;G|0.094	0.094	strong	.	ANXA9	28	.	NM_003568	exon8	c.A497G	p.D166G	TGGATGACATCAC	.	PASS	Atlas-SNP
TROAP	10024	hgsc.bcm.edu	37	12	49723963	49723963	+	Silent	SNP	A	A	G	rs4243545	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	158	79	192	0	0.5	0	A|0.789;G|0.211	0.211	strong	TROAP,NS,carcinoma,0,1	TROAP	80	1	NM_005480	exon13	c.A1335G	p.E445E	ACAGGAAGTAGAG	.	PASS	Atlas-SNP
VCX3B	425054	hgsc.bcm.edu	37	X	8434367	8434367	+	Silent	SNP	C	C	T	rs139169782	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	514	489	873	0	0.951362	0	C|0.777;T|0.223	0.223	strong	.	VCX3B	34	.	NM_001001888	exon3	c.C684T	p.S228S	GGAGAGCGAGATG	.	PASS	Atlas-SNP
GLI1	2735	hgsc.bcm.edu	37	12	57865321	57865321	+	Missense_Mutation	SNP	G	G	A	rs2228224	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	43	16	56	0	0.372093	0	G|0.547;A|0.452	0.452	strong	.	GLI1	141	.	NM_005269	exon12	c.G2798A	p.G933D	TGGGGGGTTCCCA	.	PASS	Atlas-SNP
KRT17	3872	hgsc.bcm.edu	37	17	39775870	39775870	+	Silent	SNP	C	C	T	rs117941474	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	551	274	607	0	0.497278	0	C|0.977;T|0.023	0.023	strong	.	KRT17	57	.	NM_000422	exon8	c.G1275A	p.E425E	GACCTGCTCGCGG	.	PASS	Atlas-SNP
CLEC18C	283971	hgsc.bcm.edu	37	16	70211218	70211218	+	Silent	SNP	G	G	A	rs149087931	byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	1057	159	779	2	0.150426	0.00256739	G|0.925;A|0.075	0.075	strong	CLEC18C,NS,carcinoma,0,1	CLEC18C	15	1	NM_173619	exon3	c.G291A	p.A97A	CCTGGCGTCCGGC	.	scavenged	Atlas-SNP
GOLGA1	2800	hgsc.bcm.edu	37	9	127643456	127643456	+	Silent	SNP	T	T	C	rs687434	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	185	100	203	1	0.540541	0.00492611	T|0.661;C|0.339	0.339	strong	.	GOLGA1	60	.	NM_002077	exon22	c.A2217G	p.E739E	CTTATATTCCAGA	.	PASS	Atlas-SNP
AIFM2	84883	hgsc.bcm.edu	37	10	71874734	71874734	+	Silent	SNP	G	G	A	rs2271695	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	46	24	67	0	0.521739	0	G|0.880;A|0.120	0.120	strong	.	AIFM2	33	.	NM_001198696	exon8	c.C912T	p.I304I	CACGGCGATGTTG	.	PASS	Atlas-SNP
CACNA1S	779	hgsc.bcm.edu	37	1	201058530	201058530	+	Silent	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	117	72	133	0	0.615385	0	.	.	none	CACNA1S,colon,carcinoma,-2,1	CACNA1S	249	1	NM_000069	exon6	c.C756T	p.R252R	GCACCGGCGCCCT	.	PASS	Atlas-SNP
PDZRN4	29951	hgsc.bcm.edu	37	12	41967677	41967677	+	Silent	SNP	G	G	A	rs3747556	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	53	116	0	0.524752	0	G|0.870;A|0.130	0.130	strong	.	PDZRN4	346	.	NM_001164595	exon10	c.G3096A	p.S1032S	CTTGTCGGTGACC	.	PASS	Atlas-SNP
MAP3K6	9064	hgsc.bcm.edu	37	1	27686373	27686373	+	Silent	SNP	G	G	A	rs138787990		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	183	89	176	0	0.486339	0	G|1.000;A|0.000	0.000	weak	.	MAP3K6	134	.	NM_004672	exon17	c.C2295T	p.N765N	GATGTGGTTGTCG	.	PASS	Atlas-SNP
AKAP6	9472	hgsc.bcm.edu	37	14	33004975	33004975	+	Silent	SNP	G	G	A	rs35436895	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	145	143	175	0	0.986207	0	G|0.924;A|0.076	0.076	strong	.	AKAP6	308	.	NM_004274	exon3	c.G540A	p.T180T	GCAGACGGACATT	.	PASS	Atlas-SNP
MARCH10	162333	hgsc.bcm.edu	37	17	60814632	60814632	+	Silent	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	277	3	388	1	0.0108303	0.00257732	.	.	none	MARCH10,NS,carcinoma,-2,1	MARCH10	102	1	NM_001100875	exon6	c.G597A	p.E199E	TCTTCTCTCTTGA	.	scavenged	Atlas-SNP
WDR45B	56270	hgsc.bcm.edu	37	17	80585094	80585094	+	Silent	SNP	C	C	T	rs2291393	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	66	24	53	0	0.363636	0	C|0.797;T|0.203	0.203	strong	.	.	.	.	NM_019613	exon4	c.G318A	p.K106K	CCGCAGCTTGACT	.	PASS	Atlas-SNP
PROM1	8842	hgsc.bcm.edu	37	4	16077475	16077475	+	Missense_Mutation	SNP	A	A	C	rs189108830	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	63	36	74	0	0.571429	0	A|0.990;C|0.010	0.010	strong	PROM1,NS,carcinoma,+1,1	PROM1	91	1	NM_001145847	exon2	c.T55G	p.S19A	CTCCTGAAAAGGA	.	PASS	Atlas-SNP
HSP90B1	7184	hgsc.bcm.edu	37	12	104327979	104327979	+	Silent	SNP	C	C	T	rs6615	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	95	47	123	0	0.494737	0	C|0.892;T|0.108	0.108	strong	.	HSP90B1	72	.	NM_003299	exon5	c.C657T	p.T219T	CGATACCCAGCAC	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105410417	105410417	+	Silent	SNP	G	G	A	rs200284292	byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	117	9	140	0	0.0769231	0	G|0.993;A|0.007	0.007	strong	.	AHNAK2	719	.	NM_138420	exon7	c.C11371T	p.L3791L	CGGCCAGGGACAG	.	PASS	Atlas-SNP
SRD5A1	6715	hgsc.bcm.edu	37	5	6651970	6651970	+	Silent	SNP	A	A	G	rs3822430	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	138	62	191	0	0.449275	0	A|0.667;G|0.333	0.333	strong	SRD5A1,NS,carcinoma,0,1	SRD5A1	31	1	NM_001047	exon2	c.A309G	p.P103P	TTACCCATTTCTG	.	PASS	Atlas-SNP
KRT6C	286887	hgsc.bcm.edu	37	12	52866060	52866060	+	Missense_Mutation	SNP	C	C	T	rs11608915	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	201	87	18	0	0.432836	0	C|0.677;T|0.323	0.323	strong	.	KRT6C	55	.	NM_173086	exon2	c.G545A	p.R182Q	AGGAACCGCACCT	.	PASS	Atlas-SNP
PAIP2B	400961	hgsc.bcm.edu	37	2	71417134	71417134	+	Silent	SNP	C	C	T	rs357776	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	60	27	51	0	0.45	0	C|0.699;T|0.301	0.301	strong	.	PAIP2B	7	.	NM_020459	exon3	c.G156A	p.Q52Q	TTGCTCCTGCAGT	.	PASS	Atlas-SNP
SLC39A13	91252	hgsc.bcm.edu	37	11	47434986	47434986	+	Silent	SNP	G	G	A	rs2293576	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	107	86	115	0	0.803738	0	G|0.756;A|0.244	0.244	strong	SLC39A13,NS,carcinoma,+2,1	SLC39A13	18	1	NM_152264	exon5	c.G573A	p.A191A	CGCCGCGCTCAAT	.	PASS	Atlas-SNP
NCK1	4690	hgsc.bcm.edu	37	3	136664737	136664737	+	Missense_Mutation	SNP	C	C	T	rs13320485	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	122	59	149	0	0.483607	0	C|0.989;T|0.011	0.011	strong	.	NCK1	26	.	NM_006153	exon3	c.C539T	p.A180V	AATTAGCAGCAGT	.	PASS	Atlas-SNP
PLIN4	729359	hgsc.bcm.edu	37	19	4512636	4512636	+	Missense_Mutation	SNP	A	A	C	rs140230284	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	13	137	0	0.158537	0	A|0.966;C|0.034	0.034	strong	PLIN4_ENST00000301286,caecum,carcinoma,0,4	PLIN4	191	4	NM_001080400	exon3	c.T1294G	p.L432V	TGGCCAAATTCAT	.	PASS	Atlas-SNP
CASP5	838	hgsc.bcm.edu	37	11	104877927	104877927	+	Missense_Mutation	SNP	T	T	C	rs507879	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	76	75	87	0	0.986842	0	T|0.536;G|0.002	.	strong	.	CASP5	213	.	NM_001136112	exon3	c.A355G	p.T119A	TTTTGGTATCATA	.	PASS	Atlas-SNP
ATXN1	6310	hgsc.bcm.edu	37	6	16327909	16327909	+	Missense_Mutation	SNP	A	A	C	rs59310777	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	41	15	43	0	0.365854	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
RNF17	56163	hgsc.bcm.edu	37	13	25378476	25378476	+	Missense_Mutation	SNP	A	A	G	rs9511451	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	108	48	104	0	0.444444	0	A|0.776;G|0.224	0.224	strong	RNF17_ENST00000255324,NS,carcinoma,+1,1	RNF17	259	1	NM_001184993	exon15	c.A2000G	p.H667R	CTTTACACTATCA	.	PASS	Atlas-SNP
CIB4	130106	hgsc.bcm.edu	37	2	26804247	26804247	+	Missense_Mutation	SNP	T	T	C	rs935172	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	56	22	75	0	0.392857	0	C|0.532;N|0.000	0.532	strong	.	CIB4	15	.	NM_001029881	exon7	c.A542G	p.H181R	CAGAAGTGAATCC	.	PASS	Atlas-SNP
ZFC3H1	196441	hgsc.bcm.edu	37	12	72008421	72008421	+	Missense_Mutation	SNP	T	T	C	rs11541286	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	59	27	60	0	0.457627	0	T|0.956;C|0.044	0.044	strong	.	ZFC3H1	172	.	NM_144982	exon30	c.A5420G	p.K1807R	AAAAATTTGAATT	.	PASS	Atlas-SNP
MYH7B	57644	hgsc.bcm.edu	37	20	33585437	33585437	+	Silent	SNP	C	C	T	rs55734215	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	90	38	98	0	0.422222	0	C|0.922;T|0.078	0.078	strong	.	MYH7B	145	.	NM_020884	exon32	c.C3867T	p.R1289R	GACCCGCGCCAAG	.	PASS	Atlas-SNP
EAF1	85403	hgsc.bcm.edu	37	3	15477861	15477861	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	161	32	151	0	0.198758	0	.	.	none	.	EAF1	16	.	NM_033083	exon5	c.A539G	p.E180G	GGGCTGAAGTTGA	.	PASS	Atlas-SNP
MICB	4277	hgsc.bcm.edu	37	6	31473561	31473561	+	Missense_Mutation	SNP	A	A	G	rs1065075	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	50	34	82	0	0.68	0	A|0.712;G|0.288	0.288	strong	.	MICB	26	.	NM_005931	exon2	c.A238G	p.K80E	GGAGCTAAGACCT	.	PASS	Atlas-SNP
ZNF254	9534	hgsc.bcm.edu	37	19	24310032	24310032	+	Missense_Mutation	SNP	A	A	T	rs61737180	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	19	6	39	0	0.315789	0	A|0.852;T|0.148	0.148	strong	ZNF254_ENST00000357002,colon,carcinoma,0,1	ZNF254	88	1	NM_203282	exon4	c.A1230T	p.E410D	TGAAGAATGCGGC	.	PASS	Atlas-SNP
RPGRIP1	57096	hgsc.bcm.edu	37	14	21770730	21770730	+	Missense_Mutation	SNP	A	A	G	rs6571751	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	99	36	128	0	0.363636	0	A|0.546;G|0.454	0.454	strong	.	RPGRIP1	213	.	NM_020366	exon4	c.A574G	p.K192E	GCCAGTAAACCCA	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1270691	1270691	+	Missense_Mutation	SNP	G	G	C	rs201822010	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	1023	155	882	1	0.151515	0.00113379	G|0.996;C|0.004	0.004	strong	.	MUC5B	473	.	NM_002458	exon31	c.G12581C	p.S4194T	AATGCAGCCTGGA	.	PASS	Atlas-SNP
C2orf62	375307	hgsc.bcm.edu	37	2	219221846	219221846	+	Silent	SNP	G	G	A	rs4324314	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	63	24	71	0	0.380952	0	G|0.843;A|0.157	0.157	strong	.	C2orf62	28	.	NM_198559	exon2	c.G54A	p.S18S	GCCCTCGGGTCCG	.	PASS	Atlas-SNP
TSFM	10102	hgsc.bcm.edu	37	12	58176614	58176614	+	Silent	SNP	T	T	C	rs10747783	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	55	30	70	0	0.545455	0	T|0.714;C|0.286	0.286	strong	.	TSFM	26	.	NM_005726	exon1	c.T30C	p.F10F	CGTGTTTCTGGTC	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	103	46	126	1	0.446602	0.00793651	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	.	scavenged	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149484798	149484798	+	Missense_Mutation	SNP	C	C	T	rs62490656	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	46	19	78	0	0.413043	0	C|0.826;T|0.174	0.174	strong	.	.	.	.	NM_198455	exon25	c.C3620T	p.A1207V	GTGGGGCGCTGCT	.	PASS	Atlas-SNP
DNAH5	1767	hgsc.bcm.edu	37	5	13716796	13716796	+	Missense_Mutation	SNP	C	C	T	rs138045391	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	103	43	88	0	0.417476	0	A|0.001;C|0.999	.	weak	.	DNAH5	868	.	NM_001369	exon74	c.G12709A	p.V4237I	AGGAGACACCCTG	.	PASS	Atlas-SNP
TMEM194B	100131211	hgsc.bcm.edu	37	2	191379268	191379268	+	Silent	SNP	G	G	A	rs4586658	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	288	285	341	2	0.989583	0.0058651	G|0.492;A|0.508	0.508	strong	.	TMEM194B	18	.	NM_001142645	exon7	c.C864T	p.A288A	AGGCACGGCCACA	.	PASS	Atlas-SNP
PPAN	56342	hgsc.bcm.edu	37	19	10217248	10217248	+	Silent	SNP	C	C	T	rs11559190	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	47	19	34	0	0.404255	0	C|0.992;T|0.008	0.008	strong	.	PPAN	43	.	NM_020230	exon2	c.C90T	p.H30H	CCCGCACTCGTTC	.	PASS	Atlas-SNP
NRCAM	4897	hgsc.bcm.edu	37	7	107824889	107824889	+	Silent	SNP	C	C	G	rs401433	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	84	89	0	0.988235	0	C|0.317;G|0.683	0.683	strong	.	NRCAM	267	.	NM_001037132	exon18	c.G2205C	p.A735A	CTCAGACGCCTCG	.	PASS	Atlas-SNP
TMC8	147138	hgsc.bcm.edu	37	17	76131070	76131070	+	Silent	SNP	G	G	A	rs12452890	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	93	49	94	0	0.526882	0	G|0.421;A|0.579	0.579	strong	.	TMC8	44	.	NM_152468	exon9	c.G1107A	p.E369E	CACGGAGGTCAAC	.	PASS	Atlas-SNP
ZNF93	81931	hgsc.bcm.edu	37	19	20044886	20044886	+	Silent	SNP	T	T	C	rs10401345	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	36	36	56	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
GRIN3A	116443	hgsc.bcm.edu	37	9	104433235	104433235	+	Missense_Mutation	SNP	C	C	T	rs10989589	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	214	109	237	1	0.509346	0.00421941	C|0.670;T|0.330	0.330	strong	GRIN3A,caecum,carcinoma,+1,1	GRIN3A	186	1	NM_133445	exon3	c.G1459A	p.G487R	TCTTTCCCCCCTG	.	PASS	Atlas-SNP
PTCHD2	57540	hgsc.bcm.edu	37	1	11579504	11579504	+	Missense_Mutation	SNP	G	G	C	rs2072993	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	53	31	62	0	0.584906	0	G|0.811;C|0.189	0.189	strong	.	PTCHD2	193	.	NM_020780	exon8	c.G1982C	p.G661A	CCCAGGGCCCCAT	.	PASS	Atlas-SNP
DSP	1832	hgsc.bcm.edu	37	6	7581636	7581636	+	Missense_Mutation	SNP	G	G	A	rs6929069	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	116	37	88	0	0.318966	0	G|0.792;A|0.208	0.208	strong	DSP,NS,carcinoma,0,2	DSP	306	2	NM_004415	exon23	c.G5213A	p.R1738Q	GAGGACGAAGCGA	.	PASS	Atlas-SNP
SNED1	25992	hgsc.bcm.edu	37	2	242003487	242003487	+	Silent	SNP	C	C	T	rs17852471	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	155	70	162	0	0.451613	0	C|0.733;T|0.267	0.267	strong	.	SNED1	76	.	NM_001080437	exon19	c.C2544T	p.G848G	CGGCGGCGGGGCC	.	PASS	Atlas-SNP
SH2D4A	63898	hgsc.bcm.edu	37	8	19221700	19221700	+	Missense_Mutation	SNP	G	G	A	rs34608771	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	11	68	0	0.15942	0	G|0.764;A|0.236	0.236	strong	.	SH2D4A	49	.	NM_022071	exon7	c.G824A	p.S275N	TGCAAAGCCCCTT	.	PASS	Atlas-SNP
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33037639	33037639	+	Missense_Mutation	SNP	G	G	A	rs1126534	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	22	120	0	0.293333	0	G|0.875;A|0.125	0.125	strong	HLA-DPA1,NS,carcinoma,0,4	HLA-DPA1	20	4	NM_033554	exon2	c.C125T	p.A42V	ACAAACGCGGCAT	.	scavenged	Atlas-SNP
KRTAP10-11	386678	hgsc.bcm.edu	37	21	46067180	46067180	+	Missense_Mutation	SNP	C	C	T	rs462007	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	109	107	97	0	0.981651	0	C|0.202;T|0.798	0.798	strong	.	KRTAP10-11	36	.	NM_198692	exon1	c.C805T	p.R269C	TGCTGCCGCCCGG	.	PASS	Atlas-SNP
TMEM173	340061	hgsc.bcm.edu	37	5	138857925	138857925	+	Missense_Mutation	SNP	C	C	G	rs78233829	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	119	57	139	0	0.478992	0	C|0.807;G|0.193	0.193	strong	.	TMEM173	19	.	NM_198282	exon6	c.G689C	p.G230A	TGGTCACCGGTCT	.	PASS	Atlas-SNP
TRIM31	11074	hgsc.bcm.edu	37	6	30075864	30075864	+	Silent	SNP	A	A	G	rs2023472	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	138	68	224	0	0.492754	0	A|0.348;G|0.652	0.652	strong	TRIM31,NS,carcinoma,0,1	TRIM31	40	1	NM_007028	exon6	c.T849C	p.H283H	GGAGTCATGTCTT	.	PASS	Atlas-SNP
LCE1F	353137	hgsc.bcm.edu	37	1	152749091	152749091	+	Missense_Mutation	SNP	C	C	T	rs41268480	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	63	36	81	0	0.571429	0	C|0.867;T|0.133	0.133	strong	LCE1F,right_lower_lobe,carcinoma,-1,1	LCE1F	42	1	NM_178354	exon1	c.C244T	p.R82W	CACAGACGGCGTA	.	PASS	Atlas-SNP
DOCK2	1794	hgsc.bcm.edu	37	5	169435713	169435713	+	Silent	SNP	A	A	C	rs2287727	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	241	240	242	0	0.995851	0	A|0.770;C|0.230	0.230	strong	.	DOCK2	389	.	NM_004946	exon32	c.A3195C	p.L1065L	ACGGCTAATTGGC	.	PASS	Atlas-SNP
PCSK1N	27344	hgsc.bcm.edu	37	X	48690749	48690749	+	Silent	SNP	C	C	T	rs11538178	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	34	31	41	0	0.911765	0	C|0.763;T|0.237	0.237	strong	.	PCSK1N	6	.	NM_013271	exon2	c.G117A	p.E39E	GCGGGGCTCCTGC	.	PASS	Atlas-SNP
VCX3A	51481	hgsc.bcm.edu	37	X	6451834	6451834	+	Silent	SNP	C	C	T	rs146638597		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	927	82	1050	0	0.0884574	0	.	.	weak	.	VCX3A	17	.	NM_016379	exon3	c.G513A	p.E171E	TGGTTCCTCCACC	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228468244	228468244	+	Silent	SNP	G	G	A	rs12061320	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	128	64	125	0	0.5	0	G|0.865;A|0.135	0.135	strong	.	OBSCN	2142	.	NM_001271223	exon35	c.G9231A	p.V3077V	GGTGGTGTTCCTG	.	PASS	Atlas-SNP
YTHDF1	54915	hgsc.bcm.edu	37	20	61834092	61834092	+	Silent	SNP	G	G	A	rs41282994	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	62	26	69	0	0.419355	0	G|0.930;A|0.070	0.070	strong	.	YTHDF1	66	.	NM_017798	exon4	c.C1200T	p.D400D	GATGTCGTCCTCA	.	PASS	Atlas-SNP
GIGYF1	64599	hgsc.bcm.edu	37	7	100281768	100281768	+	Silent	SNP	T	T	C	rs221794	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	111	53	111	0	0.477477	0	T|0.141;C|0.859	0.859	strong	GIGYF1_ENST00000539430,NS,carcinoma,0,2	GIGYF1	113	2	NM_022574	exon15	c.A1743G	p.P581P	GCACTGTGGGAGC	.	PASS	Atlas-SNP
NUP210	23225	hgsc.bcm.edu	37	3	13364836	13364836	+	Missense_Mutation	SNP	C	C	T	rs199752879	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	64	23	78	0	0.359375	0	.	.	weak	NUP210,NS,carcinoma,0,1	NUP210	182	1	NM_024923	exon34	c.G4741A	p.V1581M	CTCCCACGGCAAC	.	PASS	Atlas-SNP
AP3B1	8546	hgsc.bcm.edu	37	5	77412011	77412011	+	Silent	SNP	A	A	G	rs42360	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	120	77	102	0	0.641667	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
ABCA7	10347	hgsc.bcm.edu	37	19	1047537	1047537	+	Missense_Mutation	SNP	A	A	C	rs3752239	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	30	48	0	0.434783	0	A|0.934;C|0.066	0.066	strong	.	ABCA7	174	.	NM_019112	exon16	c.A2153C	p.N718T	GGCACAACGTGGG	.	PASS	Atlas-SNP
PPIC	5480	hgsc.bcm.edu	37	5	122359640	122359640	+	Missense_Mutation	SNP	T	T	C	rs451195	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	240	107	240	0	0.445833	0	A|0.005;C|0.208	0.208	strong	.	PPIC	18	.	NM_000943	exon5	c.A569G	p.N190S	GAGCAGTTGGTGA	.	PASS	Atlas-SNP
SCFD2	152579	hgsc.bcm.edu	37	4	54218834	54218834	+	Missense_Mutation	SNP	G	G	A	rs147606542	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	196	90	207	1	0.459184	0.00483092	G|0.998;A|0.002	0.002	strong	SCFD2,NS,NS,0,1	SCFD2	78	1	NM_152540	exon2	c.C938T	p.A313V	GTGAGCGCTATCA	.	scavenged	Atlas-SNP
CFHR3	10878	hgsc.bcm.edu	37	1	196759282	196759282	+	Missense_Mutation	SNP	C	C	T	rs379370	byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	9	7	327	3	0.777778	0.00917431	T|0.236;G|0.236	0.236	strong	CFHR3,NS,carcinoma,0,1	CFHR3	52	1	NM_021023	exon5	c.C721T	p.P241S	TGCCAGCCCTACT	.	scavenged	Atlas-SNP
ADAMDEC1	27299	hgsc.bcm.edu	37	8	24256470	24256470	+	Silent	SNP	C	C	T	rs2291577	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	159	111	145	0	0.698113	0	C|0.670;T|0.330	0.330	strong	.	ADAMDEC1	69	.	NM_014479	exon9	c.C846T	p.S282S	GCCCAGCGCAAGC	.	PASS	Atlas-SNP
DNAH14	127602	hgsc.bcm.edu	37	1	225237950	225237950	+	Missense_Mutation	SNP	A	A	G	rs78320839	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	181	80	172	0	0.441989	0	A|0.991;G|0.009	0.009	strong	.	DNAH14	300	.	NM_001373	exon16	c.A1951G	p.I651V	CTGTCTATCTTCA	.	PASS	Atlas-SNP
GBF1	8729	hgsc.bcm.edu	37	10	104140350	104140350	+	Missense_Mutation	SNP	G	G	A	rs11191274	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	113	56	137	0	0.495575	0	G|0.918;A|0.082	0.082	strong	.	GBF1	142	.	NM_004193	exon38	c.G5077A	p.G1693S	GGAGGCGGCCCCT	.	PASS	Atlas-SNP
C11orf84	144097	hgsc.bcm.edu	37	11	63585804	63585804	+	Silent	SNP	C	C	A	rs643634	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	42	10	56	0	0.238095	0	C|0.623;A|0.377	0.377	strong	.	C11orf84	33	.	NM_138471	exon3	c.C574A	p.R192R	AGGAGCCGGCCCA	.	PASS	Atlas-SNP
PAPPA	5069	hgsc.bcm.edu	37	9	119028233	119028233	+	Missense_Mutation	SNP	A	A	C	rs117124330	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	68	39	81	0	0.573529	0	A|0.988;C|0.012	0.012	strong	.	PAPPA	243	.	NM_002581	exon8	c.A2830C	p.S944R	CATGGAAGTGGGT	.	PASS	Atlas-SNP
SLC25A38	54977	hgsc.bcm.edu	37	3	39431081	39431081	+	Silent	SNP	G	G	A	rs2270770	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	122	58	135	0	0.47541	0	G|0.592;A|0.408	0.408	strong	.	SLC25A38	25	.	NM_017875	exon2	c.G165A	p.L55L	ACGCCTGCAAACC	.	PASS	Atlas-SNP
ZNF91	7644	hgsc.bcm.edu	37	19	23545004	23545004	+	Silent	SNP	G	G	A	rs296092	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	59	21	80	0	0.355932	0	G|0.682;A|0.318	0.318	strong	.	ZNF91	349	.	NM_003430	exon4	c.C777T	p.I259I	AGCACAGATTATT	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29912068	29912068	+	Silent	SNP	A	A	G	rs145353606	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	122	36	137	0	0.295082	0	A|0.951;G|0.049	0.049	strong	.	HLA-A	89	.	NM_001242758	exon4	c.A789G	p.G263G	GGATGGAACCTTC	.	PASS	Atlas-SNP
CRIPAK	285464	hgsc.bcm.edu	37	4	1388429	1388429	+	Missense_Mutation	SNP	G	G	A	rs79298048	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	88	40	122	0	0.454545	0	G|0.725;A|0.275	0.275	strong	CRIPAK,colon,carcinoma,0,2	CRIPAK	185	2	NM_175918	exon1	c.G130A	p.A44T	GTGCCCGCCTGCT	.	PASS	Atlas-SNP
TMPRSS2	7113	hgsc.bcm.edu	37	21	42852497	42852497	+	Missense_Mutation	SNP	C	C	T	rs12329760	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	121	121	120	0	1	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
TGIF1	7050	hgsc.bcm.edu	37	18	3457776	3457776	+	Silent	SNP	T	T	G	rs2229336	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	45	23	67	0	0.511111	0	T|0.941;G|0.059	0.059	strong	.	TGIF1	41	.	NM_170695	exon3	c.T1044G	p.T348T	GGACACTTGTAAA	.	PASS	Atlas-SNP
ODF2L	57489	hgsc.bcm.edu	37	1	86847955	86847955	+	Silent	SNP	G	G	A	rs272516	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	84	37	84	0	0.440476	0	G|0.619;A|0.381	0.381	strong	.	ODF2L	53	.	NM_001184766	exon7	c.C594T	p.A198A	GTTCTCGGCTTCC	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	104	50	111	0	0.480769	0	C|0.818;T|0.182	0.182	strong	.	PAQR6	23	.	NM_024897	exon7	c.G787A	p.E263K	GGGCCTCACTGTT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195510073	195510073	+	Missense_Mutation	SNP	G	G	A	rs200663432	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	14	55	0	0.152174	0	G|0.756;A|0.244	0.244	strong	.	MUC4	1505	.	NM_018406	exon2	c.C8378T	p.A2793V	GTGGATGCTGAGG	.	PASS	Atlas-SNP
TTC28	23331	hgsc.bcm.edu	37	22	28389453	28389453	+	Silent	SNP	T	T	C	rs470101	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	113	67	125	0	0.59292	0	T|0.926;C|0.074	0.074	strong	.	TTC28	84	.	NM_001145418	exon18	c.A5298G	p.T1766T	CTGGGATGTGTAC	.	PASS	Atlas-SNP
FHL5	9457	hgsc.bcm.edu	37	6	97058567	97058567	+	Silent	SNP	A	A	G	rs2273622	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	198	84	246	0	0.424242	0	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	.	PASS	Atlas-SNP
NAGLU	4669	hgsc.bcm.edu	37	17	40696122	40696122	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	54	18	58	0	0.333333	0	.	.	none	.	NAGLU	36	.	NM_000263	exon6	c.A2098C	p.N700H	GACAAAAATGTCT	.	PASS	Atlas-SNP
DHFRL1	200895	hgsc.bcm.edu	37	3	93779860	93779860	+	Missense_Mutation	SNP	C	C	T	rs17855824	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	172	82	196	0	0.476744	0	C|0.915;T|0.085	0.085	strong	.	DHFRL1	25	.	NM_001195643	exon2	c.G496A	p.V166I	AGAGAACACCTGG	.	PASS	Atlas-SNP
HHIPL1	84439	hgsc.bcm.edu	37	14	100129327	100129327	+	Silent	SNP	G	G	A	rs34890784	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	142	58	171	0	0.408451	0	G|0.944;A|0.056	0.056	strong	HHIPL1,NS,malignant_melanoma,+2,1	HHIPL1	86	1	NM_032425	exon6	c.G1617A	p.P539P	CTACCCGTACATC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195506775	195506775	+	Silent	SNP	G	G	A	rs79609066	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	91	11	105	0	0.120879	0	G|0.767;A|0.233	0.233	strong	MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	NM_018406	exon2	c.C11676T	p.T3892T	AGTGTCGGTGACA	.	PASS	Atlas-SNP
GABRB3	2562	hgsc.bcm.edu	37	15	26825545	26825545	+	Silent	SNP	G	G	A	rs75965657	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	90	43	92	0	0.477778	0	G|0.982;A|0.018	0.018	strong	.	GABRB3	338	.	NM_021912	exon6	c.C603T	p.T201T	CACTCCGGTAACA	.	PASS	Atlas-SNP
CREB3L3	84699	hgsc.bcm.edu	37	19	4154910	4154910	+	Silent	SNP	C	C	T	rs35474881	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	43	110	0	0.505882	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
ZNF680	340252	hgsc.bcm.edu	37	7	63986829	63986829	+	Missense_Mutation	SNP	G	G	C	rs73128772	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	26	9	37	0	0.346154	0	G|0.795;C|0.205	0.205	strong	.	ZNF680	58	.	NM_001130022	exon4	c.C320G	p.S107C	TTTAGGGAGGCCA	.	PASS	Atlas-SNP
HLA-G	3135	hgsc.bcm.edu	37	6	29797639	29797639	+	Silent	SNP	C	C	T	rs1049033	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	119	117	160	0	0.983193	0	C|0.738;T|0.262	0.262	strong	.	HLA-G	90	.	NM_002127	exon6	c.C942T	p.G314G	TGCTGGCCTGGTT	.	PASS	Atlas-SNP
AXDND1	126859	hgsc.bcm.edu	37	1	179347832	179347832	+	Silent	SNP	T	T	C	rs10798674	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	96	56	103	0	0.583333	0	T|0.546;C|0.454	0.454	strong	.	AXDND1	142	.	NM_144696	exon5	c.T435C	p.V145V	GGCAGTTTGTCCC	.	PASS	Atlas-SNP
ZNF461	92283	hgsc.bcm.edu	37	19	37130419	37130419	+	Silent	SNP	G	G	A	rs61746298	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	81	39	99	0	0.481481	0	G|0.980;A|0.020	0.020	strong	.	ZNF461	73	.	NM_153257	exon6	c.C828T	p.N276N	ACATTCGTTACAT	.	PASS	Atlas-SNP
HLA-DPB1	3115	hgsc.bcm.edu	37	6	33048599	33048599	+	Missense_Mutation	SNP	C	C	A	rs707958	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	50	47	57	0	0.94	0	A|0.527;C|0.473	0.527	strong	HLA-DPB1,brain,glioma,0,1	HLA-DPB1	28	1	NM_002121	exon2	c.C251A	p.A84D	GGCCTGCTGCGGA	.	PASS	Atlas-SNP
SERPINA5	5104	hgsc.bcm.edu	37	14	95053863	95053863	+	Missense_Mutation	SNP	C	C	T	rs6118	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	43	18	82	0	0.418605	0	C|0.764;T|0.236	0.236	strong	.	SERPINA5	69	.	NM_000624	exon3	c.C164T	p.A55V	ACAGGGCCTTGGC	.	PASS	Atlas-SNP
CELSR1	9620	hgsc.bcm.edu	37	22	46805772	46805772	+	Missense_Mutation	SNP	C	C	T	rs11704506	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	43	21	59	0	0.488372	0	C|0.979;T|0.021	0.021	strong	.	CELSR1	242	.	NM_014246	exon8	c.G4939A	p.A1647T	GAGCAGCGCAGCC	.	PASS	Atlas-SNP
SSBP4	170463	hgsc.bcm.edu	37	19	18538742	18538742	+	Silent	SNP	A	A	C	rs10405636	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	113	113	90	0	1	0	A|0.545;C|0.455	0.455	strong	.	SSBP4	19	.	NM_001009998	exon4	c.A229C	p.R77R	CCTGACAGAAGAG	.	PASS	Atlas-SNP
SLC37A2	219855	hgsc.bcm.edu	37	11	124953735	124953735	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	98	4	127	0	0.0408163	0	.	.	none	.	SLC37A2	105	.	NM_001145290	exon11	c.G1001A	p.G334E	AGGCTGGGGACCT	.	PASS	Atlas-SNP
TMCO3	55002	hgsc.bcm.edu	37	13	114152755	114152755	+	Silent	SNP	C	C	T	rs2260218	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	48	25	56	0	0.520833	0	C|0.795;T|0.205	0.205	strong	.	TMCO3	77	.	NM_017905	exon3	c.C543T	p.D181D	GCTTGACGAGATT	.	PASS	Atlas-SNP
BARX2	8538	hgsc.bcm.edu	37	11	129321066	129321066	+	Silent	SNP	C	C	T	rs10791011	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	81	62	70	0	0.765432	0	C|0.769;T|0.231	0.231	strong	.	BARX2	40	.	NM_003658	exon4	c.C609T	p.P203P	AAAACCCAAAGGT	.	PASS	Atlas-SNP
PTCHD3	374308	hgsc.bcm.edu	37	10	27687437	27687437	+	Missense_Mutation	SNP	C	C	A	rs139600575	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	76	35	133	0	0.460526	0	C|0.999;A|0.001	0.001	strong	.	PTCHD3	140	.	NM_001034842	exon4	c.G2090T	p.W697L	TCTAACCAAAACT	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	103	47	106	0	0.456311	0	T|0.641;C|0.359	0.359	strong	.	DGKI	335	.	NM_004717	exon29	c.A2778G	p.E926E	ATGATCTTCTGAA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195509676	195509676	+	Missense_Mutation	SNP	C	C	G	rs372419355		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	120	60	57	1	0.5	0.0175439	.	.	weak	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.G8775C	p.Q2925H	GGTGGCCTGACCT	.	scavenged	Atlas-SNP
CCP110	9738	hgsc.bcm.edu	37	16	19548290	19548290	+	Silent	SNP	G	G	A	rs7191012	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	177	69	135	0	0.38983	0	G|0.843;A|0.157	0.157	strong	.	CCP110	57	.	NM_001199022	exon4	c.G1299A	p.A433A	TTTAGCGGGAGTT	.	PASS	Atlas-SNP
CYFIP2	26999	hgsc.bcm.edu	37	5	156741411	156741411	+	Silent	SNP	C	C	T	rs139943836	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	38	103	0	0.535211	0	C|0.999;T|0.001	0.001	strong	.	CYFIP2	354	.	NM_001037332	exon12	c.C1170T	p.F390F	GCTCTTCGACCTA	.	PASS	Atlas-SNP
CCDC110	256309	hgsc.bcm.edu	37	4	186380515	186380515	+	Missense_Mutation	SNP	G	G	A	rs11132306	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	122	56	157	0	0.459016	0	G|0.562;A|0.438	0.438	strong	.	CCDC110	78	.	NM_152775	exon6	c.C1226T	p.S409F	TTTTCAGATATTA	.	PASS	Atlas-SNP
SLC6A17	388662	hgsc.bcm.edu	37	1	110709719	110709719	+	Silent	SNP	T	T	C	rs7527375	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	90	44	89	0	0.488889	0	T|0.518;C|0.482	0.482	strong	.	SLC6A17	86	.	NM_001010898	exon2	c.T168C	p.D56D	GCTGGATGCAGAG	.	PASS	Atlas-SNP
CCDC102B	79839	hgsc.bcm.edu	37	18	66513615	66513615	+	Missense_Mutation	SNP	A	A	G	rs2187094	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	125	125	144	0	1	0	A|0.674;G|0.326	0.326	strong	CCDC102B,NS,carcinoma,0,2	CCDC102B	92	2	NM_001093729	exon6	c.A893G	p.K298R	AGTGGAAGTATGA	.	PASS	Atlas-SNP
ZNF419	79744	hgsc.bcm.edu	37	19	58002964	58002964	+	Silent	SNP	G	G	C	rs8108040	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	253	67	155	0	0.264822	0	G|0.730;C|0.270	0.270	strong	.	ZNF419	134	.	NM_001098494	exon3	c.G201C	p.L67L	CTCTCTGGGTAAG	.	PASS	Atlas-SNP
EPHA3	2042	hgsc.bcm.edu	37	3	89521693	89521693	+	Missense_Mutation	SNP	T	T	C	rs35124509	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	102	101	172	3	0.990196	0.0174419	T|0.563;C|0.437	0.437	strong	EPHA3,NS,carcinoma,-2,2	EPHA3	501	2	NM_005233	exon16	c.T2770C	p.W924R	GGTGTCTGGACAG	.	scavenged	Atlas-SNP
TAF2	6873	hgsc.bcm.edu	37	8	120803654	120803654	+	Silent	SNP	C	C	T	rs11996390	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	126	24	143	0	0.190476	0	C|0.777;T|0.223	0.223	strong	.	TAF2	204	.	NM_003184	exon11	c.G1323A	p.L441L	CCAGGACAGTGTA	.	PASS	Atlas-SNP
PRKCI	5584	hgsc.bcm.edu	37	3	169988286	169988286	+	Silent	SNP	C	C	T	rs56257047	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	96	47	125	0	0.489583	0	C|0.886;T|0.114	0.114	strong	.	PRKCI	82	.	NM_002740	exon6	c.C528T	p.L176L	CAAACTCTTGGTT	.	PASS	Atlas-SNP
PLEKHH1	57475	hgsc.bcm.edu	37	14	68035879	68035879	+	Missense_Mutation	SNP	A	A	G	rs3825725	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	48	47	45	0	0.979167	0	A|0.789;G|0.211	0.211	strong	PLEKHH1_ENST00000329153,NS,carcinoma,0,2	PLEKHH1	118	2	NM_020715	exon8	c.A1288G	p.T430A	GTGGCCACATCGG	.	PASS	Atlas-SNP
RGPD8	727851	hgsc.bcm.edu	37	2	113147666	113147666	+	Missense_Mutation	SNP	C	C	A	rs71227755		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	188	178	858	0	0.946809	0	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
KLHL23	151230	hgsc.bcm.edu	37	2	170592709	170592709	+	Silent	SNP	A	A	G	rs2288331	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	42	19	46	0	0.452381	0	A|0.835;G|0.165	0.165	strong	.	KLHL23	52	.	NM_144711	exon2	c.A1185G	p.K395K	AGAGAAATGGATT	.	PASS	Atlas-SNP
CDNF	441549	hgsc.bcm.edu	37	10	14862082	14862082	+	Missense_Mutation	SNP	C	C	G	rs61738953	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	123	64	164	0	0.520325	0	C|0.964;G|0.036	0.036	strong	.	CDNF	19	.	NM_001029954	exon4	c.G461C	p.W154S	TCCCCCCAGCTAT	.	PASS	Atlas-SNP
AXIN2	8313	hgsc.bcm.edu	37	17	63554591	63554591	+	Missense_Mutation	SNP	G	G	A	rs2240308	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	36	13	38	0	0.361111	0	G|0.641;A|0.359	0.359	strong	.	AXIN2	92	.	NM_004655	exon2	c.C148T	p.P50S	AGACAGGCATGGG	.	PASS	Atlas-SNP
PAK6	56924	hgsc.bcm.edu	37	15	40564576	40564576	+	Missense_Mutation	SNP	C	C	T	rs3743137	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	35	73	0	0.411765	0	C|0.904;T|0.096	0.096	strong	.	PAK6	49	.	NM_001128629	exon5	c.C1010T	p.P337L	CAGCCCCGGCCAC	.	PASS	Atlas-SNP
TOR3A	64222	hgsc.bcm.edu	37	1	179064145	179064145	+	Missense_Mutation	SNP	T	T	C	rs138598531	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	192	98	213	0	0.510417	0	T|0.999;C|0.001	0.001	strong	.	TOR3A	28	.	NM_022371	exon6	c.T986C	p.I329T	ACCTGATTGACTA	.	PASS	Atlas-SNP
RIN1	9610	hgsc.bcm.edu	37	11	66099987	66099987	+	Silent	SNP	C	C	T	rs1784029	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	77	27	86	0	0.350649	0	C|0.445;T|0.555	0.555	strong	.	RIN1	64	.	NM_004292	exon10	c.G2112A	p.A704A	CCACTCCGCCCGG	.	PASS	Atlas-SNP
KPTN	11133	hgsc.bcm.edu	37	19	47978739	47978739	+	Silent	SNP	C	C	T	rs1046273	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	95	31	82	0	0.326316	0	C|0.982;T|0.018	0.018	strong	.	KPTN	34	.	NM_007059	exon12	c.G1245A	p.R415R	ACGTCTCCTCTGC	.	PASS	Atlas-SNP
OR2D2	120776	hgsc.bcm.edu	37	11	6913243	6913243	+	Missense_Mutation	SNP	T	T	C	rs1965207	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	167	125	186	0	0.748503	0	T|0.866;C|0.134	0.134	strong	.	OR2D2	52	.	NM_003700	exon1	c.A489G	p.I163M	CCTCAGTATGAAG	.	PASS	Atlas-SNP
HUS1B	135458	hgsc.bcm.edu	37	6	656810	656810	+	Silent	SNP	A	A	G	rs61748571	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	37	22	32	0	0.594595	0	A|0.942;G|0.058	0.058	strong	.	HUS1B	26	.	NM_148959	exon1	c.T135C	p.G45G	GCCGGAACCCGCG	.	PASS	Atlas-SNP
FCN1	2219	hgsc.bcm.edu	37	9	137809685	137809685	+	Silent	SNP	C	C	A	rs10858293	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	65	60	61	0	0.923077	0	C|0.693;A|0.307	0.307	strong	.	FCN1	62	.	NM_002003	exon1	c.G33T	p.G11G	AGCGAGCCCCCGG	.	PASS	Atlas-SNP
EIF4G3	8672	hgsc.bcm.edu	37	1	21133836	21133836	+	Silent	SNP	T	T	C	rs146669269	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	138	60	147	0	0.434783	0	T|0.993;C|0.007	0.007	strong	.	EIF4G3	300	.	NM_001198801	exon35	c.A4842G	p.A1614A	CTCTTCTGCTTCC	.	PASS	Atlas-SNP
CGNL1	84952	hgsc.bcm.edu	37	15	57731573	57731573	+	Missense_Mutation	SNP	C	C	T	rs7182648	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	76	19	81	0	0.25	0	C|0.797;T|0.203	0.203	strong	.	CGNL1	125	.	NM_032866	exon2	c.C1376T	p.S459F	CCCACTCCAGGCC	.	PASS	Atlas-SNP
PHIP	55023	hgsc.bcm.edu	37	6	79656562	79656562	+	Silent	SNP	A	A	T	rs2275291	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	62	61	71	0	0.983871	0	A|0.719;T|0.281	0.281	strong	.	PHIP	177	.	NM_017934	exon37	c.T4236A	p.A1412A	AAAGAAAGCAGAC	.	PASS	Atlas-SNP
CFHR2	3080	hgsc.bcm.edu	37	1	196928188	196928188	+	Missense_Mutation	SNP	A	A	G	rs41310132	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	207	104	223	1	0.502415	0.00448431	A|0.988;G|0.012	0.012	strong	.	CFHR2	73	.	NM_005666	exon5	c.A791G	p.Y264C	TGGTATATCCCAG	.	PASS	Atlas-SNP
OSBPL7	114881	hgsc.bcm.edu	37	17	45890707	45890707	+	Silent	SNP	C	C	T	rs2301690	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	74	44	77	0	0.594595	0	C|0.759;T|0.241	0.241	strong	.	OSBPL7	65	.	NM_145798	exon16	c.G1662A	p.K554K	GAAGGGCTTGCAG	.	PASS	Atlas-SNP
PIEZO1	9780	hgsc.bcm.edu	37	16	88782676	88782676	+	Silent	SNP	A	A	G	rs2290902	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	79	79	89	0	1	0	A|0.131;G|0.869	0.869	strong	.	PIEZO1	79	.	NM_001142864	exon49	c.T7059C	p.P2353P	GAGATTAGGGATG	.	PASS	Atlas-SNP
IL2	3558	hgsc.bcm.edu	37	4	123377482	123377482	+	Silent	SNP	C	C	A	rs2069763	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	142	63	190	0	0.443662	0	C|0.718;A|0.282	0.282	strong	.	IL2	23	.	NM_000586	exon1	c.G114T	p.L38L	ATCCAGCAGTAAA	.	PASS	Atlas-SNP
PCMTD1	115294	hgsc.bcm.edu	37	8	52733164	52733164	+	Missense_Mutation	SNP	G	G	C	rs149898988		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	168	16	205	0	0.0952381	0	.	.	weak	PCMTD1,NS,carcinoma,0,3	PCMTD1	73	3	NM_052937	exon6	c.C821G	p.P274R	CTTTTGGGTGGAG	.	PASS	Atlas-SNP
WWC2	80014	hgsc.bcm.edu	37	4	184190233	184190233	+	Missense_Mutation	SNP	G	G	T	rs11941467	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	59	146	0	0.608247	0	G|0.917;T|0.083	0.083	strong	.	WWC2	78	.	NM_024949	exon15	c.G2317T	p.A773S	AGAGTCGCCATTT	.	PASS	Atlas-SNP
TET1	80312	hgsc.bcm.edu	37	10	70405237	70405237	+	Silent	SNP	G	G	A	rs12241767	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	48	24	40	0	0.5	0	G|0.807;A|0.193	0.193	strong	.	TET1	255	.	NM_030625	exon4	c.G2751A	p.E917E	GGATGAGGAATCA	.	PASS	Atlas-SNP
HDAC7	51564	hgsc.bcm.edu	37	12	48189061	48189061	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	46	16	42	1	0.347826	0.0238095	.	.	none	HDAC7,NS,carcinoma,+1,1	HDAC7	71	1	NM_015401	exon11	c.C1190T	p.S397L	GGCTCTGAGCGAG	.	scavenged	Atlas-SNP
KRTAP4-7	100132476	hgsc.bcm.edu	37	17	39240794	39240794	+	Silent	SNP	C	C	A	rs9894106	by2hit2allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	37	6	21	0	0.162162	0	.	.	weak	KRTAP4-7,NS,carcinoma,0,3	KRTAP4-7	49	3	NM_033061	exon1	c.C336A	p.P112P	CCGCCCCAGCTGC	.	scavenged	Atlas-SNP
FAM120B	84498	hgsc.bcm.edu	37	6	170627614	170627614	+	Missense_Mutation	SNP	T	T	C	rs6905356	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	36	7	65	0	0.194444	0	T|0.861;C|0.139	0.139	strong	.	FAM120B	108	.	NM_032448	exon2	c.T1136C	p.M379T	TTCCCATGTGTTC	.	PASS	Atlas-SNP
RP1L1	94137	hgsc.bcm.edu	37	8	10469340	10469340	+	Silent	SNP	G	G	A	rs57819090	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	21	79	0	0.247059	0	G|0.852;A|0.148	0.148	strong	.	RP1L1	453	.	NM_178857	exon4	c.C2268T	p.N756N	GGGAGCGTTGTGC	.	PASS	Atlas-SNP
MB	4151	hgsc.bcm.edu	37	22	36007075	36007075	+	Silent	SNP	C	C	T	rs7293	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	161	85	168	0	0.52795	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
EQTN	54586	hgsc.bcm.edu	37	9	27296705	27296705	+	Silent	SNP	A	A	G	rs3824406	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	180	94	264	0	0.522222	0	A|0.873;G|0.127	0.127	strong	.	.	.	.	NM_001161585	exon2	c.T108C	p.D36D	ATTAACATCTTCA	.	PASS	Atlas-SNP
ZNF469	84627	hgsc.bcm.edu	37	16	88501971	88501971	+	Missense_Mutation	SNP	T	T	A	rs3812956	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	36	17	47	0	0.472222	0	T|0.680;A|0.320	0.320	strong	.	ZNF469	121	.	NM_001127464	exon2	c.T8009A	p.L2670Q	CCACTCTGGGACC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195512212	195512212	+	Missense_Mutation	SNP	G	G	T	rs75588776	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	19	95	0	0.218391	0	G|0.816;T|0.185	0.185	strong	MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	NM_018406	exon2	c.C6239A	p.P2080H	AGAAGAGGGGTGG	.	PASS	Atlas-SNP
CDH9	1007	hgsc.bcm.edu	37	5	26902724	26902724	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	147	35	120	0	0.238095	0	.	.	none	.	CDH9	305	.	NM_016279	exon7	c.A1114C	p.I372L	CAGATATTTTGAC	.	PASS	Atlas-SNP
RNF213	57674	hgsc.bcm.edu	37	17	78262161	78262161	+	Missense_Mutation	SNP	T	T	C	rs17857135	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	93	48	99	0	0.516129	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
C10orf71	118461	hgsc.bcm.edu	37	10	50534862	50534862	+	Silent	SNP	T	T	C	rs12411843	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	35	57	0	0.486111	0	T|0.690;C|0.310	0.310	strong	.	C10orf71	179	.	NM_001135196	exon3	c.T4272C	p.D1424D	CACTGATGACCTA	.	PASS	Atlas-SNP
MYBPC2	4606	hgsc.bcm.edu	37	19	50967640	50967640	+	Missense_Mutation	SNP	G	G	A	rs25667	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	48	31	37	0	0.645833	0	A|0.143;C|0.000;G|0.857	0.143	strong	.	MYBPC2	103	.	NM_004533	exon27	c.G3266A	p.R1089H	AAATCCGTGAAGA	.	PASS	Atlas-SNP
KIF7	374654	hgsc.bcm.edu	37	15	90195948	90195948	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	120	71	100	0	0.591667	0	.	.	none	.	KIF7	130	.	NM_198525	exon2	c.C214G	p.Q72E	AGGCCTGGTACAC	.	PASS	Atlas-SNP
SFI1	9814	hgsc.bcm.edu	37	22	32000872	32000872	+	Silent	SNP	G	G	A	rs8142346	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	100	42	88	0	0.42	0	G|0.981;A|0.019	0.019	strong	.	SFI1	78	.	NM_001007467	exon20	c.G1995A	p.V665V	CAGGGTGCGAAGC	.	PASS	Atlas-SNP
TRPM8	79054	hgsc.bcm.edu	37	2	234854552	234854552	+	Missense_Mutation	SNP	A	A	G	rs17868387	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	38	68	0	0.520548	0	A|0.954;G|0.046	0.046	strong	.	TRPM8	146	.	NM_024080	exon7	c.A752G	p.Y251C	CACTGTATATCCT	.	PASS	Atlas-SNP
RNF207	388591	hgsc.bcm.edu	37	1	6279370	6279370	+	Missense_Mutation	SNP	G	G	C	rs846111	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	224	128	221	0	0.571429	0	G|0.803;C|0.197	0.197	strong	RNF207,caecum,carcinoma,0,2	RNF207	45	2	NM_207396	exon18	c.G1808C	p.G603A	CGAACGGCCTCTC	.	PASS	Atlas-SNP
SOGA2	23255	hgsc.bcm.edu	37	18	8825192	8825192	+	Silent	SNP	A	A	G	rs581894	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	111	55	120	0	0.495495	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
MCF2L	23263	hgsc.bcm.edu	37	13	113741590	113741590	+	Silent	SNP	G	G	A	rs9604022	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	111	51	112	0	0.459459	0	G|0.832;A|0.168	0.168	strong	.	MCF2L	182	.	NM_001112732	exon22	c.G2415A	p.S805S	GGGCTCGTTCAGC	.	PASS	Atlas-SNP
DPCR1	135656	hgsc.bcm.edu	37	6	30919391	30919391	+	Silent	SNP	G	G	A	rs3094086	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	91	34	86	0	0.373626	0	G|0.932;A|0.068	0.068	strong	.	DPCR1	99	.	NM_080870	exon2	c.G3150A	p.S1050S	CCCATCGGCCAAT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195508490	195508490	+	Missense_Mutation	SNP	C	C	A	rs200820395		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	37	8	112	0	0.216216	0	.	.	weak	.	MUC4	1505	.	NM_018406	exon2	c.G9961T	p.A3321S	TGGATGCTGAGGA	.	PASS	Atlas-SNP
PRRG4	79056	hgsc.bcm.edu	37	11	32874926	32874926	+	Silent	SNP	G	G	A	rs11032025	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	62	45	66	1	0.725806	0.0151515	G|0.604;A|0.396	0.396	strong	PRRG4,colon,carcinoma,0,1	PRRG4	15	1	NM_024081	exon6	c.G534A	p.P178P	ATTGCCGCCTTCT	.	scavenged	Atlas-SNP
AP5B1	91056	hgsc.bcm.edu	37	11	65547455	65547455	+	Missense_Mutation	SNP	C	C	A	rs12362011	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	46	71	0	0.630137	0	C|0.832;A|0.168	0.168	strong	.	AP5B1	40	.	NM_138368	exon2	c.G509T	p.G170V	AGCAACCCCAGGG	.	PASS	Atlas-SNP
ENOSF1	55556	hgsc.bcm.edu	37	18	674320	674320	+	Silent	SNP	A	A	G	rs3744962	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	113	45	104	0	0.39823	0	A|0.917;G|0.083	0.083	strong	.	ENOSF1	44	.	NM_202758	exon15	c.T1338C	p.P446P	TTGAGCAGGAAGG	.	PASS	Atlas-SNP
KIAA2026	158358	hgsc.bcm.edu	37	9	5969249	5969249	+	Silent	SNP	A	A	G	rs10739080	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	118	63	120	0	0.533898	0	A|0.421;G|0.579	0.579	strong	.	KIAA2026	231	.	NM_001017969	exon3	c.T982C	p.L328L	GTTCCAATTCGTA	.	PASS	Atlas-SNP
OR8J1	219477	hgsc.bcm.edu	37	11	56128031	56128031	+	Silent	SNP	G	G	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	187	49	216	0	0.262032	0	.	.	none	.	OR8J1	87	.	NM_001005205	exon1	c.G309C	p.G103G	GGGAGGGTTCTTG	.	PASS	Atlas-SNP
ZNF180	7733	hgsc.bcm.edu	37	19	44981009	44981009	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	81	15	90	0	0.185185	0	.	.	none	.	ZNF180	103	.	NM_013256	exon5	c.C1689A	p.H563Q	AACAAGGTGAGAA	.	PASS	Atlas-SNP
DENND4C	55667	hgsc.bcm.edu	37	9	19290794	19290794	+	Missense_Mutation	SNP	A	A	C	rs41269019	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	91	49	104	0	0.538462	0	A|0.979;C|0.021	0.021	strong	.	DENND4C	120	.	NM_017925	exon5	c.A721C	p.I241L	GCTACTATTGAGT	.	PASS	Atlas-SNP
NUP188	23511	hgsc.bcm.edu	37	9	131752487	131752487	+	Silent	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	187	38	202	0	0.203209	0	.	.	none	.	NUP188	140	.	NM_015354	exon25	c.G2622A	p.L874L	TCAGCTGCTGAAA	.	PASS	Atlas-SNP
OR5L2	26338	hgsc.bcm.edu	37	11	55594869	55594869	+	Missense_Mutation	SNP	G	G	A	rs56711116	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	152	114	126	0	0.75	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
SLC17A3	10786	hgsc.bcm.edu	37	6	25862466	25862466	+	Missense_Mutation	SNP	C	C	T	rs1165165	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	83	81	86	0	0.975904	0	C|0.755;T|0.245	0.245	strong	.	SLC17A3	95	.	NM_006632	exon3	c.G298A	p.A100T	CCTTTGCAGGAAG	.	PASS	Atlas-SNP
ZNF687	57592	hgsc.bcm.edu	37	1	151259043	151259043	+	Silent	SNP	C	C	T	rs2298265	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	32	54	0	0.551724	0	C|0.892;T|0.108	0.108	strong	.	ZNF687	94	.	NM_020832	exon2	c.C276T	p.P92P	GTGTCCCGAGCAG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195511142	195511142	+	Missense_Mutation	SNP	T	T	C	rs430037	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	211	44	239	1	0.208531	0.0041841	T|0.781;C|0.219	0.219	strong	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.A7309G	p.N2437D	AAACGTTGGTGAC	.	scavenged	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29910663	29910663	+	Missense_Mutation	SNP	G	G	A	rs707910	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	198	98	186	0	0.494949	0	A|0.112;G|0.888	0.112	strong	.	HLA-A	89	.	NM_001242758	exon2	c.G203A	p.R68K	GCCAGAGGATGGA	.	PASS	Atlas-SNP
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33037640	33037640	+	Missense_Mutation	SNP	C	C	T	rs1126533	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	22	120	0	0.293333	0	T|0.125;C|0.875	0.125	strong	HLA-DPA1,NS,carcinoma,+1,4	HLA-DPA1	20	4	NM_033554	exon2	c.G124A	p.A42T	CAAACGCGGCATA	.	scavenged	Atlas-SNP
NAGLU	4669	hgsc.bcm.edu	37	17	40696120	40696120	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	53	17	59	0	0.320755	0	.	.	none	.	NAGLU	36	.	NM_000263	exon6	c.A2096T	p.K699I	TTGACAAAAATGT	.	PASS	Atlas-SNP
BDH2	56898	hgsc.bcm.edu	37	4	104013796	104013796	+	Missense_Mutation	SNP	T	T	C	rs1054707	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	275	149	330	0	0.541818	0	T|0.878;C|0.122	0.122	strong	.	BDH2	18	.	NM_020139	exon4	c.A209G	p.N70S	ACTTCATTGGCAA	.	PASS	Atlas-SNP
SHISA3	152573	hgsc.bcm.edu	37	4	42400112	42400112	+	Missense_Mutation	SNP	G	G	T	rs11733156	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	39	39	49	0	1	0	G|0.801;T|0.199	0.199	strong	.	SHISA3	27	.	NM_001080505	exon1	c.G39T	p.W13C	TGGCTGGCTGCGC	.	PASS	Atlas-SNP
STK10	6793	hgsc.bcm.edu	37	5	171523436	171523436	+	Silent	SNP	G	G	A	rs4868141	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	61	32	55	0	0.52459	0	G|0.856;A|0.144	0.144	strong	.	STK10	100	.	NM_005990	exon8	c.C999T	p.A333A	GGAGGCGGCATCC	.	PASS	Atlas-SNP
ACTL7B	10880	hgsc.bcm.edu	37	9	111617650	111617650	+	Silent	SNP	G	G	A	rs11543179	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	45	24	62	0	0.533333	0	G|0.782;A|0.218	0.218	strong	.	ACTL7B	57	.	NM_006686	exon1	c.C561T	p.Y187Y	GTAGGAGTAGATG	.	PASS	Atlas-SNP
ITGA10	8515	hgsc.bcm.edu	37	1	145536082	145536082	+	Missense_Mutation	SNP	G	G	A	rs2274616	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	144	72	158	0	0.5	0	G|0.869;A|0.131	0.131	strong	ITGA10,NS,carcinoma,-1,1	ITGA10	131	1	NM_003637	exon17	c.G2174A	p.R725Q	CCCCTCGGAGGCT	.	PASS	Atlas-SNP
HJURP	55355	hgsc.bcm.edu	37	2	234749780	234749780	+	Missense_Mutation	SNP	G	G	C	rs3821238	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	57	33	81	0	0.578947	0	G|0.832;C|0.168	0.168	strong	HJURP,NS,carcinoma,0,1	HJURP	72	1	NM_018410	exon8	c.C1646G	p.S549C	ATTCCAGAACTAT	.	PASS	Atlas-SNP
CRIPAK	285464	hgsc.bcm.edu	37	4	1388553	1388553	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	102	10	116	2	0.0980392	0.0172414	.	.	none	CRIPAK,NS,carcinoma,0,1	CRIPAK	185	1	NM_175918	exon1	c.A254G	p.H85R	GTGCCCACCTGCT	.	scavenged	Atlas-SNP
ITIH4	3700	hgsc.bcm.edu	37	3	52864635	52864635	+	Silent	SNP	A	A	G	rs2276818	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	45	84	0	0.548781	0	A|0.880;G|0.120	0.120	strong	ITIH4,NS,adenocarcinoma,-1,1	ITIH4	74	1	NM_001166449	exon1	c.T24C	p.R8R	GCAGGTACGGACA	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	66	33	87	0	0.5	0	G|0.254;N|0.000	0.254	strong	.	.	.	.	NM_025138	exon11	c.T1712C	p.V571A	ACTGGCACTGACG	.	PASS	Atlas-SNP
CPAMD8	27151	hgsc.bcm.edu	37	19	17088299	17088299	+	Missense_Mutation	SNP	T	T	C	rs56376819		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	31	31	40	0	1	0	.	.	weak	.	CPAMD8	192	.	NM_015692	exon15	c.A1778G	p.H593R	GCCAGATGAAGAG	.	PASS	Atlas-SNP
ARHGAP42	143872	hgsc.bcm.edu	37	11	100847069	100847069	+	Missense_Mutation	SNP	G	G	A	rs569336	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	96	23	105	0	0.239583	0	G|0.552;A|0.448	0.448	strong	.	ARHGAP42	32	.	NM_152432	exon20	c.G2137A	p.V713I	GGAGACGTTTCCC	.	PASS	Atlas-SNP
P2RX3	5024	hgsc.bcm.edu	37	11	57137424	57137424	+	Missense_Mutation	SNP	C	C	T	rs2276038	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	90	88	100	0	0.977778	0	C|0.650;T|0.349	0.349	strong	.	P2RX3	55	.	NM_002559	exon12	c.C1148T	p.A383V	CCACAGCGGAGAA	.	PASS	Atlas-SNP
FAM151A	338094	hgsc.bcm.edu	37	1	55075062	55075062	+	Missense_Mutation	SNP	C	C	T	rs2289015	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	80	41	83	0	0.5125	0	C|0.942;T|0.058	0.058	strong	.	FAM151A	58	.	NM_176782	exon8	c.G1637A	p.G546D	TAGTCGCCCCCAG	.	PASS	Atlas-SNP
SPATA21	374955	hgsc.bcm.edu	37	1	16731510	16731510	+	Missense_Mutation	SNP	C	C	G	rs525409	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	107	40	109	0	0.373832	0	C|0.774;G|0.226	0.226	strong	.	SPATA21	47	.	NM_198546	exon8	c.G763C	p.V255L	GCGTCACAGAGAA	.	PASS	Atlas-SNP
C7orf31	136895	hgsc.bcm.edu	37	7	25194753	25194753	+	Missense_Mutation	SNP	C	C	T	rs12535348	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	177	173	183	0	0.977401	0	C|0.675;N|0.000	.	strong	C7orf31,caecum,carcinoma,0,2	C7orf31	53	2	NM_138811	exon6	c.G472A	p.A158T	ACATGGCGCCGCG	.	PASS	Atlas-SNP
ENOSF1	55556	hgsc.bcm.edu	37	18	706558	706558	+	Silent	SNP	C	C	T	rs58085394	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	83	35	97	0	0.421687	0	C|0.886;T|0.114	0.114	strong	.	ENOSF1	44	.	NM_202758	exon2	c.G168A	p.S56S	GGCAGCCGAGTAG	.	PASS	Atlas-SNP
OR5P2	120065	hgsc.bcm.edu	37	11	7817856	7817856	+	Missense_Mutation	SNP	C	C	T	rs78460198	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	183	149	196	0	0.814208	0	C|0.739;T|0.261	0.261	strong	OR5P2,colon,carcinoma,0,2	OR5P2	68	2	NM_153444	exon1	c.G634A	p.V212I	AGCAGACGGCTAT	.	PASS	Atlas-SNP
MEFV	4210	hgsc.bcm.edu	37	16	3299749	3299749	+	Silent	SNP	G	G	A	rs224213	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	127	36	130	0	0.283465	0	G|0.373;A|0.627	0.627	strong	.	MEFV	170	.	NM_000243	exon3	c.C942T	p.R314R	GTGGCAGCGGGGA	.	PASS	Atlas-SNP
CR1	1378	hgsc.bcm.edu	37	1	207790088	207790088	+	Missense_Mutation	SNP	C	C	G	rs3811381	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	190	89	245	1	0.468421	0.00408163	C|0.800;G|0.200	0.200	strong	.	CR1	354	.	NM_000651	exon41	c.C6830G	p.P2277R	GTGACCCTCAAGG	.	PASS	Atlas-SNP
PALLD	23022	hgsc.bcm.edu	37	4	169433326	169433326	+	Missense_Mutation	SNP	T	T	C	rs7655494	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	56	56	75	0	1	0	T|0.732;C|0.268	0.268	strong	.	PALLD	179	.	NM_001166108	exon2	c.T671C	p.M224T	GCCCTATGGAAGA	.	PASS	Atlas-SNP
LRP3	4037	hgsc.bcm.edu	37	19	33693785	33693785	+	Silent	SNP	G	G	A	rs1056034	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	128	58	155	0	0.453125	0	G|0.952;A|0.048	0.048	strong	LRP3,NS,carcinoma,+1,1	LRP3	46	1	NM_002333	exon3	c.G153A	p.T51T	GCACACGGAGCGG	.	PASS	Atlas-SNP
GPR112	139378	hgsc.bcm.edu	37	X	135431358	135431358	+	Silent	SNP	C	C	T	rs5930933	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	102	101	185	1	0.990196	0.00540541	C|0.507;0|0.003	.	strong	.	GPR112	459	.	NM_153834	exon6	c.C5493T	p.P1831P	TCTACCCTCTTTG	.	PASS	Atlas-SNP
NPHP4	261734	hgsc.bcm.edu	37	1	5940243	5940243	+	Missense_Mutation	SNP	G	G	A	rs17472401	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	26	111	0	0.361111	0	G|0.986;A|0.014	0.014	strong	.	NPHP4	119	.	NM_015102	exon19	c.C2542T	p.R848W	TGACCCGAGATCT	.	PASS	Atlas-SNP
FBN3	84467	hgsc.bcm.edu	37	19	8139977	8139977	+	Silent	SNP	G	G	A	rs61729621	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	56	31	64	0	0.553571	0	G|0.969;A|0.031	0.031	strong	.	FBN3	300	.	NM_032447	exon60	c.C7680T	p.H2560H	CTGGGAGTGCTGG	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	378	300	322	1	0.793651	0.00310559	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
CCDC110	256309	hgsc.bcm.edu	37	4	186382206	186382206	+	Silent	SNP	A	A	G	rs11132309	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	98	38	137	0	0.387755	0	A|0.557;G|0.443	0.443	strong	.	CCDC110	78	.	NM_152775	exon5	c.T345C	p.D115D	TACCAAATCCTTT	.	PASS	Atlas-SNP
POTEH	23784	hgsc.bcm.edu	37	22	16287673	16287673	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	94	4	15	0	0.0425532	0	.	.	none	POTEH,NS,carcinoma,0,4	POTEH	114	4	NM_001136213	exon1	c.G213C	p.W71C	CCTGCACCAGGGG	.	scavenged	Atlas-SNP
NAV3	89795	hgsc.bcm.edu	37	12	78334179	78334179	+	Silent	SNP	A	A	G	rs17817265	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	139	71	125	0	0.510791	0	A|0.971;G|0.029	0.029	strong	.	NAV3	506	.	NM_014903	exon2	c.A324G	p.A108A	CATTGCAGATGGA	.	PASS	Atlas-SNP
PCNT	5116	hgsc.bcm.edu	37	21	47836653	47836653	+	Missense_Mutation	SNP	C	C	T	rs2070425	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	26	36	0	0.346667	0	C|0.735;T|0.265	0.265	strong	.	PCNT	283	.	NM_006031	exon30	c.C6821T	p.P2274L	AGGGGCCGGGGCT	.	PASS	Atlas-SNP
NRP1	8829	hgsc.bcm.edu	37	10	33475282	33475282	+	Missense_Mutation	SNP	C	C	T	rs2228638	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	115	52	127	0	0.452174	0	C|0.910;T|0.090	0.090	strong	NRP1,NS,carcinoma,+2,1	NRP1	126	1	NM_003873	exon14	c.G2197A	p.V733I	TGCCGACGTGGGA	.	PASS	Atlas-SNP
FAM102A	399665	hgsc.bcm.edu	37	9	130742413	130742413	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	68	27	75	0	0.397059	0	.	.	none	.	FAM102A	32	.	NM_001035254	exon1	c.G4A	p.A2T	AGAAAGCCATGAG	.	PASS	Atlas-SNP
ABCB8	11194	hgsc.bcm.edu	37	7	150730999	150730999	+	Missense_Mutation	SNP	G	G	A	rs4148844	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	45	20	36	0	0.444444	0	G|0.940;A|0.060	0.060	strong	ABCB8,NS,carcinoma,-2,1	ABCB8	65	1	NM_007188	exon2	c.G403A	p.V135I	GTAGCCGTCGTGG	.	PASS	Atlas-SNP
SERPINB8	5271	hgsc.bcm.edu	37	18	61654463	61654463	+	Missense_Mutation	SNP	A	A	G	rs3826616	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	121	75	98	0	0.619835	0	A|0.466;G|0.534	0.534	strong	.	SERPINB8	42	.	NM_198833	exon7	c.A1076G	p.H359R	TCAGGCACCACAA	.	PASS	Atlas-SNP
USP8	9101	hgsc.bcm.edu	37	15	50785016	50785016	+	Missense_Mutation	SNP	A	A	G	rs41475144	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	171	22	156	0	0.128655	0	G|1.000;|0.000	1.000	weak	USP8,NS,carcinoma,0,3	USP8	90	3	NM_001128610	exon15	c.A2353G	p.T785A	GGAAATACTTGTT	.	PASS	Atlas-SNP
F5	2153	hgsc.bcm.edu	37	1	169510475	169510475	+	Missense_Mutation	SNP	G	G	T	rs1046712	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	262	130	260	0	0.496183	0	G|0.827;T|0.173	0.173	strong	.	F5	301	.	NM_000130	exon13	c.C3853A	p.L1285I	GAGAAAGGGTTGT	.	PASS	Atlas-SNP
GGTLC2	91227	hgsc.bcm.edu	37	22	22988864	22988864	+	Missense_Mutation	SNP	G	G	C	rs8192912		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	42	2	102	0	0.047619	0	.	.	weak	GGTLC2,NS,carcinoma,0,1	GGTLC2	20	1	NM_199127	exon1	c.G49C	p.D17H	TCTGACGACACCA	.	scavenged	Atlas-SNP
FAM160B1	57700	hgsc.bcm.edu	37	10	116615045	116615045	+	Silent	SNP	T	T	C	rs3180654	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	91	45	106	0	0.494505	0	C|0.312;T|0.688	0.312	strong	.	FAM160B1	107	.	NM_020940	exon14	c.T1893C	p.F631F	TTTCTTTGAAGGT	.	PASS	Atlas-SNP
LRIT1	26103	hgsc.bcm.edu	37	10	85992390	85992390	+	Missense_Mutation	SNP	G	G	T	rs12262099	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	91	48	126	0	0.527473	0	G|0.815;T|0.185	0.185	strong	.	LRIT1	73	.	NM_015613	exon4	c.C1165A	p.P389T	CAGCGGGTTTGGG	.	PASS	Atlas-SNP
IGLL5	100423062	hgsc.bcm.edu	37	22	23230428	23230428	+	Missense_Mutation	SNP	C	C	G	rs151173231	by1000genomes;alternate_allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	22	107	0	0.255814	0	C|1.000;T|0.000	.	alt	IGLL5,caecum,carcinoma,+1,1	IGLL5	26	1	NM_001178126	exon1	c.C195G	p.S65R	GCGGAGCCTGTGG	.	PASS	Atlas-SNP
GIGYF2	26058	hgsc.bcm.edu	37	2	233697708	233697708	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	77	29	68	0	0.376623	0	.	.	none	.	GIGYF2	288	.	NM_001103147	exon24	c.C2734T	p.R912W	GTCCAGCGGCAGA	.	PASS	Atlas-SNP
ANKMY1	51281	hgsc.bcm.edu	37	2	241463453	241463453	+	Missense_Mutation	SNP	C	C	A	rs3821348	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	80	42	104	0	0.525	0	C|0.846;A|0.147	0.147	strong	.	ANKMY1	112	.	NM_016552	exon7	c.G1414T	p.V472L	CACACACGTTGGA	.	PASS	Atlas-SNP
STK31	56164	hgsc.bcm.edu	37	7	23794029	23794029	+	Missense_Mutation	SNP	G	G	A	rs4722266	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	223	48	259	0	0.215247	0	G|0.817;A|0.183	0.183	strong	STK31,NS,carcinoma,+1,1	STK31	175	1	NM_031414	exon10	c.G1229A	p.G410E	TGAATGGATTAGA	.	PASS	Atlas-SNP
TXNDC11	51061	hgsc.bcm.edu	37	16	11773662	11773662	+	Missense_Mutation	SNP	C	C	G	rs3190321	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	94	92	96	0	0.978723	0	C|0.513;G|0.487	0.487	strong	.	TXNDC11	75	.	NM_015914	exon12	c.G2266C	p.V756L	TGGGGACGTCTTC	.	PASS	Atlas-SNP
DEF8	54849	hgsc.bcm.edu	37	16	90028509	90028509	+	Silent	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	107	74	78	0	0.691589	0	.	.	none	.	DEF8	28	.	NM_207514	exon9	c.C1080T	p.Y360Y	CAGCTACGTGGAG	.	PASS	Atlas-SNP
PARVA	55742	hgsc.bcm.edu	37	11	12540037	12540037	+	Silent	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	189	33	221	0	0.174603	0	.	.	none	.	PARVA	27	.	NM_018222	exon12	c.T1135C	p.L379L	GGAGGGTTGGAAA	.	PASS	Atlas-SNP
TDG	6996	hgsc.bcm.edu	37	12	104376608	104376608	+	Silent	SNP	G	G	A	rs61937629	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	343	20	335	2	0.058309	0.00597015	G|0.924;A|0.076	0.076	strong	TDG,NS,carcinoma,0,1	TDG	43	1	NM_003211	exon5	c.G510A	p.E170E	CAGTGAGGTCCAG	.	scavenged	Atlas-SNP
TMEM63B	55362	hgsc.bcm.edu	37	6	44117607	44117607	+	Silent	SNP	C	C	T	rs4714761	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	110	49	113	0	0.445455	0	C|0.921;T|0.079	0.079	strong	TMEM63B,NS,carcinoma,0,2	TMEM63B	77	2	NM_018426	exon16	c.C1425T	p.I475I	CATCATCACCCAG	.	PASS	Atlas-SNP
KIAA1217	56243	hgsc.bcm.edu	37	10	24813454	24813454	+	Missense_Mutation	SNP	G	G	A	rs10828663	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	77	40	74	0	0.519481	0	G|0.760;A|0.240	0.240	strong	KIAA1217,colon,carcinoma,0,2	KIAA1217	235	2	NM_019590	exon13	c.G2659A	p.A887T	CGCCACGCGCAGA	.	PASS	Atlas-SNP
PLIN4	729359	hgsc.bcm.edu	37	19	4512629	4512629	+	Missense_Mutation	SNP	C	C	T	rs146679364	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	18	138	0	0.211765	0	C|0.949;T|0.051	0.051	strong	PLIN4,NS,carcinoma,0,1	PLIN4	191	1	NM_001080400	exon3	c.G1301A	p.R434K	GTTCCTCTGGCCA	.	PASS	Atlas-SNP
GPRIN2	9721	hgsc.bcm.edu	37	10	47000217	47000217	+	Missense_Mutation	SNP	G	G	A	rs72780221	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	7	3	11	0	0.428571	0	G|0.901;A|0.099	0.099	strong	GPRIN2,NS,carcinoma,0,2	GPRIN2	94	2	NM_014696	exon3	c.G1337A	p.R446H	TGCGGCGCCCCAG	.	scavenged	Atlas-SNP
TRIM51	84767	hgsc.bcm.edu	37	11	55652963	55652963	+	Missense_Mutation	SNP	A	A	G	rs2063276	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	133	28	136	0	0.210526	0	A|0.360;G|0.640	0.640	strong	.	.	.	.	NM_032681	exon2	c.A59G	p.N20S	GCATGAACTACTT	.	PASS	Atlas-SNP
B4GALNT3	283358	hgsc.bcm.edu	37	12	670595	670595	+	Missense_Mutation	SNP	G	G	A	rs36078145	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	37	69	0	0.506849	0	G|0.958;A|0.042	0.042	strong	.	B4GALNT3	64	.	NM_173593	exon20	c.G2975A	p.R992H	GGAGCCGTCGCCA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195507494	195507494	+	Missense_Mutation	SNP	C	C	T	rs200217182	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	104	58	66	0	0.557692	0	.	.	weak	.	MUC4	1505	.	NM_018406	exon2	c.G10957A	p.D3653N	AAGCGTCGGTGAC	.	PASS	Atlas-SNP
WWP2	11060	hgsc.bcm.edu	37	16	69922079	69922079	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	127	51	95	0	0.401575	0	.	.	none	.	WWP2	88	.	NM_001270454	exon8	c.G841A	p.G281R	GCTGAAGGAGAGG	.	PASS	Atlas-SNP
DCAF15	90379	hgsc.bcm.edu	37	19	14065341	14065341	+	Silent	SNP	T	T	C	rs10409785	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	137	68	148	0	0.49635	0	T|0.817;C|0.183	0.183	strong	.	DCAF15	30	.	NM_138353	exon3	c.T234C	p.H78H	CAGACATATCTTC	.	PASS	Atlas-SNP
LILRB1	10859	hgsc.bcm.edu	37	19	55144208	55144208	+	Missense_Mutation	SNP	G	G	A	rs201552016	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	108	23	135	3	0.212963	0.0222222	G|0.936;A|0.064	0.064	strong	LILRB1,NS,carcinoma,0,1	LILRB1	140	1	NM_001081637	exon6	c.G955A	p.A319T	CTGATCGCAGGTG	.	scavenged	Atlas-SNP
KRT37	8688	hgsc.bcm.edu	37	17	39580310	39580310	+	Missense_Mutation	SNP	G	G	A	rs142829376		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	47	91	1	0.643836	0.010989	G|1.000;A|0.000	0.000	weak	KRT37,hand,carcinoma,0,1	KRT37	61	1	NM_003770	exon1	c.C466T	p.R156C	TTGTACGGAAGTA	.	scavenged	Atlas-SNP
C16orf46	123775	hgsc.bcm.edu	37	16	81095099	81095099	+	Silent	SNP	C	C	G	rs2287995	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	273	172	305	1	0.630037	0.00327869	C|0.916;G|0.084	0.084	strong	C16orf46_ENST00000378611,right_upper_lobe,carcinoma,-1,2	C16orf46	57	2	NM_001100873	exon3	c.G855C	p.A285A	CTGGGCCGCTGGG	.	PASS	Atlas-SNP
ADAMTSL3	57188	hgsc.bcm.edu	37	15	84651290	84651290	+	Silent	SNP	T	T	C	rs7176737	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	85	90	0	1	0	T|0.141;C|0.859	0.859	strong	.	ADAMTSL3	290	.	NM_207517	exon21	c.T2910C	p.H970H	AATCCATGGTCTT	.	PASS	Atlas-SNP
SEMA4B	10509	hgsc.bcm.edu	37	15	90771704	90771704	+	Silent	SNP	G	G	A	rs3751656	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	60	37	50	0	0.616667	0	G|0.746;A|0.254	0.254	strong	.	SEMA4B	51	.	NM_020210	exon15	c.G2343A	p.P781P	CACCCCGCTCGAT	.	PASS	Atlas-SNP
LAMA5	3911	hgsc.bcm.edu	37	20	60898654	60898654	+	Silent	SNP	G	G	A	rs11696243	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	47	58	0	0.484536	0	G|0.980;A|0.020	0.020	strong	.	LAMA5	268	.	NM_005560	exon45	c.C5922T	p.N1974N	GTCACCGTTGCCG	.	PASS	Atlas-SNP
AP4B1	10717	hgsc.bcm.edu	37	1	114438951	114438951	+	Missense_Mutation	SNP	A	A	G	rs1217401	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	123	123	161	0	1	0	A|0.589;G|0.411	0.411	strong	.	AP4B1	72	.	NM_006594	exon9	c.T1439C	p.L480S	CGCAGCAAAGCAG	.	PASS	Atlas-SNP
VPS16	64601	hgsc.bcm.edu	37	20	2840773	2840773	+	Silent	SNP	C	C	T	rs3818605	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	31	77	0	0.449275	0	C|0.867;T|0.133	0.133	strong	VPS16,NS,carcinoma,0,2	VPS16	76	2	NM_022575	exon3	c.C216T	p.S72S	TGCTTCCGGCATG	.	PASS	Atlas-SNP
C16orf46	123775	hgsc.bcm.edu	37	16	81094951	81094951	+	Missense_Mutation	SNP	A	A	G	rs10459872	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	263	153	262	0	0.581749	0	A|0.912;G|0.088	0.088	strong	.	C16orf46	57	.	NM_001100873	exon3	c.T1003C	p.Y335H	ATTTGTAGCTTTG	.	PASS	Atlas-SNP
VILL	50853	hgsc.bcm.edu	37	3	38047680	38047680	+	Silent	SNP	G	G	A	rs11707277	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	103	55	113	0	0.533981	0	G|0.881;A|0.119	0.119	strong	VILL,NS,carcinoma,+1,2	VILL	61	2	NM_015873	exon17	c.G2142A	p.P714P	CCACCCGTCCCAC	.	PASS	Atlas-SNP
OSBPL10	114884	hgsc.bcm.edu	37	3	31712393	31712393	+	Silent	SNP	C	C	T	rs3749405	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	137	74	170	0	0.540146	0	C|0.470;T|0.530	0.530	strong	OSBPL10_ENST00000396556,extremity,malignant_melanoma,-1,6	OSBPL10	160	6	NM_017784	exon9	c.G1809A	p.P603P	CACCCACGGGATG	.	PASS	Atlas-SNP
IRGC	56269	hgsc.bcm.edu	37	19	44223145	44223145	+	Silent	SNP	C	C	T	rs34439296	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	61	40	56	0	0.655738	0	C|0.927;T|0.073	0.073	strong	IRGC,NS,carcinoma,+1,1	IRGC	67	1	NM_019612	exon2	c.C435T	p.C145C	CCGCTGCGGGGCC	.	PASS	Atlas-SNP
PCDHB6	56130	hgsc.bcm.edu	37	5	140532165	140532165	+	Missense_Mutation	SNP	G	G	A	rs17844444	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	157	66	180	0	0.420382	0	G|0.864;A|0.136	0.136	strong	.	PCDHB6	161	.	NM_018939	exon1	c.G2327A	p.G776D	CTCAGGGCACTGA	.	PASS	Atlas-SNP
HSPA2	3306	hgsc.bcm.edu	37	14	65008004	65008004	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	2	101	0	0.0273973	0	.	.	none	HSPA2,NS,carcinoma,-1,1	HSPA2	83	1	NM_021979	exon1	c.C437T	p.T146M	TCATAACGGTCCC	.	scavenged	Atlas-SNP
FAM71C	196472	hgsc.bcm.edu	37	12	100042040	100042040	+	Missense_Mutation	SNP	C	C	G	rs11109968	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	122	67	141	0	0.54918	0	C|0.729;G|0.271	0.271	strong	.	FAM71C	48	.	NM_153364	exon1	c.C88G	p.R30G	CTGCAGCGGCAAC	.	PASS	Atlas-SNP
MYH4	4622	hgsc.bcm.edu	37	17	10355763	10355763	+	Missense_Mutation	SNP	T	T	C	rs917361	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	201	109	233	1	0.542289	0.00429185	C|0.466;N|0.000	0.466	strong	.	MYH4	349	.	NM_017533	exon26	c.A3318G	p.I1106M	TAGCTGTATTGCA	.	PASS	Atlas-SNP
GAR1	54433	hgsc.bcm.edu	37	4	110739212	110739212	+	Missense_Mutation	SNP	A	A	G	rs143266987	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	60	30	81	0	0.5	0	A|1.000;G|0.000	0.000	weak	.	GAR1	16	.	NM_018983	exon3	c.A335G	p.K112R	TTGGAAAAGTGGA	.	PASS	Atlas-SNP
KIAA1755	85449	hgsc.bcm.edu	37	20	36859711	36859711	+	Silent	SNP	G	G	A	rs1205418	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	36	14	42	0	0.388889	0	G|0.703;A|0.297	0.297	strong	.	KIAA1755	145	.	NM_001029864	exon5	c.C1764T	p.A588A	CCGCCCGGCCCTG	.	PASS	Atlas-SNP
TRIM38	10475	hgsc.bcm.edu	37	6	25983777	25983777	+	Silent	SNP	C	C	T	rs17528178	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	108	51	110	0	0.472222	0	C|0.942;G|0.000;T|0.058	0.058	strong	.	TRIM38	50	.	NM_006355	exon8	c.C1260T	p.A420A	TGAGGCCGGAGTT	.	PASS	Atlas-SNP
SEMA7A	8482	hgsc.bcm.edu	37	15	74703929	74703929	+	Silent	SNP	T	T	C	rs741761	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	68	47	71	0	0.691176	0	T|0.582;C|0.418	0.418	strong	.	SEMA7A	58	.	NM_003612	exon12	c.A1545G	p.Q515Q	GCGGCCTTGGTCC	.	PASS	Atlas-SNP
DIDO1	11083	hgsc.bcm.edu	37	20	61542863	61542863	+	Silent	SNP	G	G	A	rs11907248	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	146	65	159	0	0.445205	0	G|0.924;A|0.076	0.076	strong	.	DIDO1	321	.	NM_080797	exon3	c.C102T	p.I34I	CTTGGCGATAGTG	.	PASS	Atlas-SNP
ACAN	176	hgsc.bcm.edu	37	15	89398631	89398631	+	Missense_Mutation	SNP	T	T	A	rs938609	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	90	89	113	0	0.988889	0	T|0.540;A|0.460	0.460	strong	ACAN,NS,carcinoma,0,1	ACAN	220	1	NM_001135	exon12	c.T2815A	p.S939T	CTGCCCTCTGGAG	.	PASS	Atlas-SNP
EXOC6B	23233	hgsc.bcm.edu	37	2	72707874	72707874	+	Silent	SNP	A	A	G	rs653220	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	53	40	76	0	0.754717	0	A|0.639;G|0.361	0.361	strong	.	EXOC6B	93	.	NM_015189	exon17	c.T1671C	p.V557V	AATCTGAACAAGC	.	PASS	Atlas-SNP
KIAA1984	84960	hgsc.bcm.edu	37	9	139700605	139700605	+	Missense_Mutation	SNP	T	T	C	rs2811795	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	77	35	102	0	0.454545	0	T|0.130;C|0.870	0.870	strong	.	KIAA1984	39	.	NM_001039374	exon10	c.T1024C	p.W342R	GAGGAGTGGCGGG	.	PASS	Atlas-SNP
ZNF845	91664	hgsc.bcm.edu	37	19	53856349	53856349	+	Missense_Mutation	SNP	A	A	T	rs55874600	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	81	39	92	0	0.481481	0	A|0.782;T|0.218	0.218	strong	.	ZNF845	101	.	NM_138374	exon4	c.A2421T	p.E807D	TAATGAATGTGGC	.	PASS	Atlas-SNP
RYR3	6263	hgsc.bcm.edu	37	15	33954552	33954552	+	Silent	SNP	T	T	C	rs200740143	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	122	56	91	0	0.459016	0	T|0.999;C|0.001	0.001	strong	.	RYR3	760	.	NM_001243996	exon35	c.T4821C	p.Y1607Y	TTTCTATGACCTG	.	PASS	Atlas-SNP
ALPK3	57538	hgsc.bcm.edu	37	15	85405995	85405995	+	Missense_Mutation	SNP	T	T	C	rs187316	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	148	93	133	0	0.628378	0	T|0.815;C|0.185	0.185	strong	.	ALPK3	289	.	NM_020778	exon10	c.T4865C	p.L1622P	GTGGCCTTCGGAA	.	PASS	Atlas-SNP
BTN3A2	11118	hgsc.bcm.edu	37	6	26370616	26370616	+	Missense_Mutation	SNP	G	G	C	rs9379861	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	46	116	0	0.474227	0	G|0.985;C|0.015	0.015	strong	.	BTN3A2	44	.	NM_001197246	exon3	c.G500C	p.R167T	AGTGCAGGTCCAC	.	PASS	Atlas-SNP
SMARCC1	6599	hgsc.bcm.edu	37	3	47712202	47712202	+	Silent	SNP	T	T	C	rs1141601	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	232	119	291	0	0.512931	0	T|0.639;G|0.036	.	strong	.	SMARCC1	85	.	NM_003074	exon19	c.A1845G	p.K615K	AGCACCTTTACTC	.	PASS	Atlas-SNP
SSR3	6747	hgsc.bcm.edu	37	3	156266774	156266774	+	Silent	SNP	C	C	T	rs9296	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	65	31	87	0	0.476923	0	C|0.865;T|0.135	0.135	strong	.	SSR3	17	.	NM_007107	exon3	c.G279A	p.E93E	AGCATCCTCCCTC	.	PASS	Atlas-SNP
BPIFB4	149954	hgsc.bcm.edu	37	20	31671209	31671209	+	Missense_Mutation	SNP	G	G	C	rs13036385	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	99	47	110	0	0.474747	0	G|0.777;C|0.223	0.223	strong	.	.	.	.	NM_182519	exon3	c.G206C	p.R69P	ATGTCCGAGGACC	.	PASS	Atlas-SNP
CLEC2D	29121	hgsc.bcm.edu	37	12	9822387	9822387	+	Missense_Mutation	SNP	C	C	G	rs16914640	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	115	56	106	0	0.486957	0	C|0.764;G|0.236	0.236	strong	CLEC2D_ENST00000290855,NS,carcinoma,0,5	CLEC2D	54	5	NM_001197319	exon1	c.C57G	p.N19K	TGCAAACCCAGGT	.	PASS	Atlas-SNP
AQP11	282679	hgsc.bcm.edu	37	11	77301341	77301341	+	Missense_Mutation	SNP	G	G	A	rs2276415	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	103	79	114	0	0.76699	0	G|0.873;A|0.127	0.127	strong	.	AQP11	14	.	NM_173039	exon1	c.G304A	p.G102S	CCGTGCGGCGTGA	.	PASS	Atlas-SNP
NSFL1C	55968	hgsc.bcm.edu	37	20	1426393	1426393	+	Missense_Mutation	SNP	C	C	T	rs9575	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	138	59	195	0	0.427536	0	C|0.589;T|0.411	0.411	strong	NSFL1C,colon,carcinoma,+2,2	NSFL1C	38	2	NM_016143	exon8	c.G868A	p.D290N	ATTCGTCGATTAA	.	PASS	Atlas-SNP
CCDC89	220388	hgsc.bcm.edu	37	11	85396746	85396746	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	102	85	119	0	0.833333	0	.	.	none	.	CCDC89	45	.	NM_152723	exon1	c.A428G	p.Y143C	CTCTTGTATTCAT	.	PASS	Atlas-SNP
GALR1	2587	hgsc.bcm.edu	37	18	74980601	74980601	+	Missense_Mutation	SNP	A	A	T	rs77169818	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	43	31	86	0	0.72093	0	A|0.965;T|0.035	0.035	strong	.	GALR1	53	.	NM_001480	exon3	c.A793T	p.I265F	CACCACATCATCC	.	PASS	Atlas-SNP
ZNF443	10224	hgsc.bcm.edu	37	19	12541547	12541547	+	Missense_Mutation	SNP	T	T	G	rs10402252	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	64	34	46	0	0.53125	0	T|0.615;G|0.385	0.385	strong	.	ZNF443	63	.	NM_005815	exon4	c.A1439C	p.K480T	CCAAGTTTGCATT	.	PASS	Atlas-SNP
KIAA0368	23392	hgsc.bcm.edu	37	9	114146832	114146832	+	Silent	SNP	C	C	T	rs16916040	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	107	50	122	0	0.46729	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
AKAP3	10566	hgsc.bcm.edu	37	12	4735969	4735969	+	Missense_Mutation	SNP	G	G	A	rs2041291	bycluster;byfrequency;byhapmap	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	23	103	0	0.280488	0	G|0.936;A|0.064	0.064	strong	.	AKAP3	212	.	NM_006422	exon4	c.C2099T	p.S700F	TCTCCAGACTTGT	.	PASS	Atlas-SNP
C10orf128	170371	hgsc.bcm.edu	37	10	50374930	50374930	+	Silent	SNP	C	C	T	rs45563932	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	35	40	0	0.603448	0	C|0.865;T|0.135	0.135	strong	.	C10orf128	20	.	NM_001010863	exon3	c.G222A	p.T74T	CCCAGGCGTGCTT	.	PASS	Atlas-SNP
INPP5F	22876	hgsc.bcm.edu	37	10	121586827	121586827	+	Silent	SNP	A	A	G	rs56055506	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	65	28	89	0	0.430769	0	A|0.835;G|0.165	0.165	strong	INPP5F,NS,carcinoma,0,1	INPP5F	112	1	NM_014937	exon20	c.A2934G	p.R978R	GACCAGATCTGTG	.	PASS	Atlas-SNP
H2AFY	9555	hgsc.bcm.edu	37	5	134670756	134670756	+	Silent	SNP	G	G	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	236	70	250	0	0.29661	0	.	.	none	.	H2AFY	61	.	NM_138610	exon9	c.C1029G	p.S343S	GGAAGAGGACATT	.	PASS	Atlas-SNP
SPATA5L1	79029	hgsc.bcm.edu	37	15	45695695	45695695	+	Silent	SNP	G	G	A	rs1153849	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	37	49	0	0.637931	0	G|0.415;A|0.585	0.585	strong	.	SPATA5L1	40	.	NM_024063	exon1	c.G1068A	p.R356R	GCGTAGGCCCGGG	.	PASS	Atlas-SNP
DUSP5	1847	hgsc.bcm.edu	37	10	112266771	112266771	+	Silent	SNP	C	C	T	rs1889567	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	141	67	157	0	0.475177	0	C|0.692;T|0.308	0.308	strong	DUSP5_ENST00000369583,NS,carcinoma,0,1	DUSP5	62	1	NM_004419	exon3	c.C607T	p.L203L	GCCAACCTGCACA	.	PASS	Atlas-SNP
FLVCR2	55640	hgsc.bcm.edu	37	14	76045691	76045691	+	Silent	SNP	C	C	T	rs8011292	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	144	82	198	0	0.569444	0	C|0.824;T|0.176	0.176	strong	.	FLVCR2	39	.	NM_017791	exon1	c.C376T	p.L126L	GACTGGCTGTCCA	.	PASS	Atlas-SNP
WDR52	55779	hgsc.bcm.edu	37	3	113146131	113146131	+	Silent	SNP	G	G	A	rs58474121	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	221	117	245	0	0.529412	0	G|0.969;A|0.031	0.031	strong	.	WDR52	151	.	NM_001164496	exon3	c.C156T	p.T52T	CCCTTTGGTAAAT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195513493	195513493	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	243	16	175	0	0.0658436	0	.	.	none	MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	NM_018406	exon2	c.G4958T	p.S1653I	GAAGGGCTGGTGA	.	scavenged	Atlas-SNP
CTSC	1075	hgsc.bcm.edu	37	11	88027209	88027209	+	Missense_Mutation	SNP	T	T	C	rs3888798	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	96	25	82	0	0.260417	0	T|0.939;C|0.061	0.061	strong	.	CTSC	46	.	NM_001814	exon7	c.A1357G	p.I453V	CTGCTATGCTCTC	.	PASS	Atlas-SNP
PCM1	5108	hgsc.bcm.edu	37	8	17820714	17820714	+	Silent	SNP	A	A	T	rs6991775	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	154	33	175	0	0.214286	0	A|0.770;T|0.230	0.230	strong	.	PCM1	120	.	NM_006197	exon17	c.A2568T	p.L856L	AGGTCTAGCTGAA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195507193	195507193	+	Missense_Mutation	SNP	G	G	A	rs201474621	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	24	59	2	0.347826	0.0338983	G|0.993;T|0.007	.	strong	MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	NM_018406	exon2	c.C11258T	p.A3753V	GTGGATGCTGAGG	.	scavenged	Atlas-SNP
ZNF578	147660	hgsc.bcm.edu	37	19	53014787	53014787	+	Missense_Mutation	SNP	A	A	G	rs35356792	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	42	22	43	0	0.52381	0	A|0.938;G|0.062	0.062	strong	.	.	.	.	NM_001099694	exon6	c.A1153G	p.T385A	AATTCAACCCTTG	.	PASS	Atlas-SNP
HMCN1	83872	hgsc.bcm.edu	37	1	186121995	186121995	+	Missense_Mutation	SNP	A	A	T	rs114364265	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	170	87	215	0	0.511765	0	A|0.996;T|0.004	0.004	strong	.	HMCN1	797	.	NM_031935	exon96	c.A15010T	p.T5004S	GAAGTCACTGTAA	.	PASS	Atlas-SNP
ESPN	83715	hgsc.bcm.edu	37	1	6500712	6500712	+	Silent	SNP	C	C	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	12	10	9	0	0.833333	0	.	.	none	.	ESPN	32	.	NM_031475	exon4	c.C702G	p.S234S	CCTGTCCGAGCAG	.	PASS	Atlas-SNP
CCDC176	80127	hgsc.bcm.edu	37	14	74514674	74514674	+	Missense_Mutation	SNP	A	A	T	rs3784038	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	159	159	171	0	1	0	A|0.410;T|0.590	0.590	strong	.	.	.	.	NM_025057	exon7	c.A689T	p.D230V	AGAATGATTATCT	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228476366	228476366	+	Missense_Mutation	SNP	G	G	T	rs3795789	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	56	29	66	0	0.517857	0	G|0.927;T|0.073	0.073	strong	.	OBSCN	2142	.	NM_001271223	exon43	c.G11403T	p.E3801D	CCAAGAGAGCATA	.	PASS	Atlas-SNP
KRTAP12-2	353323	hgsc.bcm.edu	37	21	46086407	46086407	+	Missense_Mutation	SNP	C	C	T	rs12481809	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	324	137	237	0	0.422839	0	C|0.844;T|0.156	0.156	strong	.	KRTAP12-2	10	.	NM_181684	exon1	c.G397A	p.V133I	AGAGGACGCTGGT	.	PASS	Atlas-SNP
ATP10A	57194	hgsc.bcm.edu	37	15	25925094	25925094	+	Missense_Mutation	SNP	C	C	G	rs3816800	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	17	11	22	0	0.647059	0	C|0.531;G|0.469	0.469	strong	.	ATP10A	270	.	NM_024490	exon21	c.G3894C	p.R1298S	GAAAACCCTCCCC	.	PASS	Atlas-SNP
MFSD4	148808	hgsc.bcm.edu	37	1	205554085	205554085	+	Missense_Mutation	SNP	G	G	C	rs7526132	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	93	44	123	0	0.473118	0	G|0.514;C|0.486	0.486	strong	.	MFSD4	46	.	NM_181644	exon5	c.G941C	p.G314A	TCACGGGCGCCCT	.	PASS	Atlas-SNP
HERPUD1	9709	hgsc.bcm.edu	37	16	56969148	56969148	+	Missense_Mutation	SNP	G	G	A	rs2217332	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	169	105	140	2	0.621302	0.0142857	G|0.870;A|0.130	0.130	strong	HERPUD1,NS,carcinoma,0,1	HERPUD1	28	1	NM_014685	exon2	c.G149A	p.R50H	ATCAGCGTCCAGA	.	scavenged	Atlas-SNP
PIGG	54872	hgsc.bcm.edu	37	4	517622	517622	+	Silent	SNP	C	C	T	rs13150531	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	59	126	0	0.584158	0	C|0.779;T|0.221	0.221	strong	.	PIGG	86	.	NM_001127178	exon9	c.C1989T	p.A663A	ACTGGCCTGCTGC	.	PASS	Atlas-SNP
CADM2	253559	hgsc.bcm.edu	37	3	85935455	85935455	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	124	31	188	0	0.25	0	.	.	none	.	CADM2	195	.	NM_001167675	exon5	c.C507A	p.F169L	ATGGTTCAAAAAT	.	PASS	Atlas-SNP
NLRP8	126205	hgsc.bcm.edu	37	19	56467375	56467375	+	Missense_Mutation	SNP	C	C	T	rs41481648	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	156	72	170	0	0.461538	0	C|0.909;T|0.091	0.091	strong	.	NLRP8	225	.	NM_176811	exon3	c.C1951T	p.R651W	CTGAAGCGGTGTC	.	PASS	Atlas-SNP
UBXN6	80700	hgsc.bcm.edu	37	19	4454083	4454083	+	Missense_Mutation	SNP	C	C	T	rs1127888	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	38	14	49	0	0.368421	0	T|0.211;G|0.000;C|0.788	0.211	strong	.	UBXN6	27	.	NM_025241	exon2	c.G91A	p.A31T	TGTGGGCCTTTTC	.	PASS	Atlas-SNP
SRFBP1	153443	hgsc.bcm.edu	37	5	121356189	121356189	+	Missense_Mutation	SNP	T	T	A	rs61734326	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	124	71	139	0	0.572581	0	T|0.938;A|0.062	0.062	strong	.	SRFBP1	47	.	NM_152546	exon6	c.T759A	p.F253L	AGAATTTTGTGAA	.	PASS	Atlas-SNP
PBRM1	55193	hgsc.bcm.edu	37	3	52610651	52610651	+	Silent	SNP	T	T	A	rs17264436	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	72	84	0	1	0	T|0.652;A|0.348	0.348	strong	.	PBRM1	1252	.	NM_018313	exon23	c.A3522T	p.P1174P	TTCTTCTGGGTGA	.	PASS	Atlas-SNP
SREBF2	6721	hgsc.bcm.edu	37	22	42290890	42290890	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	21	60	0	0.287671	0	.	.	none	.	SREBF2	99	.	NM_004599	exon13	c.T2444C	p.L815S	AGTCCTTGGTGAA	.	PASS	Atlas-SNP
LAMB2	3913	hgsc.bcm.edu	37	3	49161660	49161660	+	Silent	SNP	T	T	C	rs34290943	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	142	60	135	0	0.422535	0	T|0.914;C|0.086	0.086	strong	.	LAMB2	156	.	NM_002292	exon23	c.A3387G	p.Q1129Q	GAGCTCTTGGCAC	.	PASS	Atlas-SNP
IRF8	3394	hgsc.bcm.edu	37	16	85942659	85942659	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	107	24	87	0	0.224299	0	.	.	none	IRF8,NS,neuroblastoma,-1,1	IRF8	65	1	NM_002163	exon3	c.A238G	p.T80A	TGGAAGACGAGGT	.	PASS	Atlas-SNP
KCNAB2	8514	hgsc.bcm.edu	37	1	6142308	6142308	+	Silent	SNP	T	T	C	rs2227911	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	24	102	0	0.347826	0	T|0.887;C|0.113	0.113	strong	KCNAB2,colon,carcinoma,+2,2	KCNAB2	23	2	NM_001199862	exon5	c.T354C	p.D118D	CTTCGATACAGCA	.	PASS	Atlas-SNP
SLC35F1	222553	hgsc.bcm.edu	37	6	118556737	118556737	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	177	3	185	0	0.0169492	0	.	.	none	SLC35F1,NS,carcinoma,0,1	SLC35F1	65	1	NM_001029858	exon3	c.G415A	p.D139N	CTCATAGACCTGG	.	scavenged	Atlas-SNP
LRRC15	131578	hgsc.bcm.edu	37	3	194080174	194080174	+	Silent	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	142	45	133	0	0.316901	0	.	.	none	.	LRRC15	137	.	NM_001135057	exon3	c.C1617T	p.T539T	GGCCTGGGTCATG	.	PASS	Atlas-SNP
OR10H2	26538	hgsc.bcm.edu	37	19	15839168	15839168	+	Silent	SNP	C	C	T	rs76355860		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	193	67	181	0	0.34715	0	T|1.000;|0.000	1.000	weak	.	OR10H2	59	.	NM_013939	exon1	c.C315T	p.F105F	CTCCTTCAGCTTC	.	PASS	Atlas-SNP
BPIFB1	92747	hgsc.bcm.edu	37	20	31876681	31876681	+	Missense_Mutation	SNP	A	A	G	rs1078761	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	53	29	65	0	0.54717	0	A|0.657;G|0.343	0.343	strong	C20orf114,NS,carcinoma,0,1	.	.	1	NM_033197	exon3	c.A250G	p.I84V	AAGCACATCATCT	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	107	21	157	0	0.196262	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
GJB7	375519	hgsc.bcm.edu	37	6	87994504	87994504	+	Missense_Mutation	SNP	C	C	T	rs35259282	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	160	79	216	0	0.49375	0	C|0.939;T|0.061	0.061	strong	.	GJB7	28	.	NM_198568	exon3	c.G127A	p.V43M	TCCACACGTGCTC	.	PASS	Atlas-SNP
PPM1A	5494	hgsc.bcm.edu	37	14	60749878	60749878	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	199	2	178	0	0.0100503	0	.	.	none	PPM1A_ENST00000325642,NS,carcinoma,0,2	PPM1A	72	2	NM_177952	exon2	c.A676G	p.R226G	CTTTGTAGGAACA	.	scavenged	Atlas-SNP
TLN2	83660	hgsc.bcm.edu	37	15	63047793	63047793	+	Silent	SNP	C	C	T	rs4775538	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	65	108	0	0.643564	0	C|0.774;T|0.226	0.226	strong	.	TLN2	253	.	NM_015059	exon34	c.C4539T	p.I1513I	CCGCATCGCCTCA	.	PASS	Atlas-SNP
SLC25A39	51629	hgsc.bcm.edu	37	17	42398802	42398802	+	Silent	SNP	G	G	A	rs34365655	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	27	73	0	0.465517	0	G|0.948;A|0.052	0.052	strong	.	SLC25A39	24	.	NM_001143780	exon7	c.C517T	p.L173L	GCTCACGGCGGGC	.	PASS	Atlas-SNP
KRTAP12-2	353323	hgsc.bcm.edu	37	21	46086718	46086718	+	Missense_Mutation	SNP	G	G	C	rs7276859	bycluster;by2hit2allele;alternate_allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	106	60	89	0	0.566038	0	.	.	alt	.	KRTAP12-2	10	.	NM_181684	exon1	c.C86G	p.S29C	TGGCAGGAGCTGG	.	PASS	Atlas-SNP
MAST4	375449	hgsc.bcm.edu	37	5	66462325	66462325	+	Missense_Mutation	SNP	T	T	A	rs3188121	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	196	55	140	0	0.280612	0	T|0.983;A|0.017	0.017	strong	.	MAST4	218	.	NM_001164664	exon29	c.T7318A	p.S2440T	AAACGGTCCCCCT	.	PASS	Atlas-SNP
ETV1	2115	hgsc.bcm.edu	37	7	13978809	13978809	+	Missense_Mutation	SNP	T	T	C	rs9639168	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	73	102	0	1	0	C|0.302;N|0.000	0.302	strong	ETV1_ENST00000403527,NS,meningioma,0,2	ETV1	138	2	NM_004956	exon7	c.A298G	p.S100G	CAGAGCTGATTTC	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228564884	228564884	+	Missense_Mutation	SNP	G	G	A	rs56174824	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	31	17	34	0	0.548387	0	G|0.852;A|0.148	0.148	strong	.	OBSCN	2142	.	NM_001271223	exon112	c.G26042A	p.R8681H	GCCTGCGCCACCC	.	PASS	Atlas-SNP
NMB	4828	hgsc.bcm.edu	37	15	85200520	85200520	+	Missense_Mutation	SNP	G	G	T	rs1051168	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	128	78	102	0	0.609375	0	G|0.833;T|0.167	0.167	strong	.	NMB	14	.	NM_205858	exon2	c.C217A	p.P73T	TGTGGGGAGCTGT	.	PASS	Atlas-SNP
RNASEH1	246243	hgsc.bcm.edu	37	2	3597974	3597974	+	Silent	SNP	T	T	C	rs10186193	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	52	18	39	0	0.346154	0	T|0.579;C|0.421	0.421	strong	.	RNASEH1	27	.	NM_002936	exon4	c.A498G	p.P166P	ATGGCCTGGCCCC	.	PASS	Atlas-SNP
KRT84	3890	hgsc.bcm.edu	37	12	52777466	52777466	+	Silent	SNP	C	C	A	rs138204915	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	129	69	144	0	0.534884	0	C|0.998;A|0.002	0.002	strong	.	KRT84	61	.	NM_033045	exon2	c.G663T	p.L221L	CCTCCGCAGGTTG	.	PASS	Atlas-SNP
FER	2241	hgsc.bcm.edu	37	5	108294979	108294979	+	Silent	SNP	T	T	C	rs34869483	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	108	64	138	0	0.592593	0	T|0.988;C|0.012	0.012	strong	.	FER	100	.	NM_005246	exon13	c.T1587C	p.D529D	TATAGATCATCAC	.	PASS	Atlas-SNP
LYPD4	147719	hgsc.bcm.edu	37	19	42342319	42342319	+	Silent	SNP	A	A	G	rs2290695	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	29	29	29	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
TRIML1	339976	hgsc.bcm.edu	37	4	189061106	189061106	+	Missense_Mutation	SNP	G	G	A	rs13131525	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	294	159	263	0	0.540816	0	G|0.670;A|0.330	0.330	strong	.	TRIML1	126	.	NM_178556	exon1	c.G394A	p.E132K	GAGGCTGAGGAGC	.	PASS	Atlas-SNP
AKR1B15	441282	hgsc.bcm.edu	37	7	134264286	134264286	+	Silent	SNP	C	C	T	rs6467538	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	90	45	120	0	0.5	0	C|0.651;T|0.349	0.349	strong	.	AKR1B15	105	.	NM_001080538	exon12	c.C1020T	p.F340F	TCCCTTCGATGCA	.	PASS	Atlas-SNP
FUT10	84750	hgsc.bcm.edu	37	8	33246591	33246591	+	Missense_Mutation	SNP	G	G	C	rs17855838	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	332	330	479	1	0.993976	0.00208768	G|0.815;C|0.185	0.185	strong	FUT10,NS,carcinoma,0,1	FUT10	62	1	NM_032664	exon4	c.C1102G	p.L368V	CCCTGAGAGCTGT	.	PASS	Atlas-SNP
CTU2	348180	hgsc.bcm.edu	37	16	88781125	88781125	+	Silent	SNP	T	T	C	rs8043637	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	69	102	0	0.985714	0	T|0.117;C|0.883	0.883	strong	.	CTU2	66	.	NM_001012759	exon12	c.T1332C	p.C444C	GCGCTGTGGCCAG	.	PASS	Atlas-SNP
ALPK2	115701	hgsc.bcm.edu	37	18	56202394	56202394	+	Silent	SNP	C	C	T	rs7240355	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	44	28	73	0	0.636364	0	C|0.906;T|0.094	0.094	strong	.	ALPK2	487	.	NM_052947	exon5	c.G5025A	p.K1675K	GGTGCCCTTTTGA	.	PASS	Atlas-SNP
ZFP64	55734	hgsc.bcm.edu	37	20	50769183	50769183	+	Silent	SNP	G	G	A	rs3746415	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	20	13	33	0	0.65	0	G|0.839;A|0.161	0.161	strong	.	ZFP64	240	.	NM_018197	exon6	c.C1548T	p.A516A	TGCAGCGGCGGCA	.	PASS	Atlas-SNP
CYP4B1	1580	hgsc.bcm.edu	37	1	47280884	47280884	+	Missense_Mutation	SNP	C	C	T	rs4646491	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	121	56	134	0	0.46281	0	C|0.863;T|0.137	0.137	strong	.	CYP4B1	81	.	NM_001099772	exon8	c.C1021T	p.R341C	CAGCATCGTTGTA	.	PASS	Atlas-SNP
MLX	6945	hgsc.bcm.edu	37	17	40722029	40722029	+	Missense_Mutation	SNP	A	A	G	rs665268	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	108	54	141	0	0.5	0	A|0.732;G|0.268	0.268	strong	.	MLX	17	.	NM_170607	exon7	c.A668G	p.Q223R	CACACCAGGACAA	.	PASS	Atlas-SNP
DSPP	1834	hgsc.bcm.edu	37	4	88537258	88537258	+	Silent	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	91	30	99	0	0.32967	0	.	.	none	DSPP,NS,carcinoma,0,2	DSPP	174	2	NM_014208	exon5	c.T3444C	p.S1148S	CAGCAGTGAAAGC	.	PASS	Atlas-SNP
CMYA5	202333	hgsc.bcm.edu	37	5	79027030	79027030	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	100	20	139	0	0.2	0	.	.	none	.	CMYA5	643	.	NM_153610	exon2	c.A2442T	p.K814N	AAAGAAAATAATC	.	PASS	Atlas-SNP
SAMD8	142891	hgsc.bcm.edu	37	10	76910705	76910705	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	88	20	115	0	0.227273	0	.	.	none	.	SAMD8	57	.	NM_144660	exon2	c.A419T	p.H140L	ACAAACATTCTGT	.	PASS	Atlas-SNP
TGFBR3	7049	hgsc.bcm.edu	37	1	92177938	92177938	+	Silent	SNP	A	A	G	rs1805113	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	105	105	150	1	1	0.00666667	A|0.655;G|0.345	0.345	strong	.	TGFBR3	103	.	NM_003243	exon13	c.T2028C	p.F676F	GATAGGAAAGTGC	.	PASS	Atlas-SNP
HIST1H4H	8365	hgsc.bcm.edu	37	6	26285503	26285503	+	Silent	SNP	C	C	T	rs41266829	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	95	41	143	1	0.431579	0.00699301	C|0.869;T|0.131	0.131	strong	HIST1H4H,colon,carcinoma,0,1	HIST1H4H	16	1	NM_003543	exon1	c.G225A	p.E75E	GGCGTGCTCTGTG	.	scavenged	Atlas-SNP
LRRC16B	90668	hgsc.bcm.edu	37	14	24529209	24529209	+	Silent	SNP	C	C	T	rs61564890	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	80	79	91	0	0.9875	0	C|0.908;T|0.092	0.092	strong	.	LRRC16B	120	.	NM_138360	exon23	c.C1899T	p.P633P	CTTCCCCGTGAGC	.	PASS	Atlas-SNP
TRIML2	205860	hgsc.bcm.edu	37	4	189020293	189020293	+	Silent	SNP	G	G	A	rs11736108	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	50	88	0	0.49505	0	G|0.966;A|0.034	0.034	strong	.	TRIML2	80	.	NM_173553	exon4	c.C367T	p.L123L	CCTTCAGTTTCTC	.	PASS	Atlas-SNP
OR6S1	341799	hgsc.bcm.edu	37	14	21109385	21109385	+	Missense_Mutation	SNP	C	C	T	rs11622969	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	38	118	0	0.506667	0	C|0.498;T|0.502	0.502	strong	.	OR6S1	49	.	NM_001001968	exon1	c.G466A	p.V156I	CAGGGACGAGTCC	.	PASS	Atlas-SNP
CCDC88C	440193	hgsc.bcm.edu	37	14	91792320	91792320	+	Silent	SNP	G	G	A	rs17127245	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	46	107	0	0.474227	0	G|0.922;A|0.078	0.078	strong	.	CCDC88C	192	.	NM_001080414	exon11	c.C1131T	p.G377G	TTTATCGCCCCGG	.	PASS	Atlas-SNP
SETD7	80854	hgsc.bcm.edu	37	4	140450204	140450204	+	Silent	SNP	G	G	A	rs35062373	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	164	77	207	0	0.469512	0	G|0.974;A|0.026	0.026	strong	.	SETD7	35	.	NM_030648	exon4	c.C543T	p.H181H	TTCAAAGTGAGGC	.	PASS	Atlas-SNP
ANKLE1	126549	hgsc.bcm.edu	37	19	17397244	17397244	+	Silent	SNP	C	C	T	rs10425939	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	111	52	141	0	0.468468	0	C|0.850;T|0.150	0.150	strong	.	ANKLE1	27	.	NM_152363	exon9	c.C1731T	p.G577G	GGCAGGCTGGCCA	.	PASS	Atlas-SNP
RXFP2	122042	hgsc.bcm.edu	37	13	32360547	32360547	+	Silent	SNP	A	A	G	rs7325513	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	147	69	190	0	0.469388	0	A|0.387;G|0.613	0.613	strong	.	RXFP2	95	.	NM_130806	exon12	c.A957G	p.E319E	AACGGAACTATCA	.	PASS	Atlas-SNP
TUT1	64852	hgsc.bcm.edu	37	11	62343141	62343141	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	133	111	152	0	0.834586	0	.	.	none	.	TUT1	122	.	NM_022830	exon9	c.G2164A	p.G722S	CCCCACCGTCCCC	.	PASS	Atlas-SNP
ANPEP	290	hgsc.bcm.edu	37	15	90349558	90349558	+	Missense_Mutation	SNP	C	C	T	rs25653	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	201	127	225	0	0.631841	0	C|0.373;T|0.627	0.627	strong	.	ANPEP	124	.	NM_001150	exon2	c.G257A	p.R86Q	GTCACCCGGTAGG	.	PASS	Atlas-SNP
TTC28	23331	hgsc.bcm.edu	37	22	28504183	28504183	+	Silent	SNP	G	G	A	rs9625408	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	117	57	113	0	0.487179	0	G|0.949;A|0.051	0.051	strong	.	TTC28	84	.	NM_001145418	exon7	c.C1650T	p.R550R	TGAGGCGCGGTCA	.	PASS	Atlas-SNP
KRTAP10-2	386679	hgsc.bcm.edu	37	21	45971152	45971152	+	Missense_Mutation	SNP	G	G	A	rs199607801	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	142	41	55	0	0.288732	0	G|0.978;A|0.022	0.022	strong	KRTAP10-2,colon,carcinoma,0,1	KRTAP10-2	21	1	NM_198693	exon1	c.C190T	p.P64S	CGCTGGGCTCACA	.	scavenged	Atlas-SNP
ANKRD30A	91074	hgsc.bcm.edu	37	10	37442545	37442545	+	Missense_Mutation	SNP	G	G	T	rs200557667	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	714	132	779	0	0.184874	0	G|0.999;T|0.001	0.001	weak	ANKRD30A,NS,carcinoma,0,1	ANKRD30A	448	1	NM_052997	exon13	c.G1585T	p.A529S	CCCAAGGCTACAC	.	scavenged	Atlas-SNP
CCP110	9738	hgsc.bcm.edu	37	16	19548116	19548116	+	Missense_Mutation	SNP	G	G	A	rs7190666	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	306	121	284	0	0.395425	0	G|0.843;A|0.157	0.157	strong	.	CCP110	57	.	NM_001199022	exon4	c.G1125A	p.M375I	TAAAATGCACCGA	.	PASS	Atlas-SNP
TEKT5	146279	hgsc.bcm.edu	37	16	10788624	10788624	+	Missense_Mutation	SNP	T	T	C	rs145995713	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	56	73	0	0.811594	0	T|0.994;C|0.006	0.006	strong	.	TEKT5	66	.	NM_144674	exon1	c.A107G	p.Y36C	GGCTGATAGCATT	.	PASS	Atlas-SNP
SERPINA5	5104	hgsc.bcm.edu	37	14	95053849	95053849	+	Silent	SNP	T	T	C	rs6113	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	50	21	91	0	0.42	0	C|0.249;N|0.000	0.249	strong	.	SERPINA5	69	.	NM_000624	exon3	c.T150C	p.F50F	TACCTTTGACCTC	.	PASS	Atlas-SNP
KIF27	55582	hgsc.bcm.edu	37	9	86504005	86504005	+	Missense_Mutation	SNP	C	C	T	rs13289566	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	117	42	114	0	0.358974	0	C|0.798;T|0.202	0.202	strong	.	KIF27	103	.	NM_017576	exon7	c.G1973A	p.G658E	CTAGTTCCAGATT	.	PASS	Atlas-SNP
MFHAS1	9258	hgsc.bcm.edu	37	8	8748686	8748686	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	39	15	55	0	0.384615	0	.	.	none	.	MFHAS1	58	.	NM_004225	exon1	c.G1883C	p.S628T	CTGCAGCTAACAG	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179432185	179432185	+	Missense_Mutation	SNP	A	A	G	rs12463674	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	84	39	115	0	0.464286	0	A|0.847;G|0.153	0.153	strong	.	TTN	18412	.	NM_001267550	exon326	c.T78674C	p.I26225T	CACTCAATGGTAG	.	PASS	Atlas-SNP
ZFPM1	161882	hgsc.bcm.edu	37	16	88599659	88599659	+	Missense_Mutation	SNP	G	G	T	rs71395304	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	20	20	6	0	1	0	G|0.858;T|0.142	0.142	strong	.	ZFPM1	32	.	NM_153813	exon10	c.G1293T	p.K431N	CAGAAAGGCCCTG	.	PASS	Atlas-SNP
NUP62	23636	hgsc.bcm.edu	37	19	50412516	50412516	+	Silent	SNP	C	C	T	rs1984656	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	143	76	145	0	0.531469	0	C|0.978;T|0.022	0.022	strong	.	NUP62	50	.	NM_153719	exon3	c.G549A	p.T183T	AGGTGCCGTGGGC	.	PASS	Atlas-SNP
FARSA	2193	hgsc.bcm.edu	37	19	13035006	13035006	+	Silent	SNP	G	G	A	rs1045913	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	33	20	51	0	0.606061	0	G|0.920;A|0.080	0.080	strong	.	FARSA	46	.	NM_004461	exon12	c.C1347T	p.P449P	GTTCTCGGGAAGC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195507372	195507372	+	Missense_Mutation	SNP	C	C	G	rs147904363	by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	52	37	68	0	0.711538	0	C|0.539;G|0.461	0.461	strong	.	MUC4	1505	.	NM_018406	exon2	c.G11079C	p.Q3693H	GGTGGCCTGACCT	.	PASS	Atlas-SNP
SCLY	51540	hgsc.bcm.edu	37	2	238990388	238990388	+	Missense_Mutation	SNP	G	G	A	rs3210400	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	86	113	0	1	0	G|0.715;A|0.285	0.285	strong	.	SCLY	51	.	NM_016510	exon5	c.G547A	p.A183T	GGGCAGGCAGAGG	.	PASS	Atlas-SNP
TMEM8A	58986	hgsc.bcm.edu	37	16	427479	427479	+	Missense_Mutation	SNP	T	T	C	rs11248931	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	85	156	0	1	0	T|0.463;C|0.537	0.537	strong	TMEM8A,colon,carcinoma,0,1	TMEM8A	49	1	NM_021259	exon3	c.A406G	p.T136A	TCGGTGTGGTGCT	.	PASS	Atlas-SNP
KIF6	221458	hgsc.bcm.edu	37	6	39507889	39507889	+	Missense_Mutation	SNP	C	C	T	rs2273063	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	127	58	143	0	0.456693	0	C|0.941;T|0.059	0.059	strong	KIF6_ENST00000287152,NS,carcinoma,-1,2	KIF6	233	2	NM_145027	exon13	c.G1535A	p.R512H	CCTAGGCGGAAGG	.	PASS	Atlas-SNP
CCT8	10694	hgsc.bcm.edu	37	21	30433615	30433615	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	178	3	141	0	0.0168539	0	.	.	none	CCT8,NS,carcinoma,+1,1	CCT8	38	1	NM_006585	exon13	c.G1408A	p.V470I	GATGTACTGCATA	.	scavenged	Atlas-SNP
GPR126	57211	hgsc.bcm.edu	37	6	142688827	142688827	+	Silent	SNP	C	C	T	rs35699755	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	117	31	149	0	0.264957	0	C|0.964;T|0.036	0.036	strong	.	GPR126	192	.	NM_198569	exon3	c.C225T	p.T75T	CCCCACCGGTTAT	.	PASS	Atlas-SNP
PRSS41	360226	hgsc.bcm.edu	37	16	2854507	2854507	+	Missense_Mutation	SNP	T	T	G	rs61747737	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	148	107	160	0	0.722973	0	T|0.963;G|0.037	0.037	strong	.	.	.	.	NM_001135086	exon4	c.T698G	p.F233C	CCATGTTTTGTGC	.	PASS	Atlas-SNP
MCPH1	79648	hgsc.bcm.edu	37	8	6303025	6303025	+	Silent	SNP	G	G	A	rs2584	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	169	127	209	0	0.751479	0	G|0.814;A|0.186	0.186	strong	MCPH1,caecum,carcinoma,+1,1	MCPH1	65	1	NM_001172574	exon8	c.G1782A	p.T594T	GGAGACGTCTACA	.	PASS	Atlas-SNP
ENGASE	64772	hgsc.bcm.edu	37	17	77073776	77073776	+	Silent	SNP	A	A	T	rs62063818	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	56	27	81	0	0.482143	0	A|0.929;T|0.071	0.071	strong	.	ENGASE	55	.	NM_001042573	exon3	c.A246T	p.P82P	CAAACCAATCAGC	.	PASS	Atlas-SNP
ALPK2	115701	hgsc.bcm.edu	37	18	56202470	56202470	+	Missense_Mutation	SNP	G	G	A	rs55656447	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	40	21	62	0	0.525	0	G|0.987;A|0.013	0.013	strong	.	ALPK2	487	.	NM_052947	exon5	c.C4949T	p.A1650V	GTCTTCGCTGAGG	.	PASS	Atlas-SNP
TLR1	7096	hgsc.bcm.edu	37	4	38800214	38800214	+	Missense_Mutation	SNP	C	C	G	rs5743611	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	36	113	0	0.514286	0	C|0.950;G|0.050	0.050	strong	.	TLR1	70	.	NM_003263	exon4	c.G239C	p.R80T	TGGATTCTATTAT	.	PASS	Atlas-SNP
CENPM	79019	hgsc.bcm.edu	37	22	42341308	42341308	+	Silent	SNP	A	A	G	rs7293091	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	94	93	98	0	0.989362	0	A|0.729;G|0.271	0.271	strong	.	CENPM	8	.	NM_024053	exon4	c.T231C	p.S77S	CTGGAGACTGGGG	.	PASS	Atlas-SNP
MFSD3	113655	hgsc.bcm.edu	37	8	145735120	145735120	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	32	18	29	0	0.5625	0	.	.	none	.	MFSD3	17	.	NM_138431	exon1	c.G404C	p.G135A	GGCCGGGCAATAC	.	PASS	Atlas-SNP
PPIG	9360	hgsc.bcm.edu	37	2	170493103	170493103	+	Missense_Mutation	SNP	T	T	A	rs1050354	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	139	71	126	0	0.510791	0	A|0.574;N|0.000	0.574	strong	PPIG,NS,carcinoma,0,1	PPIG	100	1	NM_004792	exon14	c.T1335A	p.D445E	AAAAGATGACAAG	.	PASS	Atlas-SNP
SWAP70	23075	hgsc.bcm.edu	37	11	9685781	9685781	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	251	57	161	0	0.227092	0	.	.	none	.	SWAP70	40	.	NM_015055	exon1	c.C55G	p.L19V	ACCGCACTCGACC	.	PASS	Atlas-SNP
KIAA1551	55196	hgsc.bcm.edu	37	12	32138410	32138410	+	Silent	SNP	A	A	G	rs12827942	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	54	26	84	0	0.481481	0	A|0.921;G|0.079	0.079	strong	.	.	.	.	NM_018169	exon4	c.A4521G	p.E1507E	TAAAGAATCATTA	.	PASS	Atlas-SNP
CEP170B	283638	hgsc.bcm.edu	37	14	105344823	105344823	+	Silent	SNP	G	G	A	rs41314519	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	74	28	63	0	0.378378	0	G|0.969;A|0.031	0.031	strong	KIAA0284_ENST00000414716,NS,carcinoma,0,1	.	.	1	NM_001112726	exon5	c.G318A	p.P106P	AGTCCCGGAGGAG	.	PASS	Atlas-SNP
PCSK1	5122	hgsc.bcm.edu	37	5	95728898	95728898	+	Missense_Mutation	SNP	C	C	G	rs6235	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	381	191	381	0	0.501312	0	C|0.756;G|0.244	0.244	strong	.	PCSK1	93	.	NM_000439	exon14	c.G2069C	p.S690T	TTTGCACTTGGGG	.	PASS	Atlas-SNP
ZNRF4	148066	hgsc.bcm.edu	37	19	5455990	5455990	+	Missense_Mutation	SNP	G	G	A	rs17304380	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	23	17	16	0	0.73913	0	G|0.813;A|0.187	0.187	strong	.	ZNRF4	59	.	NM_181710	exon1	c.G488A	p.R163H	TCCGCCGCTACGA	.	PASS	Atlas-SNP
DCLK3	85443	hgsc.bcm.edu	37	3	36759599	36759599	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	89	28	67	0	0.314607	0	.	.	none	.	DCLK3	95	.	NM_033403	exon4	c.C1655G	p.P552R	CGGAATGGGGGAA	.	PASS	Atlas-SNP
SNX5	27131	hgsc.bcm.edu	37	20	17932210	17932210	+	Silent	SNP	C	C	T	rs2273448	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	321	158	351	0	0.492212	0	C|0.749;T|0.251	0.251	strong	.	SNX5	38	.	NM_014426	exon6	c.G543A	p.E181E	AAACATCTCTTTA	.	PASS	Atlas-SNP
SYNE1	23345	hgsc.bcm.edu	37	6	152466674	152466674	+	Silent	SNP	T	T	C	rs2747662	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	36	108	0	0.62069	0	T|0.660;C|0.340	0.340	strong	.	SYNE1	3227	.	NM_033071	exon137	c.A24780G	p.E8260E	AGGGCTTTCGGGG	.	PASS	Atlas-SNP
CRIPAK	285464	hgsc.bcm.edu	37	4	1389046	1389046	+	Silent	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	59	9	82	0	0.152542	0	.	.	none	CRIPAK,colon,carcinoma,0,1	CRIPAK	185	1	NM_175918	exon1	c.C747T	p.A249A	GAGTGCCCGCCTG	.	PASS	Atlas-SNP
EPHB3	2049	hgsc.bcm.edu	37	3	184299068	184299068	+	Silent	SNP	G	G	A	rs9881589	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	210	104	210	0	0.495238	0	G|0.834;A|0.166	0.166	strong	.	EPHB3	114	.	NM_004443	exon15	c.G2760A	p.T920T	CCGCACGGTCCCA	.	PASS	Atlas-SNP
FGF6	2251	hgsc.bcm.edu	37	12	4554413	4554413	+	Silent	SNP	C	C	T	rs11611403	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	50	29	49	0	0.58	0	C|0.833;T|0.167	0.167	strong	.	FGF6	40	.	NM_020996	exon1	c.G324A	p.G108G	GTGGGTCCCGCTG	.	PASS	Atlas-SNP
SLC36A2	153201	hgsc.bcm.edu	37	5	150723127	150723127	+	Silent	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	193	6	193	2	0.0310881	0.0103627	.	.	none	SLC36A2,NS,malignant_melanoma,0,2	SLC36A2	71	2	NM_181776	exon3	c.C288T	p.F96F	GGCAATGAAGCCC	.	scavenged	Atlas-SNP
ZNF554	115196	hgsc.bcm.edu	37	19	2833864	2833864	+	Missense_Mutation	SNP	G	G	A	rs867169	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	77	40	102	0	0.519481	0	G|0.741;A|0.259	0.259	strong	.	ZNF554	47	.	NM_001102651	exon5	c.G631A	p.V211I	GTGGCCGTTCCTC	.	PASS	Atlas-SNP
ACTR3C	653857	hgsc.bcm.edu	37	7	149983566	149983566	+	Nonsense_Mutation	SNP	G	G	A	rs78661149		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	122	33	201	0	0.270492	0	G|0.500;A|0.500	0.500	weak	Q9C0K3_HUMAN,NS,carcinoma,+1,1	.	.	1	NM_001164459	exon5	c.C361T	p.Q121X	ACTTCTGGGGATC	.	scavenged	Atlas-SNP
WDR66	144406	hgsc.bcm.edu	37	12	122413481	122413481	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	132	59	150	0	0.44697	0	.	.	none	.	WDR66	143	.	NM_144668	exon19	c.C2896T	p.R966C	CAGCTCCGCAGTC	.	PASS	Atlas-SNP
LCE1E	353135	hgsc.bcm.edu	37	1	152760096	152760096	+	Silent	SNP	A	A	T	rs115864544	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	287	43	514	1	0.149826	0.00194553	A|0.901;T|0.099	0.099	strong	LCE1E,NS,carcinoma,0,1	LCE1E	26	1	NM_178353	exon2	c.A321T	p.G107G	CTGTGGAGGGGGC	.	scavenged	Atlas-SNP
CNTNAP4	85445	hgsc.bcm.edu	37	16	76461474	76461474	+	Silent	SNP	C	C	T	rs76327478	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	196	76	163	0	0.387755	0	C|0.993;T|0.007	0.007	strong	.	CNTNAP4	600	.	NM_138994	exon4	c.C441T	p.I147I	GCGAATCGAAGTG	.	PASS	Atlas-SNP
DFNA5	1687	hgsc.bcm.edu	37	7	24758795	24758795	+	Silent	SNP	T	T	C	rs876305	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	60	8	96	0	0.133333	0	T|0.394;C|0.606	0.606	strong	.	DFNA5	51	.	NM_001127453	exon4	c.A447G	p.E149E	CCTTCCTTCCAGC	.	PASS	Atlas-SNP
UTRN	7402	hgsc.bcm.edu	37	6	144869785	144869785	+	Missense_Mutation	SNP	A	A	G	rs1534443	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	79	78	131	0	0.987342	0	A|0.684;G|0.316	0.316	strong	.	UTRN	327	.	NM_007124	exon46	c.A6605G	p.N2202S	ATCCTAATGTCCA	.	PASS	Atlas-SNP
MRGPRX3	117195	hgsc.bcm.edu	37	11	18158993	18158993	+	Missense_Mutation	SNP	T	T	C	rs12291017	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	84	67	126	0	0.797619	0	T|0.747;C|0.253	0.253	strong	.	MRGPRX3	59	.	NM_054031	exon3	c.T244C	p.C82R	ATTATATGTTCGC	.	PASS	Atlas-SNP
PTBP1	5725	hgsc.bcm.edu	37	19	808586	808586	+	Silent	SNP	C	C	G	rs13169	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	69	100	0	1	0	C|0.867;G|0.133	0.133	strong	PTBP1,NS,lymphoid_neoplasm,0,1	PTBP1	43	1	NM_002819	exon13	c.C1287G	p.P429P	GAAGCCCATCCGC	.	PASS	Atlas-SNP
SYNE1	23345	hgsc.bcm.edu	37	6	152763258	152763258	+	Silent	SNP	T	T	C	rs138705766	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	43	33	66	0	0.767442	0	T|0.983;C|0.017	0.017	strong	.	SYNE1	3227	.	NM_033071	exon31	c.A3981G	p.T1327T	ATCCAGTGTGCTC	.	PASS	Atlas-SNP
OPLAH	26873	hgsc.bcm.edu	37	8	145114643	145114643	+	Silent	SNP	G	G	A	rs6558292	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	56	55	55	0	0.982143	0	G|0.920;A|0.080	0.080	strong	.	OPLAH	78	.	NM_017570	exon3	c.C222T	p.I74I	GCTGGCGATATGA	.	PASS	Atlas-SNP
CTAGE5	4253	hgsc.bcm.edu	37	14	39818028	39818028	+	Missense_Mutation	SNP	A	A	G	rs1140952	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	105	62	130	0	0.590476	0	A|0.632;G|0.368	0.368	strong	CTAGE5,rectum,carcinoma,0,1	CTAGE5	75	1	NM_001247989	exon23	c.A2110G	p.I704V	GCTCCAATCAGAG	.	PASS	Atlas-SNP
USP42	84132	hgsc.bcm.edu	37	7	6189780	6189780	+	Silent	SNP	T	T	C	rs3764814	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	37	27	67	0	0.72973	0	T|0.728;C|0.272	0.272	strong	.	USP42	138	.	NM_032172	exon13	c.T1953C	p.L651L	CGAGCTTCAAGAA	.	PASS	Atlas-SNP
SCML4	256380	hgsc.bcm.edu	37	6	108029180	108029180	+	Missense_Mutation	SNP	G	G	A	rs56215636	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	49	108	0	0.563218	0	G|0.984;A|0.016	0.016	strong	.	SCML4	65	.	NM_198081	exon7	c.C1009T	p.R337W	GTGGCCGCCTGGC	.	PASS	Atlas-SNP
ZNF831	128611	hgsc.bcm.edu	37	20	57769140	57769140	+	Missense_Mutation	SNP	G	G	C	rs55786258	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	34	16	44	0	0.470588	0	G|0.829;C|0.171	0.171	strong	.	ZNF831	287	.	NM_178457	exon1	c.G3066C	p.L1022F	ACAGTTGGGGGGG	.	PASS	Atlas-SNP
TOR1AIP1	26092	hgsc.bcm.edu	37	1	179858444	179858444	+	Splice_Site	SNP	G	G	A	rs2245425	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	60	26	88	0	0.433333	0	G|0.377;A|0.623	0.623	strong	.	TOR1AIP1	58	.	NM_001267578	exon3	c.554-1G>A	.	ATATTAGCAGTGA	.	PASS	Atlas-SNP
SNAPC4	6621	hgsc.bcm.edu	37	9	139276448	139276448	+	Silent	SNP	A	A	G	rs150900916	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	112	62	157	0	0.553571	0	A|0.999;G|0.001	0.001	strong	.	SNAPC4	82	.	NM_003086	exon17	c.T2145C	p.H715H	CTGCACATGGGAT	.	PASS	Atlas-SNP
PCDHGA2	56113	hgsc.bcm.edu	37	5	140719090	140719090	+	Silent	SNP	G	G	A	rs6861047	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	68	33	66	0	0.485294	0	G|0.884;A|0.116	0.116	strong	.	PCDHGA2	205	.	NM_018915	exon1	c.G552A	p.R184R	GCGAAGGGGAGCT	.	PASS	Atlas-SNP
IGFN1	91156	hgsc.bcm.edu	37	1	201163306	201163306	+	Missense_Mutation	SNP	C	C	G	rs41313898	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	116	116	122	0	1	0	C|0.999;G|0.001	0.001	strong	.	IGFN1	220	.	NM_001164586	exon3	c.C32G	p.P11R	ACATCCCTGGAGT	.	PASS	Atlas-SNP
SPAG17	200162	hgsc.bcm.edu	37	1	118693217	118693217	+	Silent	SNP	T	T	C	rs1935992	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	222	107	226	0	0.481982	0	C|0.210;N|0.000	0.210	strong	SPAG17,NS,carcinoma,0,1	SPAG17	263	1	NM_206996	exon3	c.A264G	p.S88S	TTTAGATGAAGCA	.	PASS	Atlas-SNP
PON3	5446	hgsc.bcm.edu	37	7	95001555	95001555	+	Silent	SNP	C	C	T	rs1053275	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	218	97	237	0	0.444954	0	C|0.417;T|0.583	0.583	strong	.	PON3	59	.	NM_000940	exon4	c.G297A	p.A99A	TTCTAGCGCTTGT	.	PASS	Atlas-SNP
OR2T34	127068	hgsc.bcm.edu	37	1	248737329	248737329	+	Missense_Mutation	SNP	C	C	T	rs75095367	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	227	114	302	0	0.502203	0	C|0.816;T|0.184	0.184	strong	.	OR2T34	72	.	NM_001001821	exon1	c.G730A	p.A244T	AGGTGGCCAAGGC	.	PASS	Atlas-SNP
ATP2A3	489	hgsc.bcm.edu	37	17	3840928	3840928	+	Silent	SNP	A	A	G	rs3179783	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	56	29	63	0	0.517857	0	A|0.782;G|0.218	0.218	strong	.	ATP2A3	148	.	NM_174956	exon15	c.T2103C	p.T701T	ATCGCCAGTCTGT	.	PASS	Atlas-SNP
TGFBR2	7048	hgsc.bcm.edu	37	3	30713842	30713842	+	Silent	SNP	C	C	T	rs2228048	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	149	60	129	0	0.402685	0	C|0.947;T|0.053	0.053	strong	.	TGFBR2	139	.	NM_001024847	exon5	c.C1242T	p.N414N	GAAGAACGACCTA	.	PASS	Atlas-SNP
APMAP	57136	hgsc.bcm.edu	37	20	24964558	24964558	+	Missense_Mutation	SNP	T	T	C	rs12242	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	43	23	50	0	0.534884	0	T|0.964;C|0.036	0.036	strong	.	APMAP	3	.	NM_020531	exon2	c.A193G	p.I65V	GATCTATAGGAGA	.	PASS	Atlas-SNP
ATP2A3	489	hgsc.bcm.edu	37	17	3839685	3839685	+	Silent	SNP	G	G	A	rs1062683	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	168	86	186	0	0.511905	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
PCNXL3	399909	hgsc.bcm.edu	37	11	65386029	65386029	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	53	16	47	0	0.301887	0	.	.	none	.	PCNXL3	140	.	NM_032223	exon6	c.G1196A	p.R399Q	CCCTGCGAAGACA	.	PASS	Atlas-SNP
OR10H2	26538	hgsc.bcm.edu	37	19	15838967	15838967	+	Silent	SNP	G	G	A	rs45442392	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	191	65	130	0	0.340314	0	G|0.611;A|0.389	0.389	strong	OR10H2,NS,carcinoma,+1,1	OR10H2	59	1	NM_013939	exon1	c.G114A	p.T38T	GTTCACGCTGCTG	.	PASS	Atlas-SNP
UGT1A7	54577	hgsc.bcm.edu	37	2	234590975	234590975	+	Missense_Mutation	SNP	G	G	A	rs78725335	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	22	119	0	0.30137	0	.	.	weak	.	UGT1A7	74	.	NM_019077	exon1	c.G392A	p.R131Q	ATGACCGAAAATT	.	PASS	Atlas-SNP
PCDHB7	56129	hgsc.bcm.edu	37	5	140553664	140553664	+	Silent	SNP	G	G	A	rs3733695	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	161	87	141	0	0.540373	0	G|0.819;A|0.181	0.181	strong	.	PCDHB7	231	.	NM_018940	exon1	c.G1248A	p.E416E	CACTGAGTACAAC	.	PASS	Atlas-SNP
ZZEF1	23140	hgsc.bcm.edu	37	17	3926110	3926110	+	Missense_Mutation	SNP	C	C	G	rs711177	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	46	23	43	0	0.5	0	C|0.870;G|0.130	0.130	strong	.	ZZEF1	195	.	NM_015113	exon44	c.G7105C	p.E2369Q	TCTCCTCAAAACC	.	PASS	Atlas-SNP
ZNF345	25850	hgsc.bcm.edu	37	19	37368492	37368492	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	41	13	64	0	0.317073	0	.	.	none	.	ZNF345	68	.	NM_001242476	exon4	c.G760C	p.G254R	CATACCGGTGAGA	.	PASS	Atlas-SNP
SPAG9	9043	hgsc.bcm.edu	37	17	49067870	49067870	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	146	75	192	0	0.513699	0	.	.	none	.	SPAG9	151	.	NM_001130528	exon20	c.C2558T	p.T853M	GCTCCCGTCACAC	.	PASS	Atlas-SNP
ATP13A2	23400	hgsc.bcm.edu	37	1	17326767	17326767	+	Missense_Mutation	SNP	C	C	T	rs56367069	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	106	62	113	0	0.584906	0	C|0.989;T|0.011	0.011	strong	.	ATP13A2	85	.	NM_022089	exon10	c.G881A	p.R294Q	CACACCCGCATGG	.	PASS	Atlas-SNP
PKD1	5310	hgsc.bcm.edu	37	16	2156021	2156021	+	Silent	SNP	A	A	G	rs28575767	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	15	9	10	1	0.6	0.1	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
RHBG	57127	hgsc.bcm.edu	37	1	156347131	156347131	+	Missense_Mutation	SNP	G	G	A	rs2245623	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	192	189	252	0	0.984375	0	G|0.713;A|0.287	0.287	strong	.	RHBG	133	.	NM_020407	exon2	c.G227A	p.G76D	GCTTTGGCTTCCT	.	PASS	Atlas-SNP
LDLR	3949	hgsc.bcm.edu	37	19	11224265	11224265	+	Silent	SNP	A	A	G	rs5930	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	68	67	83	0	0.985294	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
PCM1	5108	hgsc.bcm.edu	37	8	17817553	17817553	+	Missense_Mutation	SNP	G	G	T	rs17635381	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	116	35	112	0	0.301724	0	G|0.834;N|0.000	.	strong	.	PCM1	120	.	NM_006197	exon14	c.G2071T	p.A691S	ATCTCTGCCAGTG	.	PASS	Atlas-SNP
TEK	7010	hgsc.bcm.edu	37	9	27203002	27203002	+	Silent	SNP	G	G	A	rs45563539	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	170	84	190	0	0.494118	0	G|0.961;A|0.039	0.039	strong	.	TEK	250	.	NM_000459	exon13	c.G2094A	p.Q698Q	GTATCAGCTCAAG	.	PASS	Atlas-SNP
ZNF366	167465	hgsc.bcm.edu	37	5	71739602	71739602	+	Missense_Mutation	SNP	G	G	C	rs13188519	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	116	43	114	0	0.37069	0	G|0.916;C|0.084	0.084	strong	.	ZNF366	108	.	NM_152625	exon5	c.C2216G	p.A739G	AGCACTGCTTGTT	.	PASS	Atlas-SNP
LAMC2	3918	hgsc.bcm.edu	37	1	183184616	183184616	+	Silent	SNP	C	C	T	rs2274980	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	145	80	129	1	0.551724	0.00775194	C|0.732;T|0.268	0.268	strong	LAMC2,NS,carcinoma,+1,1	LAMC2	113	1	NM_005562	exon3	c.C297T	p.S99S	CAACTCCGGACGG	.	scavenged	Atlas-SNP
DAPP1	27071	hgsc.bcm.edu	37	4	100784980	100784980	+	Silent	SNP	C	C	T	rs3737484	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	23	68	0	0.396552	0	C|0.705;T|0.295	0.295	strong	.	DAPP1	47	.	NM_014395	exon7	c.C654T	p.F218F	ACAATTCGATTAT	.	PASS	Atlas-SNP
ZNF417	147687	hgsc.bcm.edu	37	19	58420152	58420152	+	Silent	SNP	C	C	A	rs17845779	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	217	96	248	1	0.442396	0.00403226	C|0.765;A|0.235	0.235	strong	ZNF417,NS,carcinoma,0,1	ZNF417	44	1	NM_152475	exon3	c.G1494T	p.G498G	TGATTTCCCACAT	.	PASS	Atlas-SNP
SPICE1	152185	hgsc.bcm.edu	37	3	113222036	113222036	+	Silent	SNP	G	G	A	rs11537650	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	98	45	117	0	0.459184	0	T|0.051;G|0.602;C|0.139;A|0.208	0.208	strong	.	SPICE1	130	.	NM_144718	exon3	c.C138T	p.P46P	ATCTTCGGGAGTT	.	PASS	Atlas-SNP
SPG20	23111	hgsc.bcm.edu	37	13	36886469	36886469	+	Silent	SNP	T	T	C	rs2274293	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	211	96	289	0	0.454976	0	T|0.736;C|0.264	0.264	strong	.	SPG20	87	.	NM_015087	exon7	c.A1629G	p.A543A	ACTACTTGCTGCT	.	PASS	Atlas-SNP
TRIM31	11074	hgsc.bcm.edu	37	6	30080274	30080274	+	Silent	SNP	G	G	A	rs2517598	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	123	45	143	0	0.365854	0	G|0.878;A|0.122	0.122	strong	.	TRIM31	40	.	NM_007028	exon2	c.C309T	p.H103H	GAAATAGTGGAAC	.	PASS	Atlas-SNP
GRK4	2868	hgsc.bcm.edu	37	4	2993980	2993980	+	Silent	SNP	T	T	C	rs2515941	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	118	116	122	0	0.983051	0	T|0.639;C|0.361	0.361	strong	.	GRK4	72	.	NM_182982	exon4	c.T300C	p.D100D	AAGTGATTGTGGA	.	PASS	Atlas-SNP
UMODL1	89766	hgsc.bcm.edu	37	21	43504228	43504228	+	Silent	SNP	T	T	C	rs7278485	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	149	148	137	2	0.993289	0.0145985	T|0.347;C|0.653	0.653	strong	UMODL1_ENST00000408989,NS,carcinoma,+1,4	UMODL1	186	4	NM_173568	exon3	c.T354C	p.P118P	AAGACCTGGGGCC	.	scavenged	Atlas-SNP
CDRT1	374286	hgsc.bcm.edu	37	17	15510888	15510888	+	Missense_Mutation	SNP	G	G	A	rs62070401	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	206	206	223	0	1	0	G|0.754;A|0.246	0.246	strong	.	CDRT1	83	.	NM_006382	exon6	c.C1232T	p.T411M	ACCTACGTGTCAG	.	PASS	Atlas-SNP
C19orf45	374877	hgsc.bcm.edu	37	19	7569245	7569245	+	Missense_Mutation	SNP	A	A	G	rs145077335	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	116	70	111	0	0.603448	0	A|0.999;G|0.001	0.001	strong	.	C19orf45	36	.	NM_198534	exon4	c.A730G	p.T244A	GGATCAACGTGTT	.	PASS	Atlas-SNP
ZNF783	0	hgsc.bcm.edu	37	7	148963652	148963652	+	Missense_Mutation	SNP	C	C	T	rs61729506	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	50	17	54	0	0.34	0	C|0.942;T|0.058	0.058	strong	.	ZNF783	28	.	NM_001195220	exon2	c.C251T	p.T84I	AGAAGACAGCTGT	.	PASS	Atlas-SNP
TMCO4	255104	hgsc.bcm.edu	37	1	20072082	20072082	+	Missense_Mutation	SNP	C	C	T	rs35760408	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	130	54	160	0	0.415385	0	C|0.981;T|0.019	0.019	strong	.	TMCO4	46	.	NM_181719	exon10	c.G820A	p.G274S	GCCTGCCCTCCGT	.	PASS	Atlas-SNP
C5	727	hgsc.bcm.edu	37	9	123725926	123725926	+	Missense_Mutation	SNP	T	T	G	rs17612	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	251	120	294	0	0.478088	0	T|0.954;G|0.046	0.046	strong	.	C5	124	.	NM_001735	exon34	c.A4311C	p.E1437D	TAAGTCTTCTTCA	.	PASS	Atlas-SNP
RGS12	6002	hgsc.bcm.edu	37	4	3429856	3429856	+	Missense_Mutation	SNP	A	A	G	rs2269497	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	153	68	162	0	0.444444	0	A|0.964;G|0.036	0.036	strong	.	RGS12	128	.	NM_002926	exon15	c.A3371G	p.N1124S	AACAGAACACAGC	.	PASS	Atlas-SNP
SLC9C1	285335	hgsc.bcm.edu	37	3	111962851	111962851	+	Missense_Mutation	SNP	T	T	C	rs6768523	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	135	133	141	0	0.985185	0	T|0.708;C|0.292	0.292	strong	.	.	.	.	NM_183061	exon11	c.A1270G	p.T424A	GTATAGTAACTGC	.	PASS	Atlas-SNP
PCNX	22990	hgsc.bcm.edu	37	14	71502824	71502824	+	Missense_Mutation	SNP	G	G	T	rs117405927	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	191	98	242	0	0.513089	0	G|0.999;T|0.001	0.001	strong	.	PCNX	198	.	NM_014982	exon19	c.G3817T	p.G1273C	GTAATTGGTGTGC	.	PASS	Atlas-SNP
GPR146	115330	hgsc.bcm.edu	37	7	1097952	1097952	+	Silent	SNP	C	C	T	rs6953080	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	33	23	31	0	0.69697	0	C|0.925;T|0.075	0.075	strong	.	GPR146	20	.	NM_138445	exon1	c.C801T	p.D267D	CGTGGACGCACAC	.	PASS	Atlas-SNP
KHDC3L	154288	hgsc.bcm.edu	37	6	74072937	74072937	+	Missense_Mutation	SNP	G	G	C	rs564533	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	122	65	152	0	0.532787	0	G|0.916;C|0.084	0.084	strong	.	.	.	.	NM_001017361	exon2	c.G289C	p.E97Q	TACCAGGAGGACA	.	PASS	Atlas-SNP
BTN2A1	11120	hgsc.bcm.edu	37	6	26463660	26463660	+	Missense_Mutation	SNP	G	G	A	rs13195509	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	84	43	94	0	0.511905	0	G|0.939;A|0.061	0.061	strong	.	BTN2A1	118	.	NM_001197234	exon4	c.G619A	p.V207M	ACGGCTGTGATCA	.	PASS	Atlas-SNP
ASB17	127247	hgsc.bcm.edu	37	1	76397871	76397871	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	147	42	172	0	0.285714	0	.	.	none	.	ASB17	53	.	NM_080868	exon1	c.G106A	p.G36S	ACTGACCCAAAAA	.	PASS	Atlas-SNP
MIER3	166968	hgsc.bcm.edu	37	5	56242774	56242774	+	Silent	SNP	T	T	C	rs2034244	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	283	279	312	1	0.985866	0.00320513	T|0.666;C|0.334	0.334	strong	.	MIER3	33	.	NM_152622	exon3	c.A159G	p.S53S	AATTTCTGAACTG	.	PASS	Atlas-SNP
SEMA3A	10371	hgsc.bcm.edu	37	7	83764113	83764113	+	Silent	SNP	T	T	C	rs74349534	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	38	56	0	0.527778	0	T|0.993;C|0.007	0.007	strong	.	SEMA3A	121	.	NM_006080	exon2	c.A267G	p.Q89Q	TACCTTTTGAAAA	.	PASS	Atlas-SNP
LMF2	91289	hgsc.bcm.edu	37	22	50944128	50944128	+	Silent	SNP	G	G	A	rs743615	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	159	80	170	0	0.503145	0	G|0.706;A|0.294	0.294	strong	.	LMF2	40	.	NM_033200	exon6	c.C891T	p.H297H	GCTGCCGTGGCCA	.	PASS	Atlas-SNP
PANK4	55229	hgsc.bcm.edu	37	1	2449631	2449631	+	Missense_Mutation	SNP	C	C	G	rs144881953	alternate_allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	26	8	47	0	0.307692	0	C|1.000;T|0.000	.	alt	.	PANK4	64	.	NM_018216	exon9	c.G1190C	p.G397A	GCCGGGCCGAGCT	.	PASS	Atlas-SNP
ZNF429	353088	hgsc.bcm.edu	37	19	21719401	21719401	+	Silent	SNP	T	T	C	rs35782355	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	32	14	48	0	0.4375	0	T|0.444;C|0.556	0.556	strong	.	ZNF429	338	.	NM_001001415	exon4	c.T546C	p.F182F	ATCATTTTGCATG	.	PASS	Atlas-SNP
KIAA2026	158358	hgsc.bcm.edu	37	9	6007500	6007500	+	Silent	SNP	G	G	A	rs1061767	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	67	33	69	0	0.492537	0	G|0.786;A|0.214	0.214	strong	.	KIAA2026	231	.	NM_001017969	exon1	c.C288T	p.G96G	GGTGAGGCCCCGG	.	PASS	Atlas-SNP
RUFY1	80230	hgsc.bcm.edu	37	5	179020622	179020622	+	Silent	SNP	T	T	C	rs4701135	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	132	83	127	0	0.628788	0	T|0.912;C|0.088	0.088	strong	.	RUFY1	101	.	NM_025158	exon11	c.T1389C	p.N463N	GATTAATTTACAG	.	PASS	Atlas-SNP
VEZT	55591	hgsc.bcm.edu	37	12	95694111	95694111	+	Missense_Mutation	SNP	T	T	G	rs17855934	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	39	153	0	0.448276	0	T|0.924;G|0.076	0.076	strong	.	VEZT	106	.	NM_017599	exon12	c.T2002G	p.S668A	GAAAACTCTCTAG	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105417765	105417765	+	Silent	SNP	A	A	C	rs2894636	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	64	62	0	0	0.96875	.	A|0.831;C|0.169	0.169	strong	.	AHNAK2	719	.	NM_138420	exon7	c.T4023G	p.S1341S	TGGGGCAGACACC	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	63	63	64	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
SLC15A2	6565	hgsc.bcm.edu	37	3	121648168	121648168	+	Missense_Mutation	SNP	G	G	A	rs1143672	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	109	45	142	0	0.412844	0	G|0.523;A|0.477	0.477	strong	.	SLC15A2	92	.	NM_021082	exon17	c.G1526A	p.R509K	AAAGCAGAACAAC	.	PASS	Atlas-SNP
PRDM16	63976	hgsc.bcm.edu	37	1	3301721	3301721	+	Silent	SNP	C	C	T	rs2282198	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	31	153	0	0.364706	0	C|0.713;T|0.287	0.287	strong	.	PRDM16	147	.	NM_022114	exon4	c.C444T	p.S148S	GATCTCCGAAGAC	.	PASS	Atlas-SNP
SLFN14	342618	hgsc.bcm.edu	37	17	33881718	33881718	+	Missense_Mutation	SNP	G	G	A	rs321613	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	62	29	80	0	0.467742	0	G|0.352;A|0.648	0.648	strong	.	SLFN14	43	.	NM_001129820	exon2	c.C1066T	p.P356S	AACTGGGAGGAGC	.	PASS	Atlas-SNP
TBC1D1	23216	hgsc.bcm.edu	37	4	38138856	38138856	+	Missense_Mutation	SNP	G	G	A	rs13110318	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	77	44	101	0	0.571429	0	G|0.914;A|0.086	0.086	strong	.	TBC1D1	94	.	NM_015173	exon20	c.G3407A	p.R1136Q	TGGAGCGGTCGGC	.	PASS	Atlas-SNP
DSPP	1834	hgsc.bcm.edu	37	4	88536451	88536451	+	Silent	SNP	C	C	T	rs141946550		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	12	104	0	0.169014	0	.	.	weak	DSPP,colon,carcinoma,0,1	DSPP	174	1	NM_014208	exon5	c.C2637T	p.S879S	TGACAGCAGTGAT	.	PASS	Atlas-SNP
HIST1H1C	3006	hgsc.bcm.edu	37	6	26056484	26056484	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	96	3	114	0	0.03125	0	.	.	none	HIST1H1C,colon,carcinoma,0,1	HIST1H1C	80	1	NM_005319	exon1	c.C173T	p.S58F	GCCAGAGAAACTC	.	scavenged	Atlas-SNP
RBFOX1	54715	hgsc.bcm.edu	37	16	7629841	7629841	+	Silent	SNP	A	A	G	rs140174146	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	132	103	155	0	0.780303	0	A|0.991;G|0.009	0.009	strong	.	RBFOX1	341	.	NM_145891	exon3	c.A393G	p.E131E	CACGGAAAACAAG	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105418234	105418234	+	Missense_Mutation	SNP	G	G	A	rs76024300	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	173	17	77	0	0.0982659	0	.	.	weak	.	AHNAK2	719	.	NM_138420	exon7	c.C3554T	p.S1185L	TCCACCGAGGCCT	.	PASS	Atlas-SNP
CTDP1	9150	hgsc.bcm.edu	37	18	77473086	77473086	+	Silent	SNP	G	G	A	rs599554	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	22	138	0	0.30137	0	A|0.215;C|0.003	0.215	strong	.	CTDP1	67	.	NM_004715	exon7	c.G978A	p.T326T	GGGCACGGGTGAT	.	PASS	Atlas-SNP
LILRA6	79168	hgsc.bcm.edu	37	19	54744711	54744711	+	Missense_Mutation	SNP	C	C	G	rs77137660	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	147	16	202	0	0.108844	0	C|0.976;G|0.024	0.024	strong	.	LILRA6	75	.	NM_024318	exon5	c.G951C	p.M317I	ACCTGCCATCAGG	.	PASS	Atlas-SNP
BTC	685	hgsc.bcm.edu	37	4	75719517	75719517	+	Missense_Mutation	SNP	A	A	C	rs28549760	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	9	5	15	0	0.555556	0	A|0.802;C|0.198	0.198	strong	BTC,NS,carcinoma,0,1	BTC	23	1	NM_001729	exon1	c.T19G	p.C7G	CGCTGCACCGGGC	.	PASS	Atlas-SNP
ANKEF1	63926	hgsc.bcm.edu	37	20	10030452	10030452	+	Missense_Mutation	SNP	G	G	A	rs524625	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	39	21	35	0	0.538462	0	G|0.769;A|0.231	0.231	strong	.	.	.	.	NM_198798	exon6	c.G1235A	p.G412E	CGTATGGACCTAA	.	PASS	Atlas-SNP
LINGO1	84894	hgsc.bcm.edu	37	15	77907784	77907784	+	Silent	SNP	G	G	A	rs2271398	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	188	188	194	0	1	0	G|0.300;A|0.700	0.700	strong	.	LINGO1	76	.	NM_032808	exon2	c.C465T	p.I155I	GATAACGATCTTG	.	PASS	Atlas-SNP
SPATA31C2	645961	hgsc.bcm.edu	37	9	90746159	90746159	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	20	106	0	0.25641	0	.	.	none	.	.	.	.	NM_001166137	exon4	c.G1793A	p.R598Q	CAGGATCGACGCA	.	PASS	Atlas-SNP
GALC	2581	hgsc.bcm.edu	37	14	88414211	88414211	+	Silent	SNP	G	G	A	rs398076	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	44	102	0	0.478261	0	G|0.650;A|0.350	0.350	strong	.	GALC	48	.	NM_000153	exon13	c.C1350T	p.S450S	GCCATCGCTGTCA	.	PASS	Atlas-SNP
MCPH1	79648	hgsc.bcm.edu	37	8	6479042	6479042	+	Missense_Mutation	SNP	C	C	T	rs1057090	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	28	27	52	0	0.964286	0	C|0.519;A|0.008	.	strong	.	MCPH1	65	.	NM_024596	exon13	c.C2282T	p.A761V	AGCCAGCGATGTT	.	PASS	Atlas-SNP
ADCY9	115	hgsc.bcm.edu	37	16	4033436	4033436	+	Missense_Mutation	SNP	T	T	C	rs2230739	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	77	59	114	0	0.766234	0	T|0.736;C|0.264	0.264	strong	ADCY9,NS,carcinoma,0,1	ADCY9	151	1	NM_001116	exon7	c.A2316G	p.I772M	GTTCTTTATGACC	.	PASS	Atlas-SNP
GPR162	27239	hgsc.bcm.edu	37	12	6933787	6933787	+	Silent	SNP	A	A	G	rs1051409	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	63	31	51	0	0.492063	0	A|0.507;G|0.493	0.493	strong	.	GPR162	55	.	NM_019858	exon2	c.A723G	p.V241V	TGAGGTACCAGCC	.	PASS	Atlas-SNP
ZNF701	55762	hgsc.bcm.edu	37	19	53077411	53077411	+	Missense_Mutation	SNP	T	T	C	rs162832	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	24	24	20	0	1	0	T|0.261;C|0.739	0.739	strong	.	ZNF701	44	.	NM_001172655	exon3	c.T209C	p.L70P	CTCTTCTTCAGGT	.	PASS	Atlas-SNP
PIGQ	9091	hgsc.bcm.edu	37	16	624101	624101	+	Silent	SNP	G	G	A	rs61753370	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	64	50	56	0	0.78125	0	G|0.978;A|0.022	0.022	strong	PIGQ,NS,carcinoma,0,1	PIGQ	43	1	NM_148920	exon2	c.G27A	p.T9T	CCCCACGTGCTGC	.	PASS	Atlas-SNP
FMO1	2326	hgsc.bcm.edu	37	1	171250044	171250044	+	Silent	SNP	C	C	T	rs742350	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	162	68	248	0	0.419753	0	C|0.784;T|0.216	0.216	strong	.	FMO1	79	.	NM_002021	exon6	c.C747T	p.T249T	CCCAACCCCAATT	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	120	56	130	0	0.466667	0	G|0.675;C|0.325	0.325	strong	.	PCSK5	329	.	NM_001190482	exon31	c.G4240C	p.E1414Q	GAAAAGGAGACTA	.	PASS	Atlas-SNP
DIRAS3	9077	hgsc.bcm.edu	37	1	68512893	68512893	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	23	100	2	0.267442	0.02	.	.	none	DIRAS3,NS,carcinoma,+2,1	DIRAS3	31	1	NM_004675	exon2	c.A88C	p.K30Q	GGGGCTTGAAGGC	.	scavenged	Atlas-SNP
USH2A	7399	hgsc.bcm.edu	37	1	215848587	215848587	+	Silent	SNP	T	T	C	rs2797234	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	156	72	184	1	0.461538	0.00543478	T|0.680;C|0.320	0.320	strong	USH2A,NS,carcinoma,0,2	USH2A	1168	2	NM_206933	exon63	c.A12666G	p.T4222T	CATAAATGTATTC	.	scavenged	Atlas-SNP
ENPP2	5168	hgsc.bcm.edu	37	8	120594802	120594802	+	Silent	SNP	A	A	G	rs4871364	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	140	30	161	0	0.214286	0	A|0.735;G|0.265	0.265	strong	.	ENPP2	254	.	NM_006209	exon19	c.T1740C	p.H580H	ACTTCCATGGGTC	.	PASS	Atlas-SNP
MPP3	4356	hgsc.bcm.edu	37	17	41891437	41891437	+	Silent	SNP	G	G	A	rs17742929	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	76	35	81	0	0.460526	0	G|0.872;A|0.128	0.128	strong	.	MPP3	42	.	NM_001932	exon16	c.C1197T	p.H399H	CAGCTCGTGCAGT	.	PASS	Atlas-SNP
RAET1L	154064	hgsc.bcm.edu	37	6	150342232	150342232	+	Missense_Mutation	SNP	G	G	A	rs61730071	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	253	176	313	0	0.695652	0	G|0.611;A|0.389	0.389	strong	.	RAET1L	21	.	NM_130900	exon3	c.C440T	p.T147I	AGGAAGGTCTGTC	.	PASS	Atlas-SNP
VWF	7450	hgsc.bcm.edu	37	12	6174423	6174423	+	Silent	SNP	T	T	A	rs1800375	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	48	48	89	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
BMP3	651	hgsc.bcm.edu	37	4	81967150	81967150	+	Missense_Mutation	SNP	G	G	A	rs3733549	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	60	31	77	0	0.516667	0	G|0.923;A|0.077	0.077	strong	.	BMP3	59	.	NM_001201	exon2	c.G575A	p.R192Q	CTCATCGAGATAT	.	PASS	Atlas-SNP
CRYBB2	1415	hgsc.bcm.edu	37	22	25627604	25627604	+	Silent	SNP	G	G	A	rs8140949	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	133	133	138	0	1	0	G|0.756;A|0.244	0.244	strong	.	CRYBB2	18	.	NM_000496	exon6	c.G483A	p.G161G	CCGTGGGCTGCAG	.	PASS	Atlas-SNP
GALNT7	51809	hgsc.bcm.edu	37	4	174090004	174090004	+	Silent	SNP	G	G	A	rs3733477	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	72	76	0	1	0	T|0.000;G|0.353;A|0.647	0.647	strong	.	GALNT7	61	.	NM_017423	exon1	c.G18A	p.G6G	GATTGGGTTCATC	.	PASS	Atlas-SNP
GPR88	54112	hgsc.bcm.edu	37	1	101005554	101005554	+	Silent	SNP	C	C	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	16	5	5	0	0.3125	0	.	.	none	.	GPR88	17	.	NM_022049	exon2	c.C1032A	p.R344R	GTTCCGCCGCTCC	.	PASS	Atlas-SNP
SCUBE2	57758	hgsc.bcm.edu	37	11	9051475	9051475	+	Missense_Mutation	SNP	G	G	C	rs3751057	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	350	60	309	0	0.171429	0	G|0.908;C|0.092	0.092	strong	.	SCUBE2	102	.	NM_020974	exon18	c.C2288G	p.T763S	GTCGTAGTATTTC	.	PASS	Atlas-SNP
CCDC37	348807	hgsc.bcm.edu	37	3	126137558	126137558	+	Silent	SNP	C	C	T	rs4679242	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	67	28	86	0	0.41791	0	C|0.760;T|0.240	0.240	strong	.	CCDC37	69	.	NM_182628	exon7	c.C591T	p.A197A	GGACGCCGCCTTG	.	PASS	Atlas-SNP
PJA2	9867	hgsc.bcm.edu	37	5	108672946	108672946	+	Missense_Mutation	SNP	C	C	T	rs246105	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	189	86	188	0	0.455026	0	C|0.735;T|0.265	0.265	strong	.	PJA2	53	.	NM_014819	exon10	c.G2113A	p.A705T	CTTCTGCAATACT	.	PASS	Atlas-SNP
ADRM1	11047	hgsc.bcm.edu	37	20	60883192	60883192	+	Silent	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	48	12	72	0	0.25	0	.	.	none	.	ADRM1	28	.	NM_175573	exon8	c.G972A	p.A324A	GACCGCGGATGAG	.	PASS	Atlas-SNP
GSTA2	2939	hgsc.bcm.edu	37	6	52617738	52617738	+	Missense_Mutation	SNP	G	G	A	rs2234951	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	158	88	172	0	0.556962	0	G|0.960;A|0.040	0.040	strong	.	GSTA2	33	.	NM_000846	exon5	c.C328T	p.P110S	TAAAGGGCAGAAG	.	PASS	Atlas-SNP
ABCB5	340273	hgsc.bcm.edu	37	7	20767981	20767981	+	Missense_Mutation	SNP	T	T	C	rs117749018	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	134	31	160	0	0.231343	0	T|0.992;C|0.008	0.008	strong	.	ABCB5	357	.	NM_001163941	exon23	c.T2770C	p.F924L	TATGCATTCAGCC	.	PASS	Atlas-SNP
ARHGEF11	9826	hgsc.bcm.edu	37	1	156907081	156907081	+	Missense_Mutation	SNP	T	T	C	rs945508	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	211	210	282	0	0.995261	0	T|0.310;C|0.690	0.690	strong	.	ARHGEF11	168	.	NM_198236	exon39	c.A4400G	p.H1467R	ATGGTATGGAAGA	.	PASS	Atlas-SNP
ABCC5	10057	hgsc.bcm.edu	37	3	183699516	183699516	+	Silent	SNP	T	T	C	rs7636910	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	114	60	141	0	0.526316	0	T|0.657;C|0.343	0.343	strong	ABCC5,NS,carcinoma,0,1	ABCC5	142	1	NM_005688	exon8	c.A1146G	p.Q382Q	CTCACTTTGAACA	.	PASS	Atlas-SNP
TMEM86B	255043	hgsc.bcm.edu	37	19	55739605	55739605	+	Silent	SNP	C	C	T	rs4606850	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	67	26	57	0	0.38806	0	C|0.829;T|0.171	0.171	strong	.	TMEM86B	12	.	NM_173804	exon2	c.G252A	p.S84S	CACAGCCGAGCAC	.	PASS	Atlas-SNP
TTC3	7267	hgsc.bcm.edu	37	21	38563639	38563639	+	Missense_Mutation	SNP	C	C	T	rs61740519	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	246	139	226	0	0.565041	0	C|0.974;T|0.026	0.026	strong	.	TTC3	182	.	NM_001001894	exon40	c.C5029T	p.P1677S	AGTGATCCTGCAG	.	PASS	Atlas-SNP
ZNF283	284349	hgsc.bcm.edu	37	19	44352639	44352639	+	Missense_Mutation	SNP	G	G	A	rs1061768	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	57	21	94	0	0.368421	0	G|0.832;A|0.168	0.168	strong	.	ZNF283	83	.	NM_181845	exon7	c.G1886A	p.R629H	ATCAACGTAAGGA	.	PASS	Atlas-SNP
PLA2G3	50487	hgsc.bcm.edu	37	22	31532960	31532960	+	Missense_Mutation	SNP	C	C	T	rs2232183	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	165	73	151	0	0.442424	0	C|0.845;T|0.155	0.155	strong	.	PLA2G3	85	.	NM_015715	exon5	c.G1133A	p.R378Q	ATTTCCCGGGGCC	.	PASS	Atlas-SNP
MAP7D2	256714	hgsc.bcm.edu	37	X	20071046	20071046	+	Missense_Mutation	SNP	T	T	C	rs34519770	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	201	201	263	0	1	0	T|0.544;C|0.456	0.456	strong	.	MAP7D2	165	.	NM_152780	exon5	c.A545G	p.N182S	CGTTTATTCATGG	.	PASS	Atlas-SNP
OR51F1	256892	hgsc.bcm.edu	37	11	4790948	4790948	+	Missense_Mutation	SNP	C	C	A	rs11033800	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	88	15	98	0	0.170455	0	C|0.707;A|0.293	0.293	strong	.	OR51F1	60	.	NM_001004752	exon1	c.G200T	p.R67M	GATAGCCTGAAGA	.	PASS	Atlas-SNP
COL4A1	1282	hgsc.bcm.edu	37	13	110833702	110833702	+	Silent	SNP	C	C	T	rs16975492	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	104	52	94	0	0.5	0	C|0.691;T|0.309	0.309	strong	.	COL4A1	372	.	NM_001845	exon29	c.G2130A	p.P710P	AGTCCCCGGTGGC	.	PASS	Atlas-SNP
TGM2	7052	hgsc.bcm.edu	37	20	36770588	36770588	+	Silent	SNP	C	C	T	rs2076390	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	179	79	191	0	0.441341	0	C|0.831;T|0.169	0.169	strong	.	TGM2	88	.	NM_198951	exon7	c.G873A	p.L291L	GATGCCCAGGCAC	.	PASS	Atlas-SNP
ANXA9	8416	hgsc.bcm.edu	37	1	150955582	150955582	+	Missense_Mutation	SNP	A	A	G	rs267731	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	45	20	56	0	0.444444	0	A|0.983;G|0.017	0.017	strong	.	ANXA9	28	.	NM_003568	exon3	c.A1G	p.M1V	AGCACCATGTCTG	.	PASS	Atlas-SNP
SLC26A3	1811	hgsc.bcm.edu	37	7	107423254	107423254	+	Silent	SNP	C	C	T	rs3735605	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	88	44	147	0	0.5	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
SLC4A4	8671	hgsc.bcm.edu	37	4	72363294	72363294	+	Missense_Mutation	SNP	A	A	T	rs35891845	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	140	66	126	0	0.471429	0	A|0.998;T|0.002	0.002	strong	.	SLC4A4	269	.	NM_001098484	exon16	c.A2051T	p.N684I	TCGGGAACAACTG	.	PASS	Atlas-SNP
IFT140	9742	hgsc.bcm.edu	37	16	1652418	1652418	+	Missense_Mutation	SNP	C	C	T	rs146128830	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	15	79	0	0.176471	0	C|0.993;T|0.007	0.007	strong	IFT140,NS,carcinoma,0,1	IFT140	128	1	NM_014714	exon4	c.G322A	p.V108M	GGAGCACGGTGAT	.	PASS	Atlas-SNP
SIRPG	55423	hgsc.bcm.edu	37	20	1616137	1616137	+	Missense_Mutation	SNP	G	G	A	rs6034239	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	258	132	243	0	0.511628	0	G|0.459;A|0.541	0.541	strong	.	SIRPG	61	.	NM_018556	exon4	c.C857T	p.S286L	TTCTCCGACCAGG	.	PASS	Atlas-SNP
OR5K3	403277	hgsc.bcm.edu	37	3	98109640	98109640	+	Missense_Mutation	SNP	G	G	A	rs13068323	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	295	155	339	0	0.525424	0	G|0.846;A|0.154	0.154	strong	OR5K3,rectum,carcinoma,-1,1	OR5K3	60	1	NM_001005516	exon1	c.G131A	p.G44D	ACATTGGTTTGGT	.	PASS	Atlas-SNP
IGLL5	100423062	hgsc.bcm.edu	37	22	23230394	23230394	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	114	24	135	0	0.210526	0	.	.	none	.	IGLL5	26	.	NM_001178126	exon1	c.C161T	p.A54V	CTGGAGCCTCAGT	.	PASS	Atlas-SNP
GJA9	81025	hgsc.bcm.edu	37	1	39340875	39340875	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	275	3	305	0	0.0109091	0	.	.	none	GJA9,rectum,carcinoma,-1,1	GJA9	55	1	NM_030772	exon2	c.G896A	p.S299N	TTTAAACTAGGGT	.	scavenged	Atlas-SNP
POLE4	56655	hgsc.bcm.edu	37	2	75185856	75185856	+	Missense_Mutation	SNP	G	G	T	rs12366	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	53	52	51	0	0.981132	0	G|0.638;T|0.362	0.362	strong	.	POLE4	2	.	NM_019896	exon1	c.G50T	p.G17V	AGGAGGGACCTGC	.	PASS	Atlas-SNP
OR51G1	79324	hgsc.bcm.edu	37	11	4944892	4944892	+	Silent	SNP	G	G	C	rs34583466	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	99	20	111	0	0.20202	0	G|0.903;C|0.097	0.097	strong	.	OR51G1	74	.	NM_001005237	exon1	c.C678G	p.T226T	GAGCACGGTGCGA	.	PASS	Atlas-SNP
BRD2	6046	hgsc.bcm.edu	37	6	32942302	32942302	+	Silent	SNP	G	G	A	rs516535	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	123	44	104	0	0.357724	0	G|0.363;A|0.637	0.637	strong	.	BRD2	70	.	NM_005104	exon3	c.G93A	p.K31K	AGGGAAGAGGATT	.	PASS	Atlas-SNP
C6orf222	389384	hgsc.bcm.edu	37	6	36287312	36287312	+	Missense_Mutation	SNP	G	G	C	rs743852	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	38	42	0	0.550725	0	G|0.540;C|0.460	0.460	strong	.	C6orf222	72	.	NM_001010903	exon11	c.C1744G	p.L582V	TGCGCAGGGTGGC	.	PASS	Atlas-SNP
MUC20	200958	hgsc.bcm.edu	37	3	195453014	195453014	+	Missense_Mutation	SNP	G	G	A	rs3828410	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	367	123	400	1	0.33515	0.0025	G|0.800;A|0.200	0.200	strong	.	MUC20	84	.	NM_152673	exon3	c.G1027A	p.G343R	GCACCCGGGGCCA	.	PASS	Atlas-SNP
CDH11	1009	hgsc.bcm.edu	37	16	65022114	65022114	+	Silent	SNP	C	C	T	rs28216	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	329	329	276	0	1	0	C|0.715;T|0.285	0.285	strong	CDH11_ENST00000394156,NS,carcinoma,-1,2	CDH11	260	2	NM_001797	exon7	c.G945A	p.S315S	TTCAAACGATTCC	.	PASS	Atlas-SNP
NUAK1	9891	hgsc.bcm.edu	37	12	106460938	106460938	+	Missense_Mutation	SNP	G	G	C	rs3741883	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	87	79	0	1	0	G|0.796;C|0.204	0.204	strong	NUAK1_ENST00000261402,NS,carcinoma,0,2	NUAK1	196	2	NM_014840	exon7	c.C1628G	p.P543R	ATTTCAGGGCTGA	.	PASS	Atlas-SNP
COL15A1	1306	hgsc.bcm.edu	37	9	101804329	101804329	+	Silent	SNP	T	T	C	rs7854112	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	33	14	41	0	0.424242	0	T|0.871;C|0.129	0.129	strong	.	COL15A1	211	.	NM_001855	exon24	c.T2514C	p.G838G	CCAGGGTCCTAGA	.	PASS	Atlas-SNP
SLC37A1	54020	hgsc.bcm.edu	37	21	43979127	43979127	+	Silent	SNP	C	C	T	rs118032072	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	59	102	0	0.584158	0	C|0.961;T|0.039	0.039	strong	.	SLC37A1	48	.	NM_018964	exon12	c.C909T	p.H303H	GAACCACGTCGTC	.	PASS	Atlas-SNP
KIAA0226	9711	hgsc.bcm.edu	37	3	197432036	197432036	+	Missense_Mutation	SNP	C	C	T	rs61743568	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	52	29	63	0	0.557692	0	C|0.929;T|0.071	0.071	strong	.	KIAA0226	136	.	NM_014687	exon3	c.G230A	p.R77H	GTCTGGCGGCGGC	.	PASS	Atlas-SNP
ALMS1	7840	hgsc.bcm.edu	37	2	73679956	73679956	+	Missense_Mutation	SNP	C	C	T	rs28730854	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	89	32	111	0	0.359551	0	C|0.972;T|0.028	0.028	strong	.	ALMS1	384	.	NM_015120	exon8	c.C6299T	p.S2100L	AGAAATCGAATAT	.	PASS	Atlas-SNP
TCP11L1	55346	hgsc.bcm.edu	37	11	33090362	33090362	+	Silent	SNP	C	C	T	rs34745218	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	8	89	0	0.114286	0	C|0.980;T|0.020	0.020	strong	.	TCP11L1	40	.	NM_001145541	exon9	c.C1284T	p.I428I	CCAGATCCAGGCC	.	PASS	Atlas-SNP
BUD13	84811	hgsc.bcm.edu	37	11	116633862	116633862	+	Missense_Mutation	SNP	G	G	A	rs11820589	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	77	17	84	0	0.220779	0	G|0.905;A|0.095	0.095	strong	.	BUD13	41	.	NM_001159736	exon4	c.C443T	p.P148L	GGATCCGGGGTGT	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228464303	228464303	+	Missense_Mutation	SNP	G	G	T	rs75280352	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	232	134	234	0	0.577586	0	G|0.993;T|0.007	0.007	strong	.	OBSCN	2142	.	NM_001271223	exon26	c.G7498T	p.A2500S	CACCTGGCTGTGC	.	PASS	Atlas-SNP
DNAJC1	64215	hgsc.bcm.edu	37	10	22048330	22048330	+	Silent	SNP	C	C	T	rs9045	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	131	69	120	0	0.526718	0	C|0.861;T|0.139	0.139	strong	DNAJC1,colon,carcinoma,0,2	DNAJC1	42	2	NM_022365	exon11	c.G1365A	p.A455A	CGGCTTCGCTGTA	.	PASS	Atlas-SNP
SMARCA2	6595	hgsc.bcm.edu	37	9	2039793	2039793	+	Missense_Mutation	SNP	A	A	C	rs62534884	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	74	33	58	0	0.445946	0	A|0.970;C|0.030	0.030	strong	SMARCA2_ENST00000349721,caecum,carcinoma,0,2	SMARCA2	313	2	NM_139045	exon4	c.A683C	p.Q228P	AGCAGCAGCAGCA	.	PASS	Atlas-SNP
ESYT2	57488	hgsc.bcm.edu	37	7	158528233	158528233	+	Silent	SNP	A	A	G	rs3816462	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	66	26	88	0	0.393939	0	A|0.703;G|0.297	0.297	strong	.	ESYT2	70	.	NM_020728	exon20	c.T2547C	p.S849S	GCCGCCACTGTTC	.	PASS	Atlas-SNP
NOTCH2NL	388677	hgsc.bcm.edu	37	1	145281656	145281656	+	Missense_Mutation	SNP	A	A	T	rs4649852	bycluster;byfrequency;by2hit2allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	840	127	955	3	0.15119	0.00314136	A|0.863;T|0.137	0.137	strong	NOTCH2NL_ENST00000362074,NS,carcinoma,-2,6	NOTCH2NL	100	6	NM_203458	exon4	c.A586T	p.T196S	GGAGGCACCTGTC	.	scavenged	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195506483	195506483	+	Missense_Mutation	SNP	T	T	G	rs201375109	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	49	14	56	3	0.285714	0.0535714	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.A11968C	p.T3990P	AGGAAGTGTCGGT	.	scavenged	Atlas-SNP
TMCC3	57458	hgsc.bcm.edu	37	12	95044161	95044161	+	Missense_Mutation	SNP	A	A	C	rs1274523	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	7	7	0	0	1	.	A|0.034;C|0.966	0.966	strong	.	TMCC3	63	.	NM_020698	exon1	c.T46G	p.Y16D	CGGGGTACGAGTA	.	PASS	Atlas-SNP
ZAK	0	hgsc.bcm.edu	37	2	174055646	174055646	+	Silent	SNP	T	T	C	rs35853276	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	63	35	114	0	0.555556	0	T|0.858;C|0.142	0.142	strong	.	ZAK	62	.	NM_133646	exon6	c.T439C	p.L147L	GGAGTATTGAAGG	.	PASS	Atlas-SNP
IFT140	9742	hgsc.bcm.edu	37	16	1608082	1608082	+	Silent	SNP	A	A	G	rs2076436	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	149	29	145	0	0.194631	0	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	.	PASS	Atlas-SNP
DSC1	1823	hgsc.bcm.edu	37	18	28734749	28734749	+	Silent	SNP	A	A	G	rs2249810	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	41	41	73	0	1	0	G|0.484;N|0.000	0.484	strong	.	DSC1	240	.	NM_004948	exon5	c.T615C	p.Y205Y	CTGTTCATATTTC	.	PASS	Atlas-SNP
LRIG1	26018	hgsc.bcm.edu	37	3	66433676	66433676	+	Silent	SNP	A	A	G	rs900171	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	118	60	121	0	0.508475	0	A|0.361;G|0.639	0.639	strong	.	LRIG1	138	.	NM_015541	exon15	c.T2221C	p.L741L	GGGTCAAGTGGTG	.	PASS	Atlas-SNP
TRIM17	51127	hgsc.bcm.edu	37	1	228602660	228602660	+	Silent	SNP	G	G	C	rs503203	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	116	63	113	0	0.543103	0	G|0.745;C|0.255	0.255	strong	.	TRIM17	66	.	NM_001024940	exon2	c.C114G	p.A38A	GATGCAGGCTCGG	.	PASS	Atlas-SNP
XPO5	57510	hgsc.bcm.edu	37	6	43492578	43492578	+	Silent	SNP	G	G	A	rs2257082	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	71	85	0	1	0	G|0.652;N|0.002	.	strong	.	XPO5	79	.	NM_020750	exon30	c.C3303T	p.Y1101Y	TGCCTCGTATATC	.	PASS	Atlas-SNP
ALOX12	239	hgsc.bcm.edu	37	17	6904934	6904934	+	Missense_Mutation	SNP	A	A	G	rs434473	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	32	64	0	0.450704	0	A|0.648;G|0.352	0.352	strong	.	ALOX12	49	.	NM_000697	exon8	c.A965G	p.N322S	CTCCCAACCCCAG	.	PASS	Atlas-SNP
HIST1H2BE	8344	hgsc.bcm.edu	37	6	26184041	26184041	+	Silent	SNP	A	A	G	rs16891375	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	32	80	0	0.376471	0	A|0.936;G|0.064	0.064	strong	.	HIST1H2BE	10	.	NM_003523	exon1	c.A18G	p.K6K	AGCGAAATCCGCT	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29912280	29912280	+	Missense_Mutation	SNP	T	T	C	rs35946537	alternate_allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	115	43	159	0	0.373913	0	.	.	alt	.	HLA-A	89	.	NM_001242758	exon5	c.T899C	p.L300P	CAGAGCTGTCTTC	.	PASS	Atlas-SNP
ACAN	176	hgsc.bcm.edu	37	15	89391160	89391160	+	Silent	SNP	C	C	A	rs2272023	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	98	94	80	0	0.959184	0	C|0.305;A|0.695	0.695	strong	ACAN,NS,carcinoma,0,1	ACAN	220	1	NM_001135	exon9	c.C1623A	p.P541P	GAGCCCCCGGACC	.	PASS	Atlas-SNP
ENTPD2	954	hgsc.bcm.edu	37	9	139945971	139945971	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	153	3	142	0	0.0196078	0	.	.	none	ENTPD2,NS,carcinoma,-1,1	ENTPD2	30	1	NM_203468	exon3	c.G377A	p.R126H	AGCAGGCGCATAC	.	scavenged	Atlas-SNP
UBXN11	91544	hgsc.bcm.edu	37	1	26608873	26608873	+	Missense_Mutation	SNP	T	T	A	rs1134583	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	27	12	19	1	0.444444	0.0526316	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
PDXDC1	23042	hgsc.bcm.edu	37	16	15098047	15098047	+	Missense_Mutation	SNP	C	C	G	rs11549900	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	264	99	318	0	0.375	0	C|0.742;G|0.258	0.258	strong	.	PDXDC1	59	.	NM_015027	exon5	c.C246G	p.I82M	CAGAATCCAAAAT	.	PASS	Atlas-SNP
MTIF3	219402	hgsc.bcm.edu	37	13	28009851	28009851	+	Silent	SNP	G	G	A	rs7669	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	54	121	0	0.534653	0	A|0.137;C|0.000;G|0.863	0.137	strong	.	MTIF3	21	.	NM_001166263	exon6	c.C798T	p.D266D	TCCATGGTCTTTG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195513779	195513779	+	Missense_Mutation	SNP	C	C	T	rs3103959	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	36	12	56	0	0.333333	0	.	.	weak	.	MUC4	1505	.	NM_018406	exon2	c.G4672A	p.A1558T	AGGAAGCGTCGGT	.	PASS	Atlas-SNP
PYGB	5834	hgsc.bcm.edu	37	20	25276297	25276297	+	Silent	SNP	G	G	A	rs1130694	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	187	99	196	0	0.529412	0	G|0.542;A|0.458	0.458	strong	.	PYGB	84	.	NM_002862	exon19	c.G2370A	p.Q790Q	GGACCAGCTGTAC	.	PASS	Atlas-SNP
ADCY9	115	hgsc.bcm.edu	37	16	4016943	4016943	+	Silent	SNP	A	A	G	rs2230741	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	11	62	0	0.150685	0	A|0.856;G|0.144	0.144	strong	.	ADCY9	151	.	NM_001116	exon11	c.T2895C	p.S965S	CACCGAACTATTG	.	PASS	Atlas-SNP
DNAH1	25981	hgsc.bcm.edu	37	3	52407041	52407041	+	Silent	SNP	C	C	T	rs1546737	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	27	85	0	0.465517	0	C|0.781;T|0.219	0.219	strong	.	DNAH1	534	.	NM_015512	exon44	c.C6957T	p.H2319H	GGACCACGGCGGC	.	PASS	Atlas-SNP
SLC2A2	6514	hgsc.bcm.edu	37	3	170715830	170715830	+	Silent	SNP	G	G	A	rs5398	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	87	110	0	1	0	G|0.622;A|0.378	0.378	strong	.	SLC2A2	71	.	NM_000340	exon11	c.C1437T	p.F479F	AAATGTGAACAGG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195507251	195507251	+	Missense_Mutation	SNP	G	G	T	rs201456607	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	91	19	78	0	0.208791	0	.	.	weak	MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	NM_018406	exon2	c.C11200A	p.P3734T	AGGAAGGGCTGGT	.	PASS	Atlas-SNP
ZC2HC1A	51101	hgsc.bcm.edu	37	8	79610710	79610710	+	Silent	SNP	A	A	G	rs1054283	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	51	95	0	0.708333	0	A|0.323;G|0.677	0.677	strong	FAM164A,rectum,carcinoma,0,1	.	.	1	NM_016010	exon7	c.A666G	p.L222L	GACCTTATCTCCC	.	PASS	Atlas-SNP
SCML4	256380	hgsc.bcm.edu	37	6	108068003	108068003	+	Missense_Mutation	SNP	C	C	T	rs6934505	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	106	106	122	0	1	0	C|0.875;T|0.125	0.125	strong	.	SCML4	65	.	NM_198081	exon4	c.G377A	p.R126Q	GATGGCCGCTCGG	.	PASS	Atlas-SNP
GGCX	2677	hgsc.bcm.edu	37	2	85788528	85788528	+	Silent	SNP	C	C	T	rs371622780		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	137	67	126	0	0.489051	0	.	.	weak	.	GGCX	44	.	NM_000821	exon1	c.G24A	p.A8A	GGTCCGCGCGGAC	.	PASS	Atlas-SNP
CD8A	925	hgsc.bcm.edu	37	2	87017662	87017662	+	Silent	SNP	G	G	T	rs2229239	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	42	19	60	0	0.452381	0	G|0.932;T|0.068	0.068	strong	.	CD8A	28	.	NM_001145873	exon5	c.C192A	p.A64A	ACTGGCGGCGGCG	.	PASS	Atlas-SNP
FAM53A	152877	hgsc.bcm.edu	37	4	1656801	1656801	+	Silent	SNP	A	A	C	rs62287700	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	38	14	46	1	0.368421	0.0217391	A|0.738;C|0.262	0.262	strong	FAM53A,NS,carcinoma,0,1	FAM53A	25	1	NM_001013622	exon4	c.T786G	p.P262P	CACGCAAGGCTGT	.	scavenged	Atlas-SNP
ZKSCAN4	387032	hgsc.bcm.edu	37	6	28213527	28213527	+	Silent	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	138	54	152	0	0.391304	0	.	.	none	.	ZKSCAN4	42	.	NM_019110	exon5	c.G1005A	p.L335L	TTTAGTCAGGCCT	.	PASS	Atlas-SNP
LRIG1	26018	hgsc.bcm.edu	37	3	66430870	66430870	+	Silent	SNP	G	G	A	rs61754218	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	41	84	0	0.482353	0	A|0.049;C|0.000;G|0.950	0.049	strong	.	LRIG1	138	.	NM_015541	exon19	c.C3099T	p.S1033S	CTCTGTGGAGTCC	.	PASS	Atlas-SNP
ARHGEF11	9826	hgsc.bcm.edu	37	1	156907115	156907115	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	226	224	296	0	0.99115	0	.	.	none	.	ARHGEF11	168	.	NM_198236	exon39	c.A4366G	p.S1456G	CCAGGCTTGGAGG	.	PASS	Atlas-SNP
NOMO2	283820	hgsc.bcm.edu	37	16	18532182	18532182	+	Missense_Mutation	SNP	A	A	T	rs62038475		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	769	52	1013	1	0.0676203	0.000987167	.	.	weak	NOMO2,NS,carcinoma,0,1	NOMO2	36	1	NM_173614	exon19	c.T2178A	p.N726K	TTCCTCATTGCCG	.	scavenged	Atlas-SNP
SGCG	6445	hgsc.bcm.edu	37	13	23898509	23898509	+	Silent	SNP	T	T	C	rs1800353	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	34	86	0	0.472222	0	T|0.406;C|0.594	0.594	strong	.	SGCG	64	.	NM_000231	exon8	c.T705C	p.L235L	CCAGCTTGTGCTT	.	PASS	Atlas-SNP
TDRD5	163589	hgsc.bcm.edu	37	1	179562740	179562740	+	Missense_Mutation	SNP	G	G	C	rs61310274	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	267	129	295	0	0.483146	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
TEF	7008	hgsc.bcm.edu	37	22	41783659	41783659	+	Silent	SNP	C	C	T	rs11546403	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	53	26	51	0	0.490566	0	C|0.825;T|0.175	0.175	strong	.	TEF	21	.	NM_003216	exon2	c.C462T	p.T154T	TGAAACCGTGTCC	.	PASS	Atlas-SNP
CLDND2	125875	hgsc.bcm.edu	37	19	51871194	51871194	+	Missense_Mutation	SNP	C	C	T	rs61736500	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	118	68	133	0	0.576271	0	C|0.995;T|0.005	0.005	strong	.	CLDND2	11	.	NM_152353	exon2	c.G256A	p.D86N	CCTCGTCGCACCG	.	PASS	Atlas-SNP
ARHGEF10	9639	hgsc.bcm.edu	37	8	1817367	1817367	+	Silent	SNP	G	G	A	rs7003969	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	198	153	263	1	0.772727	0.00380228	G|0.777;A|0.223	0.223	strong	.	ARHGEF10	255	.	NM_014629	exon7	c.G630A	p.E210E	TCCAGAGGAAGCA	.	PASS	Atlas-SNP
CNTN3	5067	hgsc.bcm.edu	37	3	74334560	74334560	+	Missense_Mutation	SNP	C	C	T	rs143021649	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	175	80	202	0	0.457143	0	C|0.976;T|0.024	0.024	strong	CNTN3,caecum,carcinoma,+1,1	CNTN3	174	1	NM_020872	exon19	c.G2600A	p.R867Q	AGGCCCCGTAGTC	.	PASS	Atlas-SNP
MTRR	4552	hgsc.bcm.edu	37	5	7900056	7900056	+	Missense_Mutation	SNP	A	A	G	rs148909799	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	129	67	153	0	0.51938	0	A|0.998;G|0.002	0.002	strong	.	MTRR	74	.	NM_024010	exon15	c.A2063G	p.H688R	ATGTACATGATGC	.	PASS	Atlas-SNP
XYLB	9942	hgsc.bcm.edu	37	3	38404472	38404472	+	Missense_Mutation	SNP	C	C	A	rs17118	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	54	22	73	1	0.407407	0.0136986	C|0.731;A|0.269	0.269	strong	XYLB,caecum,carcinoma,+2,1	XYLB	50	1	NM_005108	exon4	c.C255A	p.D85E	CTTCGACTTCTCT	.	scavenged	Atlas-SNP
TAAR8	83551	hgsc.bcm.edu	37	6	132874814	132874814	+	Missense_Mutation	SNP	A	A	C	rs8192627	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	44	26	62	0	0.590909	0	A|0.949;C|0.051	0.051	strong	.	TAAR8	38	.	NM_053278	exon1	c.A983C	p.D328A	GTGGAGATGTTTT	.	PASS	Atlas-SNP
VEZT	55591	hgsc.bcm.edu	37	12	95660182	95660182	+	Missense_Mutation	SNP	A	A	G	rs17855933	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	210	107	231	1	0.509524	0.004329	A|0.925;G|0.075	0.075	strong	.	VEZT	106	.	NM_017599	exon5	c.A484G	p.T162A	CTTCCCACTTGGT	.	PASS	Atlas-SNP
WDR93	56964	hgsc.bcm.edu	37	15	90245253	90245253	+	Silent	SNP	C	C	T	rs4316730	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	98	32	112	0	0.326531	0	C|0.564;T|0.436	0.436	strong	.	WDR93	63	.	NM_020212	exon2	c.C276T	p.T92T	GCCCACCGTCTAC	.	PASS	Atlas-SNP
FYCO1	79443	hgsc.bcm.edu	37	3	46009487	46009487	+	Missense_Mutation	SNP	G	G	A	rs33910087	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	110	58	130	0	0.527273	0	G|0.916;A|0.084	0.084	strong	.	FYCO1	115	.	NM_024513	exon8	c.C1339T	p.R447C	CCAGGCGCTCCAG	.	PASS	Atlas-SNP
ITPRIPL1	150771	hgsc.bcm.edu	37	2	96993884	96993884	+	Silent	SNP	A	A	G	rs1048675	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	106	50	142	0	0.471698	0	A|0.691;C|0.000;G|0.309	0.309	strong	ITPRIPL1,NS,carcinoma,0,1	ITPRIPL1	58	1	NM_178495	exon1	c.A1539G	p.P513P	CATCCCAATCCCT	.	PASS	Atlas-SNP
SCAF11	9169	hgsc.bcm.edu	37	12	46322449	46322449	+	Silent	SNP	C	C	T	rs10880868	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	181	80	201	0	0.441989	0	C|0.857;T|0.143	0.143	strong	SCAF11,NS,carcinoma,0,1	SCAF11	145	1	NM_004719	exon11	c.G1035A	p.G345G	ATCACACCCAGAA	.	PASS	Atlas-SNP
FRY	10129	hgsc.bcm.edu	37	13	32776616	32776616	+	Missense_Mutation	SNP	T	T	A	rs61750791	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	98	47	92	0	0.479592	0	T|0.916;A|0.084	0.084	strong	.	FRY	312	.	NM_023037	exon31	c.T3970A	p.C1324S	TTGTCATGTGAGC	.	PASS	Atlas-SNP
GLYATL2	219970	hgsc.bcm.edu	37	11	58602309	58602309	+	Missense_Mutation	SNP	C	C	T	rs11229651	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	29	94	0	0.298969	0	C|0.732;T|0.268	0.268	strong	GLYATL2,NS,carcinoma,0,1	GLYATL2	40	1	NM_145016	exon6	c.G478A	p.E160K	TTCCTTCCCTGTG	.	PASS	Atlas-SNP
ZFHX4	79776	hgsc.bcm.edu	37	8	77745635	77745635	+	Silent	SNP	G	G	A	rs2733733	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	124	124	155	1	1	0.00645161	G|0.387;A|0.613	0.613	strong	.	ZFHX4	878	.	NM_024721	exon5	c.G3387A	p.S1129S	GAGATCGACCTCA	.	PASS	Atlas-SNP
PBK	55872	hgsc.bcm.edu	37	8	27667969	27667969	+	Silent	SNP	C	C	G	rs2294092	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	127	126	142	0	0.992126	0	C|0.567;G|0.433	0.433	strong	.	PBK	29	.	NM_018492	exon8	c.G822C	p.A274A	TCCCAACGCTGCA	.	PASS	Atlas-SNP
ATP10B	23120	hgsc.bcm.edu	37	5	160115007	160115007	+	Silent	SNP	C	C	T	rs201071012	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	146	86	177	1	0.589041	0.00564972	C|0.996;T|0.005	0.005	strong	.	ATP10B	201	.	NM_025153	exon5	c.G75A	p.S25S	GGTTTCCGATGGA	.	PASS	Atlas-SNP
BPIFB4	149954	hgsc.bcm.edu	37	20	31671663	31671663	+	Silent	SNP	T	T	C	rs2424945	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	32	19	42	0	0.59375	0	T|0.623;C|0.377	0.377	strong	.	.	.	.	NM_182519	exon3	c.T660C	p.T220T	CAGCACTGTGCAA	.	PASS	Atlas-SNP
PMPCA	23203	hgsc.bcm.edu	37	9	139305140	139305140	+	Missense_Mutation	SNP	C	C	A	rs149055087	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	150	88	74	0	0.586667	0	C|0.991;A|0.009	0.009	strong	.	PMPCA	29	.	NM_015160	exon1	c.C20A	p.A7E	TGCTGGCGGCGAC	.	PASS	Atlas-SNP
GRIN3A	116443	hgsc.bcm.edu	37	9	104335682	104335682	+	Missense_Mutation	SNP	C	C	T	rs3739722	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	189	96	186	0	0.507937	0	C|0.831;T|0.169	0.169	strong	.	GRIN3A	186	.	NM_133445	exon9	c.G3122A	p.R1041Q	TGGATCCGGATGC	.	PASS	Atlas-SNP
GPRC5D	55507	hgsc.bcm.edu	37	12	13102605	13102605	+	Silent	SNP	G	G	A	rs4630382	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	112	57	91	0	0.508929	0	G|0.739;A|0.261	0.261	strong	.	GPRC5D	23	.	NM_018654	exon1	c.C714T	p.D238D	CGGGTCGTCCCAC	.	PASS	Atlas-SNP
RIT2	6014	hgsc.bcm.edu	37	18	40323497	40323497	+	Silent	SNP	G	G	T	rs1804730	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	77	43	65	0	0.558442	0	G|0.455;T|0.545	0.545	strong	.	RIT2	56	.	NM_002930	exon5	c.C615A	p.L205L	ACCTTTGAGCTTC	.	PASS	Atlas-SNP
SLFN13	146857	hgsc.bcm.edu	37	17	33769034	33769034	+	Silent	SNP	G	G	A	rs76823120	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	686	310	764	6	0.451895	0.0078534	.	.	weak	SLFN13,rectum,carcinoma,0,1	SLFN13	79	1	NM_144682	exon5	c.C1470T	p.T490T	AAAGGCGGTGCGA	.	scavenged	Atlas-SNP
CHDH	55349	hgsc.bcm.edu	37	3	53855738	53855738	+	Silent	SNP	G	G	C	rs35064726	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	38	96	0	0.535211	0	G|0.958;C|0.042	0.042	strong	.	CHDH	34	.	NM_018397	exon5	c.C921G	p.L307L	GCCAGAGAGCATG	.	PASS	Atlas-SNP
NES	10763	hgsc.bcm.edu	37	1	156640156	156640156	+	Missense_Mutation	SNP	G	G	A	rs3748570	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	60	25	58	0	0.416667	0	G|0.310;A|0.690	0.690	strong	.	NES	196	.	NM_006617	exon4	c.C3824T	p.P1275L	TCCTGGGGGCCCT	.	PASS	Atlas-SNP
TRIM31	11074	hgsc.bcm.edu	37	6	30075843	30075843	+	Silent	SNP	T	T	C	rs3132679	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	124	123	207	0	0.991935	0	T|0.196;C|0.804	0.804	strong	.	TRIM31	40	.	NM_007028	exon6	c.A870G	p.L290L	TTTTTTTAGGCTC	.	PASS	Atlas-SNP
HAS1	3036	hgsc.bcm.edu	37	19	52217174	52217174	+	Missense_Mutation	SNP	C	C	T	rs45625331	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	17	8	21	0	0.470588	0	C|0.997;T|0.003	0.003	strong	.	HAS1	61	.	NM_001523	exon5	c.G1243A	p.V415M	CCGCCACGAAGAA	.	PASS	Atlas-SNP
PLEKHH2	130271	hgsc.bcm.edu	37	2	43931176	43931176	+	Silent	SNP	T	T	C	rs4953002	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	68	68	46	0	1	0	T|0.587;C|0.413	0.413	strong	PLEKHH2,NS,carcinoma,0,1	PLEKHH2	156	1	NM_172069	exon9	c.T1707C	p.N569N	CTTCAATATGGAG	.	PASS	Atlas-SNP
TTLL9	164395	hgsc.bcm.edu	37	20	30527065	30527065	+	Silent	SNP	T	T	C	rs6061043	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	39	16	58	0	0.410256	0	T|0.572;C|0.428	0.428	strong	TTLL9,NS,carcinoma,0,1	TTLL9	95	1	NM_001008409	exon14	c.T1239C	p.H413H	CACACATCTCGGT	.	PASS	Atlas-SNP
RBM44	375316	hgsc.bcm.edu	37	2	238733016	238733016	+	Silent	SNP	G	G	A	rs4663795	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	102	46	91	0	0.45098	0	G|0.738;A|0.262	0.262	strong	.	RBM44	167	.	NM_001080504	exon10	c.G2406A	p.Q802Q	GACACAGGGAAAT	.	PASS	Atlas-SNP
WBSCR28	135886	hgsc.bcm.edu	37	7	73275565	73275565	+	Missense_Mutation	SNP	T	T	A	rs11770052	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	43	42	71	0	0.976744	0	T|0.385;A|0.615	0.615	strong	.	WBSCR28	24	.	NM_182504	exon1	c.T41A	p.I14N	TGGGGATCCTGTT	.	PASS	Atlas-SNP
METTL11B	149281	hgsc.bcm.edu	37	1	170135765	170135765	+	Silent	SNP	T	T	C	rs6669514	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	131	73	141	0	0.557252	0	T|0.746;C|0.254	0.254	strong	.	METTL11B	18	.	NM_001136107	exon3	c.T453C	p.F151F	ATCCTTTCTCCTT	.	PASS	Atlas-SNP
ELP2	55250	hgsc.bcm.edu	37	18	33718326	33718326	+	Missense_Mutation	SNP	A	A	C	rs1785934	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	89	47	85	0	0.52809	0	A|0.654;C|0.346	0.346	strong	.	ELP2	70	.	NM_001242879	exon4	c.A382C	p.T128P	TTATGTACACTGA	.	PASS	Atlas-SNP
OR5L2	26338	hgsc.bcm.edu	37	11	55595017	55595017	+	Missense_Mutation	SNP	G	G	T	rs117277709		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	36	139	0	0.514286	0	.	.	weak	OR5L2,NS,carcinoma,-1,2	OR5L2	135	2	NM_001004739	exon1	c.G323T	p.G108V	CATGTGGAGTCAC	.	PASS	Atlas-SNP
CHD5	26038	hgsc.bcm.edu	37	1	6211183	6211183	+	Silent	SNP	G	G	A	rs9434711	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	121	47	155	0	0.38843	0	G|0.588;A|0.412	0.412	strong	.	CHD5	267	.	NM_015557	exon7	c.C903T	p.F301F	GCTGTCGAAGTCC	.	PASS	Atlas-SNP
KRTAP4-11	653240	hgsc.bcm.edu	37	17	39274266	39274266	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	32	8	37	0	0.25	0	.	.	none	.	KRTAP4-11	94	.	NM_033059	exon1	c.G302A	p.R101H	CTGGGGCGGCAGC	.	PASS	Atlas-SNP
GPRIN1	114787	hgsc.bcm.edu	37	5	176026122	176026122	+	Silent	SNP	C	C	T	rs3797464		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	125	29	172	0	0.232	0	.	.	weak	GPRIN1,rectum,carcinoma,-1,2	GPRIN1	77	2	NM_052899	exon2	c.G714A	p.L238L	CTTTCTCAAAGAC	.	PASS	Atlas-SNP
RNF111	54778	hgsc.bcm.edu	37	15	59347929	59347929	+	Silent	SNP	C	C	A	rs1446239	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	154	100	126	1	0.649351	0.00793651	C|0.554;A|0.446	0.446	strong	RNF111_ENST00000434298,rectum,carcinoma,0,4	RNF111	179	4	NM_017610	exon4	c.C1056A	p.S352S	GGGTTCCAGTTCT	.	scavenged	Atlas-SNP
DPH3	285381	hgsc.bcm.edu	37	3	16305674	16305674	+	Silent	SNP	C	C	G	rs14080	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	117	114	106	0	0.974359	0	C|0.590;G|0.410	0.410	strong	DPH3,NS,adenoma,0,1	DPH3	7	1	NM_206831	exon2	c.G171C	p.V57V	ATAAATCACTTTT	.	PASS	Atlas-SNP
HIST1H3C	8352	hgsc.bcm.edu	37	6	26045905	26045905	+	Silent	SNP	G	G	C	rs3752417	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	88	41	84	0	0.465909	0	G|0.908;C|0.092	0.092	strong	.	HIST1H3C	34	.	NM_003531	exon1	c.G267C	p.A89A	CTCTGCGGTGATG	.	PASS	Atlas-SNP
KIF13A	63971	hgsc.bcm.edu	37	6	17794494	17794494	+	Silent	SNP	G	G	A	rs3734234	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	91	90	96	0	0.989011	0	G|0.609;A|0.391	0.391	strong	.	KIF13A	276	.	NM_001105567	exon25	c.C3208T	p.L1070L	TGTCCAGCCCTCT	.	PASS	Atlas-SNP
DAPK1	1612	hgsc.bcm.edu	37	9	90252966	90252966	+	Silent	SNP	C	C	T	rs55800264	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	32	110	0	0.426667	0	C|0.991;T|0.009	0.009	strong	.	DAPK1	329	.	NM_004938	exon4	c.C393T	p.H131H	CCTGCACTCCCTT	.	PASS	Atlas-SNP
PMEL	6490	hgsc.bcm.edu	37	12	56351346	56351346	+	Silent	SNP	G	G	A	rs1052165	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	84	47	74	0	0.559524	0	G|0.799;N|0.000	.	strong	.	PMEL	60	.	NM_001200054	exon6	c.C741T	p.P247P	GCCACTGGGGTCA	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	175	90	170	0	0.514286	0	A|0.770;G|0.230	0.230	strong	.	.	.	.	NM_014283	exon14	c.A1368G	p.E456E	GGAAGAATATGAA	.	PASS	Atlas-SNP
RCAN3	11123	hgsc.bcm.edu	37	1	24859665	24859665	+	Silent	SNP	G	G	A	rs196430	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	67	28	86	0	0.41791	0	A|0.338;C|0.003	0.338	strong	.	RCAN3	22	.	NM_001251979	exon4	c.G462A	p.P154P	TCCCCCGGTGGGG	.	PASS	Atlas-SNP
PKHD1L1	93035	hgsc.bcm.edu	37	8	110460488	110460488	+	Missense_Mutation	SNP	G	G	T	rs1673407	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	90	68	104	0	0.755556	0	G|0.427;T|0.573	0.573	strong	PKHD1L1,colon,carcinoma,0,1	PKHD1L1	522	1	NM_177531	exon39	c.G5893T	p.V1965L	AGTGTGGTGCAGT	.	PASS	Atlas-SNP
OR13C3	138803	hgsc.bcm.edu	37	9	107298270	107298270	+	Silent	SNP	C	C	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	108	22	141	0	0.203704	0	.	.	none	.	OR13C3	45	.	NM_001001961	exon1	c.G825T	p.L275L	CACAGTCAGGTGA	.	PASS	Atlas-SNP
PKD1L1	168507	hgsc.bcm.edu	37	7	47840387	47840387	+	Missense_Mutation	SNP	C	C	T	rs13231277	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	60	42	97	0	0.7	0	C|0.858;T|0.142	0.142	strong	.	PKD1L1	328	.	NM_138295	exon54	c.G8053A	p.A2685T	GGAAGGCGTCTGT	.	PASS	Atlas-SNP
KRTAP4-6	81871	hgsc.bcm.edu	37	17	39296361	39296361	+	Missense_Mutation	SNP	A	A	G	rs146882220	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	26	72	3	0.282609	0.0416667	.	.	weak	KRTAP4-6,NS,carcinoma,0,3	KRTAP4-6	46	3	NM_030976	exon1	c.T379C	p.S127P	ACTGGGACCTGCA	.	scavenged	Atlas-SNP
FAM218A	152756	hgsc.bcm.edu	37	4	165878335	165878335	+	Missense_Mutation	SNP	A	A	G	rs3733418	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	164	87	231	0	0.530488	0	A|0.813;G|0.187	0.187	strong	.	.	.	.	NM_153027	exon1	c.A161G	p.H54R	GCCGCCATGGCAG	.	PASS	Atlas-SNP
DOK7	285489	hgsc.bcm.edu	37	4	3494956	3494956	+	Missense_Mutation	SNP	C	C	T	rs16844464	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	34	74	0	0.435897	0	C|0.935;T|0.065	0.065	strong	DOK7,NS,carcinoma,0,1	DOK7	44	1	NM_173660	exon7	c.C1243T	p.P415S	CTGGCTCCTAGAG	.	PASS	Atlas-SNP
LPCAT1	79888	hgsc.bcm.edu	37	5	1466919	1466919	+	Silent	SNP	G	G	A	rs2277006	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	111	66	136	0	0.594595	0	G|0.696;A|0.304	0.304	strong	LPCAT1,NS,carcinoma,0,1	LPCAT1	70	1	NM_024830	exon13	c.C1365T	p.T455T	GGTCACGGTGAGC	.	PASS	Atlas-SNP
C9orf43	257169	hgsc.bcm.edu	37	9	116187302	116187302	+	Missense_Mutation	SNP	C	C	G	rs111748634	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	31	17	27	0	0.548387	0	C|0.957;G|0.043	0.043	strong	.	C9orf43	49	.	NM_152786	exon9	c.C811G	p.P271A	CAGAGACCAGCAC	.	PASS	Atlas-SNP
ANO2	57101	hgsc.bcm.edu	37	12	6030437	6030437	+	Silent	SNP	A	A	G	rs3741904	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	95	44	98	0	0.463158	0	A|0.917;G|0.083	0.083	strong	.	ANO2	309	.	NM_020373	exon3	c.T291C	p.Y97Y	AAGTACATAGTCG	.	PASS	Atlas-SNP
UTS2	10911	hgsc.bcm.edu	37	1	7909737	7909737	+	Missense_Mutation	SNP	C	C	T	rs2890565	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	98	49	130	0	0.5	0	C|0.928;T|0.072	0.072	strong	.	UTS2	18	.	NM_021995	exon4	c.G266A	p.S89N	TTGGTACTTGAGT	.	PASS	Atlas-SNP
MIS12	79003	hgsc.bcm.edu	37	17	5392791	5392791	+	Silent	SNP	A	A	G	rs74577983	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	23	87	0	0.323944	0	A|0.972;G|0.028	0.028	strong	.	MIS12	19	.	NM_001258220	exon2	c.A609G	p.K203K	ACTGAAAATATCT	.	PASS	Atlas-SNP
SP140L	93349	hgsc.bcm.edu	37	2	231256812	231256812	+	Silent	SNP	A	A	G	rs7559665	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	113	113	134	0	1	0	A|0.801;G|0.199	0.199	strong	.	SP140L	68	.	NM_138402	exon12	c.A975G	p.A325A	CTTGGCAAAGTGT	.	PASS	Atlas-SNP
PKHD1L1	93035	hgsc.bcm.edu	37	8	110465060	110465060	+	Silent	SNP	G	G	C	rs1673404	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	53	38	79	0	0.716981	0	G|0.517;C|0.483	0.483	strong	PKHD1L1,NS,carcinoma,+2,1	PKHD1L1	522	1	NM_177531	exon43	c.G6621C	p.L2207L	CATTCTGCTGGAT	.	PASS	Atlas-SNP
CCDC110	256309	hgsc.bcm.edu	37	4	186380243	186380243	+	Missense_Mutation	SNP	A	A	C	rs59319722	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	43	22	85	0	0.511628	0	A|0.548;C|0.452	0.452	strong	.	CCDC110	78	.	NM_152775	exon6	c.T1498G	p.Y500D	TGCTGTATTCTTC	.	PASS	Atlas-SNP
CCDC168	643677	hgsc.bcm.edu	37	13	103392127	103392127	+	Missense_Mutation	SNP	T	T	A	rs74435572	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	33	124	0	0.423077	0	T|0.933;A|0.067	0.067	strong	.	.	.	.	NM_001146197	exon4	c.A10920T	p.K3640N	TGTTTCTTTATTC	.	PASS	Atlas-SNP
ADRA2B	151	hgsc.bcm.edu	37	2	96780716	96780716	+	Silent	SNP	T	T	G	rs2229169	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	89	89	82	0	1	0	T|0.317;G|0.683	0.683	strong	.	ADRA2B	115	.	NM_000682	exon1	c.A1173C	p.G391G	GATGGCTCCCAGG	.	PASS	Atlas-SNP
RFX6	222546	hgsc.bcm.edu	37	6	117243260	117243260	+	Silent	SNP	T	T	C	rs7764347	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	45	22	47	0	0.488889	0	T|0.750;C|0.250	0.250	strong	.	RFX6	141	.	NM_173560	exon13	c.T1383C	p.T461T	TGCCACTGTGGAG	.	PASS	Atlas-SNP
CFH	3075	hgsc.bcm.edu	37	1	196695742	196695742	+	Silent	SNP	A	A	G	rs3753396	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	148	70	215	1	0.472973	0.00465116	A|0.777;G|0.223	0.223	strong	CFH,NS,carcinoma,+2,3	CFH	251	3	NM_000186	exon13	c.A2016G	p.Q672Q	AATTCAATGTGTT	.	PASS	Atlas-SNP
PTPRA	5786	hgsc.bcm.edu	37	20	2996497	2996497	+	Silent	SNP	C	C	T	rs1178016	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	56	27	78	0	0.482143	0	C|0.453;T|0.547	0.547	strong	.	PTPRA	75	.	NM_002836	exon16	c.C909T	p.G303G	CCAGGGCTACCAA	.	PASS	Atlas-SNP
PTHLH	5744	hgsc.bcm.edu	37	12	28116465	28116465	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	169	38	214	0	0.224852	0	.	.	none	.	PTHLH	36	.	NM_198964	exon3	c.T340C	p.Y114H	CTTTGTACGTCTC	.	PASS	Atlas-SNP
CPED1	79974	hgsc.bcm.edu	37	7	120906785	120906785	+	Silent	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	354	5	392	0	0.0141243	0	.	.	none	C7orf58,NS,carcinoma,+2,1	.	.	1	NM_024913	exon20	c.C2556T	p.G852G	TACTGGCCAGACT	.	scavenged	Atlas-SNP
UBN1	29855	hgsc.bcm.edu	37	16	4925291	4925291	+	Silent	SNP	T	T	G	rs17137364	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	60	48	73	0	0.8	0	T|0.912;G|0.088	0.088	strong	.	UBN1	88	.	NM_001079514	exon15	c.T2880G	p.V960V	GCCTGTTTCCCAG	.	PASS	Atlas-SNP
PSD3	23362	hgsc.bcm.edu	37	8	18729459	18729459	+	Silent	SNP	T	T	C	rs13273954	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	250	175	238	0	0.7	0	C|0.267;N|0.001	0.267	strong	.	PSD3	142	.	NM_015310	exon3	c.A915G	p.E305E	CAGTATTTCCACT	.	PASS	Atlas-SNP
SPATA31E1	286234	hgsc.bcm.edu	37	9	90502458	90502458	+	Missense_Mutation	SNP	T	T	A	rs10868670	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	102	49	129	0	0.480392	0	T|0.313;A|0.687	0.687	strong	.	.	.	.	NM_178828	exon4	c.T3056A	p.V1019E	TGCAAGTGCTCAG	.	PASS	Atlas-SNP
ITGA3	3675	hgsc.bcm.edu	37	17	48149386	48149386	+	Silent	SNP	C	C	T	rs2269772	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	27	124	0	0.375	0	C|0.807;T|0.193	0.193	strong	.	ITGA3	128	.	NM_005501	exon7	c.C996T	p.F332F	CTACTTCGAGAGG	.	PASS	Atlas-SNP
C1orf110	339512	hgsc.bcm.edu	37	1	162824960	162824960	+	Silent	SNP	G	G	A	rs190249067	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	215	103	242	0	0.47907	0	G|0.999;A|0.001	0.001	strong	.	C1orf110	22	.	NM_178550	exon4	c.C504T	p.D168D	GTCTACGTCCTTA	.	PASS	Atlas-SNP
STK11IP	114790	hgsc.bcm.edu	37	2	220473355	220473355	+	Missense_Mutation	SNP	G	G	A	rs673951	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	228	109	241	0	0.47807	0	G|0.643;A|0.357	0.357	strong	.	STK11IP	152	.	NM_052902	exon15	c.G1687A	p.V563I	GAGGGCGTACGGG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195512742	195512742	+	Silent	SNP	G	G	A	rs113755990	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	115	30	55	0	0.26087	0	G|0.992;A|0.008	0.008	strong	MUC4_ENST00000463781,NS,haematopoietic_neoplasm,0,6	MUC4	1505	6	NM_018406	exon2	c.C5709T	p.T1903T	AAGAGGGGTGGTG	.	PASS	Atlas-SNP
ZNF80	7634	hgsc.bcm.edu	37	3	113955820	113955820	+	Silent	SNP	G	G	C	rs3732780	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	123	48	124	0	0.390244	0	G|0.703;C|0.297	0.297	strong	.	ZNF80	75	.	NM_007136	exon1	c.C102G	p.S34S	TCCCTGGGAGTCA	.	PASS	Atlas-SNP
PHPT1	29085	hgsc.bcm.edu	37	9	139744578	139744578	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	146	39	111	0	0.267123	0	.	.	none	.	PHPT1	14	.	NM_001135861	exon2	c.G274A	p.G92S	GTGTACGGCTATT	.	PASS	Atlas-SNP
PSME4	23198	hgsc.bcm.edu	37	2	54127041	54127041	+	Silent	SNP	C	C	T	rs805423	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	503	376	297	1	0.747515	0.003367	C|0.452;T|0.548	0.548	strong	.	PSME4	247	.	NM_014614	exon29	c.G3399A	p.Q1133Q	CTTTTCCTGTTGG	.	PASS	Atlas-SNP
TUBG2	27175	hgsc.bcm.edu	37	17	40818699	40818699	+	Missense_Mutation	SNP	A	A	G	rs1046097	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	177	93	241	0	0.525424	0	A|0.531;G|0.469	0.469	strong	.	TUBG2	43	.	NM_016437	exon11	c.A1237G	p.M413V	GAGGACATGTTCA	.	PASS	Atlas-SNP
MYH7B	57644	hgsc.bcm.edu	37	20	33581955	33581955	+	Silent	SNP	G	G	A	rs2425012	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	223	106	224	0	0.475336	0	G|0.585;A|0.415	0.415	strong	.	MYH7B	145	.	NM_020884	exon27	c.G2577A	p.A859A	GGATGCGCTGTTC	.	PASS	Atlas-SNP
GBP3	2635	hgsc.bcm.edu	37	1	89475135	89475135	+	Missense_Mutation	SNP	C	C	T	rs10493821	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	254	142	272	0	0.559055	0	C|0.773;T|0.227	0.227	strong	.	GBP3	53	.	NM_018284	exon9	c.G1405A	p.V469M	CGGTCACAGACTC	.	PASS	Atlas-SNP
PPP1R26	9858	hgsc.bcm.edu	37	9	138377853	138377853	+	Silent	SNP	A	A	G	rs2004074	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	56	25	50	0	0.446429	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
CACNA1H	8912	hgsc.bcm.edu	37	16	1252369	1252369	+	Missense_Mutation	SNP	C	C	T	rs61734410	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	54	43	0	0.739726	0	C|0.556;T|0.444	0.444	strong	CACNA1H_ENST00000358590,bladder,carcinoma,-1,2	CACNA1H	317	2	NM_021098	exon9	c.C1919T	p.P640L	GTGGACCGCCAGG	.	PASS	Atlas-SNP
GLYATL3	389396	hgsc.bcm.edu	37	6	49479775	49479775	+	Silent	SNP	A	A	T	rs1480615	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	35	14	64	0	0.4	0	T|0.431;N|0.000	0.431	strong	GLYATL3,trunk,malignant_melanoma,+1,1	GLYATL3	19	1	NM_001010904	exon2	c.A72T	p.S24S	TGAATCACTCAAG	.	PASS	Atlas-SNP
FAM135B	51059	hgsc.bcm.edu	37	8	139165068	139165068	+	Silent	SNP	C	C	T	rs3763590	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	94	94	113	0	1	0	C|0.632;T|0.368	0.368	strong	.	FAM135B	423	.	NM_015912	exon13	c.G1650A	p.V550V	GGTCAGCACTGGG	.	PASS	Atlas-SNP
AKAP6	9472	hgsc.bcm.edu	37	14	33014869	33014869	+	Missense_Mutation	SNP	C	C	T	rs3742926	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	78	100	0	1	0	C|0.859;T|0.141	0.141	strong	.	AKAP6	308	.	NM_004274	exon4	c.C1010T	p.A337V	ATGCTGCTCAACC	.	PASS	Atlas-SNP
MMP3	4314	hgsc.bcm.edu	37	11	102713465	102713465	+	Silent	SNP	A	A	G	rs602128	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	127	126	160	0	0.992126	0	A|0.461;G|0.539	0.539	strong	MMP3,NS,carcinoma,0,1	MMP3	60	1	NM_002422	exon2	c.T288C	p.D96D	ACCAACATCAGGA	.	PASS	Atlas-SNP
KRTAP4-6	81871	hgsc.bcm.edu	37	17	39296422	39296422	+	Silent	SNP	A	A	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	50	6	65	2	0.12	0.0307692	.	.	none	KRTAP4-6,NS,carcinoma,-1,2	KRTAP4-6	46	2	NM_030976	exon1	c.T318C	p.R106R	GCTGGGACGGCAG	.	scavenged	Atlas-SNP
LDLR	3949	hgsc.bcm.edu	37	19	11222300	11222300	+	Missense_Mutation	SNP	G	G	A	rs11669576	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	24	13	36	0	0.541667	0	G|0.916;A|0.084	0.084	strong	.	LDLR	72	.	NM_001195798	exon8	c.G1171A	p.A391T	ACGAAGGCCTGCA	.	PASS	Atlas-SNP
ARHGAP19	84986	hgsc.bcm.edu	37	10	99006083	99006083	+	Silent	SNP	G	G	A	rs13439	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	52	27	83	0	0.519231	0	G|0.724;A|0.276	0.276	strong	ARHGAP19_ENST00000358531,caecum,carcinoma,-2,3	ARHGAP19	72	3	NM_032900	exon7	c.C939T	p.Y313Y	CCGAATGTAAGCA	.	PASS	Atlas-SNP
GCLC	2729	hgsc.bcm.edu	37	6	53387242	53387242	+	Silent	SNP	C	C	A	rs2066508	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	66	28	91	0	0.424242	0	C|0.975;A|0.025	0.025	strong	.	GCLC	58	.	NM_001197115	exon2	c.G234T	p.L78L	CTCTTGCAGAGTT	.	PASS	Atlas-SNP
TMEM82	388595	hgsc.bcm.edu	37	1	16069644	16069644	+	Silent	SNP	C	C	T	rs11584945	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	88	49	83	0	0.556818	0	C|0.766;T|0.234	0.234	strong	.	TMEM82	30	.	NM_001013641	exon3	c.C291T	p.L97L	GGTGCTCGAGTTC	.	PASS	Atlas-SNP
RADIL	55698	hgsc.bcm.edu	37	7	4841614	4841614	+	Missense_Mutation	SNP	C	C	T	rs117943885	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	119	22	89	0	0.184874	0	C|0.984;T|0.016	0.016	strong	.	RADIL	110	.	NM_018059	exon12	c.G2512A	p.V838M	GGACCACGTGGTG	.	PASS	Atlas-SNP
PPP2R3A	5523	hgsc.bcm.edu	37	3	135721208	135721208	+	Missense_Mutation	SNP	A	A	G	rs146596318	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	44	22	51	0	0.5	0	A|1.000;G|0.000	0.000	strong	.	PPP2R3A	114	.	NM_002718	exon2	c.A868G	p.K290E	TATCTGAAAAAGT	.	PASS	Atlas-SNP
RC3H2	54542	hgsc.bcm.edu	37	9	125639808	125639808	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	60	37	73	0	0.616667	0	.	.	none	.	RC3H2	150	.	NM_018835	exon9	c.G1267A	p.G423R	AACCCCCTTGCTG	.	PASS	Atlas-SNP
C10orf71	118461	hgsc.bcm.edu	37	10	50533237	50533237	+	Missense_Mutation	SNP	G	G	A	rs12217617	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	26	59	0	0.448276	0	G|0.803;A|0.197	0.197	strong	.	C10orf71	179	.	NM_001135196	exon3	c.G2647A	p.D883N	TTGGAGGACTCCC	.	PASS	Atlas-SNP
KDM2B	84678	hgsc.bcm.edu	37	12	122018761	122018761	+	Missense_Mutation	SNP	T	T	C	rs191586330	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	172	78	153	0	0.453488	0	T|0.997;C|0.003	0.003	strong	.	KDM2B	218	.	NM_032590	exon1	c.A56G	p.H19R	GCTGCATGTCTTT	.	PASS	Atlas-SNP
PTK2B	2185	hgsc.bcm.edu	37	8	27293865	27293865	+	Silent	SNP	C	C	T	rs7005936	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	275	45	342	0	0.163636	0	C|0.638;T|0.362	0.362	strong	PTK2B_ENST00000544172,brain,glioma,0,6	PTK2B	304	6	NM_173174	exon20	c.C1341T	p.H447H	AAATCACGTGAGT	.	PASS	Atlas-SNP
KRTAP10-2	386679	hgsc.bcm.edu	37	21	45971162	45971162	+	Silent	SNP	C	C	T	rs76415521		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	131	37	53	0	0.282443	0	.	.	weak	KRTAP10-2,colon,carcinoma,0,1	KRTAP10-2	21	1	NM_198693	exon1	c.G180A	p.A60A	ACAGGCCGCCTGG	.	scavenged	Atlas-SNP
KRTAP3-3	85293	hgsc.bcm.edu	37	17	39150284	39150284	+	Silent	SNP	A	A	G	rs2010201	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	133	66	161	0	0.496241	0	A|0.598;G|0.402	0.402	strong	.	KRTAP3-3	11	.	NM_033185	exon1	c.T66C	p.S22S	TTTGTCAGAGGAG	.	PASS	Atlas-SNP
ABCF3	55324	hgsc.bcm.edu	37	3	183904049	183904049	+	Silent	SNP	A	A	G	rs11539876	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	138	61	145	0	0.442029	0	A|0.835;G|0.165	0.165	strong	.	ABCF3	72	.	NM_018358	exon1	c.A54G	p.Q18Q	CGGACAAGTCTTC	.	PASS	Atlas-SNP
IGSF3	3321	hgsc.bcm.edu	37	1	117122130	117122130	+	Missense_Mutation	SNP	T	T	C	rs6703791	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	23	122	0	0.328571	0	T|0.725;C|0.275	0.275	strong	.	IGSF3	294	.	NM_001542	exon11	c.A3278G	p.Q1093R	GTATCTTGGGGGC	.	PASS	Atlas-SNP
ZNF334	55713	hgsc.bcm.edu	37	20	45131665	45131665	+	Missense_Mutation	SNP	T	T	C	rs111517766	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	301	137	331	0	0.45515	0	T|0.986;C|0.014	0.014	strong	ZNF334,NS,carcinoma,+1,1	ZNF334	101	1	NM_018102	exon5	c.A313G	p.N105D	TTTTGTTGCTGAA	.	PASS	Atlas-SNP
OPN1SW	611	hgsc.bcm.edu	37	7	128415195	128415195	+	Silent	SNP	T	T	G	rs1799922	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	49	22	61	0	0.44898	0	T|0.710;G|0.290	0.290	strong	OPN1SW,NS,carcinoma,0,1	OPN1SW	52	1	NM_001708	exon2	c.A366C	p.G122G	TGACCATCCTGTA	.	PASS	Atlas-SNP
PNPLA6	10908	hgsc.bcm.edu	37	19	7606908	7606908	+	Missense_Mutation	SNP	G	G	C	rs17854645	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	24	8	28	0	0.333333	0	G|0.837;C|0.163	0.163	strong	.	PNPLA6	163	.	NM_001166111	exon12	c.G1234C	p.A412P	CCCTCGGCCCCTC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195511204	195511204	+	Missense_Mutation	SNP	T	T	G	rs423290	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	167	13	211	6	0.0778443	0.028436	T|0.987;G|0.013	0.013	strong	MUC4_ENST00000463781,extremity,malignant_melanoma,0,2	MUC4	1505	2	NM_018406	exon2	c.A7247C	p.H2416P	GGAAGATGGGTGG	.	scavenged	Atlas-SNP
PIPOX	51268	hgsc.bcm.edu	37	17	27371919	27371919	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	108	18	109	0	0.166667	0	.	.	none	PIPOX,NS,carcinoma,-1,1	PIPOX	42	1	NM_016518	exon2	c.C157T	p.R53W	CAAAGCCGGATAA	.	PASS	Atlas-SNP
MED13L	23389	hgsc.bcm.edu	37	12	116457158	116457158	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	132	3	161	0	0.0227273	0	.	.	none	MED13L,NS,carcinoma,0,1	MED13L	193	1	NM_015335	exon7	c.G880A	p.V294I	GAGGAACCGGGAT	.	scavenged	Atlas-SNP
SLC35G5	83650	hgsc.bcm.edu	37	8	11189591	11189591	+	Missense_Mutation	SNP	C	C	T	rs62488717	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	106	40	76	0	0.377358	0	.	.	weak	AMAC1L2,NS,carcinoma,-1,1	.	.	1	NM_054028	exon1	c.C976T	p.R326W	ACAGCCCGGAACC	.	PASS	Atlas-SNP
KIAA0825	285600	hgsc.bcm.edu	37	5	93812885	93812885	+	Silent	SNP	C	C	T	rs10057902	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	145	65	167	0	0.448276	0	C|0.879;T|0.121	0.121	strong	.	KIAA0825	172	.	NM_001145678	exon7	c.G1158A	p.E386E	TACAACCTCTCTA	.	PASS	Atlas-SNP
EPS15	2060	hgsc.bcm.edu	37	1	51873951	51873951	+	Silent	SNP	G	G	A	rs1065754	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	266	263	340	0	0.988722	0	G|0.242;A|0.758	0.758	strong	.	EPS15	72	.	NM_001981	exon15	c.C1329T	p.Y443Y	TTCTTCGTAAGTG	.	PASS	Atlas-SNP
ATMIN	23300	hgsc.bcm.edu	37	16	81077204	81077204	+	Silent	SNP	T	T	A	rs16954513	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	145	83	97	0	0.572414	0	T|0.929;A|0.071	0.071	strong	.	ATMIN	50	.	NM_015251	exon4	c.T1101A	p.P367P	CCTACCTCTTTTC	.	PASS	Atlas-SNP
AAMDC	28971	hgsc.bcm.edu	37	11	77553638	77553638	+	Silent	SNP	T	T	C	rs585721	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	52	34	72	1	0.653846	0.0138889	T|0.588;C|0.412	0.412	strong	C11orf67,NS,carcinoma,0,1	.	.	1	NM_024684	exon2	c.T96C	p.G32G	AGGGGGTAGTCGG	.	scavenged	Atlas-SNP
STYXL1	51657	hgsc.bcm.edu	37	7	75659815	75659815	+	Silent	SNP	T	T	C	rs1044483	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	181	94	216	0	0.519337	0	T|0.452;C|0.548;A|0.000	0.548	strong	.	STYXL1	35	.	NM_016086	exon2	c.A27G	p.P9P	CTCTGTTGGTTCA	.	PASS	Atlas-SNP
ALDH18A1	5832	hgsc.bcm.edu	37	10	97388162	97388162	+	Missense_Mutation	SNP	G	G	A	rs2275272	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	64	18	77	0	0.28125	0	G|0.912;A|0.088	0.088	strong	.	ALDH18A1	63	.	NM_002860	exon8	c.C896T	p.T299I	GACTTGGTTCCAA	.	PASS	Atlas-SNP
DUOX1	53905	hgsc.bcm.edu	37	15	45444133	45444133	+	Missense_Mutation	SNP	T	T	C	rs16939752	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	198	119	165	0	0.60101	0	C|0.231;N|0.000	0.231	strong	DUOX1,NS,carcinoma,0,1	DUOX1	125	1	NM_017434	exon25	c.T3076C	p.C1026R	CGCAGCTGTCTCC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195506676	195506676	+	Silent	SNP	G	G	A	rs147667126	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	117	112	205	0	0.957265	0	G|0.740;A|0.260	0.260	strong	.	MUC4	1505	.	NM_018406	exon2	c.C11775T	p.D3925D	GGAAACGTCGGTG	.	PASS	Atlas-SNP
FCGBP	8857	hgsc.bcm.edu	37	19	40399508	40399508	+	Missense_Mutation	SNP	C	C	T	rs6508919	bycluster;by2hit2allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	126	22	128	0	0.174603	0	.	.	weak	FCGBP,NS,carcinoma,0,1	FCGBP	416	1	NM_003890	exon13	c.G6187A	p.G2063S	GGCAGCCGTGCTG	.	scavenged	Atlas-SNP
DSCAML1	57453	hgsc.bcm.edu	37	11	117309989	117309989	+	Silent	SNP	C	C	T	rs11216386	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	21	91	0	0.216495	0	C|0.805;T|0.195	0.195	strong	.	DSCAML1	286	.	NM_020693	exon23	c.G4317A	p.L1439L	TTGCACCAGAAGG	.	PASS	Atlas-SNP
C1QTNF6	114904	hgsc.bcm.edu	37	22	37581422	37581422	+	Missense_Mutation	SNP	G	G	C	rs229526	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	60	30	42	0	0.5	0	G|0.791;C|0.208	0.208	strong	.	C1QTNF6	32	.	NM_182486	exon2	c.C125G	p.P42R	ACCATAGGGATCT	.	PASS	Atlas-SNP
KIF13A	63971	hgsc.bcm.edu	37	6	17764896	17764896	+	Missense_Mutation	SNP	G	G	C	rs41267712	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	67	37	83	0	0.552239	0	G|0.995;C|0.005	0.005	strong	.	KIF13A	276	.	NM_022113	exon39	c.C4863G	p.D1621E	CAGCTGGTCTGAG	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	51	51	74	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
PDE3A	5139	hgsc.bcm.edu	37	12	20522252	20522252	+	Missense_Mutation	SNP	G	G	A	rs12305038	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	14	6	19	1	0.428571	0.0526316	G|0.663;A|0.337	0.337	strong	PDE3A,NS,carcinoma,0,1	PDE3A	184	1	NM_000921	exon1	c.G34A	p.D12N	GTCAGGGACAAGC	.	scavenged	Atlas-SNP
PPP1R32	220004	hgsc.bcm.edu	37	11	61252200	61252200	+	Missense_Mutation	SNP	A	A	G	rs146231065	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	84	48	106	0	0.571429	0	A|0.995;G|0.005	0.005	strong	.	.	.	.	NM_001170753	exon5	c.A422G	p.Q141R	GGCCTCAGGCCAT	.	PASS	Atlas-SNP
PSAPL1	768239	hgsc.bcm.edu	37	4	7435901	7435901	+	Missense_Mutation	SNP	C	C	T	rs56269914	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	55	29	76	0	0.527273	0	C|0.986;T|0.014	0.014	strong	.	PSAPL1	51	.	NM_001085382	exon1	c.G706A	p.D236N	CTTGGTCAGCAGG	.	PASS	Atlas-SNP
TRIM63	84676	hgsc.bcm.edu	37	1	26384973	26384973	+	Nonsense_Mutation	SNP	G	G	A	rs148395034	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	160	73	153	0	0.45625	0	G|0.999;A|0.001	0.001	strong	.	TRIM63	33	.	NM_032588	exon5	c.C739T	p.Q247X	ACTGCTGGATGAG	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100683796	100683796	+	Silent	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	35	2	24	0	0.0571429	0	.	.	none	MUC17,caecum,carcinoma,+2,2	MUC17	804	2	NM_001040105	exon3	c.T9099C	p.G3033G	TGAAGGTACCGGC	.	scavenged	Atlas-SNP
KRTAP1-4	728255	hgsc.bcm.edu	37	17	39186031	39186031	+	Silent	SNP	C	C	T	rs8074117	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	112	53	141	0	0.473214	0	C|0.701;T|0.299	0.299	strong	.	KRTAP1-4	4	.	NM_001257305	exon1	c.G300A	p.P100P	GTAGGACGGGCGG	.	PASS	Atlas-SNP
FAM120B	84498	hgsc.bcm.edu	37	6	170628009	170628009	+	Missense_Mutation	SNP	T	T	G	rs9348266	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	62	23	130	0	0.370968	0	T|0.851;G|0.149	0.149	strong	.	FAM120B	108	.	NM_032448	exon2	c.T1531G	p.C511G	CCCATATGTACAG	.	PASS	Atlas-SNP
OR10Q1	219960	hgsc.bcm.edu	37	11	57996084	57996084	+	Silent	SNP	G	G	A	rs61902844	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	55	50	78	0	0.909091	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
CHSY1	22856	hgsc.bcm.edu	37	15	101718097	101718097	+	Silent	SNP	C	C	G	rs28364839	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	108	57	95	0	0.527778	0	C|0.724;G|0.276	0.276	strong	.	CHSY1	60	.	NM_014918	exon3	c.G1905C	p.V635V	AGTAAACACGAGG	.	PASS	Atlas-SNP
ARHGAP29	9411	hgsc.bcm.edu	37	1	94643531	94643531	+	Silent	SNP	T	T	C	rs1048854	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	34	115	0	0.4	0	T|0.826;C|0.174	0.174	strong	.	ARHGAP29	132	.	NM_004815	exon21	c.A2673G	p.Q891Q	TTGTGGTTGTAGG	.	PASS	Atlas-SNP
ATP9B	374868	hgsc.bcm.edu	37	18	77067000	77067000	+	Silent	SNP	T	T	G	rs3760541	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	47	29	77	0	0.617021	0	T|0.570;G|0.430	0.430	strong	.	ATP9B	96	.	NM_198531	exon15	c.T1539G	p.A513A	TCAAGCTGGTGGA	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105417837	105417837	+	Silent	SNP	A	A	G	rs76231332	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	70	0	0	1	.	A|0.777;G|0.223	0.223	strong	.	AHNAK2	719	.	NM_138420	exon7	c.T3951C	p.A1317A	CTTGTCAGCCAGG	.	PASS	Atlas-SNP
SCAPER	49855	hgsc.bcm.edu	37	15	77025687	77025687	+	Silent	SNP	C	C	T	rs144694379	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	189	103	180	0	0.544974	0	C|0.988;T|0.012	0.012	strong	SCAPER_ENST00000538941,NS,carcinoma,-2,2	SCAPER	160	2	NM_020843	exon15	c.G1905A	p.Q635Q	TTTATTCTGGGCT	.	PASS	Atlas-SNP
FAR2	55711	hgsc.bcm.edu	37	12	29423460	29423460	+	Silent	SNP	G	G	A	rs2216854	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	121	120	139	0	0.991736	0	G|0.554;A|0.446	0.446	strong	FAR2,NS,carcinoma,0,1	FAR2	60	1	NM_018099	exon2	c.G78A	p.L26L	AGTGCTGATGGAG	.	PASS	Atlas-SNP
RASSF7	8045	hgsc.bcm.edu	37	11	562437	562437	+	Silent	SNP	G	G	A	rs11246189	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	143	114	115	0	0.797203	0	G|0.827;A|0.173	0.173	strong	.	RASSF7	22	.	NM_001143994	exon3	c.G483A	p.R161R	GCTCAGGGTGCAG	.	PASS	Atlas-SNP
SETX	23064	hgsc.bcm.edu	37	9	135203838	135203838	+	Silent	SNP	G	G	A	rs3739921	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	39	122	0	0.402062	0	G|0.910;A|0.090	0.090	strong	.	SETX	234	.	NM_015046	exon10	c.C3147T	p.H1049H	TGAAACGTGCTGC	.	PASS	Atlas-SNP
CMAS	55907	hgsc.bcm.edu	37	12	22213786	22213786	+	Silent	SNP	C	C	T	rs10841930	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	30	16	66	0	0.533333	0	C|0.831;G|0.000;T|0.169	0.169	strong	.	CMAS	45	.	NM_018686	exon5	c.C714T	p.Y238Y	ATACTACGAAATG	.	PASS	Atlas-SNP
TRIM66	9866	hgsc.bcm.edu	37	11	8662649	8662649	+	Missense_Mutation	SNP	A	A	G	rs61743935	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	128	114	108	0	0.890625	0	A|0.964;G|0.036	0.036	strong	.	TRIM66	45	.	NM_014818	exon9	c.T838C	p.Y280H	CTCCATAAGCAGG	.	PASS	Atlas-SNP
CDK17	5128	hgsc.bcm.edu	37	12	96676330	96676330	+	Silent	SNP	C	C	A	rs35751611	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	160	85	188	0	0.53125	0	C|0.924;A|0.076	0.076	strong	.	CDK17	71	.	NM_001170464	exon15	c.G1413T	p.V471V	AAAGTACACATGT	.	PASS	Atlas-SNP
MKRN1	23608	hgsc.bcm.edu	37	7	140159721	140159721	+	Silent	SNP	T	T	C	rs10243155	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	90	39	149	0	0.433333	0	T|0.721;C|0.279	0.279	strong	.	MKRN1	35	.	NM_013446	exon3	c.A330G	p.K110K	CAATGGTTTGCTA	.	PASS	Atlas-SNP
PTPRH	5794	hgsc.bcm.edu	37	19	55708573	55708573	+	Silent	SNP	G	G	A	rs2288520	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	252	118	270	1	0.468254	0.0037037	G|0.925;A|0.075	0.075	strong	.	PTPRH	139	.	NM_002842	exon9	c.C1902T	p.A634A	TTCCAGGGCCTCC	.	PASS	Atlas-SNP
TMEM44	93109	hgsc.bcm.edu	37	3	194346704	194346704	+	Missense_Mutation	SNP	A	A	G	rs140271606	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	195	90	218	0	0.461538	0	A|0.998;G|0.002	0.002	strong	.	TMEM44	42	.	NM_138399	exon3	c.T280C	p.Y94H	CTAGGTAGGCACC	.	PASS	Atlas-SNP
XRN1	54464	hgsc.bcm.edu	37	3	142078759	142078759	+	Missense_Mutation	SNP	C	C	T	rs73238159	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	34	8	59	0	0.235294	0	C|0.901;T|0.099	0.099	strong	.	XRN1	138	.	NM_001042604	exon30	c.G3409A	p.D1137N	GTACATCGGCTTC	.	PASS	Atlas-SNP
ROS1	6098	hgsc.bcm.edu	37	6	117683821	117683821	+	Missense_Mutation	SNP	G	G	A	rs2229079	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	110	47	106	0	0.427273	0	G|0.939;A|0.061	0.061	strong	.	ROS1	728	.	NM_002944	exon21	c.C3326T	p.S1109L	ATCACTGAGGGAG	.	PASS	Atlas-SNP
NPC1L1	29881	hgsc.bcm.edu	37	7	44555406	44555406	+	Silent	SNP	G	G	A	rs10264715	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	43	38	59	0	0.883721	0	G|0.866;A|0.134	0.134	strong	.	NPC1L1	141	.	NM_013389	exon19	c.C3873T	p.Y1291Y	ACCCACGTAGCTG	.	PASS	Atlas-SNP
HSPA6	3310	hgsc.bcm.edu	37	1	161495344	161495344	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	17	101	0	0.226667	0	.	.	none	.	HSPA6	53	.	NM_002155	exon1	c.T896C	p.I299T	CGTCCATCACTCG	.	PASS	Atlas-SNP
IRAK4	51135	hgsc.bcm.edu	37	12	44177511	44177511	+	Missense_Mutation	SNP	G	G	A	rs55944915	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	64	30	57	0	0.46875	0	G|0.989;A|0.011	0.011	strong	.	IRAK4	77	.	NM_016123	exon10	c.G1172A	p.R391H	AACACCGTGAACC	.	PASS	Atlas-SNP
ELP2	55250	hgsc.bcm.edu	37	18	33725931	33725931	+	Missense_Mutation	SNP	G	G	A	rs1785928	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	174	76	215	0	0.436782	0	G|0.656;A|0.344	0.344	strong	ELP2,colon,carcinoma,0,1	ELP2	70	1	NM_001242875	exon11	c.G1108A	p.V370M	CAGCCAGTGAGAT	.	PASS	Atlas-SNP
PPP1R26	9858	hgsc.bcm.edu	37	9	138377433	138377433	+	Silent	SNP	G	G	A	rs3827827	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	105	47	109	0	0.447619	0	G|0.824;A|0.176	0.176	strong	KIAA0649,NS,carcinoma,0,1	.	.	1	NM_014811	exon4	c.G1077A	p.A359A	CGAGGCGTCCGAC	.	PASS	Atlas-SNP
PPIG	9360	hgsc.bcm.edu	37	2	170441001	170441001	+	Splice_Site	SNP	G	G	A	rs2276611	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	67	33	64	0	0.492537	0	G|0.830;A|0.170	0.170	strong	.	PPIG	100	.	.	.	.	.	GTGCAGGTAAGTG	.	PASS	Atlas-SNP
ADAP1	11033	hgsc.bcm.edu	37	7	943868	943868	+	Silent	SNP	G	G	A	rs61730955	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	118	26	123	0	0.220339	0	G|0.946;A|0.054	0.054	strong	.	ADAP1	23	.	NM_006869	exon6	c.C543T	p.N181N	GGTGGCGTTCAGG	.	PASS	Atlas-SNP
COL5A3	50509	hgsc.bcm.edu	37	19	10078589	10078589	+	Silent	SNP	T	T	C	rs3815748	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	83	40	94	0	0.481928	0	T|0.837;C|0.163	0.163	strong	.	COL5A3	243	.	NM_015719	exon61	c.A4395G	p.K1465K	AGACCCTTTTGAG	.	PASS	Atlas-SNP
CLDN6	9074	hgsc.bcm.edu	37	16	3065596	3065596	+	Missense_Mutation	SNP	T	T	C	rs2257295	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	65	158	0	0.706522	0	T|0.645;C|0.355	0.355	strong	CLDN6,rectum,carcinoma,0,3	CLDN6	31	3	NM_021195	exon2	c.A427G	p.I143V	GGATGATGGCATG	.	PASS	Atlas-SNP
CDH18	1016	hgsc.bcm.edu	37	5	19591174	19591174	+	Silent	SNP	A	A	G	rs17285716	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	105	51	116	0	0.485714	0	A|0.879;G|0.121	0.121	strong	CDH18_ENST00000507958,NS,adenoma,0,4	CDH18	561	4	NM_001167667	exon7	c.T991C	p.L331L	TCTTTAAAGAAAG	.	PASS	Atlas-SNP
SLIT2	9353	hgsc.bcm.edu	37	4	20487867	20487867	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	163	45	269	0	0.276074	0	.	.	none	.	SLIT2	290	.	NM_004787	exon7	c.T584C	p.F195S	CAAGTTTCAACCA	.	PASS	Atlas-SNP
ITIH1	3697	hgsc.bcm.edu	37	3	52825585	52825585	+	Silent	SNP	T	T	C	rs9324	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	49	47	68	0	0.959184	0	T|0.568;C|0.432	0.432	strong	.	ITIH1	108	.	NM_002215	exon21	c.T2547C	p.S849S	AGGCTCTGACCCC	.	PASS	Atlas-SNP
MYO9B	4650	hgsc.bcm.edu	37	19	17273893	17273893	+	Silent	SNP	G	G	T	rs7256689	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	106	52	102	0	0.490566	0	G|0.238;T|0.762	0.762	strong	.	MYO9B	264	.	NM_001130065	exon10	c.G1632T	p.L544L	GCAGCTGCAGTAT	.	PASS	Atlas-SNP
HIST1H1A	3024	hgsc.bcm.edu	37	6	26017542	26017542	+	Missense_Mutation	SNP	T	T	C	rs16891235	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	177	94	210	0	0.531073	0	T|0.908;C|0.092	0.092	strong	.	HIST1H1A	25	.	NM_005325	exon1	c.A419G	p.K140R	GCCTTTTTGAGCT	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228492220	228492220	+	Missense_Mutation	SNP	C	C	T	rs41270183	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	95	61	114	0	0.642105	0	C|0.988;T|0.012	0.012	strong	.	OBSCN	2142	.	NM_001271223	exon53	c.C14219T	p.S4740L	AGTACTCGTGCGT	.	PASS	Atlas-SNP
ZNF804A	91752	hgsc.bcm.edu	37	2	185801917	185801917	+	Silent	SNP	A	A	G	rs728534	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	74	76	0	0.986667	0	A|0.840;G|0.160	0.160	strong	.	ZNF804A	322	.	NM_194250	exon4	c.A1794G	p.K598K	GAAAAAAAGAAAA	.	PASS	Atlas-SNP
ZNF215	7762	hgsc.bcm.edu	37	11	6953858	6953858	+	Missense_Mutation	SNP	A	A	G	rs11041108	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	94	11	92	0	0.117021	0	A|0.721;G|0.279	0.279	strong	.	ZNF215	72	.	NM_013250	exon3	c.A355G	p.M119V	AAAGATATGGTGA	.	PASS	Atlas-SNP
SEMA4D	10507	hgsc.bcm.edu	37	9	92003679	92003679	+	Missense_Mutation	SNP	C	C	T	rs11526468	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	31	14	37	0	0.451613	0	C|0.774;T|0.226	0.226	strong	.	SEMA4D	81	.	NM_006378	exon13	c.G979A	p.A327T	TGTAGGCGCACAC	.	PASS	Atlas-SNP
JPH3	57338	hgsc.bcm.edu	37	16	87678441	87678441	+	Silent	SNP	C	C	T	rs8051448	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	56	69	0	0.658824	0	C|0.876;G|0.000;T|0.124	0.124	strong	.	JPH3	95	.	NM_020655	exon2	c.C960T	p.R320R	CCGGCGCCATGGC	.	PASS	Atlas-SNP
IRF8	3394	hgsc.bcm.edu	37	16	85945231	85945231	+	Silent	SNP	C	C	T	rs8052064	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	53	39	97	0	0.735849	0	C|0.882;T|0.118	0.118	strong	.	IRF8	65	.	NM_002163	exon4	c.C414T	p.C138C	GGAGTGCGGTCGC	.	PASS	Atlas-SNP
COL5A3	50509	hgsc.bcm.edu	37	19	10077419	10077419	+	Missense_Mutation	SNP	C	C	G	rs3745584	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	9	7	14	0	0.777778	0	C|0.641;G|0.359	0.359	strong	.	COL5A3	243	.	NM_015719	exon63	c.G4462C	p.A1488P	CAGGGGCACCCTG	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	121	56	141	1	0.46281	0.0070922	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	.	scavenged	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195508133	195508133	+	Missense_Mutation	SNP	G	G	A	rs202065387		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	90	5	61	0	0.0555556	0	.	.	weak	MUC4_ENST00000463781,NS,carcinoma,0,4	MUC4	1505	4	NM_018406	exon2	c.C10318T	p.P3440S	GAACAGGGGTGGC	.	scavenged	Atlas-SNP
WDR48	57599	hgsc.bcm.edu	37	3	39111140	39111140	+	Silent	SNP	C	C	A	rs2293312	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	64	40	91	0	0.625	0	C|0.529;N|0.000	.	strong	.	WDR48	41	.	NM_020839	exon7	c.C577A	p.R193R	GTGTTACGGGTAT	.	PASS	Atlas-SNP
FCGR3A	2214	hgsc.bcm.edu	37	1	161514542	161514542	+	Missense_Mutation	SNP	A	A	C	rs396991	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	235	108	271	0	0.459574	0	A|0.681;C|0.319	0.319	strong	.	FCGR3A	38	.	NM_000569	exon4	c.T634G	p.F212V	TCCCAAAAAGCCC	.	PASS	Atlas-SNP
PER3	8863	hgsc.bcm.edu	37	1	7887605	7887605	+	Silent	SNP	G	G	A	rs17031614	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	174	74	211	0	0.425287	0	G|0.940;A|0.060	0.060	strong	.	PER3	95	.	NM_016831	exon17	c.G2592A	p.S864S	GCCATCGTTTTTG	.	PASS	Atlas-SNP
NCOR2	9612	hgsc.bcm.edu	37	12	124821416	124821416	+	Missense_Mutation	SNP	C	C	T	rs2227277	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	35	27	12	0	0.771429	0	C|0.959;T|0.041	0.041	strong	.	NCOR2	475	.	NM_006312	exon40	c.G5998A	p.A2000T	GAGGTGCGAGGTT	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105417683	105417683	+	Missense_Mutation	SNP	C	C	T	rs367930189		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	88	4	0	0	0.0454545	.	.	.	weak	AHNAK2_ENST00000333244,NS,carcinoma,+2,1	AHNAK2	719	1	NM_138420	exon7	c.G4105A	p.G1369R	GGTCCCCCTGCAT	.	PASS	Atlas-SNP
FKBP15	23307	hgsc.bcm.edu	37	9	115968797	115968797	+	Missense_Mutation	SNP	C	C	T	rs1133618	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	44	120	0	0.511628	0	C|0.805;T|0.195	0.195	strong	.	FKBP15	128	.	NM_015258	exon4	c.G316A	p.A106T	CTCTGGCTGTGTG	.	PASS	Atlas-SNP
LGALS14	56891	hgsc.bcm.edu	37	19	40196548	40196548	+	Missense_Mutation	SNP	A	A	G	rs140242272	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	156	72	157	0	0.461538	0	A|0.999;G|0.001	0.001	strong	.	LGALS14	38	.	NM_203471	exon2	c.A1G	p.M1V	CCAGTTATGTCCC	.	PASS	Atlas-SNP
GATA5	140628	hgsc.bcm.edu	37	20	61039958	61039958	+	Silent	SNP	T	T	C	rs6061550	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	61	32	80	0	0.52459	0	T|0.412;C|0.588	0.588	strong	.	GATA5	22	.	NM_080473	exon7	c.A1128G	p.P376P	GGGGCTTGGGGCC	.	PASS	Atlas-SNP
FSCB	84075	hgsc.bcm.edu	37	14	44975606	44975606	+	Missense_Mutation	SNP	G	G	T	rs3809429	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	112	56	119	1	0.5	0.00840336	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	.	scavenged	Atlas-SNP
HEATR5A	25938	hgsc.bcm.edu	37	14	31790886	31790886	+	Missense_Mutation	SNP	T	T	G	rs28396248	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	35	126	0	0.507246	0	T|0.909;G|0.091	0.091	strong	HEATR5A_ENST00000389961,NS,carcinoma,0,1	HEATR5A	181	1	NM_015473	exon25	c.A3788C	p.N1263T	AAGTCATCTATAA	.	PASS	Atlas-SNP
KIF19	124602	hgsc.bcm.edu	37	17	72350362	72350362	+	Silent	SNP	G	G	A	rs72852235	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	35	35	25	0	1	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
UNC93A	54346	hgsc.bcm.edu	37	6	167728775	167728775	+	Missense_Mutation	SNP	G	G	A	rs9459921	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	57	41	183	0	0.719298	0	G|0.806;A|0.194	0.194	strong	.	UNC93A	66	.	NM_018974	exon8	c.G1209A	p.M403I	CAGCATGTTTTTG	.	PASS	Atlas-SNP
HPS4	89781	hgsc.bcm.edu	37	22	26866723	26866723	+	Silent	SNP	C	C	T	rs13054747	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	163	88	182	1	0.539877	0.00549451	C|0.968;T|0.032	0.032	strong	HPS4_ENST00000398141,colon,carcinoma,0,2	HPS4	123	2	NM_022081	exon7	c.G558A	p.S186S	GTGAGGCGAGCGC	.	scavenged	Atlas-SNP
ARHGEF5	7984	hgsc.bcm.edu	37	7	144060802	144060802	+	Missense_Mutation	SNP	C	C	T	rs76491286		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	943	212	402	0	0.224814	0	.	.	weak	ARHGEF5,colon,carcinoma,+1,1	ARHGEF5	73	1	NM_005435	exon2	c.C1040T	p.T347I	GTCAAACCTTTTT	.	scavenged	Atlas-SNP
KRT32	3882	hgsc.bcm.edu	37	17	39619193	39619193	+	Missense_Mutation	SNP	C	C	T	rs11078993	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	40	91	0	0.434783	0	C|0.935;T|0.065	0.065	strong	KRT32,NS,carcinoma,0,1	KRT32	57	1	NM_002278	exon6	c.G1106A	p.R369Q	TCAGCCCGGATCT	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	178	94	199	0	0.52809	0	T|0.805;C|0.195	0.195	strong	.	AIM1	161	.	NM_001624	exon2	c.T1471C	p.C491R	TTCCCATGCACTG	.	PASS	Atlas-SNP
LAMA1	284217	hgsc.bcm.edu	37	18	6986259	6986259	+	Silent	SNP	G	G	A	rs62081531	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	163	91	156	0	0.558282	0	G|0.810;A|0.190	0.190	strong	LAMA1,colon,carcinoma,0,2	LAMA1	458	2	NM_005559	exon37	c.C5256T	p.H1752H	AAGGACGTGGCTT	.	PASS	Atlas-SNP
ENGASE	64772	hgsc.bcm.edu	37	17	77082174	77082174	+	Missense_Mutation	SNP	C	C	T	rs117014247	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	63	42	70	0	0.666667	0	C|0.982;T|0.018	0.018	strong	.	ENGASE	55	.	NM_001042573	exon14	c.C1975T	p.R659C	CAAGTCCGTTGCT	.	PASS	Atlas-SNP
CLDN14	23562	hgsc.bcm.edu	37	21	37833931	37833931	+	Silent	SNP	C	C	T	rs117560775	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	66	40	56	0	0.606061	0	C|0.978;T|0.022	0.022	strong	.	CLDN14	25	.	NM_144492	exon3	c.G63A	p.T21T	GATCAACGTGCCC	.	PASS	Atlas-SNP
ADAMTS7	11173	hgsc.bcm.edu	37	15	79058951	79058951	+	Missense_Mutation	SNP	T	T	C	rs28699256	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	105	55	103	0	0.52381	0	T|0.695;C|0.305	0.305	strong	.	ADAMTS7	142	.	NM_014272	exon19	c.A3302G	p.H1101R	GCAGGATGGCTGT	.	PASS	Atlas-SNP
PLEKHG5	57449	hgsc.bcm.edu	37	1	6528589	6528589	+	Silent	SNP	C	C	T	rs3138150	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	147	73	148	0	0.496599	0	C|0.939;T|0.061	0.061	strong	.	PLEKHG5	66	.	NM_001265592	exon21	c.G2544A	p.T848T	GGACAGCGTGTCC	.	PASS	Atlas-SNP
UTP20	27340	hgsc.bcm.edu	37	12	101685852	101685852	+	Silent	SNP	G	G	A	rs11110737	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	90	36	117	0	0.4	0	G|0.888;A|0.112	0.112	strong	.	UTP20	222	.	NM_014503	exon10	c.G1143A	p.P381P	CTTGCCGGAGACC	.	PASS	Atlas-SNP
ABCA7	10347	hgsc.bcm.edu	37	19	1062192	1062192	+	Silent	SNP	T	T	C	rs4147921	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	153	59	143	0	0.385621	0	T|0.960;C|0.040	0.040	strong	.	ABCA7	174	.	NM_019112	exon42	c.T5592C	p.A1864A	CAGTGCTGCGCAC	.	PASS	Atlas-SNP
SH3RF1	57630	hgsc.bcm.edu	37	4	170038894	170038894	+	Silent	SNP	A	A	G	rs74798922	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	40	120	0	0.487805	0	A|0.982;G|0.018	0.018	strong	.	SH3RF1	60	.	NM_020870	exon9	c.T1557C	p.S519S	AGCTGTAGACATA	.	PASS	Atlas-SNP
VCAN	1462	hgsc.bcm.edu	37	5	82815170	82815170	+	Missense_Mutation	SNP	A	A	G	rs61749613	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	81	37	129	0	0.45679	0	A|0.973;G|0.027	0.027	strong	.	VCAN	498	.	NM_004385	exon7	c.A1045G	p.K349E	CTAGCTAAAGAGG	.	PASS	Atlas-SNP
TPRX1	284355	hgsc.bcm.edu	37	19	48305654	48305654	+	Missense_Mutation	SNP	C	C	T	rs73036913	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	27	9	19	0	0.333333	0	C|0.949;T|0.051	0.051	strong	TPRX1,colon,carcinoma,0,1	TPRX1	46	1	NM_198479	exon2	c.G614A	p.G205D	ATCGGGCCTGGGA	.	PASS	Atlas-SNP
UTRN	7402	hgsc.bcm.edu	37	6	144774982	144774982	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	30	87	0	0.517241	0	.	.	none	.	UTRN	327	.	NM_007124	exon18	c.T2261G	p.I754S	GACAAATCCTTGT	.	PASS	Atlas-SNP
CEP112	201134	hgsc.bcm.edu	37	17	63898348	63898348	+	Silent	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	149	3	166	0	0.0201342	0	.	.	none	CEP112,NS,carcinoma,-2,1	CEP112	192	1	NM_001199165	exon20	c.A2085G	p.E695E	CAGGTTTTCAATT	.	scavenged	Atlas-SNP
T	6862	hgsc.bcm.edu	37	6	166579270	166579270	+	Missense_Mutation	SNP	C	C	T	rs2305089	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	128	36	195	0	0.28125	0	C|0.583;T|0.417	0.417	strong	.	T	77	.	NM_003181	exon4	c.G530A	p.G177D	TGTGGACCCCCAA	.	PASS	Atlas-SNP
UNC45B	146862	hgsc.bcm.edu	37	17	33476001	33476001	+	Missense_Mutation	SNP	G	G	A	rs16970659	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	120	61	125	0	0.508333	0	G|0.963;A|0.037	0.037	strong	UNC45B,NS,carcinoma,0,1	UNC45B	133	1	NM_001267052	exon3	c.G178A	p.V60I	AGCTACGTCCAGG	.	PASS	Atlas-SNP
MECOM	2122	hgsc.bcm.edu	37	3	169098992	169098992	+	Missense_Mutation	SNP	G	G	A	rs7622799	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	132	56	128	0	0.424242	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
LILRA3	11026	hgsc.bcm.edu	37	19	54802548	54802548	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	193	13	181	5	0.0673575	0.0276243	.	.	none	LILRA3,NS,malignant_melanoma,0,1	LILRA3	65	1	NM_006865	exon5	c.C893A	p.S298Y	GCACCGGAGCATG	.	scavenged	Atlas-SNP
IGLL5	100423062	hgsc.bcm.edu	37	22	23230312	23230312	+	Silent	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	159	41	152	0	0.257862	0	.	.	none	IGLL5,NS,lymphoid_neoplasm,-2,1	IGLL5	26	1	NM_001178126	exon1	c.C79T	p.L27L	CCCCTGCTGCTGC	.	PASS	Atlas-SNP
VPS33B	26276	hgsc.bcm.edu	37	15	91543761	91543761	+	Missense_Mutation	SNP	C	C	T	rs11073964	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	70	74	0	1	0	C|0.359;T|0.641	0.641	strong	.	VPS33B	42	.	NM_018668	exon20	c.G1540A	p.G514S	CACCACCGAAGAC	.	PASS	Atlas-SNP
OR5L2	26338	hgsc.bcm.edu	37	11	55595114	55595114	+	Silent	SNP	G	G	T	rs34929168	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	205	143	249	0	0.697561	0	G|0.913;T|0.087	0.087	strong	.	OR5L2	135	.	NM_001004739	exon1	c.G420T	p.L140L	GAAGCTGCGTGTG	.	PASS	Atlas-SNP
CHD2	1106	hgsc.bcm.edu	37	15	93536197	93536197	+	Silent	SNP	C	C	T	rs2272457	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	79	30	57	0	0.379747	0	C|0.770;T|0.230	0.230	strong	.	CHD2	280	.	NM_001271	exon28	c.C3564T	p.Y1188Y	GGAATACGAAGAG	.	PASS	Atlas-SNP
SEMA5B	54437	hgsc.bcm.edu	37	3	122642590	122642590	+	Silent	SNP	G	G	A	rs2276778	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	93	89	78	0	0.956989	0	G|0.514;A|0.486	0.486	strong	.	SEMA5B	303	.	NM_001256347	exon10	c.C1308T	p.I436I	AGCCGCGATGCTG	.	PASS	Atlas-SNP
C7orf31	136895	hgsc.bcm.edu	37	7	25182405	25182405	+	Missense_Mutation	SNP	G	G	T	rs11984293	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	112	12	116	0	0.107143	0	G|0.777;T|0.223	0.223	strong	.	C7orf31	53	.	NM_138811	exon8	c.C713A	p.P238Q	AATACTGGCTTAT	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	166	70	131	0	0.421687	0	C|0.702;G|0.298	0.298	strong	.	KRTAP10-2	21	.	NM_198693	exon1	c.G349C	p.A117P	AAGAAGCCCCACA	.	PASS	Atlas-SNP
CLUAP1	23059	hgsc.bcm.edu	37	16	3558389	3558389	+	Missense_Mutation	SNP	C	C	T	rs79133712	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	80	64	88	0	0.8	0	C|0.975;T|0.025	0.025	strong	.	CLUAP1	32	.	NM_015041	exon4	c.C320T	p.A107V	ATAATGCTATGAA	.	PASS	Atlas-SNP
GOSR2	9570	hgsc.bcm.edu	37	17	45000565	45000565	+	Missense_Mutation	SNP	C	C	A	rs12944167	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	122	47	126	0	0.385246	0	C|0.984;A|0.016	0.016	strong	.	GOSR2	38	.	NM_001012511	exon1	c.C7A	p.P3T	ATGGATCCCCTGT	.	PASS	Atlas-SNP
WNK1	65125	hgsc.bcm.edu	37	12	939268	939268	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	293	72	280	0	0.245734	0	.	.	none	.	WNK1	403	.	NM_001184985	exon4	c.C1253A	p.S418Y	CTACATCTGAATA	.	PASS	Atlas-SNP
SRD5A1	6715	hgsc.bcm.edu	37	5	6652009	6652009	+	Silent	SNP	G	G	A	rs8192186	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	179	79	211	0	0.441341	0	G|0.652;A|0.348	0.348	strong	SRD5A1,NS,carcinoma,0,1	SRD5A1	31	1	NM_001047	exon2	c.G348A	p.A116A	GTTGGCGTGTACA	.	PASS	Atlas-SNP
HCN4	10021	hgsc.bcm.edu	37	15	73615097	73615097	+	Missense_Mutation	SNP	T	T	C	rs142735148	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	33	19	24	0	0.575758	0	T|0.992;C|0.008	0.008	strong	.	HCN4	150	.	NM_005477	exon8	c.A3337G	p.M1113V	CAGCCATGGACTC	.	PASS	Atlas-SNP
CNST	163882	hgsc.bcm.edu	37	1	246829147	246829147	+	Missense_Mutation	SNP	C	C	G	rs138848173	alternate_allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	128	54	137	0	0.421875	0	C|1.000;T|0.000	.	alt	.	CNST	73	.	NM_152609	exon11	c.C2118G	p.F706L	GGACTTCTATTAC	.	PASS	Atlas-SNP
SVIL	6840	hgsc.bcm.edu	37	10	29754609	29754609	+	Silent	SNP	T	T	C	rs1057952	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	273	130	296	1	0.47619	0.00337838	T|0.629;C|0.371	0.371	strong	SVIL,NS,carcinoma,0,1	SVIL	226	1	NM_021738	exon34	c.A6048G	p.T2016T	AAACTCTGTGGCT	.	PASS	Atlas-SNP
PYGB	5834	hgsc.bcm.edu	37	20	25264814	25264814	+	Silent	SNP	T	T	C	rs2227892	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	113	50	162	0	0.442478	0	T|0.523;C|0.477	0.477	strong	.	PYGB	84	.	NM_002862	exon14	c.T1695C	p.D565D	GTTCGATGTGCAT	.	PASS	Atlas-SNP
MAP4K4	9448	hgsc.bcm.edu	37	2	102314984	102314984	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	312	90	402	1	0.288462	0.00248756	.	.	none	.	MAP4K4	111	.	NM_004834	exon2	c.A107T	p.Y36F	GCACCTATGGACA	.	PASS	Atlas-SNP
DPCR1	135656	hgsc.bcm.edu	37	6	30920124	30920124	+	Missense_Mutation	SNP	G	G	A	rs3132580	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	191	97	214	1	0.507853	0.0046729	G|0.913;A|0.087	0.087	strong	.	DPCR1	99	.	NM_080870	exon2	c.G3883A	p.E1295K	GGAAACGAGAGCC	.	PASS	Atlas-SNP
GRIN2B	2904	hgsc.bcm.edu	37	12	13720043	13720043	+	Silent	SNP	G	G	A	rs3026160	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	106	48	111	0	0.45283	0	G|0.922;A|0.078	0.078	strong	.	GRIN2B	303	.	NM_000834	exon12	c.C2514T	p.C838C	GTGTTCGCAGATG	.	PASS	Atlas-SNP
TF	7018	hgsc.bcm.edu	37	3	133474328	133474328	+	Silent	SNP	G	G	A	rs12769	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	67	32	72	0	0.477612	0	G|0.727;A|0.273	0.273	strong	.	TF	116	.	NM_001063	exon5	c.G624A	p.S208S	CTACTCGGGAGCC	.	PASS	Atlas-SNP
KRTAP4-8	728224	hgsc.bcm.edu	37	17	39254054	39254054	+	Missense_Mutation	SNP	A	A	T	rs76270529	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	41	4	45	0	0.097561	0	A|0.500;T|0.500	0.500	weak	KRTAP4-8,rectum,carcinoma,0,8	KRTAP4-8	57	8	NM_031960	exon1	c.T283A	p.C95S	AGATGCAGCAGCT	.	PASS	Atlas-SNP
ITLN1	55600	hgsc.bcm.edu	37	1	160851826	160851826	+	Missense_Mutation	SNP	A	A	T	rs2274907	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	156	80	210	0	0.512821	0	A|0.411;N|0.001	.	strong	.	ITLN1	45	.	NM_017625	exon4	c.T326A	p.V109D	GGGTAGACTGCTT	.	PASS	Atlas-SNP
HIVEP3	59269	hgsc.bcm.edu	37	1	42050366	42050366	+	Missense_Mutation	SNP	C	C	T	rs2146315	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	109	109	95	0	1	0	C|0.726;T|0.274	0.274	strong	HIVEP3,colon,carcinoma,0,1	HIVEP3	235	1	NM_024503	exon4	c.G103A	p.V35I	ATGGGACGCTGGA	.	PASS	Atlas-SNP
KEAP1	9817	hgsc.bcm.edu	37	19	10600442	10600442	+	Silent	SNP	G	G	C	rs1048290	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	114	114	95	0	1	0	G|0.511;C|0.489	0.489	strong	KEAP1,NS,carcinoma,0,1	KEAP1	182	1	NM_012289	exon4	c.C1413G	p.L471L	ATAAAGGAGACGA	.	PASS	Atlas-SNP
SH2D4B	387694	hgsc.bcm.edu	37	10	82363404	82363404	+	Missense_Mutation	SNP	A	A	G	rs7075840	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	76	31	70	0	0.407895	0	A|0.661;G|0.339	0.339	strong	SH2D4B,NS,carcinoma,0,1	SH2D4B	44	1	NM_207372	exon5	c.A713G	p.H238R	ACCGACACCACTC	.	PASS	Atlas-SNP
TEAD4	7004	hgsc.bcm.edu	37	12	3120180	3120180	+	Silent	SNP	G	G	A	rs147476820	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	139	78	127	0	0.561151	0	G|0.999;A|0.001	0.001	strong	.	TEAD4	45	.	NM_003213	exon4	c.G237A	p.E79E	GAACGAGCTGATT	.	PASS	Atlas-SNP
OR2M3	127062	hgsc.bcm.edu	37	1	248366632	248366632	+	Missense_Mutation	SNP	G	G	T	rs139107079	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	142	68	207	0	0.478873	0	G|0.999;T|0.001	0.001	strong	.	OR2M3	116	.	NM_001004689	exon1	c.G263T	p.G88V	TGTCTGGCAGCAA	.	PASS	Atlas-SNP
GLT6D1	360203	hgsc.bcm.edu	37	9	138516119	138516119	+	Missense_Mutation	SNP	G	G	A	rs17040344	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	51	21	75	0	0.411765	0	G|0.955;A|0.045	0.045	strong	GLT6D1,NS,carcinoma,+2,1	GLT6D1	56	1	NM_182974	exon5	c.C655T	p.P219S	CAAACGGGATGCA	.	PASS	Atlas-SNP
MINA	84864	hgsc.bcm.edu	37	3	97686159	97686159	+	Silent	SNP	C	C	T	rs34097037	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	107	51	103	0	0.476636	0	C|0.996;T|0.004	0.004	strong	.	MINA	39	.	NM_001261829	exon2	c.G279A	p.G93G	GTACATCCCCCGG	.	PASS	Atlas-SNP
FYCO1	79443	hgsc.bcm.edu	37	3	46007823	46007823	+	Missense_Mutation	SNP	G	G	T	rs71622515	alternate_allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	181	72	187	0	0.39779	0	GTT|0.500;TTC|0.500	.	alt	.	FYCO1	115	.	NM_024513	exon8	c.C3003A	p.N1001K	GAGGGTGTTGAGC	.	PASS	Atlas-SNP
KRTAP10-3	386682	hgsc.bcm.edu	37	21	45978488	45978488	+	Silent	SNP	G	G	A	rs12483390	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	68	38	43	0	0.558824	0	G|0.755;A|0.245	0.245	strong	.	KRTAP10-3	17	.	NM_198696	exon1	c.C111T	p.C37C	CGGGGCGCAGCAG	.	PASS	Atlas-SNP
LAMA3	3909	hgsc.bcm.edu	37	18	21453038	21453038	+	Silent	SNP	C	C	T	rs145044428	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	41	97	0	0.476744	0	C|0.999;T|0.001	0.001	strong	.	LAMA3	397	.	NM_001127718	exon1	c.C30T	p.C10C	AGCCTGCAGCATG	.	PASS	Atlas-SNP
TENC1	23371	hgsc.bcm.edu	37	12	53453456	53453456	+	Silent	SNP	C	C	T	rs34044566	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	77	41	70	0	0.532468	0	C|0.947;T|0.053	0.053	strong	TENC1_ENST00000314276,NS,carcinoma,0,2	TENC1	148	2	NM_015319	exon18	c.C2061T	p.V687V	GGTGGTCATCCTG	.	PASS	Atlas-SNP
CDSN	1041	hgsc.bcm.edu	37	6	31088145	31088145	+	Missense_Mutation	SNP	T	T	A	rs3095318	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	186	79	204	1	0.424731	0.00490196	T|0.831;A|0.169	0.169	strong	CDSN,NS,carcinoma,0,1	CDSN	48	1	NM_001264	exon1	c.A52T	p.M18L	GTGCCATCATCCC	.	scavenged	Atlas-SNP
OR13D1	286365	hgsc.bcm.edu	37	9	107456763	107456763	+	Missense_Mutation	SNP	T	T	C	rs10991359	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	91	50	144	0	0.549451	0	T|0.800;C|0.200	0.200	strong	OR13D1,NS,carcinoma,0,1	OR13D1	42	1	NM_001004484	exon1	c.T61C	p.F21L	GTCCTTTTCTATA	.	PASS	Atlas-SNP
DDX52	11056	hgsc.bcm.edu	37	17	35988672	35988672	+	Silent	SNP	C	C	T	rs7224513	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	95	48	87	0	0.505263	0	C|0.357;T|0.643	0.643	strong	.	DDX52	40	.	NM_007010	exon6	c.G792A	p.R264R	GTGTATCCTGAAT	.	PASS	Atlas-SNP
TRIOBP	11078	hgsc.bcm.edu	37	22	38129332	38129332	+	Silent	SNP	G	G	A	rs7284476	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	176	77	199	0	0.4375	0	G|0.639;A|0.361	0.361	strong	.	TRIOBP	262	.	NM_001039141	exon8	c.G3975A	p.Q1325Q	CTTCCAGGCCCAG	.	PASS	Atlas-SNP
MCM10	55388	hgsc.bcm.edu	37	10	13230915	13230915	+	Missense_Mutation	SNP	C	C	T	rs35114749	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	88	38	106	0	0.431818	0	C|0.991;T|0.009	0.009	strong	.	MCM10	76	.	NM_182751	exon10	c.C1253T	p.A418V	TCCAGGCTCAGTA	.	PASS	Atlas-SNP
ANKRD27	84079	hgsc.bcm.edu	37	19	33096816	33096816	+	Silent	SNP	C	C	T	rs7248273	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	115	45	200	0	0.391304	0	C|0.838;N|0.000	.	strong	ANKRD27,NS,NS,0,1	ANKRD27	86	1	NM_032139	exon24	c.G2418A	p.K806K	GAGGTCCTTCTTA	.	PASS	Atlas-SNP
ACSBG2	81616	hgsc.bcm.edu	37	19	6156483	6156483	+	Missense_Mutation	SNP	T	T	C	rs4807840	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	213	117	246	1	0.549296	0.00406504	T|0.289;C|0.711	0.711	strong	ACSBG2,NS,carcinoma,+1,1	ACSBG2	83	1	NM_030924	exon5	c.T428C	p.V143A	CCGAGGTTTGTCA	.	PASS	Atlas-SNP
CMKLR1	1240	hgsc.bcm.edu	37	12	108686572	108686572	+	Silent	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	117	28	169	0	0.239316	0	.	.	none	CMKLR1,NS,carcinoma,-2,1	CMKLR1	67	1	NM_001142344	exon3	c.G168A	p.L56L	ATTGCCCAGAATC	.	PASS	Atlas-SNP
SUSD5	26032	hgsc.bcm.edu	37	3	33194990	33194990	+	Missense_Mutation	SNP	C	C	A	rs6810039	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	173	85	233	0	0.491329	0	C|0.374;A|0.626	0.626	strong	.	SUSD5	53	.	NM_015551	exon5	c.G1134T	p.E378D	AGCCCCCTCTGTC	.	PASS	Atlas-SNP
KLHL13	90293	hgsc.bcm.edu	37	X	117035896	117035896	+	Silent	SNP	A	A	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	112	34	157	0	0.303571	0	.	.	none	.	KLHL13	87	.	NM_001168299	exon7	c.T1389C	p.C463C	ATTGTAACATTCT	.	PASS	Atlas-SNP
B9D1	27077	hgsc.bcm.edu	37	17	19247075	19247075	+	Missense_Mutation	SNP	G	G	A	rs4924987	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	30	18	27	0	0.6	0	G|0.579;A|0.421	0.421	strong	.	B9D1	8	.	NM_001243473	exon6	c.C559T	p.H187Y	GGGGATGGGGGTA	.	PASS	Atlas-SNP
STOX2	56977	hgsc.bcm.edu	37	4	184930961	184930961	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	51	11	64	0	0.215686	0	.	.	none	.	STOX2	142	.	NM_020225	exon3	c.G970A	p.V324M	CTGACCGTGGAAA	.	PASS	Atlas-SNP
CLEC18B	497190	hgsc.bcm.edu	37	16	74451970	74451970	+	Missense_Mutation	SNP	G	G	C	rs3869428		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	638	44	266	0	0.0689655	0	.	.	weak	CLEC18B,mouth,carcinoma,0,1	CLEC18B	45	1	NM_001011880	exon3	c.C443G	p.T148S	TAGTGGGTGCAGG	.	scavenged	Atlas-SNP
DNAJC30	84277	hgsc.bcm.edu	37	7	73097238	73097238	+	Silent	SNP	G	G	A	rs1569062	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	64	37	62	0	0.578125	0	G|0.763;A|0.237	0.237	strong	.	DNAJC30	12	.	NM_032317	exon1	c.C516T	p.Y172Y	TTCCCCGTAGTGG	.	PASS	Atlas-SNP
KIF13A	63971	hgsc.bcm.edu	37	6	17764530	17764530	+	Silent	SNP	C	C	T	rs9371018	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	109	53	172	0	0.486239	0	C|0.684;T|0.316	0.316	strong	.	KIF13A	276	.	NM_022113	exon39	c.G5229A	p.E1743E	TTTTCCCTCTGAC	.	PASS	Atlas-SNP
TRPV3	162514	hgsc.bcm.edu	37	17	3447914	3447914	+	Silent	SNP	C	C	T	rs1039519	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	17	6	21	0	0.352941	0	C|0.383;T|0.617	0.617	strong	.	TRPV3	85	.	NM_001258205	exon4	c.G270A	p.Q90Q	ATCATCCTGAGGA	.	PASS	Atlas-SNP
POFUT1	23509	hgsc.bcm.edu	37	20	30795819	30795819	+	Silent	SNP	T	T	C	rs1923095	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	34	33	56	0	0.970588	0	T|0.236;C|0.764	0.764	strong	POFUT1_ENST00000375730,NS,carcinoma,0,2	POFUT1	52	2	NM_172236	exon1	c.T75C	p.P25P	GATGCCTGCGGGC	.	PASS	Atlas-SNP
BTBD6	90135	hgsc.bcm.edu	37	14	105716854	105716854	+	Missense_Mutation	SNP	G	G	A	rs146426875	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	56	29	70	0	0.517857	0	G|0.997;A|0.003	0.003	strong	.	BTBD6	24	.	NM_033271	exon5	c.G1303A	p.V435I	AGTGCCGTCCTGG	.	PASS	Atlas-SNP
FAT1	2195	hgsc.bcm.edu	37	4	187542755	187542755	+	Missense_Mutation	SNP	T	T	C	rs28489116	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	181	81	250	0	0.447514	0	T|0.794;C|0.206	0.206	strong	FAT1,NS,carcinoma,0,2	FAT1	500	2	NM_005245	exon10	c.A4985G	p.N1662S	GAGGCGTTGTCAG	.	PASS	Atlas-SNP
DMBT1	1755	hgsc.bcm.edu	37	10	124351954	124351954	+	Silent	SNP	G	G	A	rs4752722	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	42	30	46	0	0.714286	0	G|0.732;A|0.268	0.268	strong	.	DMBT1	677	.	NM_007329	exon20	c.G2343A	p.S781S	CACGTCGGCCCCA	.	PASS	Atlas-SNP
CRIPAK	285464	hgsc.bcm.edu	37	4	1388378	1388378	+	Missense_Mutation	SNP	T	T	C	rs55884223	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	90	23	127	2	0.255556	0.015748	T|0.993;C|0.007	0.007	strong	CRIPAK,NS,carcinoma,-1,1	CRIPAK	185	1	NM_175918	exon1	c.T79C	p.C27R	TGCTCATGTGCCC	.	scavenged	Atlas-SNP
ZNF585A	199704	hgsc.bcm.edu	37	19	37644051	37644051	+	Silent	SNP	T	T	C	rs57916401	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	156	97	236	0	0.621795	0	T|0.630;C|0.370	0.370	strong	.	ZNF585A	117	.	NM_199126	exon6	c.A585G	p.A195A	TGTGAATGCTTTG	.	PASS	Atlas-SNP
CC2D2B	387707	hgsc.bcm.edu	37	10	97772358	97772358	+	Missense_Mutation	SNP	A	A	G	rs17383738	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	112	64	108	0	0.571429	0	A|0.889;G|0.111	0.111	strong	.	CC2D2B	46	.	NM_001001732	exon4	c.A190G	p.N64D	TTTCCCAACCGAA	.	PASS	Atlas-SNP
BIN3	55909	hgsc.bcm.edu	37	8	22481449	22481449	+	Silent	SNP	A	A	G	rs1871900	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	64	48	85	0	0.75	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
LRIG3	121227	hgsc.bcm.edu	37	12	59282702	59282702	+	Silent	SNP	T	T	C	rs17533647	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	171	73	156	0	0.426901	0	T|0.928;C|0.072	0.072	strong	LRIG3,NS,carcinoma,-2,1	LRIG3	120	1	NM_153377	exon6	c.A702G	p.T234T	TTGGAATGTCAGT	.	PASS	Atlas-SNP
CTR9	9646	hgsc.bcm.edu	37	11	10786175	10786175	+	Silent	SNP	C	C	T	rs7118399	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	188	25	156	0	0.132979	0	C|0.772;T|0.228	0.228	strong	CTR9,NS,carcinoma,0,1	CTR9	94	1	NM_014633	exon12	c.C1494T	p.T498T	CGTTACCACGTCA	.	PASS	Atlas-SNP
WDR78	79819	hgsc.bcm.edu	37	1	67390468	67390468	+	Missense_Mutation	SNP	C	C	G	rs1886686	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	42	41	72	0	0.97619	0	C|0.209;G|0.791	0.791	strong	.	WDR78	102	.	NM_207014	exon1	c.G47C	p.G16A	GCTCCTCCGTTAG	.	PASS	Atlas-SNP
CHGB	1114	hgsc.bcm.edu	37	20	5903894	5903894	+	Silent	SNP	A	A	G	rs236153	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	27	13	37	0	0.481481	0	A|0.533;G|0.467	0.467	strong	.	CHGB	112	.	NM_001819	exon4	c.A1104G	p.E368E	AAGTGAAGAATAC	.	PASS	Atlas-SNP
ERMAP	114625	hgsc.bcm.edu	37	1	43296173	43296173	+	Silent	SNP	C	C	T	rs33950227	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	102	102	112	0	1	0	C|0.814;T|0.186	0.186	strong	.	ERMAP	30	.	NM_001017922	exon3	c.C54T	p.L18L	CCCTCTCGTCTTC	.	PASS	Atlas-SNP
PLIN4	729359	hgsc.bcm.edu	37	19	4512613	4512613	+	Silent	SNP	T	T	G	rs74327986	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	99	30	132	0	0.30303	0	T|0.916;G|0.084	0.084	strong	.	PLIN4	191	.	NM_001080400	exon3	c.A1317C	p.T439T	CACGCCTGTCTGG	.	PASS	Atlas-SNP
DPT	1805	hgsc.bcm.edu	37	1	168683476	168683476	+	Silent	SNP	C	C	T	rs35449613	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	66	33	79	0	0.5	0	C|0.957;G|0.000;T|0.043	0.043	strong	.	DPT	29	.	NM_001937	exon2	c.G414A	p.R138R	TGGGCACCTCTTG	.	PASS	Atlas-SNP
SP110	3431	hgsc.bcm.edu	37	2	231042276	231042276	+	Missense_Mutation	SNP	A	A	G	rs1135791	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	291	168	336	0	0.57732	0	A|0.640;G|0.360	0.360	strong	.	SP110	105	.	NM_001185015	exon15	c.T1586C	p.M529T	AGGGTCATTCCTT	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	74	38	120	0	0.513514	0	C|0.812;A|0.188	0.188	strong	.	HTT	221	.	NM_002111	exon39	c.C5159A	p.T1720N	ACAGTACTTCAAC	.	PASS	Atlas-SNP
ZFAT	57623	hgsc.bcm.edu	37	8	135622851	135622851	+	Missense_Mutation	SNP	G	G	A	rs75596750	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	286	62	309	0	0.216783	0	G|0.999;A|0.001	0.001	strong	.	ZFAT	265	.	NM_020863	exon4	c.C496T	p.R166W	TTTCCCGATCATC	.	PASS	Atlas-SNP
KIAA1217	56243	hgsc.bcm.edu	37	10	24669877	24669877	+	Missense_Mutation	SNP	C	C	G	rs17506606	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	60	23	46	0	0.383333	0	C|0.845;G|0.155	0.155	strong	KIAA1217,caecum,carcinoma,+1,1	KIAA1217	235	1	NM_019590	exon3	c.C434G	p.A145G	CGTCCGCTGATTC	.	PASS	Atlas-SNP
TPM1	7168	hgsc.bcm.edu	37	15	63351840	63351840	+	Silent	SNP	C	C	A	rs1071646	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	53	53	68	0	1	0	C|0.339;A|0.661	0.661	strong	.	TPM1	59	.	NM_001018007	exon4	c.C453A	p.A151A	AGAGGCCAAGCAC	.	PASS	Atlas-SNP
UNC13A	23025	hgsc.bcm.edu	37	19	17749893	17749893	+	Missense_Mutation	SNP	G	G	A	rs200328448	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	67	39	86	0	0.58209	0	G|0.996;A|0.004	0.004	strong	UNC13A_ENST00000519716,NS,carcinoma,0,2	UNC13A	299	2	NM_001080421	exon24	c.C3080T	p.P1027L	CTCACCGGGTCTG	.	PASS	Atlas-SNP
C4orf36	132989	hgsc.bcm.edu	37	4	87809025	87809025	+	Missense_Mutation	SNP	T	T	C	rs28664715	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	94	94	158	0	1	0	T|0.938;C|0.062	0.062	strong	.	C4orf36	10	.	NM_144645	exon4	c.A242G	p.Y81C	ACTTCATACTCCC	.	PASS	Atlas-SNP
NACC2	138151	hgsc.bcm.edu	37	9	138905136	138905136	+	Silent	SNP	C	C	T	rs2280486	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	149	76	150	0	0.510067	0	C|0.543;T|0.457	0.457	strong	.	NACC2	16	.	NM_144653	exon5	c.G1164A	p.T388T	GGCCAGCGTGTTC	.	PASS	Atlas-SNP
DDR1	780	hgsc.bcm.edu	37	6	30862423	30862423	+	Missense_Mutation	SNP	C	C	T	rs1264319	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	60	26	46	0	0.433333	0	C|0.820;T|0.180	0.180	strong	.	DDR1	213	.	NM_001202522	exon10	c.C1406T	p.P469L	CCACTCCGCTCCC	.	PASS	Atlas-SNP
ANO7	50636	hgsc.bcm.edu	37	2	242157228	242157228	+	Silent	SNP	G	G	T	rs78605785	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	91	53	90	0	0.582418	0	C|0.028;G|0.842;T|0.131	0.131	strong	.	ANO7	136	.	NM_001001891	exon20	c.G2262T	p.P754P	GCGCCCGGTGGCC	.	PASS	Atlas-SNP
OR10H1	26539	hgsc.bcm.edu	37	19	15918380	15918380	+	Silent	SNP	C	C	T	rs28426969	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	153	86	186	0	0.562092	0	C|0.618;T|0.382	0.382	strong	OR10H1,NS,carcinoma,0,1	OR10H1	59	1	NM_013940	exon1	c.G468A	p.G156G	CACCATCCCCATG	.	PASS	Atlas-SNP
SH3BP4	23677	hgsc.bcm.edu	37	2	235951183	235951183	+	Silent	SNP	G	G	A	rs140262787	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	38	104	0	0.520548	0	G|0.992;A|0.008	0.008	strong	SH3BP4,NS,carcinoma,+2,1	SH3BP4	109	1	NM_014521	exon4	c.G1770A	p.R590R	GCTGCGGGTTCAG	.	PASS	Atlas-SNP
KIAA1143	57456	hgsc.bcm.edu	37	3	44794881	44794881	+	Missense_Mutation	SNP	A	A	C	rs3853404	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	112	50	100	0	0.446429	0	A|1.000;|0.000	.	weak	.	KIAA1143	10	.	NM_020696	exon3	c.T417G	p.I139M	ATTTTTAATTTGT	.	PASS	Atlas-SNP
NCKAP1	10787	hgsc.bcm.edu	37	2	183848053	183848053	+	Silent	SNP	A	A	G	rs35142583	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	126	54	94	0	0.428571	0	A|0.961;G|0.039	0.039	strong	.	NCKAP1	105	.	NM_205842	exon12	c.T1080C	p.A360A	GACAGTAGCCAAT	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	205	92	231	0	0.44878	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
MKI67	4288	hgsc.bcm.edu	37	10	129901501	129901501	+	Missense_Mutation	SNP	G	G	C	rs2071496	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	100	55	119	0	0.55	0	G|0.798;C|0.202	0.202	strong	MKI67,NS,carcinoma,0,1	MKI67	363	1	NM_002417	exon13	c.C8603G	p.T2868S	TGCGTGGTCTCCC	.	PASS	Atlas-SNP
OR10G2	26534	hgsc.bcm.edu	37	14	22102439	22102439	+	Missense_Mutation	SNP	C	C	G	rs41361344	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	236	46	394	2	0.194915	0.00507614	C|0.586;G|0.414	0.414	strong	OR10G2,NS,carcinoma,0,2	OR10G2	35	2	NM_001005466	exon1	c.G560C	p.R187P	ACTGCGCGGATGT	.	scavenged	Atlas-SNP
SLC12A5	57468	hgsc.bcm.edu	37	20	44680412	44680412	+	Silent	SNP	C	C	T	rs3746522	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	74	43	77	0	0.581081	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
HIVEP2	3097	hgsc.bcm.edu	37	6	143091769	143091769	+	Silent	SNP	G	G	A	rs34947356	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	56	44	85	0	0.785714	0	G|0.859;A|0.141	0.141	strong	.	HIVEP2	225	.	NM_006734	exon5	c.C4107T	p.V1369V	CTCATCGACTTTG	.	PASS	Atlas-SNP
C3orf30	152405	hgsc.bcm.edu	37	3	118865332	118865332	+	Missense_Mutation	SNP	A	A	G	rs11550908	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	107	48	105	0	0.448598	0	A|0.855;G|0.145	0.145	strong	.	C3orf30	64	.	NM_152539	exon1	c.A296G	p.D99G	TTTCTGACCTTAG	.	PASS	Atlas-SNP
FKBP9	11328	hgsc.bcm.edu	37	7	33035785	33035785	+	Silent	SNP	C	C	T	rs141599926	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	119	90	127	0	0.756303	0	C|0.988;T|0.012	0.012	strong	.	FKBP9	335	.	NM_007270	exon7	c.C1050T	p.P350P	TATCCCCGGCTCG	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	76	41	100	0	0.539474	0	C|0.772;T|0.228	0.228	strong	.	PCDH15	1715	.	NM_001142763	exon12	c.G1153A	p.G385S	GTAGACCGGCAAA	.	PASS	Atlas-SNP
PALLD	23022	hgsc.bcm.edu	37	4	169433327	169433327	+	Missense_Mutation	SNP	G	G	A	rs7671781	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	57	74	0	0.982759	0	G|0.733;A|0.267	0.267	strong	.	PALLD	179	.	NM_001166108	exon2	c.G672A	p.M224I	CCCTATGGAAGAC	.	PASS	Atlas-SNP
HTT	3064	hgsc.bcm.edu	37	4	3234980	3234980	+	Missense_Mutation	SNP	G	G	A	rs362272	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	139	62	159	0	0.446043	0	G|0.759;T|0.008	.	strong	HTT,NS,carcinoma,0,1	HTT	221	1	NM_002111	exon61	c.G8356A	p.V2786I	CACGGCGTCCTCT	.	PASS	Atlas-SNP
TMEM176A	55365	hgsc.bcm.edu	37	7	150500729	150500729	+	Missense_Mutation	SNP	A	A	G	rs741064	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	38	37	36	0	0.973684	0	A|0.127;G|0.873	0.873	strong	TMEM176A,NS,carcinoma,0,1	TMEM176A	35	1	NM_018487	exon5	c.A364G	p.T122A	CTGCTAACGCTGG	.	PASS	Atlas-SNP
CRIP3	401262	hgsc.bcm.edu	37	6	43273604	43273604	+	Missense_Mutation	SNP	A	A	G	rs2242416	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	95	95	115	1	1	0.00869565	G|0.469;N|0.000	0.469	strong	.	CRIP3	30	.	NM_206922	exon8	c.T563C	p.I188T	TCGCCAATGTTCA	.	PASS	Atlas-SNP
NEDD9	4739	hgsc.bcm.edu	37	6	11193860	11193860	+	Silent	SNP	G	G	A	rs16871074	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	156	58	150	2	0.371795	0.0133333	G|0.813;A|0.187	0.187	strong	NEDD9_ENST00000379446,NS,carcinoma,0,1	NEDD9	191	1	NM_001142393	exon4	c.C525T	p.D175D	ATAGACGTCCTTT	.	scavenged	Atlas-SNP
MLL3	58508	hgsc.bcm.edu	37	7	151970858	151970858	+	Missense_Mutation	SNP	C	C	T	rs2775344	bycluster;byfrequency;by2hit2allele;byhapmap	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	339	6	332	2	0.0176991	0.0060241	C|0.600;T|0.400	0.400	strong	MLL3_ENST00000355193,NS,carcinoma,-1,14	MLL3	1564	14	NM_170606	exon7	c.G944A	p.G315D	AAGGTGCCGGCTC	.	scavenged	Atlas-SNP
MS4A14	84689	hgsc.bcm.edu	37	11	60184191	60184191	+	Missense_Mutation	SNP	G	G	A	rs3825020	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	67	16	81	0	0.238806	0	G|0.445;A|0.555	0.555	strong	.	MS4A14	120	.	NM_001261828	exon6	c.G1849A	p.G617R	AAAGATGGACAAG	.	PASS	Atlas-SNP
OR5L1	219437	hgsc.bcm.edu	37	11	55579419	55579419	+	Silent	SNP	T	T	C	rs34948392	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	302	234	358	0	0.774834	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
ATAD5	79915	hgsc.bcm.edu	37	17	29167653	29167653	+	Missense_Mutation	SNP	A	A	C	rs3764421	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	38	135	0	0.391753	0	A|0.885;C|0.115	0.115	strong	ATAD5,NS,carcinoma,0,1	ATAD5	150	1	NM_024857	exon4	c.A2095C	p.N699H	TCAAAAAACATAT	.	PASS	Atlas-SNP
PIGS	94005	hgsc.bcm.edu	37	17	26881923	26881923	+	Silent	SNP	C	C	T	rs146249165	byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	111	53	134	0	0.477477	0	C|1.000;T|0.000	0.000	strong	.	PIGS	42	.	NM_033198	exon11	c.G1338A	p.A446A	AAGCTGCGCCAGG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195513420	195513420	+	Silent	SNP	G	G	A	rs71321842	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	171	44	205	0	0.25731	0	G|0.500;A|0.500	0.500	strong	.	MUC4	1505	.	NM_018406	exon2	c.C5031T	p.H1677H	GGTGGCGTGACCG	.	PASS	Atlas-SNP
RPS6KA1	6195	hgsc.bcm.edu	37	1	26883511	26883511	+	Missense_Mutation	SNP	A	A	C	rs2229712	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	125	45	134	0	0.36	0	A|0.833;C|0.167	0.167	strong	.	RPS6KA1	65	.	NM_001006665	exon12	c.A1031C	p.K344T	AGATCAAGCCACC	.	PASS	Atlas-SNP
SF3B1	23451	hgsc.bcm.edu	37	2	198257075	198257075	+	Silent	SNP	G	G	A	rs78516934	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	106	40	111	0	0.377358	0	G|0.993;A|0.007	0.007	strong	.	SF3B1	1038	.	NM_012433	exon25	c.C3867T	p.N1289N	ATCATCGTTGTAG	.	PASS	Atlas-SNP
C19orf59	199675	hgsc.bcm.edu	37	19	7743821	7743821	+	Missense_Mutation	SNP	A	A	G	rs72996468	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	184	91	165	0	0.494565	0	A|0.897;G|0.103	0.103	strong	.	C19orf59	15	.	NM_174918	exon6	c.A499G	p.I167V	AAAAACATTGACA	.	PASS	Atlas-SNP
OSBPL6	114880	hgsc.bcm.edu	37	2	179201048	179201048	+	Silent	SNP	G	G	T	rs16866263	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	51	30	55	0	0.588235	0	G|0.955;T|0.045	0.045	strong	OSBPL6_ENST00000392505,mucosal,malignant_melanoma,+2,2	OSBPL6	178	2	NM_001201482	exon9	c.G678T	p.P226P	CTTTCCGTGGCAG	.	PASS	Atlas-SNP
PITRM1	10531	hgsc.bcm.edu	37	10	3214942	3214942	+	Missense_Mutation	SNP	T	T	C	rs11818724	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	45	19	48	0	0.422222	0	T|0.938;C|0.062	0.062	strong	.	PITRM1	109	.	NM_014889	exon1	c.A23G	p.Q8R	AGGCCCTGCCGCC	.	PASS	Atlas-SNP
NOM1	64434	hgsc.bcm.edu	37	7	156761818	156761818	+	Missense_Mutation	SNP	G	G	A	rs2302445	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	74	74	110	0	1	0	G|0.508;A|0.492	0.492	strong	.	NOM1	73	.	NM_138400	exon10	c.G2336A	p.R779H	GAGTCCGTTTTTT	.	PASS	Atlas-SNP
MANSC1	54682	hgsc.bcm.edu	37	12	12496086	12496086	+	Missense_Mutation	SNP	C	C	T	rs3741798	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	124	60	141	0	0.483871	0	C|0.898;T|0.102	0.102	strong	.	MANSC1	38	.	NM_018050	exon2	c.G163A	p.V55I	TATATACGGGCTC	.	PASS	Atlas-SNP
AKAP9	10142	hgsc.bcm.edu	37	7	91708898	91708898	+	Missense_Mutation	SNP	A	A	G	rs35759833	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	52	19	52	0	0.365385	0	A|0.911;G|0.089	0.089	strong	AKAP9_ENST00000356239,colon,carcinoma,0,2	AKAP9	788	2	NM_005751	exon31	c.A7451G	p.K2484R	ACTTCAAATCTTT	.	PASS	Atlas-SNP
DFNA5	1687	hgsc.bcm.edu	37	7	24758818	24758818	+	Missense_Mutation	SNP	G	G	T	rs754554	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	47	5	76	0	0.106383	0	G|0.798;T|0.202	0.202	strong	DFNA5,colon,carcinoma,+1,1	DFNA5	51	1	NM_001127453	exon4	c.C424A	p.P142T	GCACAGGGTTTCT	.	PASS	Atlas-SNP
BRD8	10902	hgsc.bcm.edu	37	5	137475787	137475787	+	Silent	SNP	C	C	T	rs423258	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	141	140	183	0	0.992908	0	C|0.714;T|0.286	0.286	strong	BRD8,NS,carcinoma,0,1	BRD8	192	1	NM_139199	exon27	c.G3684A	p.V1228V	ATCATCCACTGGG	.	PASS	Atlas-SNP
PGLS	25796	hgsc.bcm.edu	37	19	17628587	17628587	+	Silent	SNP	A	A	G	rs6743	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	70	93	0	1	0	A|0.390;G|0.610	0.610	strong	.	PGLS	12	.	NM_012088	exon4	c.A567G	p.T189T	CCTCACACTACCT	.	PASS	Atlas-SNP
SULT4A1	25830	hgsc.bcm.edu	37	22	44234792	44234792	+	Nonsense_Mutation	SNP	G	G	A	rs199511302	alternate_allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	124	2	169	0	0.016129	0	G|0.999;T|0.001	.	alt	SULT4A1,NS,carcinoma,+1,1	SULT4A1	26	1	NM_014351	exon4	c.C463T	p.R155X	TGCCTCGGTAGCT	.	scavenged	Atlas-SNP
USP24	23358	hgsc.bcm.edu	37	1	55620442	55620442	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	178	3	204	0	0.0168539	0	.	.	none	USP24_ENST00000294383,NS,carcinoma,+2,2	USP24	323	2	NM_015306	exon13	c.T1456C	p.S486P	TAGATGATTGTCC	.	scavenged	Atlas-SNP
CAV1	857	hgsc.bcm.edu	37	7	116165140	116165140	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	37	122	0	0.402174	0	.	.	none	.	CAV1	13	.	NM_001753	exon1	c.C24A	p.D8E	CGTAGACTCGGAG	.	PASS	Atlas-SNP
RAVER1	125950	hgsc.bcm.edu	37	19	10439501	10439501	+	Silent	SNP	C	C	T	rs3745263	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	187	86	249	0	0.459893	0	C|0.971;T|0.029	0.029	strong	.	RAVER1	67	.	NM_133452	exon3	c.G624A	p.S208S	CAGGTCCGACTTG	.	PASS	Atlas-SNP
C17orf97	400566	hgsc.bcm.edu	37	17	263645	263645	+	Silent	SNP	C	C	T	rs200761914	byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	115	6	210	6	0.0521739	0.0285714	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
C14orf37	145407	hgsc.bcm.edu	37	14	58563694	58563694	+	Missense_Mutation	SNP	G	G	C	rs2273442	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	91	91	92	0	1	0	G|0.481;C|0.519	0.519	strong	.	C14orf37	87	.	NM_001001872	exon5	c.C1837G	p.Q613E	CTTCTTGTCCCTC	.	PASS	Atlas-SNP
ACSM5	54988	hgsc.bcm.edu	37	16	20441077	20441077	+	Missense_Mutation	SNP	A	A	G	rs12931877	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	40	12	50	0	0.3	0	A|0.969;G|0.031	0.031	strong	.	ACSM5	101	.	NM_017888	exon8	c.A1079G	p.H360R	GGAAACACCAGAC	.	PASS	Atlas-SNP
TMPRSS11E	28983	hgsc.bcm.edu	37	4	69337325	69337325	+	Missense_Mutation	SNP	C	C	G	rs2603188	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	325	324	412	0	0.996923	0	C|0.887;G|0.113	0.113	strong	.	TMPRSS11E	40	.	NM_014058	exon5	c.C474G	p.H158Q	TCCTCACTCAGTT	.	PASS	Atlas-SNP
CBX3	11335	hgsc.bcm.edu	37	7	26245986	26245986	+	Splice_Site	SNP	A	A	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	26	6	37	1	0.230769	0.027027	.	.	none	CBX3,colon,adenoma,0,1	CBX3	25	1	NM_007276	exon3	c.25-2A>T	.	TATTTTAGCAAAA	.	scavenged	Atlas-SNP
DHDH	27294	hgsc.bcm.edu	37	19	49447713	49447713	+	Missense_Mutation	SNP	G	G	A	rs3765148	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	145	75	178	0	0.517241	0	G|0.920;A|0.080	0.080	strong	.	DHDH	35	.	NM_014475	exon6	c.G844A	p.G282R	GACAACGGGGCAG	.	PASS	Atlas-SNP
FAM46C	54855	hgsc.bcm.edu	37	1	118165691	118165691	+	Missense_Mutation	SNP	C	C	G	rs1630312	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	157	70	168	0	0.44586	0	T|0.288;G|0.015;C|0.697	0.015	strong	.	FAM46C	25	.	NM_017709	exon2	c.C201G	p.H67Q	AGTGCACGACGTC	.	PASS	Atlas-SNP
PCNXL4	64430	hgsc.bcm.edu	37	14	60592491	60592491	+	Missense_Mutation	SNP	A	A	G	rs145320435	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	48	99	0	0.475248	0	A|0.998;G|0.002	0.002	strong	.	.	.	.	NM_022495	exon9	c.A2515G	p.I839V	GAAGCAATTTTAC	.	PASS	Atlas-SNP
ZNF681	148213	hgsc.bcm.edu	37	19	23926916	23926916	+	Missense_Mutation	SNP	T	T	C	rs1852432	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	19	9	19	0	0.473684	0	T|0.898;C|0.102	0.102	strong	.	ZNF681	76	.	NM_138286	exon4	c.A1436G	p.K479R	TCACATTTGTAGG	.	PASS	Atlas-SNP
TDRD10	126668	hgsc.bcm.edu	37	1	154516578	154516578	+	Missense_Mutation	SNP	G	G	A	rs3811448	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	99	47	106	0	0.474747	0	G|0.821;A|0.179	0.179	strong	.	TDRD10	48	.	NM_182499	exon9	c.G643A	p.V215I	ATGCACGTCACTG	.	PASS	Atlas-SNP
CDC42BPA	8476	hgsc.bcm.edu	37	1	227504794	227504794	+	Silent	SNP	T	T	C	rs11804613	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	155	86	213	0	0.554839	0	T|0.768;C|0.232	0.232	strong	.	CDC42BPA	528	.	NM_003607	exon1	c.A90G	p.T30T	CAGTAATGTCTCC	.	PASS	Atlas-SNP
VIT	5212	hgsc.bcm.edu	37	2	37041480	37041480	+	Silent	SNP	G	G	A	rs17441812	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	37	82	0	0.528571	0	G|0.956;A|0.044	0.044	strong	.	VIT	138	.	NM_053276	exon16	c.G2058A	p.E686E	TACAGAGTTCAAC	.	PASS	Atlas-SNP
CAPZA1	829	hgsc.bcm.edu	37	1	113197203	113197203	+	Silent	SNP	A	A	G	rs3790599	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	216	105	233	0	0.486111	0	A|0.935;G|0.065	0.065	strong	.	CAPZA1	16	.	NM_006135	exon5	c.A336G	p.E112E	AGAAGAAGCAGAT	.	PASS	Atlas-SNP
ELFN2	114794	hgsc.bcm.edu	37	22	37770357	37770357	+	Silent	SNP	A	A	G	rs7292751	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	80	38	124	0	0.475	0	A|0.542;G|0.458	0.458	strong	.	ELFN2	89	.	NM_052906	exon3	c.T1218C	p.F406F	CATGCCAAAGAGG	.	PASS	Atlas-SNP
AP1M1	8907	hgsc.bcm.edu	37	19	16339715	16339715	+	Silent	SNP	C	C	T	rs3752797	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	96	96	118	0	1	0	C|0.486;T|0.514	0.514	strong	.	AP1M1	48	.	NM_001130524	exon10	c.C1059T	p.I353I	CGAGATCGTGTGG	.	PASS	Atlas-SNP
HSD17B3	3293	hgsc.bcm.edu	37	9	99064378	99064378	+	Silent	SNP	G	G	A	rs139582148	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	109	56	97	0	0.513761	0	G|0.999;A|0.001	0.001	strong	.	HSD17B3	32	.	NM_000197	exon1	c.C9T	p.D3D	CAGGACGTCCCCC	.	PASS	Atlas-SNP
HEG1	57493	hgsc.bcm.edu	37	3	124748226	124748226	+	Silent	SNP	G	G	A	rs2860440	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	61	25	51	0	0.409836	0	G|0.528;A|0.472	0.472	strong	HEG1,colon,carcinoma,0,1	HEG1	109	1	NM_020733	exon2	c.C423T	p.G141G	CATCACGCCCTCT	.	scavenged	Atlas-SNP
FSTL4	23105	hgsc.bcm.edu	37	5	132535046	132535046	+	Missense_Mutation	SNP	G	G	A	rs3749817	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	85	100	0	1	0	G|0.785;N|0.000	.	strong	.	FSTL4	74	.	NM_015082	exon16	c.C2270T	p.T757M	GGCTCCGTGTGCA	.	PASS	Atlas-SNP
SYNGR2	9144	hgsc.bcm.edu	37	17	76167047	76167047	+	Silent	SNP	C	C	T	rs1062668	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	98	38	105	0	0.387755	0	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	.	PASS	Atlas-SNP
IQCB1	9657	hgsc.bcm.edu	37	3	121500699	121500699	+	Missense_Mutation	SNP	C	C	T	rs17849995	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	37	76	0	0.521127	0	C|0.759;T|0.241	0.241	strong	.	IQCB1	50	.	NM_001023570	exon13	c.G1301A	p.C434Y	TTACGGCACTTCG	.	PASS	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149520553	149520553	+	Silent	SNP	G	G	A	rs141884347	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	45	18	37	0	0.4	0	G|0.990;A|0.010	0.010	strong	.	.	.	.	NM_198455	exon92	c.G13371A	p.P4457P	CCAGCCGGGCTGC	.	PASS	Atlas-SNP
PPP6R2	9701	hgsc.bcm.edu	37	22	50878196	50878196	+	Missense_Mutation	SNP	G	G	A	rs13057311	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	145	66	128	0	0.455172	0	G|0.783;A|0.217	0.217	strong	.	PPP6R2	71	.	NM_001242898	exon20	c.G2195A	p.R732K	TGGTGAGGGACGT	.	PASS	Atlas-SNP
HIST1H2AC	8334	hgsc.bcm.edu	37	6	26124563	26124563	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	100	32	99	0	0.32	0	.	.	none	.	HIST1H2AC	29	.	NM_003512	exon1	c.C103G	p.L35V	CGCCTGCTCCGTA	.	PASS	Atlas-SNP
MTMR10	54893	hgsc.bcm.edu	37	15	31267147	31267147	+	Silent	SNP	C	C	T	rs1133642	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	73	95	0	1	0	A|0.000;C|0.421;T|0.579	0.579	strong	.	MTMR10	74	.	NM_017762	exon4	c.G318A	p.E106E	AATTTGCTCAATA	.	PASS	Atlas-SNP
CEP70	80321	hgsc.bcm.edu	37	3	138244400	138244400	+	Silent	SNP	C	C	T	rs9878436	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	16	15	28	0	0.9375	0	C|0.619;T|0.381	0.381	strong	.	CEP70	51	.	NM_024491	exon11	c.G876A	p.T292T	ATGCTGCGTAGGC	.	PASS	Atlas-SNP
FBLN2	2199	hgsc.bcm.edu	37	3	13612020	13612020	+	Silent	SNP	T	T	C	rs3732667	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	162	60	174	0	0.37037	0	T|0.745;G|0.000;C|0.255	0.255	strong	.	FBLN2	137	.	NM_001998	exon2	c.T165C	p.C55C	CTGCTGTGCCACG	.	PASS	Atlas-SNP
LIMD1	8994	hgsc.bcm.edu	37	3	45637253	45637253	+	Silent	SNP	C	C	T	rs267237	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	81	36	100	0	0.444444	0	C|0.394;T|0.606	0.606	strong	LIMD1,NS,carcinoma,0,1	LIMD1	34	1	NM_014240	exon1	c.C882T	p.T294T	CAGGACCCCTTCT	.	PASS	Atlas-SNP
PSPH	5723	hgsc.bcm.edu	37	7	56084977	56084977	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	508	130	548	1	0.255906	0.00182482	.	.	none	.	PSPH	23	.	NM_004577	exon6	c.A371G	p.N124S	GGGATATTGAGCT	.	PASS	Atlas-SNP
HNRNPCL1	343069	hgsc.bcm.edu	37	1	12907385	12907385	+	Missense_Mutation	SNP	G	G	A	rs150590256	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	156	14	163	15	0.0897436	0.0920245	.	.	weak	HNRNPCL1,NS,carcinoma,0,1	HNRNPCL1	68	1	NM_001013631	exon2	c.C758T	p.P253L	TCCAGTGGGTCCC	.	scavenged	Atlas-SNP
PROSER1	80209	hgsc.bcm.edu	37	13	39587889	39587889	+	Silent	SNP	T	T	C	rs3751377	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	35	100	0	0.466667	0	T|0.809;C|0.191	0.191	strong	.	.	.	.	NM_025138	exon11	c.A1500G	p.L500L	AGAAGATAGTGAA	.	PASS	Atlas-SNP
ARHGAP42	143872	hgsc.bcm.edu	37	11	100847050	100847050	+	Silent	SNP	A	A	G	rs569270	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	21	112	0	0.207921	0	A|0.479;G|0.521	0.521	strong	.	ARHGAP42	32	.	NM_152432	exon20	c.A2118G	p.S706S	TGCTTCAGTCACT	.	PASS	Atlas-SNP
MUC6	4588	hgsc.bcm.edu	37	11	1017068	1017068	+	Silent	SNP	C	C	T	rs78992004		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	509	62	396	40	0.121807	0.10101	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
AVPR1B	553	hgsc.bcm.edu	37	1	206230958	206230958	+	Missense_Mutation	SNP	G	G	A	rs28632197	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	32	18	38	0	0.5625	0	G|0.894;A|0.106	0.106	strong	.	AVPR1B	47	.	NM_000707	exon2	c.G1091A	p.R364H	GGATGCGCCGGCG	.	PASS	Atlas-SNP
VWA8	23078	hgsc.bcm.edu	37	13	42385446	42385446	+	Missense_Mutation	SNP	T	T	C	rs9562353	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	88	47	89	0	0.534091	0	T|0.931;C|0.069	0.069	strong	KIAA0564,lymph_node,lymphoid_neoplasm,0,1	.	.	1	NM_015058	exon17	c.A1978G	p.R660G	GTTGTCTGGTAGA	.	PASS	Atlas-SNP
BTN2A1	11120	hgsc.bcm.edu	37	6	26468545	26468545	+	Missense_Mutation	SNP	G	G	C	rs78126484		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	256	112	279	0	0.4375	0	.	.	weak	BTN2A1_ENST00000265424,NS,carcinoma,-1,2	BTN2A1	118	2	NM_007049	exon8	c.G1352C	p.G451A	GGGTGGGCGTCTT	.	PASS	Atlas-SNP
BOD1	91272	hgsc.bcm.edu	37	5	173036394	173036394	+	Missense_Mutation	SNP	C	C	T	rs72822197	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	286	34	186	0	0.118881	0	C|0.946;T|0.054	0.054	strong	.	BOD1	15	.	NM_138369	exon3	c.G406A	p.V136M	CCACCACCTGAGA	.	PASS	Atlas-SNP
C5orf55	116349	hgsc.bcm.edu	37	5	442790	442790	+	Missense_Mutation	SNP	G	G	A	rs10035653	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	124	61	140	0	0.491935	0	G|0.917;A|0.083	0.083	strong	.	C5orf55	11	.	NM_138464	exon1	c.C148T	p.P50S	TGGCAGGTATGAC	.	PASS	Atlas-SNP
MKS1	54903	hgsc.bcm.edu	37	17	56294075	56294075	+	Missense_Mutation	SNP	G	G	C	rs142813109	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	151	71	158	0	0.470199	0	G|0.996;C|0.004	0.004	strong	MKS1_ENST00000337050,NS,carcinoma,0,2	MKS1	100	2	NM_017777	exon3	c.C213G	p.D71E	CTCTTCGTCTTCC	.	PASS	Atlas-SNP
FAM135B	51059	hgsc.bcm.edu	37	8	139164192	139164192	+	Silent	SNP	G	G	A	rs3750306	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	60	59	95	0	0.983333	0	G|0.665;A|0.335	0.335	strong	.	FAM135B	423	.	NM_015912	exon13	c.C2526T	p.P842P	GTATCCGGGGCCC	.	PASS	Atlas-SNP
UBE2D1	7321	hgsc.bcm.edu	37	10	60127732	60127732	+	Silent	SNP	C	C	G	rs61749178	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	40	87	0	0.547945	0	C|0.984;G|0.016	0.016	strong	.	UBE2D1	16	.	NM_003338	exon6	c.C354G	p.P118P	TGACCCCTTAGTA	.	PASS	Atlas-SNP
SH2D4B	387694	hgsc.bcm.edu	37	10	82363340	82363340	+	Silent	SNP	C	C	A	rs7069048	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	46	22	74	0	0.478261	0	C|0.624;A|0.376	0.376	strong	SH2D4B,NS,carcinoma,-1,2	SH2D4B	44	2	NM_207372	exon5	c.C649A	p.R217R	GTGCGCCGGTCCA	.	PASS	Atlas-SNP
GLI3	2737	hgsc.bcm.edu	37	7	42005678	42005678	+	Missense_Mutation	SNP	G	G	A	rs929387	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	2	2	0	0	1	.	G|0.565;A|0.435	0.435	strong	GLI3,NS,adenocarcinoma,+1,1	GLI3	312	1	NM_000168	exon15	c.C2993T	p.P998L	TGGCCCGGCGCAT	.	scavenged	Atlas-SNP
MYO9B	4650	hgsc.bcm.edu	37	19	17316782	17316782	+	Missense_Mutation	SNP	T	T	C	rs7248508	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	31	10	35	0	0.322581	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
SPATA31E1	286234	hgsc.bcm.edu	37	9	90502819	90502819	+	Silent	SNP	T	T	C	rs10868671	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	45	95	0	0.642857	0	T|0.461;C|0.539	0.539	strong	.	.	.	.	NM_178828	exon4	c.T3417C	p.T1139T	GCTCACTGCCGCA	.	PASS	Atlas-SNP
KIF17	57576	hgsc.bcm.edu	37	1	21031042	21031042	+	Missense_Mutation	SNP	T	T	C	rs2296225	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	250	138	237	0	0.552	0	T|0.885;C|0.115	0.115	strong	.	KIF17	130	.	NM_001122819	exon5	c.A1021G	p.I341V	CATTGATGCGCGG	.	PASS	Atlas-SNP
ZFAT	57623	hgsc.bcm.edu	37	8	135524797	135524797	+	Silent	SNP	G	G	T	rs3739429	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	109	81	134	0	0.743119	0	G|0.797;T|0.203	0.203	strong	.	ZFAT	265	.	NM_020863	exon14	c.C3282A	p.I1094I	CTCTGTGATGTGG	.	PASS	Atlas-SNP
PRCC	5546	hgsc.bcm.edu	37	1	156756948	156756948	+	Silent	SNP	C	C	T	rs201827573	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	327	157	405	0	0.480122	0	C|0.999;T|0.001	0.001	strong	.	PRCC	39	.	NM_005973	exon3	c.C1065T	p.A355A	CAATGCCGCTGGT	.	PASS	Atlas-SNP
NCOA2	10499	hgsc.bcm.edu	37	8	71126255	71126255	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	77	4	108	0	0.0519481	0	.	.	none	NCOA2,NS,carcinoma,0,1	NCOA2	147	1	NM_006540	exon4	c.G142A	p.E48K	CAAGTTCTTCTAT	.	PASS	Atlas-SNP
C12orf65	91574	hgsc.bcm.edu	37	12	123738494	123738494	+	Silent	SNP	C	C	T	rs2280424	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	64	29	56	0	0.453125	0	C|0.929;T|0.071	0.071	strong	.	C12orf65	15	.	NM_001194995	exon2	c.C273T	p.I91I	AGGCATCGTTGTA	.	PASS	Atlas-SNP
KCNAB1	7881	hgsc.bcm.edu	37	3	156249214	156249214	+	Silent	SNP	T	T	C	rs2280031	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	119	59	114	0	0.495798	0	T|0.756;C|0.244	0.244	strong	.	KCNAB1	176	.	NM_172160	exon13	c.T1098C	p.N366N	GAGAAATGAAGGT	.	PASS	Atlas-SNP
L3HYPDH	112849	hgsc.bcm.edu	37	14	59950690	59950690	+	Silent	SNP	A	A	C	rs2296842	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	13	6	7	0	0.461538	0	A|0.786;C|0.214	0.214	strong	C14orf149,NS,carcinoma,0,1	.	.	1	NM_144581	exon1	c.T345G	p.A115A	GTCCAAAGCGAAG	.	PASS	Atlas-SNP
OR9G9	504191	hgsc.bcm.edu	37	11	56468155	56468155	+	Missense_Mutation	SNP	T	T	G	rs11228732	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	178	69	193	0	0.38764	0	T|0.749;G|0.251	0.251	strong	.	.	.	.	NM_001013358	exon1	c.T292G	p.C98G	TGCCTGTGTCAGT	.	PASS	Atlas-SNP
LILRA1	11024	hgsc.bcm.edu	37	19	55106239	55106239	+	Silent	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	122	4	175	0	0.0327869	0	.	.	none	LILRA1,NS,carcinoma,0,3	LILRA1	105	3	NM_006863	exon4	c.G180A	p.L60L	CCGTCTGTATAGA	.	scavenged	Atlas-SNP
GGT1	2678	hgsc.bcm.edu	37	22	25023881	25023881	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	431	104	538	0	0.241299	0	.	.	none	.	GGT1	68	.	NM_013430	exon13	c.T1271G	p.F424C	ACGACTTCAGCTC	.	PASS	Atlas-SNP
STOX1	219736	hgsc.bcm.edu	37	10	70645697	70645697	+	Silent	SNP	C	C	T	rs10509306	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	158	80	174	0	0.506329	0	C|0.912;T|0.088	0.088	strong	.	STOX1	75	.	NM_152709	exon3	c.C2145T	p.N715N	TTCTAACGATGAC	.	PASS	Atlas-SNP
OR5M1	390168	hgsc.bcm.edu	37	11	56380134	56380134	+	Missense_Mutation	SNP	C	C	G	rs4939078	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	359	94	401	0	0.261838	0	C|0.621;G|0.379	0.379	strong	.	OR5M1	92	.	NM_001004740	exon1	c.G845C	p.S282T	ATTGGGCTCAAAA	.	PASS	Atlas-SNP
FGF6	2251	hgsc.bcm.edu	37	12	4553332	4553332	+	Silent	SNP	A	A	G	rs2241280	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	144	62	147	0	0.430556	0	A|0.554;G|0.446	0.446	strong	FGF6,NS,carcinoma,-2,1	FGF6	40	1	NM_020996	exon2	c.T417C	p.V139V	CATGGCAACGAAG	.	PASS	Atlas-SNP
FAM194A	131831	hgsc.bcm.edu	37	3	150384657	150384657	+	Missense_Mutation	SNP	G	G	A	rs114572143	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	134	61	139	0	0.455224	0	G|0.986;A|0.014	0.014	strong	.	FAM194A	91	.	NM_152394	exon13	c.C1645T	p.R549C	AGATGCGGACTCC	.	PASS	Atlas-SNP
SNAPC4	6621	hgsc.bcm.edu	37	9	139270901	139270901	+	Silent	SNP	G	G	A	rs61745672	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	122	44	154	0	0.360656	0	G|0.934;A|0.066	0.066	strong	.	SNAPC4	82	.	NM_003086	exon22	c.C4317T	p.S1439S	GCAGGAGGAAGCA	.	PASS	Atlas-SNP
TMEM132C	92293	hgsc.bcm.edu	37	12	129153986	129153986	+	Missense_Mutation	SNP	G	G	A	rs4272850	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	148	72	145	0	0.486486	0	G|0.692;A|0.308	0.308	strong	.	TMEM132C	142	.	NM_001136103	exon5	c.G1330A	p.V444I	ACCGCCGTACTCA	.	PASS	Atlas-SNP
IGLL5	100423062	hgsc.bcm.edu	37	22	23230419	23230419	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	25	113	0	0.257732	0	.	.	none	.	IGLL5	26	.	NM_001256296	exon1	c.C80T	p.A27V	ATCCAGCCTGCGG	.	PASS	Atlas-SNP
POT1	25913	hgsc.bcm.edu	37	7	124481185	124481185	+	Missense_Mutation	SNP	C	C	A	rs35536751	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	106	47	124	0	0.443396	0	C|0.990;A|0.010	0.010	strong	.	POT1	186	.	NM_015450	exon14	c.G1211T	p.G404V	GTTGCACCATCCT	.	PASS	Atlas-SNP
SSPN	8082	hgsc.bcm.edu	37	12	26383959	26383959	+	Missense_Mutation	SNP	G	G	A	rs12313736	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	57	28	68	0	0.491228	0	G|0.913;A|0.087	0.087	strong	.	SSPN	19	.	NM_005086	exon3	c.G682A	p.V228I	GTGGGTGTCAGGA	.	PASS	Atlas-SNP
SIPA1L2	57568	hgsc.bcm.edu	37	1	232650867	232650867	+	Silent	SNP	C	C	T	rs4649383	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	150	150	198	1	1	0.00505051	C|0.410;T|0.590	0.590	strong	.	SIPA1L2	218	.	NM_020808	exon1	c.G219A	p.K73K	ACCCATCTTGGGC	.	PASS	Atlas-SNP
DARS2	55157	hgsc.bcm.edu	37	1	173822936	173822936	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	63	15	93	0	0.238095	0	.	.	none	.	DARS2	61	.	NM_018122	exon15	c.C1567T	p.R523C	TAGGCCCGTAGCC	.	PASS	Atlas-SNP
MST1L	11223	hgsc.bcm.edu	37	1	17085452	17085452	+	Silent	SNP	A	A	G	rs3981980		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	211	41	197	3	0.194313	0.0152284	A|1.000;|0.000	.	weak	Q13209_HUMAN,NS,carcinoma,0,1	.	.	1	NM_001271733	exon10	c.T1239C	p.F413F	GGGAGCAAAATCG	.	scavenged	Atlas-SNP
LAMA1	284217	hgsc.bcm.edu	37	18	6985270	6985270	+	Missense_Mutation	SNP	C	C	T	rs11664063	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	165	70	172	0	0.424242	0	C|0.823;T|0.177	0.177	strong	LAMA1,NS,carcinoma,0,1	LAMA1	458	1	NM_005559	exon39	c.G5626A	p.A1876T	ACTCAGCGGCATG	.	PASS	Atlas-SNP
TRAPPC10	7109	hgsc.bcm.edu	37	21	45506819	45506819	+	Silent	SNP	T	T	C	rs1131999	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	132	131	104	0	0.992424	0	T|0.658;C|0.342	0.342	strong	.	TRAPPC10	109	.	NM_003274	exon16	c.T2517C	p.A839A	CAGGGCTGTGGTC	.	PASS	Atlas-SNP
GH1	2688	hgsc.bcm.edu	37	17	61995189	61995189	+	Silent	SNP	G	G	A	rs370785603		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	30	131	1	0.29703	0.00763359	.	.	weak	GH1,caecum,carcinoma,0,1	GH1	39	1	NM_000515	exon4	c.C387T	p.Y129Y	GGCGCCGTACACC	.	scavenged	Atlas-SNP
MARCH10	162333	hgsc.bcm.edu	37	17	60814273	60814273	+	Missense_Mutation	SNP	A	A	G	rs9891498	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	139	139	183	0	1	0	A|0.682;G|0.318	0.318	strong	.	MARCH10	102	.	NM_001100875	exon6	c.T956C	p.F319S	CCCCCAAATCTAC	.	PASS	Atlas-SNP
HTR3D	200909	hgsc.bcm.edu	37	3	183755822	183755822	+	Missense_Mutation	SNP	G	G	A	rs1000952	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	80	41	102	0	0.5125	0	G|0.272;A|0.728	0.728	strong	.	HTR3D	65	.	NM_001163646	exon6	c.G674A	p.R225H	TCAGGCGCAGGTG	.	PASS	Atlas-SNP
HSPG2	3339	hgsc.bcm.edu	37	1	22154845	22154845	+	Silent	SNP	A	A	G	rs2228347	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	57	26	81	0	0.45614	0	T|0.000;G|0.250;A|0.750	0.250	strong	.	HSPG2	311	.	NM_005529	exon89	c.T12312C	p.D4104D	GGAGCTATCATAG	.	PASS	Atlas-SNP
HTR3A	3359	hgsc.bcm.edu	37	11	113857365	113857365	+	Silent	SNP	G	G	A	rs56232120	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	56	80	0	0.777778	0	G|0.986;A|0.014	0.014	strong	.	HTR3A	93	.	NM_000869	exon7	c.G849A	p.K283K	TTTCAAGATTACA	.	PASS	Atlas-SNP
SLBP	7884	hgsc.bcm.edu	37	4	1701317	1701317	+	Silent	SNP	G	G	A	rs2247341	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	217	91	273	0	0.419355	0	G|0.647;T|0.001	.	strong	.	SLBP	12	.	NM_006527	exon5	c.C453T	p.Y151Y	ACGATCGTAGGCA	.	PASS	Atlas-SNP
GPR37	2861	hgsc.bcm.edu	37	7	124387092	124387092	+	Silent	SNP	C	C	G	rs3735270	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	71	63	1	1	0.015873	C|0.590;G|0.410	0.410	strong	GPR37,NS,carcinoma,0,1	GPR37	89	1	NM_005302	exon2	c.G1329C	p.L443L	CCACCACAGTCTC	.	scavenged	Atlas-SNP
PARL	55486	hgsc.bcm.edu	37	3	183558402	183558402	+	Missense_Mutation	SNP	C	C	G	rs3732581	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	224	106	327	0	0.473214	0	C|0.516;G|0.484	0.484	strong	PARL,NS,carcinoma,0,1	PARL	32	1	NM_018622	exon7	c.G784C	p.V262L	TACCCACGTAACT	.	PASS	Atlas-SNP
TLN2	83660	hgsc.bcm.edu	37	15	62994208	62994208	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	129	65	104	0	0.503876	0	.	.	none	.	TLN2	253	.	NM_015059	exon15	c.G1714A	p.D572N	GACACTGACTACA	.	PASS	Atlas-SNP
TMF1	7110	hgsc.bcm.edu	37	3	69073223	69073223	+	Missense_Mutation	SNP	G	G	A	rs185749329	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	138	70	132	0	0.507246	0	G|0.999;A|0.001	0.001	strong	.	TMF1	77	.	NM_007114	exon16	c.C3121T	p.L1041F	TTCTAAGTTTGGG	.	PASS	Atlas-SNP
ALX4	60529	hgsc.bcm.edu	37	11	44289071	44289071	+	Silent	SNP	G	G	A	rs12419361	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	66	16	72	0	0.242424	0	G|0.905;A|0.095	0.095	strong	.	ALX4	58	.	NM_021926	exon3	c.C879T	p.L293L	GGTGAGGAGGGGC	.	PASS	Atlas-SNP
DSPP	1834	hgsc.bcm.edu	37	4	88535869	88535869	+	Silent	SNP	C	C	T	rs200233307		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	93	12	132	1	0.129032	0.00757576	.	.	weak	DSPP,NS,carcinoma,0,2	DSPP	174	2	NM_014208	exon5	c.C2055T	p.N685N	CAGCAACAGCAGT	.	scavenged	Atlas-SNP
MET	4233	hgsc.bcm.edu	37	7	116339282	116339282	+	Silent	SNP	G	G	A	rs11762213	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	136	69	126	0	0.507353	0	G|0.974;A|0.026	0.026	strong	MET,NS,adenocarcinoma,+1,2	MET	412	2	NM_000245	exon2	c.G144A	p.A48A	CACCGCGGAAACA	.	PASS	Atlas-SNP
KIF15	56992	hgsc.bcm.edu	37	3	44881909	44881909	+	Silent	SNP	A	A	G	rs76526953	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	31	106	0	0.360465	0	A|0.943;G|0.057	0.057	strong	.	KIF15	103	.	NM_020242	exon28	c.A3381G	p.Q1127Q	GAGGCAACTAGAA	.	PASS	Atlas-SNP
MORC3	23515	hgsc.bcm.edu	37	21	37741352	37741352	+	Silent	SNP	G	G	A	rs61739936	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	185	62	138	0	0.335135	0	G|0.919;A|0.081	0.081	strong	MORC3,NS,carcinoma,+2,1	MORC3	78	1	NM_015358	exon15	c.G1686A	p.Q562Q	TAGTCAGTTTGAA	.	PASS	Atlas-SNP
PLAUR	5329	hgsc.bcm.edu	37	19	44156472	44156472	+	Missense_Mutation	SNP	T	T	C	rs2302524	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	119	44	152	0	0.369748	0	T|0.832;C|0.168	0.168	strong	PLAUR,NS,carcinoma,0,1	PLAUR	71	1	NM_001005376	exon6	c.A659G	p.K220R	TTCCCCTTGCAGC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195512567	195512567	+	Missense_Mutation	SNP	G	G	A	rs150659095	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	118	33	54	1	0.279661	0.0185185	.	.	weak	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.C5884T	p.P1962S	CTGTGGGTACTGA	.	scavenged	Atlas-SNP
BTN1A1	696	hgsc.bcm.edu	37	6	26509382	26509382	+	Missense_Mutation	SNP	C	C	T	rs35555795	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	67	29	92	0	0.432836	0	C|0.934;T|0.066	0.066	strong	.	BTN1A1	68	.	NM_001732	exon7	c.C1561T	p.P521S	ACCCAACCCAGCC	.	PASS	Atlas-SNP
OR5B3	441608	hgsc.bcm.edu	37	11	58170025	58170025	+	Silent	SNP	C	C	G	rs12271646	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	169	109	200	0	0.64497	0	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	.	PASS	Atlas-SNP
TRIM66	9866	hgsc.bcm.edu	37	11	8646763	8646763	+	Missense_Mutation	SNP	G	G	C	rs7935453	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	61	56	40	0	0.918033	0	G|0.719;C|0.281	0.281	strong	.	TRIM66	45	.	NM_014818	exon11	c.C1888G	p.L630V	TGCTCAGCGAGGT	.	PASS	Atlas-SNP
L3MBTL2	83746	hgsc.bcm.edu	37	22	41613188	41613188	+	Silent	SNP	C	C	T	rs9611519	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	34	14	39	0	0.411765	0	C|0.775;T|0.225	0.225	strong	L3MBTL2,NS,carcinoma,0,1	L3MBTL2	61	1	NM_031488	exon5	c.C582T	p.P194P	TGCTCCCGTCAGC	.	PASS	Atlas-SNP
FSIP1	161835	hgsc.bcm.edu	37	15	39910404	39910404	+	Missense_Mutation	SNP	G	G	A	rs12908846	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	135	68	128	0	0.503704	0	G|0.862;A|0.138	0.138	strong	.	FSIP1	53	.	NM_152597	exon11	c.C1231T	p.L411F	CCAGAAGACACTT	.	PASS	Atlas-SNP
KANK3	256949	hgsc.bcm.edu	37	19	8389405	8389405	+	Silent	SNP	G	G	A	rs12981073	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	130	64	148	0	0.492308	0	G|0.840;A|0.159	0.159	strong	.	KANK3	35	.	NM_198471	exon10	c.C2310T	p.A770A	CTCCAGGGCGATG	.	PASS	Atlas-SNP
CDSN	1041	hgsc.bcm.edu	37	6	31084639	31084639	+	Silent	SNP	C	C	T	rs4713436	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	45	18	46	0	0.4	0	C|0.838;T|0.162	0.162	strong	.	CDSN	48	.	NM_001264	exon2	c.G753A	p.R251R	CACAGGCCTCTGA	.	PASS	Atlas-SNP
FAT3	120114	hgsc.bcm.edu	37	11	92088177	92088177	+	Silent	SNP	C	C	T	rs7479732	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	24	115	0	0.275862	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
PRDM9	56979	hgsc.bcm.edu	37	5	23527469	23527469	+	Missense_Mutation	SNP	C	C	A	rs112501567	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	66	15	87	2	0.227273	0.0229885	C|0.978;A|0.022	0.022	strong	PRDM9,NS,carcinoma,-1,2	PRDM9	344	2	NM_020227	exon11	c.C2272A	p.R758S	GGCTTTCGCGATA	.	scavenged	Atlas-SNP
KIAA1841	84542	hgsc.bcm.edu	37	2	61304271	61304271	+	Silent	SNP	A	A	G	rs1729659	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	236	187	149	1	0.792373	0.00671141	A|0.639;G|0.361	0.361	strong	KIAA1841,NS,carcinoma,0,1	KIAA1841	95	1	NM_032506	exon6	c.A648G	p.K216K	GAATAAAGATTGT	.	PASS	Atlas-SNP
GPR123	84435	hgsc.bcm.edu	37	10	134942832	134942832	+	Silent	SNP	G	G	A	rs45586231	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	45	24	39	0	0.533333	0	G|0.756;A|0.244	0.244	strong	.	GPR123	118	.	NM_001083909	exon7	c.G1500A	p.P500P	GCAGCCGGGCAGG	.	PASS	Atlas-SNP
PDILT	204474	hgsc.bcm.edu	37	16	20370816	20370816	+	Missense_Mutation	SNP	C	C	T	rs9652589	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	271	94	233	0	0.346863	0	C|0.584;T|0.416	0.416	strong	.	PDILT	120	.	NM_174924	exon12	c.G1580A	p.R527K	CCTTTCCTCATCA	.	PASS	Atlas-SNP
UGT2B7	7364	hgsc.bcm.edu	37	4	69964271	69964271	+	Silent	SNP	A	A	G	rs28365062	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	45	87	0	0.576923	0	A|0.854;G|0.146	0.146	strong	.	UGT2B7	79	.	NM_001074	exon2	c.A735G	p.T245T	CACTACATTATCT	.	PASS	Atlas-SNP
WBSCR27	155368	hgsc.bcm.edu	37	7	73249299	73249299	+	Missense_Mutation	SNP	G	G	C	rs13232463	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	59	59	49	0	1	0	G|0.360;C|0.640	0.640	strong	.	WBSCR27	21	.	NM_152559	exon6	c.C512G	p.S171W	TTGGACGAGTTGG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195513680	195513680	+	Missense_Mutation	SNP	A	A	T	rs7372250	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	67	22	76	0	0.328358	0	A|1.000;|0.000	.	weak	.	MUC4	1505	.	NM_018406	exon2	c.T4771A	p.S1591T	CTGAGGAAGTGTC	.	PASS	Atlas-SNP
LRRN1	57633	hgsc.bcm.edu	37	3	3887093	3887093	+	Silent	SNP	A	A	G	rs9844909	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	37	66	0	0.513889	0	A|0.775;G|0.225	0.225	strong	.	LRRN1	82	.	NM_020873	exon2	c.A768G	p.Q256Q	CCCTCAACTTGCC	.	PASS	Atlas-SNP
CHGB	1114	hgsc.bcm.edu	37	20	5903067	5903067	+	Missense_Mutation	SNP	T	T	A	rs6085324	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	91	41	89	0	0.450549	0	T|0.776;A|0.224	0.224	strong	CHGB,colon,carcinoma,0,2	CHGB	112	2	NM_001819	exon4	c.T277A	p.S93T	GATGCCTCGGAAG	.	PASS	Atlas-SNP
CPAMD8	27151	hgsc.bcm.edu	37	19	17108135	17108135	+	Missense_Mutation	SNP	C	C	T	rs3745340	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	146	137	165	0	0.938356	0	C|0.647;T|0.353	0.353	strong	.	CPAMD8	192	.	NM_015692	exon11	c.G1022A	p.R341Q	AAGTCCCGGGAGC	.	PASS	Atlas-SNP
MCCC1	56922	hgsc.bcm.edu	37	3	182755209	182755209	+	Missense_Mutation	SNP	T	T	G	rs2270968	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	133	133	124	0	1	0	T|0.479;G|0.521	0.521	strong	.	MCCC1	87	.	NM_020166	exon13	c.A1391C	p.H464P	TTGGTGTGCAGTC	.	PASS	Atlas-SNP
ZNF862	643641	hgsc.bcm.edu	37	7	149559177	149559177	+	Silent	SNP	C	C	T	rs370165112		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	145	3	163	0	0.0206897	0	.	.	weak	ZNF862,NS,carcinoma,0,2	ZNF862	97	2	NM_001099220	exon7	c.C2928T	p.F976F	GTATTTCGAGTGC	.	scavenged	Atlas-SNP
NXNL1	115861	hgsc.bcm.edu	37	19	17566634	17566634	+	Missense_Mutation	SNP	T	T	A	rs56248314	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	19	5	24	0	0.263158	0	T|0.913;A|0.087	0.087	strong	.	NXNL1	13	.	NM_138454	exon2	c.A461T	p.E154V	GCCGCCTCCTGCC	.	PASS	Atlas-SNP
PARP4	143	hgsc.bcm.edu	37	13	25000617	25000617	+	Missense_Mutation	SNP	C	C	T	rs7571	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes;alternate_allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	263	3	334	0	0.0114068	0	C|0.568;G|0.432	.	alt	PARP4,NS,carcinoma,0,1	PARP4	142	1	NM_006437	exon33	c.G4966A	p.A1656T	TAGAAGCGTCATC	.	scavenged	Atlas-SNP
LRRC72	100506049	hgsc.bcm.edu	37	7	16566645	16566645	+	Missense_Mutation	SNP	C	C	G	rs2301968	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	21	7	18	0	0.333333	0	C|0.908;G|0.092	0.092	strong	.	.	.	.	NM_001195280	exon1	c.C68G	p.T23S	CCGAAACTGCCCT	.	PASS	Atlas-SNP
CAMK2B	816	hgsc.bcm.edu	37	7	44282928	44282928	+	Silent	SNP	G	G	A	rs17172630	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	103	76	108	0	0.737864	0	G|0.945;A|0.055	0.055	strong	CAMK2B,NS,carcinoma,0,1	CAMK2B	56	1	NM_172081	exon8	c.C522T	p.F174F	GCCAGCGAAACCT	.	PASS	Atlas-SNP
ESYT2	57488	hgsc.bcm.edu	37	7	158536267	158536267	+	Missense_Mutation	SNP	T	T	C	rs2305473	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	127	56	143	0	0.440945	0	T|0.712;C|0.288	0.288	strong	.	ESYT2	70	.	NM_020728	exon16	c.A1828G	p.S610G	AGTTACTGAGCTG	.	PASS	Atlas-SNP
TGM7	116179	hgsc.bcm.edu	37	15	43579566	43579566	+	Silent	SNP	A	A	G	rs513970	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	121	53	97	0	0.438017	0	A|0.492;G|0.508	0.508	strong	.	TGM7	86	.	NM_052955	exon6	c.T777C	p.S259S	GGCCACACTGCCC	.	PASS	Atlas-SNP
P2RX7	5027	hgsc.bcm.edu	37	12	121605355	121605355	+	Missense_Mutation	SNP	G	G	A	rs7958311	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	124	41	126	0	0.330645	0	A|0.265;G|0.735;N|0.000	0.265	strong	P2RX7,NS,carcinoma,0,1	P2RX7	53	1	NM_002562	exon8	c.G809A	p.R270H	ACTGCCGTCCCAA	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100681751	100681751	+	Missense_Mutation	SNP	A	A	G	rs73712044	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	49	22	52	0	0.44898	0	A|0.965;G|0.035	0.035	strong	.	MUC17	804	.	NM_001040105	exon3	c.A7054G	p.S2352G	GTGGCCAGTTTTG	.	PASS	Atlas-SNP
PPAT	5471	hgsc.bcm.edu	37	4	57268328	57268328	+	Silent	SNP	T	T	C	rs2271924	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	32	76	0	0.457143	0	T|0.907;C|0.093	0.093	strong	.	PPAT	41	.	NM_002703	exon6	c.A681G	p.T227T	TCCTTCTGTTTCT	.	PASS	Atlas-SNP
PRDM12	59335	hgsc.bcm.edu	37	9	133553993	133553993	+	Silent	SNP	C	C	T	rs7021384	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	93	38	103	0	0.408602	0	C|0.650;T|0.350	0.350	strong	.	PRDM12	24	.	NM_021619	exon4	c.C648T	p.P216P	TGTGCCCGGGCTA	.	PASS	Atlas-SNP
UGCG	7357	hgsc.bcm.edu	37	9	114694486	114694486	+	Silent	SNP	A	A	G	rs7850023	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	221	129	206	0	0.58371	0	A|0.701;G|0.299	0.299	strong	.	UGCG	32	.	NM_003358	exon8	c.A861G	p.T287T	TGCTACAATAATT	.	PASS	Atlas-SNP
ALKBH3	221120	hgsc.bcm.edu	37	11	43940602	43940602	+	Missense_Mutation	SNP	C	C	G	rs1130290	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	49	49	61	0	1	0	C|0.827;G|0.173	0.173	strong	ALKBH3,NS,carcinoma,0,1	ALKBH3	33	1	NM_139178	exon9	c.C684G	p.D228E	TGGAGACTACACA	.	PASS	Atlas-SNP
PHTF2	57157	hgsc.bcm.edu	37	7	77567051	77567051	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	83	5	94	0	0.060241	0	.	.	none	.	PHTF2	104	.	NM_001127357	exon11	c.T1261C	p.S421P	CATAGTTCCCACC	.	PASS	Atlas-SNP
INSL3	3640	hgsc.bcm.edu	37	19	17932289	17932289	+	Silent	SNP	C	C	T	rs2286663	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	16	9	7	0	0.5625	0	C|0.875;T|0.125	0.125	strong	.	INSL3	8	.	NM_005543	exon1	c.G27A	p.A9A	CACCAGCGCCCAG	.	PASS	Atlas-SNP
ATP2A1	487	hgsc.bcm.edu	37	16	28898778	28898778	+	Silent	SNP	C	C	G	rs113803159	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	74	43	61	0	0.581081	0	C|0.995;G|0.005	0.005	strong	.	ATP2A1	116	.	NM_004320	exon8	c.C663G	p.G221G	CTTGGGCATCGTG	.	PASS	Atlas-SNP
ACACB	32	hgsc.bcm.edu	37	12	109577735	109577735	+	Silent	SNP	C	C	T	rs2878960	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	103	55	94	0	0.533981	0	C|0.511;T|0.489	0.489	strong	.	ACACB	330	.	NM_001093	exon1	c.C525T	p.S175S	CTCCTCCGACGAG	.	PASS	Atlas-SNP
SLC19A3	80704	hgsc.bcm.edu	37	2	228563835	228563835	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	90	23	117	0	0.255556	0	.	.	none	.	SLC19A3	62	.	NM_025243	exon3	c.T596G	p.F199C	GCATGAAAAAACA	.	PASS	Atlas-SNP
LGR6	59352	hgsc.bcm.edu	37	1	202287813	202287813	+	Silent	SNP	T	T	C	rs788793	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	140	65	135	0	0.464286	0	T|0.445;C|0.555	0.555	strong	.	LGR6	102	.	NM_001017403	exon18	c.T2382C	p.F794F	CAGCTTTGCCTCC	.	PASS	Atlas-SNP
VCAN	1462	hgsc.bcm.edu	37	5	82815408	82815408	+	Missense_Mutation	SNP	G	G	A	rs2287926	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	158	78	218	0	0.493671	0	G|0.819;A|0.181	0.181	strong	.	VCAN	498	.	NM_004385	exon7	c.G1283A	p.G428D	CTACTGGCAGTAC	.	PASS	Atlas-SNP
TARBP1	6894	hgsc.bcm.edu	37	1	234546245	234546245	+	Silent	SNP	C	C	T	rs1141264	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	196	85	251	0	0.433673	0	C|0.658;T|0.342	0.342	strong	.	TARBP1	111	.	NM_005646	exon23	c.G3738A	p.T1246T	TAAAAACGTACAA	.	PASS	Atlas-SNP
PRKD1	5587	hgsc.bcm.edu	37	14	30066914	30066914	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	38	9	60	0	0.236842	0	.	.	none	.	PRKD1	316	.	NM_002742	exon16	c.C2217A	p.F739L	CCTCCGGAAAGAC	.	PASS	Atlas-SNP
ANKRD30A	91074	hgsc.bcm.edu	37	10	37508450	37508450	+	Silent	SNP	A	A	C	rs1148259	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	125	123	161	0	0.984	0	A|0.458;C|0.542	0.542	strong	.	ANKRD30A	448	.	NM_052997	exon34	c.A3642C	p.A1214A	TTATGCAGGAGAT	.	PASS	Atlas-SNP
SIGLEC10	89790	hgsc.bcm.edu	37	19	51919949	51919949	+	Missense_Mutation	SNP	G	G	A	rs9304711	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	174	94	232	0	0.54023	0	G|0.682;A|0.318	0.318	strong	.	SIGLEC10	112	.	NM_001171157	exon3	c.C677T	p.A226V	CTCTGTGCGCTCA	.	PASS	Atlas-SNP
C3orf67	200844	hgsc.bcm.edu	37	3	58870321	58870321	+	Missense_Mutation	SNP	C	C	T	rs116534917	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	170	78	188	0	0.458824	0	C|0.994;T|0.006	0.006	strong	C3orf67,NS,carcinoma,-1,1	C3orf67	45	1	NM_198463	exon7	c.G290A	p.R97H	GTTTGGCGAAGTT	.	PASS	Atlas-SNP
SAFB2	9667	hgsc.bcm.edu	37	19	5622579	5622579	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	105	37	93	0	0.352381	0	.	.	none	.	SAFB2	90	.	NM_014649	exon1	c.G148A	p.G50S	TGCCGCCCGTGTC	.	PASS	Atlas-SNP
LRRTM1	347730	hgsc.bcm.edu	37	2	80529595	80529595	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	91	22	83	0	0.241758	0	.	.	none	.	LRRTM1	251	.	NM_178839	exon2	c.G1350A	p.W450X	ACACTTCCAGGAC	.	PASS	Atlas-SNP
BCL2L2-PABPN1	100529063	hgsc.bcm.edu	37	14	23777099	23777099	+	Silent	SNP	G	G	A	rs2231301	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	98	52	89	0	0.530612	0	G|0.792;A|0.208	0.208	strong	.	.	.	.	NM_001199864	exon3	c.G123A	p.P41P	TGACCCGCTGCAC	.	PASS	Atlas-SNP
THBS2	7058	hgsc.bcm.edu	37	6	169641971	169641971	+	Silent	SNP	C	C	T	rs61730651	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	44	10	67	0	0.227273	0	C|0.871;T|0.129	0.129	strong	.	THBS2	230	.	NM_003247	exon6	c.G777A	p.S259S	CCTCTCCGAGCTG	.	PASS	Atlas-SNP
ATR	545	hgsc.bcm.edu	37	3	142178144	142178144	+	Missense_Mutation	SNP	C	C	T	rs2229032	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	114	68	143	0	0.596491	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
CATSPER1	117144	hgsc.bcm.edu	37	11	65793454	65793454	+	Missense_Mutation	SNP	C	C	T	rs1203998	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	56	106	0	0.767123	0	C|0.656;T|0.344	0.344	strong	.	CATSPER1	101	.	NM_053054	exon1	c.G397A	p.G133S	ACCCACCGTATTG	.	PASS	Atlas-SNP
PHACTR3	116154	hgsc.bcm.edu	37	20	58342349	58342349	+	Missense_Mutation	SNP	C	C	T	rs73598372	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	109	58	128	0	0.53211	0	C|0.989;T|0.011	0.011	strong	.	PHACTR3	104	.	NM_080672	exon5	c.C650T	p.P217L	ACAGTCCTCCCAG	.	PASS	Atlas-SNP
BCL7A	605	hgsc.bcm.edu	37	12	122460048	122460048	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	47	8	32	0	0.170213	0	.	.	none	.	BCL7A	31	.	NM_020993	exon1	c.T51G	p.D17E	AGATGATATCAAG	.	PASS	Atlas-SNP
FAM188B	84182	hgsc.bcm.edu	37	7	30818128	30818128	+	Silent	SNP	A	A	G	rs200053449	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	205	47	224	0	0.229268	0	A|0.998;G|0.002	0.002	strong	FAM188B,colon,carcinoma,+2,4	FAM188B	62	4	NM_032222	exon2	c.A144G	p.R48R	TCTTCGAAAGGTT	.	PASS	Atlas-SNP
CES1	1066	hgsc.bcm.edu	37	16	55862712	55862712	+	Missense_Mutation	SNP	C	C	T	rs2307240	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	109	32	154	0	0.293578	0	C|0.956;T|0.044	0.044	strong	.	CES1	78	.	NM_001025195	exon2	c.G227A	p.S76N	ACAAAGCTCCATG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195509171	195509171	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	125	12	43	0	0.096	0	.	.	none	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.C9280T	p.L3094F	AGGAAAGGCTGGT	.	scavenged	Atlas-SNP
LMF1	64788	hgsc.bcm.edu	37	16	961054	961054	+	Silent	SNP	C	C	T	rs2277892	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	65	19	77	0	0.292308	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
LRPPRC	10128	hgsc.bcm.edu	37	2	44201317	44201317	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	555	64	347	0	0.115315	0	.	.	none	.	LRPPRC	105	.	NM_133259	exon9	c.T1127G	p.F376C	TGTAAAAAGAAAC	.	PASS	Atlas-SNP
DUSP27	92235	hgsc.bcm.edu	37	1	167096931	167096931	+	Missense_Mutation	SNP	A	A	C	rs267746	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	65	33	88	0	0.507692	0	A|0.780;C|0.220	0.220	strong	.	DUSP27	235	.	NM_001080426	exon5	c.A2563C	p.K855Q	GAGTACAAAATGG	.	PASS	Atlas-SNP
ARHGAP42	143872	hgsc.bcm.edu	37	11	100846936	100846936	+	Silent	SNP	A	A	G	rs654593	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	56	17	95	0	0.303571	0	A|0.462;G|0.538	0.538	strong	.	ARHGAP42	32	.	NM_152432	exon20	c.A2004G	p.P668P	AACCCCATCATCT	.	PASS	Atlas-SNP
BPIFA2	140683	hgsc.bcm.edu	37	20	31768363	31768363	+	Silent	SNP	C	C	T	rs34968847	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	122	64	118	0	0.52459	0	C|0.940;T|0.060	0.060	strong	.	.	.	.	NM_080574	exon8	c.C747T	p.I249I	CCTCATCTGAAGA	.	PASS	Atlas-SNP
USP38	84640	hgsc.bcm.edu	37	4	144130750	144130750	+	Silent	SNP	T	T	C	rs7670426	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	55	21	82	0	0.381818	0	T|0.908;C|0.092	0.092	strong	.	USP38	92	.	NM_032557	exon7	c.T1437C	p.N479N	TCTAAATGGGTGC	.	PASS	Atlas-SNP
PLEKHG1	57480	hgsc.bcm.edu	37	6	151161018	151161018	+	Silent	SNP	A	A	G	rs17348890	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	62	175	0	0.673913	0	A|0.883;G|0.117	0.117	strong	.	PLEKHG1	97	.	NM_001029884	exon17	c.A3144G	p.R1048R	ATTCAGAGAGTCT	.	PASS	Atlas-SNP
EXOC3L2	90332	hgsc.bcm.edu	37	19	45728059	45728059	+	Missense_Mutation	SNP	T	T	C	rs10411314	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	373	168	390	0	0.450402	0	T|0.896;C|0.104	0.104	strong	.	EXOC3L2	30	.	NM_138568	exon6	c.A517G	p.N173D	GCAGGTTGGCCAC	.	PASS	Atlas-SNP
ANKEF1	63926	hgsc.bcm.edu	37	20	10030188	10030188	+	Missense_Mutation	SNP	T	T	A	rs652633	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	83	50	108	0	0.60241	0	T|0.761;A|0.239	0.239	strong	.	.	.	.	NM_198798	exon6	c.T971A	p.L324Q	ATCCACTGTGGGC	.	PASS	Atlas-SNP
KLC1	3831	hgsc.bcm.edu	37	14	104166994	104166994	+	Missense_Mutation	SNP	C	C	T	rs3212102	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	53	38	43	0	0.716981	0	C|0.982;T|0.018	0.018	strong	.	KLC1	54	.	NM_001130107	exon15	c.C1784T	p.A595V	CCAGGGCGTCTCT	.	PASS	Atlas-SNP
ATL1	51062	hgsc.bcm.edu	37	14	51054598	51054598	+	Silent	SNP	A	A	G	rs35014209	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	30	84	0	0.428571	0	A|0.807;G|0.193	0.193	strong	.	ATL1	46	.	NM_015915	exon2	c.A84G	p.P28P	GGAGCCAGTGAAA	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	118	72	93	0	0.610169	0	C|0.801;T|0.199	0.199	strong	.	ALLC	61	.	NM_018436	exon6	c.C329T	p.T110I	GAGGAACCAGGAC	.	PASS	Atlas-SNP
SLC16A3	9123	hgsc.bcm.edu	37	17	80195163	80195163	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	108	34	93	0	0.314815	0	.	.	none	.	SLC16A3	19	.	NM_001206950	exon4	c.C517T	p.R173C	CAGGACCGCTACG	.	PASS	Atlas-SNP
OSBP2	23762	hgsc.bcm.edu	37	22	31091139	31091139	+	Silent	SNP	A	A	G	rs13053290	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	118	118	170	2	1	0.0117647	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	.	scavenged	Atlas-SNP
PRRC2C	23215	hgsc.bcm.edu	37	1	171486912	171486912	+	Missense_Mutation	SNP	G	G	A	rs10913157	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	42	122	0	0.56	0	G|0.869;A|0.131	0.131	strong	.	.	.	.	NM_015172	exon6	c.G703A	p.A235T	CAGCAGGCTGCTC	.	PASS	Atlas-SNP
DHRS2	10202	hgsc.bcm.edu	37	14	24114437	24114437	+	Missense_Mutation	SNP	T	T	A	rs146187363	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	84	38	108	0	0.452381	0	T|1.000;A|0.000	0.000	weak	.	DHRS2	78	.	NM_182908	exon9	c.T829A	p.W277R	TTGCGGTGGCAGG	.	PASS	Atlas-SNP
YLPM1	56252	hgsc.bcm.edu	37	14	75248652	75248652	+	Missense_Mutation	SNP	C	C	G	rs45617140	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	144	70	151	0	0.486111	0	C|0.936;G|0.064	0.064	strong	.	YLPM1	298	.	NM_019589	exon4	c.C1906G	p.P636A	CCTCCCCCTGGAG	.	PASS	Atlas-SNP
PRDM9	56979	hgsc.bcm.edu	37	5	23527492	23527492	+	Missense_Mutation	SNP	A	A	T	rs112815500	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	83	13	85	0	0.156627	0	A|0.998;T|0.002	0.002	strong	PRDM9,NS,haematopoietic_neoplasm,0,2	PRDM9	344	2	NM_020227	exon11	c.A2295T	p.R765S	CCTCAGACACCAG	.	PASS	Atlas-SNP
TOP2A	7153	hgsc.bcm.edu	37	17	38545824	38545824	+	Missense_Mutation	SNP	C	C	A	rs11540720	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	112	60	124	0	0.535714	0	C|0.957;A|0.043	0.043	strong	.	TOP2A	124	.	NM_001067	exon35	c.G4543T	p.A1515S	TCTTTGCCCGTAC	.	PASS	Atlas-SNP
RSF1	51773	hgsc.bcm.edu	37	11	77378505	77378505	+	Silent	SNP	A	A	G	rs28930682	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	34	31	52	0	0.911765	0	A|0.816;G|0.184	0.184	strong	.	RSF1	105	.	NM_016578	exon16	c.T3783C	p.D1261D	TAGCTCATCATCT	.	PASS	Atlas-SNP
CCDC27	148870	hgsc.bcm.edu	37	1	3677933	3677933	+	Missense_Mutation	SNP	T	T	C	rs1181883	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	140	96	231	1	0.685714	0.004329	T|0.530;C|0.470	0.470	strong	.	CCDC27	79	.	NM_152492	exon5	c.T800C	p.M267T	TGAAGATGCAGCT	.	PASS	Atlas-SNP
TAGLN3	29114	hgsc.bcm.edu	37	3	111719786	111719786	+	Silent	SNP	A	A	T	rs2292583	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	50	20	77	0	0.4	0	A|0.919;T|0.081	0.081	strong	.	TAGLN3	44	.	NM_001008272	exon3	c.A348T	p.L116L	GGATCTATGGGAA	.	PASS	Atlas-SNP
GIT1	28964	hgsc.bcm.edu	37	17	27903998	27903998	+	Silent	SNP	A	A	C	rs144787773		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	31	19	36	0	0.612903	0	A|0.998;C|0.002	0.002	weak	.	GIT1	84	.	NM_001085454	exon13	c.T1137G	p.S379S	CCGCAGAGACAGC	.	PASS	Atlas-SNP
CHRD	8646	hgsc.bcm.edu	37	3	184099050	184099050	+	Missense_Mutation	SNP	C	C	T	rs34095724	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	250	144	267	0	0.576	0	C|0.949;T|0.051	0.051	strong	.	CHRD	149	.	NM_003741	exon3	c.C280T	p.P94S	AGGGGCCCTGGCA	.	PASS	Atlas-SNP
TMEM132A	54972	hgsc.bcm.edu	37	11	60704213	60704213	+	Missense_Mutation	SNP	C	C	T	rs2469887	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	67	76	0	0.971014	0	C|0.570;T|0.430	0.430	strong	.	TMEM132A	135	.	NM_017870	exon11	c.C2909T	p.A970V	CATTTGCGCCAGC	.	PASS	Atlas-SNP
CCDC170	80129	hgsc.bcm.edu	37	6	151936677	151936677	+	Missense_Mutation	SNP	G	G	A	rs6929137	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	93	93	162	0	1	0	G|0.655;A|0.345	0.345	strong	.	.	.	.	NM_025059	exon10	c.G1810A	p.V604I	ATGTCTGTCAAGT	.	PASS	Atlas-SNP
SPATA5L1	79029	hgsc.bcm.edu	37	15	45695445	45695445	+	Missense_Mutation	SNP	C	C	G	rs143453038	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	22	6	5	0	0.272727	0	C|0.982;G|0.018	0.018	strong	.	SPATA5L1	40	.	NM_024063	exon1	c.C818G	p.S273C	AGGGTTCCCGGCC	.	PASS	Atlas-SNP
PCDHB10	56126	hgsc.bcm.edu	37	5	140572668	140572668	+	Silent	SNP	C	C	T	rs597064	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	152	72	155	0	0.473684	0	C|0.561;T|0.439	0.439	strong	.	PCDHB10	177	.	NM_018930	exon1	c.C543T	p.N181N	TATTAACATTAGT	.	PASS	Atlas-SNP
LAMA5	3911	hgsc.bcm.edu	37	20	60887028	60887028	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	51	5	80	0	0.0980392	0	.	.	none	.	LAMA5	268	.	NM_005560	exon70	c.G9583A	p.G3195S	CGAAGCCCGCTTG	.	PASS	Atlas-SNP
ZDHHC11	79844	hgsc.bcm.edu	37	5	837553	837553	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	372	39	322	0	0.104839	0	.	.	none	ZDHHC11_ENST00000424784,NS,carcinoma,-1,2	ZDHHC11	97	2	NM_024786	exon6	c.G827C	p.R276P	TCTTTGCGGTTAT	.	scavenged	Atlas-SNP
ITPR3	3710	hgsc.bcm.edu	37	6	33651129	33651129	+	Silent	SNP	C	C	T	rs942636	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	91	52	106	0	0.571429	0	C|0.835;T|0.165	0.165	strong	.	ITPR3	409	.	NM_002224	exon35	c.C4743T	p.P1581P	CACCCCCACCGCC	.	PASS	Atlas-SNP
ACER3	55331	hgsc.bcm.edu	37	11	76701606	76701606	+	Silent	SNP	G	G	A	rs3740767	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	148	31	199	0	0.209459	0	G|0.409;A|0.591	0.591	strong	.	ACER3	19	.	NM_018367	exon6	c.G426A	p.P142P	AGAGCCGATATTC	.	PASS	Atlas-SNP
PLA2R1	22925	hgsc.bcm.edu	37	2	160901517	160901517	+	Silent	SNP	A	A	G	rs4665143	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	108	53	124	0	0.490741	0	A|0.497;G|0.503	0.503	strong	.	PLA2R1	153	.	NM_001195641	exon2	c.T261C	p.S87S	GCAACCACTGCCT	.	PASS	Atlas-SNP
PPRC1	23082	hgsc.bcm.edu	37	10	103900729	103900729	+	Missense_Mutation	SNP	G	G	A	rs61731871	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	57	29	71	0	0.508772	0	G|0.912;A|0.088	0.088	strong	PPRC1,NS,carcinoma,0,1	PPRC1	151	1	NM_015062	exon5	c.G2464A	p.V822I	GTGCCTGTAGGTC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195513102	195513102	+	Silent	SNP	A	A	G	rs3103958	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	337	93	185	4	0.275964	0.0216216	A|0.500;G|0.500	0.500	strong	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.T5349C	p.S1783S	AGCTGAAGAAAGG	.	scavenged	Atlas-SNP
CECR5	27440	hgsc.bcm.edu	37	22	17630486	17630486	+	Silent	SNP	C	C	A	rs1034859	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	45	14	66	0	0.311111	0	C|0.487;A|0.513	0.513	strong	.	CECR5	46	.	NM_033070	exon2	c.G276T	p.G92G	GATGTTCCCAGCA	.	PASS	Atlas-SNP
SPTBN2	6712	hgsc.bcm.edu	37	11	66476403	66476403	+	Silent	SNP	G	G	A	rs74909073	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	95	28	96	0	0.294737	0	G|0.996;A|0.004	0.004	strong	SPTBN2,colon,carcinoma,-2,3	SPTBN2	188	3	NM_006946	exon10	c.C1161T	p.R387R	GCCCTCGCGGGGC	.	PASS	Atlas-SNP
KRT82	3888	hgsc.bcm.edu	37	12	52788814	52788814	+	Missense_Mutation	SNP	C	C	T	rs61730587	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	114	56	150	0	0.491228	0	C|0.991;T|0.009	0.009	strong	KRT82,NS,carcinoma,-1,1	KRT82	45	1	NM_033033	exon9	c.G1487A	p.R496Q	GATTTCCGCCCGC	.	PASS	Atlas-SNP
MANBA	4126	hgsc.bcm.edu	37	4	103611845	103611845	+	Missense_Mutation	SNP	C	C	T	rs227368	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	160	83	155	0	0.51875	0	T|0.377;G|0.002;C|0.617;A|0.004	0.377	strong	.	MANBA	78	.	NM_005908	exon6	c.G757A	p.V253I	TGGCTACGATCAC	.	PASS	Atlas-SNP
SRGN	5552	hgsc.bcm.edu	37	10	70856963	70856963	+	Missense_Mutation	SNP	C	C	G	rs67852477	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	122	62	160	0	0.508197	0	C|0.991;G|0.009	0.009	strong	SRGN,NS,carcinoid-endocrine_tumour,0,1	SRGN	15	1	NM_002727	exon2	c.C203G	p.P68R	AGATCCCCCGTCT	.	PASS	Atlas-SNP
DPP3	10072	hgsc.bcm.edu	37	11	66254085	66254085	+	Missense_Mutation	SNP	G	G	T	rs11550299	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	213	149	215	0	0.699531	0	G|0.781;T|0.219	0.219	strong	DPP3,colon,carcinoma,0,2	DPP3	61	2	NM_130443	exon4	c.G435T	p.Q145H	CTGGCAGACCTGC	.	PASS	Atlas-SNP
MYCBP2	23077	hgsc.bcm.edu	37	13	77672767	77672767	+	Missense_Mutation	SNP	C	C	T	rs142807127	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	196	2	224	0	0.0102041	0	C|0.998;T|0.002	0.002	strong	MYCBP2_ENST00000407578,colon,carcinoma,-1,4	MYCBP2	1029	4	NM_015057	exon56	c.G8522A	p.R2841H	GAGGAGCGTGGAG	.	scavenged	Atlas-SNP
CACNA1C	775	hgsc.bcm.edu	37	12	2788879	2788879	+	Silent	SNP	G	G	A	rs1051375	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	84	95	0	0.988235	0	G|0.374;A|0.626	0.626	strong	.	CACNA1C	1023	.	NM_199460	exon44	c.G5505A	p.T1835T	CAGCACGGTCAGC	.	PASS	Atlas-SNP
FBXL5	26234	hgsc.bcm.edu	37	4	15640168	15640168	+	Silent	SNP	C	C	T	rs3182730	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	84	42	89	0	0.5	0	T|0.112;G|0.000;C|0.888	0.112	strong	.	FBXL5	52	.	NM_001193534	exon4	c.G546A	p.K182K	AAAAAACTTCTGT	.	PASS	Atlas-SNP
TIAM2	26230	hgsc.bcm.edu	37	6	155500242	155500242	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	146	46	210	0	0.315068	0	.	.	none	.	TIAM2	161	.	NM_012454	exon10	c.T2593C	p.C865R	GAGTATTGCATCC	.	PASS	Atlas-SNP
PCDH15	65217	hgsc.bcm.edu	37	10	55892642	55892642	+	Missense_Mutation	SNP	T	T	C	rs61731389	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	35	76	0	0.426829	0	T|0.969;C|0.031	0.031	strong	.	PCDH15	1715	.	NM_001142763	exon16	c.A1925G	p.N642S	TGTAGATTTAATA	.	PASS	Atlas-SNP
HRNR	388697	hgsc.bcm.edu	37	1	152192549	152192549	+	Missense_Mutation	SNP	T	T	G	rs12145941	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	76	39	87	0	0.513158	0	T|0.939;G|0.061	0.061	strong	.	HRNR	403	.	NM_001009931	exon3	c.A1556C	p.Q519P	CCATGCTGACCAT	.	PASS	Atlas-SNP
CLEC18A	348174	hgsc.bcm.edu	37	16	69996928	69996928	+	Missense_Mutation	SNP	G	G	A	rs616457	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	429	64	339	1	0.149184	0.00294985	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
UNC5CL	222643	hgsc.bcm.edu	37	6	40996173	40996173	+	Missense_Mutation	SNP	G	G	C	rs742491	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	119	63	93	1	0.529412	0.0107527	G|0.992;C|0.008	0.008	strong	UNC5CL,NS,carcinoma,-1,1	UNC5CL	52	1	NM_173561	exon9	c.C1496G	p.P499R	GGGCCTGGGCTGC	.	scavenged	Atlas-SNP
CDH6	1004	hgsc.bcm.edu	37	5	31302288	31302288	+	Silent	SNP	C	C	T	rs2287582	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	265	264	234	0	0.996226	0	C|0.591;T|0.409	0.409	strong	.	CDH6	175	.	NM_004932	exon6	c.C882T	p.D294D	CAGCGACGCTGAT	.	PASS	Atlas-SNP
PBRM1	55193	hgsc.bcm.edu	37	3	52584787	52584787	+	Silent	SNP	T	T	C	rs2251219	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	125	124	136	0	0.992	0	T|0.654;C|0.346	0.346	strong	.	PBRM1	1252	.	NM_018313	exon28	c.A4335G	p.P1445P	TCCACCTGGTGCT	.	PASS	Atlas-SNP
WNK1	65125	hgsc.bcm.edu	37	12	994030	994030	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	180	62	190	0	0.344444	0	.	.	none	.	WNK1	403	.	NM_001184985	exon19	c.G4840A	p.A1614T	GCCACAGCACCAG	.	PASS	Atlas-SNP
VSIG10	54621	hgsc.bcm.edu	37	12	118509191	118509191	+	Missense_Mutation	SNP	G	G	A	rs7307331	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	106	56	106	0	0.528302	0	G|0.472;A|0.528	0.528	strong	.	VSIG10	41	.	NM_019086	exon6	c.C1303T	p.H435Y	TATAATGCAACAG	.	PASS	Atlas-SNP
TIAM1	7074	hgsc.bcm.edu	37	21	32638550	32638550	+	Missense_Mutation	SNP	C	C	T	rs2070418	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	96	60	105	0	0.625	0	C|0.874;A|0.001	.	strong	.	TIAM1	522	.	NM_003253	exon5	c.G739A	p.G247R	GCCCCCCGTTTGC	.	PASS	Atlas-SNP
BDP1	55814	hgsc.bcm.edu	37	5	70818150	70818150	+	Missense_Mutation	SNP	C	C	G	rs12187098	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	197	67	183	0	0.340102	0	C|0.971;G|0.029	0.029	strong	.	BDP1	204	.	NM_018429	exon23	c.C5026G	p.Q1676E	TCAGCACAAATGA	.	PASS	Atlas-SNP
C19orf40	91442	hgsc.bcm.edu	37	19	33467357	33467357	+	Silent	SNP	G	G	A	rs2304102	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	94	47	117	0	0.5	0	G|0.605;A|0.395	0.395	strong	.	C19orf40	21	.	NM_152266	exon5	c.G417A	p.E139E	CAAAGAGCCCAGT	.	PASS	Atlas-SNP
UGT2A1	10941	hgsc.bcm.edu	37	4	70460328	70460328	+	Missense_Mutation	SNP	C	C	T	rs4148304	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	150	77	192	1	0.513333	0.00520833	C|0.876;T|0.124	0.124	strong	UGT2A1_ENST00000457664,NS,carcinoma,0,2	UGT2A1	131	2	NM_001252274	exon6	c.G1669A	p.V557I	TGGGAACTCCCAC	.	scavenged	Atlas-SNP
TANC1	85461	hgsc.bcm.edu	37	2	160084473	160084473	+	Silent	SNP	A	A	C	rs2288110	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	26	11	34	0	0.423077	0	A|0.566;C|0.434	0.434	strong	.	TANC1	157	.	NM_033394	exon25	c.A4047C	p.T1349T	AAAAACAAATGTA	.	PASS	Atlas-SNP
FOXO3	2309	hgsc.bcm.edu	37	6	108882570	108882570	+	Silent	SNP	C	C	T	rs11757217	bycluster;byhapmap	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	43	18	57	0	0.418605	0	.	.	weak	FOXO3,brain,glioma,0,4	FOXO3	67	4	NM_001455	exon1	c.C159T	p.A53A	GGCCGCCGACTCC	.	scavenged	Atlas-SNP
PPP1R16A	84988	hgsc.bcm.edu	37	8	145722726	145722726	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	145	80	116	0	0.551724	0	.	.	none	.	PPP1R16A	25	.	NM_032902	exon1	c.C149A	p.P50H	AGGGTCCTGGGGA	.	PASS	Atlas-SNP
NEFH	4744	hgsc.bcm.edu	37	22	29881828	29881828	+	Silent	SNP	C	C	T	rs165734	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	66	33	89	0	0.5	0	C|0.890;T|0.110	0.110	strong	.	NEFH	178	.	NM_021076	exon3	c.C1200T	p.A400A	GATAGCCGCTTAC	.	PASS	Atlas-SNP
DST	667	hgsc.bcm.edu	37	6	56480500	56480500	+	Missense_Mutation	SNP	T	T	C	rs150191284	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	147	67	179	0	0.455782	0	T|0.974;C|0.026	0.026	strong	.	DST	1427	.	NM_001723	exon24	c.A7765G	p.I2589V	TGGCAATGAGGAC	.	PASS	Atlas-SNP
MYH15	22989	hgsc.bcm.edu	37	3	108179165	108179165	+	Silent	SNP	C	C	T	rs61739469	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	179	81	231	0	0.452514	0	C|0.987;T|0.013	0.013	strong	.	MYH15	223	.	NM_014981	exon18	c.G1974A	p.T658T	TGCAACCGTTTGG	.	PASS	Atlas-SNP
ITSN2	50618	hgsc.bcm.edu	37	2	24431184	24431184	+	Missense_Mutation	SNP	C	C	T	rs2303291	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	104	44	98	0	0.423077	0	C|0.829;T|0.171	0.171	strong	.	ITSN2	224	.	NM_006277	exon37	c.G4600A	p.A1534T	CCCAGGCGGTCCT	.	PASS	Atlas-SNP
SLC35G5	83650	hgsc.bcm.edu	37	8	11188743	11188743	+	Missense_Mutation	SNP	C	C	T	rs13260331	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	16	98	0	0.195122	0	C|0.705;T|0.295	0.295	strong	.	.	.	.	NM_054028	exon1	c.C128T	p.A43V	TGGTGGCCCTGCT	.	PASS	Atlas-SNP
HSD17B7	51478	hgsc.bcm.edu	37	1	162782145	162782145	+	Missense_Mutation	SNP	A	A	G	rs45459196	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	289	119	350	0	0.411765	0	.	.	weak	.	HSD17B7	25	.	NM_016371	exon9	c.A961G	p.K321E	CTGGAAAAGCACA	.	PASS	Atlas-SNP
KIR2DL1	3802	hgsc.bcm.edu	37	19	55285072	55285072	+	Missense_Mutation	SNP	A	A	G	rs202032452	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	62	26	65	0	0.419355	0	A|0.983;G|0.017	0.017	strong	.	KIR2DL1	46	.	NM_014218	exon3	c.A358G	p.I120V	CTGGACATCGTGA	.	PASS	Atlas-SNP
FAM129C	199786	hgsc.bcm.edu	37	19	17660300	17660300	+	Missense_Mutation	SNP	G	G	A	rs11666267	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	60	31	85	0	0.516667	0	G|0.543;A|0.456	0.456	strong	FAM129C,NS,carcinoma,0,1	FAM129C	110	1	NM_001098524	exon15	c.G1807A	p.G603S	CTGGACGGCTGCT	.	PASS	Atlas-SNP
GABRA5	2558	hgsc.bcm.edu	37	15	27182422	27182422	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	77	32	79	0	0.415584	0	.	.	none	GABRA5,colon,carcinoma,-1,1	GABRA5	127	1	NM_001165037	exon8	c.A671T	p.Q224L	TGAACCAGTACCA	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105417285	105417285	+	Silent	SNP	C	C	T	rs76453246	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	116	20	44	0	0.172414	0	C|0.948;T|0.052	0.052	strong	AHNAK2_ENST00000333244,colon,carcinoma,-1,1	AHNAK2	719	1	NM_138420	exon7	c.G4503A	p.P1501P	GAACGACGGCATC	.	scavenged	Atlas-SNP
DUSP2	1844	hgsc.bcm.edu	37	2	96810085	96810085	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	61	10	76	0	0.163934	0	.	.	none	.	DUSP2	20	.	NM_004418	exon3	c.C538G	p.L180V	GGAACAGGTAGGG	.	PASS	Atlas-SNP
C2orf16	84226	hgsc.bcm.edu	37	2	27799712	27799712	+	Silent	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	185	89	147	0	0.481081	0	.	.	none	.	C2orf16	357	.	NM_032266	exon1	c.G273A	p.V91V	ATCTGTGGAATTA	.	PASS	Atlas-SNP
CRYBB2	1415	hgsc.bcm.edu	37	22	25623839	25623839	+	Missense_Mutation	SNP	G	G	T	rs16986560	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	66	25	50	0	0.378788	0	G|0.985;T|0.015	0.015	strong	.	CRYBB2	18	.	NM_000496	exon4	c.G193T	p.A65S	GAACAGGCCAACT	.	PASS	Atlas-SNP
FAM22F	54754	hgsc.bcm.edu	37	9	97082699	97082699	+	Missense_Mutation	SNP	G	G	A	rs10993163	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	24	81	0	0.338028	0	G|0.856;A|0.144	0.144	strong	.	FAM22F	72	.	NM_017561	exon5	c.C1159T	p.P387S	CCTCAGGGACCTT	.	PASS	Atlas-SNP
LAMB3	3914	hgsc.bcm.edu	37	1	209823354	209823354	+	Silent	SNP	G	G	A	rs2228339	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	63	38	62	0	0.603175	0	G|0.739;A|0.261	0.261	strong	LAMB3,NS,carcinoma,0,1	LAMB3	136	1	NM_000228	exon3	c.C138T	p.T46T	TCCACAGGTAGAT	.	PASS	Atlas-SNP
TAF1L	138474	hgsc.bcm.edu	37	9	32631369	32631369	+	Silent	SNP	C	C	T	rs10971047	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	317	134	382	0	0.422713	0	C|0.873;T|0.127	0.127	strong	TAF1L,NS,carcinoma,-1,1	TAF1L	382	1	NM_153809	exon1	c.G4209A	p.T1403T	TGACAGCGTCACC	.	PASS	Atlas-SNP
RELN	5649	hgsc.bcm.edu	37	7	103155705	103155705	+	Silent	SNP	A	A	G	rs2229864	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	43	146	0	0.425743	0	A|0.467;G|0.533	0.533	strong	.	RELN	593	.	NM_173054	exon50	c.T8046C	p.H2682H	GCGCTCATGCTGG	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105415608	105415608	+	Missense_Mutation	SNP	G	G	C	rs11850848	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	55	46	0	0	0.836364	.	G|0.698;C|0.302	0.302	strong	.	AHNAK2	719	.	NM_138420	exon7	c.C6180G	p.H2060Q	GGGCACGTGGCCC	.	PASS	Atlas-SNP
TTC13	79573	hgsc.bcm.edu	37	1	231057247	231057247	+	Silent	SNP	A	A	T	rs2275333	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	56	23	102	0	0.410714	0	A|0.818;T|0.182	0.182	strong	.	TTC13	74	.	NM_024525	exon16	c.T1818A	p.G606G	CACCTGACCCCTA	.	PASS	Atlas-SNP
DUSP22	56940	hgsc.bcm.edu	37	6	350829	350829	+	Silent	SNP	G	G	A	rs1129085	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	218	79	323	1	0.362385	0.00309598	G|0.581;A|0.419	0.419	strong	.	DUSP22	55	.	NM_020185	exon8	c.G516A	p.P172P	CGCTCCGGGAATT	.	PASS	Atlas-SNP
GRM4	2914	hgsc.bcm.edu	37	6	34003928	34003928	+	Silent	SNP	C	C	T	rs34858760	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	104	44	88	0	0.423077	0	C|0.975;T|0.025	0.025	strong	.	GRM4	317	.	NM_000841	exon9	c.G1959A	p.S653S	GCGCAGCGAGCAG	.	PASS	Atlas-SNP
MYCBP2	23077	hgsc.bcm.edu	37	13	77740577	77740577	+	Missense_Mutation	SNP	T	T	C	rs111642157	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	131	73	193	0	0.557252	0	T|0.997;C|0.003	0.003	strong	.	MYCBP2	1029	.	NM_015057	exon41	c.A6227G	p.N2076S	CCTGAATTCTGAA	.	PASS	Atlas-SNP
NEK4	6787	hgsc.bcm.edu	37	3	52797634	52797634	+	Missense_Mutation	SNP	G	G	C	rs1029871	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	39	39	66	0	1	0	G|0.654;C|0.346	0.346	strong	.	NEK4	51	.	NM_003157	exon5	c.C673G	p.P225A	GCATTGGTGGCAG	.	PASS	Atlas-SNP
KCNK10	54207	hgsc.bcm.edu	37	14	88651962	88651962	+	Missense_Mutation	SNP	C	C	T	rs17762463	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	199	82	283	0	0.41206	0	C|0.833;T|0.167	0.167	strong	.	KCNK10	273	.	NM_138318	exon7	c.G1549A	p.A517T	ACTCAGCGTGCTG	.	PASS	Atlas-SNP
KCNJ3	3760	hgsc.bcm.edu	37	2	155711357	155711357	+	Silent	SNP	T	T	C	rs17642086	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	130	129	165	0	0.992308	0	T|0.753;C|0.247	0.247	strong	.	KCNJ3	126	.	NM_002239	exon3	c.T1038C	p.H346H	GTTCCATGCAACA	.	PASS	Atlas-SNP
WDR33	55339	hgsc.bcm.edu	37	2	128522383	128522383	+	Silent	SNP	T	T	C	rs11557685	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	146	67	191	0	0.458904	0	T|0.938;C|0.062	0.062	strong	WDR33_ENST00000409658,NS,carcinoma,-2,1	WDR33	136	1	NM_001006622	exon6	c.A645G	p.P215P	AGAAAATGGTATA	.	PASS	Atlas-SNP
BTN2A1	11120	hgsc.bcm.edu	37	6	26468660	26468660	+	Silent	SNP	G	G	A	rs3734544	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	172	77	246	0	0.447674	0	G|0.824;A|0.176	0.176	strong	.	BTN2A1	118	.	NM_007049	exon8	c.G1467A	p.R489R	CTTCAGGTTGGGG	.	PASS	Atlas-SNP
CCDC154	645811	hgsc.bcm.edu	37	16	1488141	1488141	+	Silent	SNP	C	C	T	rs12925639	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	15	71	0	0.205479	0	C|0.791;T|0.209	0.209	strong	.	CCDC154	27	.	NM_001143980	exon10	c.G1062A	p.G354G	CAGCTCCCCAGCC	.	PASS	Atlas-SNP
SH3BP2	6452	hgsc.bcm.edu	37	4	2826912	2826912	+	Silent	SNP	C	C	G	rs16843413	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	153	75	174	0	0.490196	0	C|0.875;G|0.125	0.125	strong	.	SH3BP2	43	.	NM_001145856	exon5	c.C588G	p.P196P	CCTGCCCTTGGAC	.	PASS	Atlas-SNP
NFE2L3	9603	hgsc.bcm.edu	37	7	26224313	26224313	+	Missense_Mutation	SNP	C	C	T	rs147199325		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	459	67	381	0	0.145969	0	.	.	weak	.	NFE2L3	77	.	NM_004289	exon4	c.C995T	p.T332I	ATCCAACAGCAAG	.	PASS	Atlas-SNP
PARP16	54956	hgsc.bcm.edu	37	15	65553246	65553246	+	Silent	SNP	C	C	T	rs2304896	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	206	86	177	0	0.417476	0	C|0.729;T|0.271	0.271	strong	.	PARP16	23	.	NM_017851	exon5	c.G810A	p.V270V	TGAATACACCAGG	.	PASS	Atlas-SNP
PKD1L2	114780	hgsc.bcm.edu	37	16	81253759	81253759	+	Missense_Mutation	SNP	A	A	G	rs9924371	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	144	144	134	1	1	0.00746269	A|0.425;G|0.575	0.575	strong	.	PKD1L2	361	.	NM_001076780	exon1	c.T217C	p.W73R	GAAACCACTGGGT	.	PASS	Atlas-SNP
CDAN1	146059	hgsc.bcm.edu	37	15	43028592	43028592	+	Silent	SNP	G	G	A	rs7167392	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	53	32	33	0	0.603774	0	G|0.766;A|0.234	0.234	strong	.	CDAN1	70	.	NM_138477	exon2	c.C477T	p.P159P	GCGGCTGGGGCTG	.	PASS	Atlas-SNP
ASCL1	429	hgsc.bcm.edu	37	12	103352649	103352649	+	Silent	SNP	C	C	G	rs731682	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	120	60	122	0	0.5	0	C|0.917;G|0.083	0.083	strong	.	ASCL1	16	.	NM_004316	exon1	c.C627G	p.V209V	GCCGGTCTCATCC	.	PASS	Atlas-SNP
PROSER1	80209	hgsc.bcm.edu	37	13	39587865	39587865	+	Silent	SNP	A	A	C	rs3751378	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	76	33	107	0	0.434211	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
ZNF879	345462	hgsc.bcm.edu	37	5	178459283	178459283	+	Missense_Mutation	SNP	A	A	G	rs17078988	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	114	57	95	0	0.5	0	A|0.634;G|0.366	0.366	strong	.	ZNF879	41	.	NM_001136116	exon5	c.A334G	p.T112A	GATGGCACATTTG	.	PASS	Atlas-SNP
KRT37	8688	hgsc.bcm.edu	37	17	39580559	39580559	+	Missense_Mutation	SNP	T	T	A	rs9916475	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	115	52	138	0	0.452174	0	T|0.606;A|0.394	0.394	strong	.	KRT37	61	.	NM_003770	exon1	c.A217T	p.S73C	TGTGACTGGTTGG	.	PASS	Atlas-SNP
OPLAH	26873	hgsc.bcm.edu	37	8	145111529	145111529	+	Silent	SNP	A	A	G	rs11993554	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	102	100	133	0	0.980392	0	A|0.879;G|0.121	0.121	strong	.	OPLAH	78	.	NM_017570	exon13	c.T1836C	p.F612F	CTCCACAAAGGCT	.	PASS	Atlas-SNP
GIPC1	10755	hgsc.bcm.edu	37	19	14589378	14589378	+	Silent	SNP	C	C	T	rs1127307	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	116	61	143	0	0.525862	0	T|0.235;G|0.000;C|0.765	0.235	strong	.	GIPC1	21	.	NM_202468	exon8	c.G852A	p.A284A	GGTGGCCGCTATT	.	PASS	Atlas-SNP
WWC3	55841	hgsc.bcm.edu	37	X	10085582	10085582	+	Missense_Mutation	SNP	G	G	A	rs5934750	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	61	60	40	0	0.983607	0	G|0.973;A|0.027	0.027	strong	.	WWC3	142	.	NM_015691	exon11	c.G1483A	p.A495T	CTGGGCGCCCTAG	.	PASS	Atlas-SNP
UBA6	55236	hgsc.bcm.edu	37	4	68562365	68562365	+	Silent	SNP	A	A	G	rs17572160	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	311	144	400	0	0.463023	0	A|0.778;G|0.222	0.222	strong	.	UBA6	98	.	NM_018227	exon2	c.T132C	p.Y44Y	TTACCTATACAAT	.	PASS	Atlas-SNP
KIF4A	24137	hgsc.bcm.edu	37	X	69561780	69561780	+	Missense_Mutation	SNP	T	T	G	rs1199457	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	229	228	313	1	0.995633	0.00319489	T|0.841;0|0.015	.	strong	.	KIF4A	118	.	NM_012310	exon11	c.T1265G	p.L422W	TCATTTTGGTAAG	.	PASS	Atlas-SNP
KIF19	124602	hgsc.bcm.edu	37	17	72351406	72351406	+	Silent	SNP	C	C	T	rs2271536	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	38	38	35	0	1	0	C|0.650;T|0.350	0.350	strong	.	KIF19	102	.	NM_153209	exon20	c.C2952T	p.H984H	GCCCCACGGCACA	.	PASS	Atlas-SNP
KRTAP10-3	386682	hgsc.bcm.edu	37	21	45978587	45978587	+	Silent	SNP	A	A	G	rs67272426	alternate_allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	119	50	92	0	0.420168	0	AGACAT|0.500;GGACGC|0.500	.	alt	.	KRTAP10-3	17	.	NM_198696	exon1	c.T12C	p.S4S	CATGGTAGACGTG	.	PASS	Atlas-SNP
ZDHHC11	79844	hgsc.bcm.edu	37	5	843815	843815	+	Silent	SNP	C	C	T	rs71591190	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	375	115	271	0	0.306667	0	C|0.856;T|0.144	0.144	strong	ZDHHC11_ENST00000424784,rectum,carcinoma,0,2	ZDHHC11	97	2	NM_024786	exon4	c.G528A	p.S176S	TGTGGCCGAGGCC	.	scavenged	Atlas-SNP
HIST1H2BL	8340	hgsc.bcm.edu	37	6	27775674	27775674	+	Missense_Mutation	SNP	A	A	G	rs200484	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	105	56	151	0	0.533333	0	A|0.876;G|0.124	0.124	strong	.	HIST1H2BL	48	.	NM_003519	exon1	c.T11C	p.L4P	TTGGCCAGCTCGG	.	PASS	Atlas-SNP
DHTKD1	55526	hgsc.bcm.edu	37	10	12131081	12131081	+	Missense_Mutation	SNP	T	T	G	rs3740015	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	94	93	107	1	0.989362	0.00934579	T|0.518;G|0.482	0.482	strong	.	DHTKD1	104	.	NM_018706	exon5	c.T814G	p.Y272D	GACCTGTACTTTG	.	PASS	Atlas-SNP
PCDHA11	56138	hgsc.bcm.edu	37	5	140249884	140249884	+	Missense_Mutation	SNP	C	C	T	rs62622798	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	178	80	239	0	0.449438	0	C|0.989;T|0.011	0.011	strong	.	PCDHA11	209	.	NM_018902	exon1	c.C1196T	p.T399I	TGTCCACCTTCAA	.	PASS	Atlas-SNP
CCDC67	159989	hgsc.bcm.edu	37	11	93129484	93129484	+	Missense_Mutation	SNP	A	A	G	rs12282288	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	115	114	152	0	0.991304	0	A|0.801;G|0.199	0.199	strong	.	CCDC67	57	.	NM_181645	exon11	c.A1319G	p.E440G	CCGGAGAATACAT	.	PASS	Atlas-SNP
CCDC110	256309	hgsc.bcm.edu	37	4	186379899	186379899	+	Missense_Mutation	SNP	G	G	C	rs35596415	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	164	77	161	0	0.469512	0	G|0.545;C|0.455	0.455	strong	.	CCDC110	78	.	NM_152775	exon6	c.C1842G	p.I614M	TAGCTGGATTATC	.	PASS	Atlas-SNP
VSX2	338917	hgsc.bcm.edu	37	14	74707911	74707911	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	49	10	36	0	0.204082	0	.	.	none	VSX2,right_upper_lobe,carcinoma,-1,1	VSX2	32	1	NM_182894	exon2	c.C397T	p.R133X	AGCGATCGAAAAA	.	PASS	Atlas-SNP
KDELC1	79070	hgsc.bcm.edu	37	13	103449202	103449202	+	Missense_Mutation	SNP	T	T	C	rs1047740	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	116	54	107	0	0.465517	0	T|0.602;C|0.398	0.398	strong	.	KDELC1	66	.	NM_024089	exon2	c.A340G	p.I114V	ATTTAATTTCCAC	.	PASS	Atlas-SNP
PCDHGC3	5098	hgsc.bcm.edu	37	5	140856265	140856265	+	Silent	SNP	G	G	C	rs2075661	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	110	110	104	1	1	0.00961538	G|0.809;C|0.191	0.191	strong	.	PCDHGC3	173	.	NM_032402	exon1	c.G582C	p.A194A	GTACGCGGAGCTG	.	PASS	Atlas-SNP
SLC37A2	219855	hgsc.bcm.edu	37	11	124951767	124951767	+	Missense_Mutation	SNP	G	G	A	rs143239155	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	68	53	68	0	0.779412	0	G|0.999;A|0.001	0.001	strong	.	SLC37A2	105	.	NM_001145290	exon9	c.G850A	p.A284T	GAGCCTGCTGCCA	.	PASS	Atlas-SNP
CD24	100133941	hgsc.bcm.edu	37	Y	21154426	21154426	+	Missense_Mutation	SNP	G	G	A	rs52812045	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	91	36	70	0	0.395604	0	G|0.500;A|0.500	0.500	weak	.	.	.	.	NM_013230	exon1	c.C170T	p.A57V	CCAGCCGCCTTGG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195513519	195513519	+	Silent	SNP	A	A	T	rs201585392	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	256	45	196	0	0.175781	0	A|0.964;T|0.036	0.036	strong	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.T4932A	p.G1644G	GGCGTGACCTGTG	.	PASS	Atlas-SNP
CD44	960	hgsc.bcm.edu	37	11	35226155	35226155	+	Missense_Mutation	SNP	A	A	G	rs9666607	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	77	75	94	0	0.974026	0	A|0.218;G|0.782	0.782	strong	.	CD44	48	.	NM_000610	exon10	c.A1250G	p.K417R	CACCCAAAGAAGA	.	PASS	Atlas-SNP
NEK3	4752	hgsc.bcm.edu	37	13	52726772	52726772	+	Missense_Mutation	SNP	C	C	T	rs56190615	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	105	51	123	0	0.485714	0	C|0.995;T|0.005	0.005	strong	.	NEK3	41	.	NM_002498	exon5	c.G365A	p.R122H	AGCACACGTTTCT	.	PASS	Atlas-SNP
SERPINI1	5274	hgsc.bcm.edu	37	3	167506937	167506937	+	Missense_Mutation	SNP	C	C	G	rs33917740	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	53	24	67	0	0.45283	0	C|0.879;G|0.121	0.121	strong	.	SERPINI1	52	.	NM_005025	exon2	c.C21G	p.F7L	ACTCTTCTCTTTG	.	PASS	Atlas-SNP
CCDC122	160857	hgsc.bcm.edu	37	13	44411421	44411421	+	Missense_Mutation	SNP	C	C	T	rs79782223	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	126	125	203	0	0.992063	0	C|0.963;T|0.037	0.037	strong	.	CCDC122	21	.	NM_144974	exon7	c.G817A	p.E273K	GTTACTCTTGCAT	.	PASS	Atlas-SNP
DSPP	1834	hgsc.bcm.edu	37	4	88536917	88536917	+	Missense_Mutation	SNP	G	G	A	rs199901845	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	65	6	90	0	0.0923077	0	.	.	weak	DSPP,NS,carcinoma,-2,3	DSPP	174	3	NM_014208	exon5	c.G3103A	p.D1035N	AGCAGCGATAGCA	.	PASS	Atlas-SNP
LGR6	59352	hgsc.bcm.edu	37	1	202276494	202276494	+	Silent	SNP	C	C	T	rs896551	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	161	68	180	0	0.42236	0	C|0.532;T|0.468	0.468	strong	.	LGR6	102	.	NM_001017403	exon14	c.C1245T	p.P415P	CCACCCCGAGGCC	.	PASS	Atlas-SNP
FBXL7	23194	hgsc.bcm.edu	37	5	15937010	15937010	+	Silent	SNP	C	C	T	rs61748187	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	145	87	97	0	0.6	0	C|0.982;T|0.018	0.018	strong	FBXL7,NS,carcinoma,+2,1	FBXL7	138	1	NM_012304	exon4	c.C1191T	p.L397L	GTACCTCGCCAAG	.	PASS	Atlas-SNP
SMYD1	150572	hgsc.bcm.edu	37	2	88407959	88407959	+	Silent	SNP	T	T	C	rs2970918	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	98	51	88	0	0.520408	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
ZNF286B	729288	hgsc.bcm.edu	37	17	18565423	18565423	+	Missense_Mutation	SNP	G	G	A	rs9912852	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	145	129	145	0	0.889655	0	G|0.698;A|0.302	0.302	strong	ZNF286B_ENST00000545289,colon,carcinoma,+2,2	ZNF286B	75	2	NM_001145045	exon5	c.C1396T	p.P466S	TGTACGGTTTCTT	.	PASS	Atlas-SNP
PHLPP2	23035	hgsc.bcm.edu	37	16	71682796	71682796	+	Silent	SNP	T	T	C	rs61733125	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	136	82	133	0	0.602941	0	T|0.817;C|0.183	0.183	strong	.	PHLPP2	96	.	NM_015020	exon18	c.A3969G	p.L1323L	CAGTCATAGTGCT	.	PASS	Atlas-SNP
CD22	933	hgsc.bcm.edu	37	19	35835739	35835739	+	Silent	SNP	G	G	A	rs7259477	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	62	35	76	0	0.564516	0	G|0.996;A|0.004	0.004	strong	.	CD22	129	.	NM_001185100	exon10	c.G2043A	p.P681P	TAGCCCGGAGACC	.	PASS	Atlas-SNP
CCDC40	55036	hgsc.bcm.edu	37	17	78059889	78059889	+	Missense_Mutation	SNP	G	G	A	rs60684213	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	186	90	182	0	0.483871	0	G|0.904;A|0.096	0.096	strong	.	CCDC40	198	.	NM_017950	exon14	c.G2323A	p.V775M	GCCCAGGTGACCT	.	PASS	Atlas-SNP
TNNT2	7139	hgsc.bcm.edu	37	1	201334382	201334382	+	Silent	SNP	G	G	A	rs3729547	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	126	126	141	1	1	0.0070922	G|0.318;A|0.682	0.682	strong	TNNT2,colon,carcinoma,0,1	TNNT2	43	1	NM_001276345	exon10	c.C348T	p.I116I	AGCCTCGATCAGC	.	PASS	Atlas-SNP
SLIRP	81892	hgsc.bcm.edu	37	14	78174473	78174473	+	Silent	SNP	A	A	C	rs11159286	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	86	105	0	0.988506	0	A|0.093;C|0.907	0.907	strong	SLIRP,NS,carcinoma,-1,1	SLIRP	6	1	NM_001267864	exon1	c.A19C	p.R7R	GCAGCGAGAGGTG	.	PASS	Atlas-SNP
ACVR1	90	hgsc.bcm.edu	37	2	158634674	158634674	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	275	3	253	0	0.0109091	0	.	.	none	ACVR1,NS,carcinoma,-1,1	ACVR1	52	1	NM_001105	exon5	c.T512C	p.I171T	GTGGTGATGAGCC	.	scavenged	Atlas-SNP
USHBP1	83878	hgsc.bcm.edu	37	19	17367435	17367435	+	Missense_Mutation	SNP	T	T	C	rs9676419	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	95	43	76	0	0.452632	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
SGK1	6446	hgsc.bcm.edu	37	6	134493397	134493397	+	Silent	SNP	G	G	A	rs1057293	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	23	187	0	0.237113	0	G|0.894;A|0.106	0.106	strong	.	SGK1	387	.	NM_001143676	exon10	c.C1005T	p.D335D	TCCGAAGTCAGTA	.	PASS	Atlas-SNP
TDRKH	11022	hgsc.bcm.edu	37	1	151747970	151747970	+	Silent	SNP	A	A	G	rs11204885	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	172	83	188	0	0.482558	0	A|0.773;G|0.227	0.227	strong	.	TDRKH	45	.	NM_001083965	exon10	c.T1332C	p.H444H	AGCACAATGAGTG	.	PASS	Atlas-SNP
PDE4DIP	9659	hgsc.bcm.edu	37	1	144859816	144859816	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	153	11	153	0	0.0718954	0	.	.	none	.	PDE4DIP	817	.	NM_014644	exon38	c.A6268G	p.I2090V	GGTTAATGGAGGA	.	PASS	Atlas-SNP
FAM179A	165186	hgsc.bcm.edu	37	2	29222070	29222070	+	Missense_Mutation	SNP	G	G	A	rs13009279	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	39	88	0	0.557143	0	G|0.655;A|0.345	0.345	strong	.	FAM179A	106	.	NM_199280	exon4	c.G163A	p.A55T	CCAAGAGCCCTGC	.	PASS	Atlas-SNP
HOXB7	3217	hgsc.bcm.edu	37	17	46688135	46688135	+	Missense_Mutation	SNP	G	G	A	rs79247310	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	40	24	48	0	0.6	0	G|0.917;A|0.083	0.083	strong	.	HOXB7	15	.	NM_004502	exon1	c.C146T	p.A49V	AAGGAAGCGCCCG	.	PASS	Atlas-SNP
CAND2	23066	hgsc.bcm.edu	37	3	12858244	12858244	+	Missense_Mutation	SNP	C	C	T	rs367818782		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	136	24	171	1	0.176471	0.00584795	.	.	weak	CAND2_ENST00000456430,NS,carcinoma,-1,2	CAND2	138	2	NM_001162499	exon10	c.C1813T	p.R605W	GGTGACCGGCTTG	.	scavenged	Atlas-SNP
CCDC168	643677	hgsc.bcm.edu	37	13	103397890	103397890	+	Silent	SNP	G	G	A	rs75285783	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	99	47	114	0	0.474747	0	G|0.930;A|0.070	0.070	strong	.	.	.	.	NM_001146197	exon4	c.C5157T	p.Y1719Y	GAGCATGTATGAA	.	PASS	Atlas-SNP
TACC2	10579	hgsc.bcm.edu	37	10	123810060	123810060	+	Silent	SNP	G	G	A	rs11200367	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	119	59	142	0	0.495798	0	G|0.885;A|0.115	0.115	strong	.	TACC2	271	.	NM_206861	exon3	c.G141A	p.A47A	AGACGCGTCCAGG	.	PASS	Atlas-SNP
CWF19L2	143884	hgsc.bcm.edu	37	11	107197640	107197640	+	Missense_Mutation	SNP	T	T	C	rs3758911	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	15	62	0	0.258621	0	T|0.725;C|0.275	0.275	strong	.	CWF19L2	135	.	NM_152434	exon18	c.A2681G	p.Y894C	CCTCAATAGTTTT	.	PASS	Atlas-SNP
ASB8	140461	hgsc.bcm.edu	37	12	48543584	48543584	+	Silent	SNP	G	G	C	rs3936179	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	156	67	176	0	0.429487	0	G|0.946;C|0.054	0.054	strong	.	ASB8	25	.	NM_024095	exon4	c.C432G	p.V144V	GGCATTGACAGAG	.	PASS	Atlas-SNP
WNK1	65125	hgsc.bcm.edu	37	12	988894	988894	+	Silent	SNP	G	G	A	rs9804992	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	47	135	0	0.484536	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
FAM135B	51059	hgsc.bcm.edu	37	8	139165273	139165273	+	Missense_Mutation	SNP	G	G	A	rs13280444	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	150	148	178	0	0.986667	0	G|0.670;A|0.330	0.330	strong	.	FAM135B	423	.	NM_015912	exon13	c.C1445T	p.P482L	TCACCTGGCTCTG	.	PASS	Atlas-SNP
HEPH	9843	hgsc.bcm.edu	37	X	65390579	65390579	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	158	54	200	0	0.341772	0	.	.	none	.	HEPH	224	.	NM_138737	exon2	c.T329C	p.I110T	GTGACATGTAGGT	.	PASS	Atlas-SNP
NES	10763	hgsc.bcm.edu	37	1	156640678	156640678	+	Missense_Mutation	SNP	G	G	A	rs2886443	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	133	49	142	0	0.368421	0	G|0.356;A|0.644	0.644	strong	NES,NS,carcinoma,0,1	NES	196	1	NM_006617	exon4	c.C3302T	p.P1101L	TGCCCCGGGCCTG	.	PASS	Atlas-SNP
SP1	6667	hgsc.bcm.edu	37	12	53777171	53777171	+	Silent	SNP	A	A	G	rs3741651	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	151	68	168	0	0.450331	0	A|0.814;G|0.186	0.186	strong	.	SP1	57	.	NM_138473	exon3	c.A1440G	p.Q480Q	AGCCCAAACAATC	.	PASS	Atlas-SNP
LRP5	4041	hgsc.bcm.edu	37	11	68193582	68193582	+	Silent	SNP	G	G	A	rs117289001	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	52	38	65	0	0.730769	0	G|0.992;A|0.008	0.008	strong	.	LRP5	136	.	NM_002335	exon16	c.G3564A	p.R1188R	CAAGCGGACTCGC	.	PASS	Atlas-SNP
TNIK	23043	hgsc.bcm.edu	37	3	170825920	170825920	+	Silent	SNP	G	G	A	rs2291900	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	45	30	48	0	0.666667	0	G|0.792;A|0.208	0.208	strong	TNIK_ENST00000436636,NS,carcinoma,0,3	TNIK	313	3	NM_015028	exon20	c.C2316T	p.L772L	ATGGGGGAGCACA	.	PASS	Atlas-SNP
CR1	1378	hgsc.bcm.edu	37	1	207669708	207669708	+	Silent	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	44	15	39	0	0.340909	0	.	.	none	.	CR1	354	.	NM_000573	exon1	c.G96A	p.V32V	TGTGGTGCTGCTT	.	PASS	Atlas-SNP
PSME4	23198	hgsc.bcm.edu	37	2	54133744	54133744	+	Silent	SNP	T	T	C	rs805316	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	340	275	164	0	0.808824	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
CCR8	1237	hgsc.bcm.edu	37	3	39373902	39373902	+	Missense_Mutation	SNP	C	C	G	rs2853699	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	283	133	288	0	0.469965	0	C|0.791;G|0.209	0.209	strong	.	CCR8	34	.	NM_005201	exon2	c.C80G	p.A27G	GTGATGCGGAACT	.	PASS	Atlas-SNP
TNFRSF6B	8771	hgsc.bcm.edu	37	20	62328267	62328267	+	Silent	SNP	C	C	T	rs2257440	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	43	24	45	0	0.55814	0	C|0.779;T|0.221	0.221	strong	.	TNFRSF6B	22	.	NM_003823	exon1	c.C147T	p.C49C	GGTGTGCGCCCAG	.	PASS	Atlas-SNP
PLRG1	5356	hgsc.bcm.edu	37	4	155459194	155459194	+	Silent	SNP	A	A	T	rs7668818	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	188	188	257	1	1	0.00389105	A|0.748;T|0.252	0.252	strong	.	PLRG1	43	.	NM_002669	exon13	c.T1218A	p.I406I	ATTTTGAATGAAA	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	166	86	198	0	0.518072	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
C6orf15	29113	hgsc.bcm.edu	37	6	31080016	31080016	+	Missense_Mutation	SNP	C	C	G	rs2233974	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	68	68	99	0	1	0	C|0.832;G|0.168	0.168	strong	.	C6orf15	29	.	NM_014070	exon2	c.G120C	p.L40F	GGTCCCCAAGTTT	.	PASS	Atlas-SNP
KIAA1755	85449	hgsc.bcm.edu	37	20	36870122	36870122	+	Silent	SNP	T	T	G	rs1205435	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	135	66	159	0	0.488889	0	T|0.674;G|0.319;A|0.007	0.319	strong	.	KIAA1755	145	.	NM_001029864	exon3	c.A411C	p.P137P	TGGCTCTGGAACA	.	PASS	Atlas-SNP
COG5	10466	hgsc.bcm.edu	37	7	106897237	106897237	+	Silent	SNP	A	A	C	rs17349904	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	46	23	73	0	0.5	0	A|0.851;C|0.149	0.149	strong	.	COG5	78	.	NM_006348	exon16	c.T1782G	p.V594V	GGAAACAACCTAG	.	PASS	Atlas-SNP
ABCA7	10347	hgsc.bcm.edu	37	19	1043748	1043748	+	Missense_Mutation	SNP	A	A	G	rs3752232	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	25	16	28	0	0.64	0	A|0.884;G|0.116	0.116	strong	.	ABCA7	174	.	NM_019112	exon10	c.A955G	p.T319A	GAGCTCACCCTGC	.	PASS	Atlas-SNP
ZNF713	349075	hgsc.bcm.edu	37	7	56007576	56007576	+	Silent	SNP	C	C	T	rs34016595	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	47	24	49	0	0.510638	0	C|0.694;T|0.306	0.306	strong	.	ZNF713	47	.	NM_182633	exon4	c.C1170T	p.C390C	TGAATGCGGGAAA	.	PASS	Atlas-SNP
F13B	2165	hgsc.bcm.edu	37	1	197009798	197009798	+	Silent	SNP	A	A	G	rs5998	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	243	240	296	1	0.987654	0.00337838	A|0.547;G|0.453	0.453	strong	.	F13B	137	.	NM_001994	exon11	c.T1806C	p.N602N	TGGTCTATTGTCA	.	PASS	Atlas-SNP
GAS2L1	10634	hgsc.bcm.edu	37	22	29704125	29704125	+	Silent	SNP	C	C	T	rs11090564	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	45	18	40	0	0.4	0	C|0.704;T|0.296	0.296	strong	GAS2L1_ENST00000333679,NS,carcinoma,0,4	GAS2L1	54	4	NM_152237	exon2	c.C30T	p.G10G	CGCGGGCTCGGCG	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105417768	105417768	+	Silent	SNP	C	C	A	rs2396458	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	63	62	0	0	0.984127	.	C|0.809;A|0.191	0.191	strong	.	AHNAK2	719	.	NM_138420	exon7	c.G4020T	p.V1340V	GGCAGACACCCCG	.	PASS	Atlas-SNP
DLG4	1742	hgsc.bcm.edu	37	17	7099811	7099811	+	Silent	SNP	G	G	A	rs17203281	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	94	46	135	0	0.489362	0	G|0.742;A|0.258	0.258	strong	.	DLG4	110	.	NM_001365	exon12	c.C1296T	p.I432I	CTGAGCGATGATC	.	PASS	Atlas-SNP
GIPC2	54810	hgsc.bcm.edu	37	1	78585086	78585086	+	Missense_Mutation	SNP	T	T	C	rs540742	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	72	62	0	0.986301	0	A|0.004;C|0.271	0.271	strong	.	GIPC2	37	.	NM_017655	exon4	c.T617C	p.L206P	TAGAGCTGAGGTC	.	PASS	Atlas-SNP
SNX13	23161	hgsc.bcm.edu	37	7	17879553	17879553	+	Silent	SNP	G	G	A	rs12720473	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	15	118	0	0.163043	0	G|0.957;A|0.043	0.043	strong	.	SNX13	113	.	NM_015132	exon13	c.C1236T	p.T412T	TTGGGCGGTAACC	.	PASS	Atlas-SNP
TBCK	93627	hgsc.bcm.edu	37	4	107133919	107133919	+	Silent	SNP	A	A	G	rs17036613	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	293	138	412	0	0.47099	0	A|0.802;G|0.198	0.198	strong	TBCK,NS,carcinoma,0,2	TBCK	89	2	NM_001163436	exon20	c.T1848C	p.G616G	AATGAAACCAATC	.	PASS	Atlas-SNP
ENDOG	2021	hgsc.bcm.edu	37	9	131584732	131584732	+	Missense_Mutation	SNP	C	C	T	rs61737987	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	139	71	151	0	0.510791	0	C|0.998;T|0.002	0.002	strong	.	ENDOG	8	.	NM_004435	exon3	c.C737T	p.T246I	TCCGCACCTACGT	.	PASS	Atlas-SNP
MLF1IP	79682	hgsc.bcm.edu	37	4	185637699	185637699	+	Missense_Mutation	SNP	A	A	G	rs6552804	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	235	116	302	0	0.493617	0	A|0.825;G|0.175	0.175	strong	.	MLF1IP	33	.	NM_024629	exon6	c.T470C	p.I157T	GTACTTATTTTCT	.	PASS	Atlas-SNP
SLC41A1	254428	hgsc.bcm.edu	37	1	205767885	205767885	+	Silent	SNP	G	G	A	rs708727	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	260	135	291	2	0.519231	0.00687285	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	.	scavenged	Atlas-SNP
ADAM21	8747	hgsc.bcm.edu	37	14	70924693	70924693	+	Silent	SNP	T	T	C	rs45480894	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	60	12	87	0	0.2	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	.	scavenged	Atlas-SNP
PLIN4	729359	hgsc.bcm.edu	37	19	4512409	4512409	+	Silent	SNP	T	T	C	rs10410197	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	131	66	104	0	0.503817	0	T|0.896;C|0.104	0.104	strong	.	PLIN4	191	.	NM_001080400	exon3	c.A1521G	p.V507V	GGTGTCTACGCCG	.	PASS	Atlas-SNP
MDN1	23195	hgsc.bcm.edu	37	6	90372574	90372574	+	Missense_Mutation	SNP	A	A	C	rs36040566	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	213	104	250	1	0.488263	0.004	A|0.909;C|0.091	0.091	strong	.	MDN1	478	.	NM_014611	exon86	c.T14349G	p.D4783E	CTCCTCATCATCA	.	PASS	Atlas-SNP
ZNF775	285971	hgsc.bcm.edu	37	7	150094853	150094853	+	Silent	SNP	G	G	A	rs7780011	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	10	10	2	0	1	0	G|0.551;A|0.449	0.449	strong	ZNF775,NS,carcinoma,0,1	ZNF775	34	1	NM_173680	exon3	c.G1284A	p.T428T	GGACACGCTGTGG	.	PASS	Atlas-SNP
SLCO4C1	353189	hgsc.bcm.edu	37	5	101592919	101592919	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	355	93	410	0	0.261972	0	.	.	none	.	SLCO4C1	113	.	NM_180991	exon8	c.G1369A	p.A457T	ACAGTGCAAACTT	.	PASS	Atlas-SNP
UGT1A7	54577	hgsc.bcm.edu	37	2	234591339	234591339	+	Silent	SNP	G	G	A	rs17864686	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	104	56	128	0	0.538462	0	G|0.822;A|0.178	0.178	strong	.	UGT1A7	74	.	NM_019077	exon1	c.G756A	p.L252L	TTGGTTGTTGCGA	.	PASS	Atlas-SNP
ZNF813	126017	hgsc.bcm.edu	37	19	53993923	53993923	+	Missense_Mutation	SNP	C	C	T	rs61743337		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	113	52	172	0	0.460177	0	C|0.986;T|0.014	0.014	weak	.	ZNF813	81	.	NM_001004301	exon4	c.C437T	p.S146L	TTCATTCGCATCT	.	PASS	Atlas-SNP
SLC6A6	6533	hgsc.bcm.edu	37	3	14489107	14489107	+	Missense_Mutation	SNP	G	G	A	rs62233560	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	118	57	134	0	0.483051	0	G|0.992;A|0.008	0.008	strong	.	SLC6A6	58	.	NM_003043	exon5	c.G382A	p.V128I	GCCTCCGTTGTAA	.	PASS	Atlas-SNP
MLF1IP	79682	hgsc.bcm.edu	37	4	185655171	185655171	+	Missense_Mutation	SNP	C	C	T	rs902174	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	16	13	17	0	0.8125	0	C|0.641;T|0.359	0.359	strong	.	MLF1IP	33	.	NM_024629	exon1	c.G46A	p.G16S	CTTACCCCTCAGA	.	PASS	Atlas-SNP
CDK10	8558	hgsc.bcm.edu	37	16	89758285	89758285	+	Missense_Mutation	SNP	C	C	T	rs143430910	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	106	3	104	0	0.0283019	0	C|1.000;T|0.000	0.000	strong	CDK10_ENST00000353379,NS,carcinoma,0,1	CDK10	26	1	NM_052988	exon5	c.C407T	p.S136L	CCTTCTCGGAGGC	.	scavenged	Atlas-SNP
UHRF1BP1L	23074	hgsc.bcm.edu	37	12	100444984	100444984	+	Missense_Mutation	SNP	G	G	A	rs7296162	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	131	61	197	0	0.465649	0	G|0.939;A|0.061	0.061	strong	.	UHRF1BP1L	144	.	NM_015054	exon16	c.C3440T	p.S1147L	GTAGTTGAGTTCT	.	PASS	Atlas-SNP
RYR3	6263	hgsc.bcm.edu	37	15	34137200	34137200	+	Silent	SNP	T	T	G	rs41279228	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	112	112	151	0	1	0	T|0.854;G|0.146	0.146	strong	RYR3,brain,glioma,0,1	RYR3	760	1	NM_001036	exon93	c.T13434G	p.R4478R	CCTGCGTGCCCTG	.	PASS	Atlas-SNP
STXBP2	6813	hgsc.bcm.edu	37	19	7711221	7711221	+	Silent	SNP	T	T	C	rs10001	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	138	69	167	0	0.5	0	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	.	PASS	Atlas-SNP
PTPRN2	5799	hgsc.bcm.edu	37	7	157959895	157959895	+	Missense_Mutation	SNP	C	C	T	rs1130496	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	60	59	72	0	0.983333	0	C|0.653;T|0.347	0.347	strong	.	PTPRN2	243	.	NM_130843	exon6	c.G638A	p.R213H	TCCTCGCGGAGCT	.	PASS	Atlas-SNP
GOLGA6C	653641	hgsc.bcm.edu	37	15	75562493	75562493	+	Missense_Mutation	SNP	C	C	A	rs2636846		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	10	79	5	0.136986	0.0632911	.	.	weak	GOLGA6C_ENST00000300576,bladder,carcinoma,-2,3	GOLGA6C	12	3	NM_001164404	exon18	c.C2035A	p.P679T	AACCCCCCGGTAC	.	scavenged	Atlas-SNP
GPR116	221395	hgsc.bcm.edu	37	6	46827239	46827239	+	Missense_Mutation	SNP	C	C	T	rs9395218	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	37	110	0	0.451219	0	C|0.761;T|0.239	0.239	strong	.	GPR116	133	.	NM_015234	exon17	c.G2401A	p.V801I	GGATGACATTAAC	.	PASS	Atlas-SNP
ITGAE	3682	hgsc.bcm.edu	37	17	3632836	3632836	+	Missense_Mutation	SNP	G	G	A	rs1716	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	153	74	174	0	0.48366	0	G|0.755;A|0.245	0.245	strong	.	ITGAE	96	.	NM_002208	exon24	c.C2848T	p.R950W	AAGACCGTCTTTC	.	PASS	Atlas-SNP
KLF14	136259	hgsc.bcm.edu	37	7	130418525	130418525	+	Silent	SNP	G	G	A	rs76603546	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	16	11	5	0	0.6875	0	G|0.582;A|0.418	0.418	strong	.	KLF14	15	.	NM_138693	exon1	c.C336T	p.S112S	GAAGCCGGACGAG	.	PASS	Atlas-SNP
MCPH1	79648	hgsc.bcm.edu	37	8	6479178	6479178	+	Silent	SNP	C	C	A	rs2912016	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	64	63	71	0	0.984375	0	C|0.615;A|0.385	0.385	strong	.	MCPH1	65	.	NM_024596	exon13	c.C2418A	p.A806A	GAAAGCCACAGTC	.	PASS	Atlas-SNP
MARCH7	64844	hgsc.bcm.edu	37	2	160604936	160604936	+	Missense_Mutation	SNP	G	G	A	rs13024801	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	152	67	154	0	0.440789	0	G|0.944;A|0.056	0.056	strong	.	MARCH7	48	.	NM_022826	exon5	c.G1135A	p.G379S	TCTGAAGGTAGAA	.	PASS	Atlas-SNP
OR2C1	4993	hgsc.bcm.edu	37	16	3406626	3406626	+	Missense_Mutation	SNP	G	G	A	rs11648783	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	73	79	0	0.793478	0	G|0.723;A|0.277	0.277	strong	.	OR2C1	38	.	NM_012368	exon1	c.G686A	p.R229H	AAATCCGCTCTGC	.	PASS	Atlas-SNP
ESPNL	339768	hgsc.bcm.edu	37	2	239039057	239039057	+	Missense_Mutation	SNP	A	A	G	rs13033248	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	50	24	58	0	0.48	0	A|0.615;G|0.385	0.385	strong	.	ESPNL	63	.	NM_194312	exon9	c.A1702G	p.I568V	GCCTCAATCCCAG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195508108	195508108	+	Missense_Mutation	SNP	G	G	A	rs374140595		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	80	17	64	0	0.2125	0	.	.	weak	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.C10343T	p.S3448L	GATGCTGAGGAAG	.	PASS	Atlas-SNP
ZNF585B	92285	hgsc.bcm.edu	37	19	37677748	37677748	+	Missense_Mutation	SNP	T	T	A	rs45626541	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	142	65	163	0	0.457746	0	T|0.676;A|0.324	0.324	strong	.	ZNF585B	91	.	NM_152279	exon5	c.A691T	p.I231L	CATGTATACTGAG	.	PASS	Atlas-SNP
LAMB3	3914	hgsc.bcm.edu	37	1	209795909	209795909	+	Silent	SNP	T	T	C	rs3179860	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	100	51	128	0	0.51	0	T|0.896;C|0.104	0.104	strong	.	LAMB3	136	.	NM_000228	exon18	c.A2673G	p.L891L	CTGGATTAGGAGC	.	PASS	Atlas-SNP
C6orf70	55780	hgsc.bcm.edu	37	6	170176647	170176647	+	Silent	SNP	C	C	T	rs4716399	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	44	13	78	0	0.295455	0	C|0.694;T|0.306	0.306	strong	.	C6orf70	63	.	NM_018341	exon16	c.C1617T	p.I539I	AAGCATCAGCGAA	.	PASS	Atlas-SNP
PTPRQ	374462	hgsc.bcm.edu	37	12	80890246	80890246	+	Silent	SNP	T	T	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	277	60	316	0	0.216606	0	.	.	none	.	PTPRQ	119	.	NM_001145026	exon11	c.T1692G	p.S564S	AAGGTCTTACACC	.	PASS	Atlas-SNP
TTC21A	199223	hgsc.bcm.edu	37	3	39152345	39152345	+	Missense_Mutation	SNP	G	G	A	rs1112438	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	137	65	150	0	0.474453	0	G|0.662;A|0.338	0.338	strong	TTC21A,caecum,carcinoma,0,1	TTC21A	96	1	NM_001105513	exon4	c.G272A	p.R91Q	CAGACCGAGAAGC	.	PASS	Atlas-SNP
SENP2	59343	hgsc.bcm.edu	37	3	185331165	185331165	+	Missense_Mutation	SNP	C	C	A	rs6762208	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	68	67	94	0	0.985294	0	C|0.610;A|0.390	0.390	strong	.	SENP2	88	.	NM_021627	exon10	c.C902A	p.T301K	CAGAGACGATGGT	.	PASS	Atlas-SNP
GPR112	139378	hgsc.bcm.edu	37	X	135496398	135496398	+	Silent	SNP	G	G	A	rs5930942	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	209	204	293	0	0.976077	0	0|0.003;A|0.709	0.709	strong	.	GPR112	459	.	NM_153834	exon25	c.G9117A	p.T3039T	GTTGACGCCATCT	.	PASS	Atlas-SNP
KIAA1109	84162	hgsc.bcm.edu	37	4	123280860	123280860	+	Silent	SNP	T	T	C	rs1127348	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	33	87	0	0.388235	0	T|0.843;C|0.157	0.157	strong	KIAA1109,colon,carcinoma,0,1	KIAA1109	424	1	NM_015312	exon83	c.T14784C	p.H4928H	ATGGCATCTAGAA	.	PASS	Atlas-SNP
HTT	3064	hgsc.bcm.edu	37	4	3162056	3162056	+	Silent	SNP	C	C	T	rs363099	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	175	87	157	1	0.497143	0.00636943	T|0.148;G|0.337	0.148	strong	HTT,NS,carcinoma,0,1	HTT	221	1	NM_002111	exon29	c.C3801T	p.L1267L	GTTTCTCCGCTCA	.	scavenged	Atlas-SNP
KDM2B	84678	hgsc.bcm.edu	37	12	121878659	121878659	+	Silent	SNP	C	C	T	rs1064951	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	88	37	98	0	0.420455	0	C|0.667;T|0.333	0.333	strong	.	KDM2B	218	.	NM_032590	exon21	c.G3570A	p.Q1190Q	CCGCATCTGGGCA	.	PASS	Atlas-SNP
TANC2	26115	hgsc.bcm.edu	37	17	61315272	61315272	+	Silent	SNP	G	G	A	rs2460111	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	115	114	155	0	0.991304	0	G|0.463;A|0.537	0.537	strong	TANC2_ENST00000389520,NS,lymphoid_neoplasm,0,2	TANC2	266	2	NM_025185	exon6	c.G645A	p.Q215Q	TTGGCAGTCTCAA	.	PASS	Atlas-SNP
FDX1L	112812	hgsc.bcm.edu	37	19	10426597	10426597	+	Missense_Mutation	SNP	T	T	C	rs62640397	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	31	86	0	0.442857	0	T|0.980;C|0.020	0.020	strong	.	FDX1L	21	.	NM_001031734	exon1	c.A76G	p.R26G	CAGGTCTGTTCCA	.	PASS	Atlas-SNP
NOL6	65083	hgsc.bcm.edu	37	9	33466219	33466219	+	Silent	SNP	A	A	C	rs3739681	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	56	29	78	0	0.517857	0	A|0.831;C|0.169	0.169	strong	.	NOL6	85	.	NM_022917	exon18	c.T2214G	p.V738V	GTGACAAACCACT	.	PASS	Atlas-SNP
ADAMTS18	170692	hgsc.bcm.edu	37	16	77327018	77327018	+	Silent	SNP	G	G	A	rs35296483	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	23	51	0	0.328571	0	G|0.891;A|0.109	0.109	strong	.	ADAMTS18	270	.	NM_199355	exon20	c.C3144T	p.C1048C	CTTGGGGCATCGT	.	PASS	Atlas-SNP
DTHD1	401124	hgsc.bcm.edu	37	4	36296443	36296443	+	Silent	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	134	60	162	0	0.447761	0	.	.	none	.	DTHD1	63	.	NM_001170700	exon4	c.G1050A	p.V350V	TCTGGTGGCACAT	.	PASS	Atlas-SNP
CCDC157	550631	hgsc.bcm.edu	37	22	30762035	30762035	+	Missense_Mutation	SNP	A	A	G	rs9606721	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	49	19	32	0	0.387755	0	A|0.987;G|0.013	0.013	strong	.	CCDC157	86	.	NM_001017437	exon3	c.A46G	p.T16A	CTGCGCACAGACC	.	PASS	Atlas-SNP
WDR41	55255	hgsc.bcm.edu	37	5	76734084	76734084	+	Missense_Mutation	SNP	C	C	T	rs33204	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	140	75	108	0	0.535714	0	C|0.490;T|0.510	0.510	strong	.	WDR41	29	.	NM_018268	exon10	c.G985A	p.V329I	TGGCAACGTGCAG	.	PASS	Atlas-SNP
OR10AD1	121275	hgsc.bcm.edu	37	12	48596546	48596546	+	Missense_Mutation	SNP	C	C	T	rs75531856	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	124	55	111	0	0.443548	0	C|0.935;T|0.065	0.065	strong	.	OR10AD1	24	.	NM_001004134	exon1	c.G530A	p.S177N	AAGAAGCTTTCTA	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	35	73	1	0.5	0.0136986	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	.	scavenged	Atlas-SNP
CCDC9	26093	hgsc.bcm.edu	37	19	47774680	47774680	+	Silent	SNP	C	C	G	rs117519030	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	55	30	44	0	0.545455	0	C|0.978;G|0.022	0.022	strong	.	CCDC9	37	.	NM_015603	exon12	c.C1341G	p.A447A	ACCAGCCCAAGAC	.	PASS	Atlas-SNP
BRD2	6046	hgsc.bcm.edu	37	6	32946133	32946133	+	Silent	SNP	T	T	C	rs206781	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	51	127	0	0.525773	0	T|0.705;C|0.295	0.295	strong	.	BRD2	70	.	NM_005104	exon10	c.T1809C	p.S603S	CCCTTCTGGCTTT	.	PASS	Atlas-SNP
TSEN54	283989	hgsc.bcm.edu	37	17	73513289	73513289	+	Silent	SNP	C	C	G	rs6501818	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	90	47	128	0	0.522222	0	C|0.822;G|0.178	0.178	strong	.	TSEN54	27	.	NM_207346	exon4	c.C333G	p.R111R	GCAGCGCCTTCAC	.	PASS	Atlas-SNP
PRDM1	639	hgsc.bcm.edu	37	6	106547372	106547372	+	Missense_Mutation	SNP	C	C	G	rs811925	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	103	43	130	0	0.417476	0	C|0.843;G|0.157	0.157	strong	.	PRDM1	195	.	NM_001198	exon4	c.C609G	p.D203E	TCGGGACTTTGCA	.	PASS	Atlas-SNP
CCDC8	83987	hgsc.bcm.edu	37	19	46915702	46915702	+	Silent	SNP	C	C	T	rs35262679	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	59	25	80	0	0.423729	0	C|0.941;T|0.059	0.059	strong	.	CCDC8	56	.	NM_032040	exon1	c.G366A	p.R122R	GCCCCGCCGCGGG	.	PASS	Atlas-SNP
AXIN1	8312	hgsc.bcm.edu	37	16	347184	347184	+	Silent	SNP	A	A	G	rs214252	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	76	13	49	0	0.171053	0	A|0.746;G|0.254	0.254	strong	.	AXIN1	290	.	NM_181050	exon7	c.T1827C	p.A609A	CGACTCAGCCTTC	.	PASS	Atlas-SNP
PDXK	8566	hgsc.bcm.edu	37	21	45168884	45168884	+	Silent	SNP	G	G	A	rs11539534	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	57	23	49	0	0.403509	0	G|0.906;A|0.094	0.094	strong	.	PDXK	17	.	NM_003681	exon6	c.G387A	p.P129P	CGTCCCGGAGGAC	.	PASS	Atlas-SNP
SGK223	0	hgsc.bcm.edu	37	8	8235523	8235523	+	Silent	SNP	G	G	A	rs55993234	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	51	7	48	0	0.137255	0	G|0.974;A|0.026	0.026	strong	.	.	.	.	NM_001080826	exon2	c.C396T	p.Y132Y	GCCCAGGTAGACG	.	PASS	Atlas-SNP
PTPRN2	5799	hgsc.bcm.edu	37	7	157959879	157959879	+	Silent	SNP	C	C	T	rs1130497	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	59	58	75	0	0.983051	0	C|0.659;T|0.341	0.341	strong	.	PTPRN2	243	.	NM_130843	exon6	c.G654A	p.P218P	GGTCCGCGGCAGG	.	PASS	Atlas-SNP
PREP	5550	hgsc.bcm.edu	37	6	105776792	105776792	+	Silent	SNP	G	G	A	rs6902415	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	102	43	118	0	0.421569	0	G|0.789;A|0.211	0.211	strong	.	PREP	65	.	NM_002726	exon9	c.C1125T	p.F375F	GAGCGGGAAGGTC	.	PASS	Atlas-SNP
TDRD9	122402	hgsc.bcm.edu	37	14	104481083	104481083	+	Silent	SNP	T	T	C	rs11160779	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	65	36	66	0	0.553846	0	T|0.678;C|0.322	0.322	strong	TDRD9_ENST00000409874,NS,carcinoma,-1,4	TDRD9	175	4	NM_153046	exon21	c.T2128C	p.L710L	GAAGAATTGAAGA	.	PASS	Atlas-SNP
OR5D14	219436	hgsc.bcm.edu	37	11	55563602	55563602	+	Missense_Mutation	SNP	G	G	A	rs68042892	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	249	189	286	0	0.759036	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
TNS1	7145	hgsc.bcm.edu	37	2	218683368	218683368	+	Silent	SNP	C	C	T	rs34144104	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	132	71	151	0	0.537879	0	C|0.774;T|0.226	0.226	strong	TNS1,NS,carcinoma,0,2	TNS1	251	2	NM_022648	exon24	c.G3375A	p.P1125P	GGCAGACGGGCTG	.	PASS	Atlas-SNP
CCDC146	57639	hgsc.bcm.edu	37	7	76916819	76916819	+	Silent	SNP	G	G	A	rs3763402	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	185	182	179	0	0.983784	0	G|0.769;A|0.231	0.231	strong	.	CCDC146	87	.	NM_020879	exon17	c.G2340A	p.Q780Q	TGAGCAGGTCTCC	.	PASS	Atlas-SNP
ZNF48	197407	hgsc.bcm.edu	37	16	30408961	30408961	+	Silent	SNP	C	C	T	rs61978578	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	52	19	55	0	0.365385	0	C|0.966;T|0.034	0.034	strong	.	ZNF48	34	.	NM_001214906	exon3	c.C390T	p.H130H	GAAACACCAGCGG	.	PASS	Atlas-SNP
OR5H2	79310	hgsc.bcm.edu	37	3	98002419	98002419	+	Missense_Mutation	SNP	A	A	G	rs16839214	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	135	69	166	0	0.511111	0	A|0.855;G|0.145	0.145	strong	.	OR5H2	63	.	NM_001005482	exon1	c.A688G	p.I230V	TTCACAATCCTAA	.	PASS	Atlas-SNP
SKIV2L2	23517	hgsc.bcm.edu	37	5	54645455	54645455	+	Missense_Mutation	SNP	C	C	G	rs142958762	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	171	98	165	0	0.573099	0	C|0.995;G|0.005	0.005	strong	.	SKIV2L2	104	.	NM_015360	exon12	c.C1295G	p.S432C	GCTTATCCGATGA	.	PASS	Atlas-SNP
GHRL	51738	hgsc.bcm.edu	37	3	10331519	10331519	+	Missense_Mutation	SNP	C	C	T	rs34911341	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	110	57	92	0	0.518182	0	C|0.996;T|0.004	0.004	strong	.	GHRL	8	.	NM_016362	exon3	c.G152A	p.R51Q	AGAGCTCGGGGCT	.	PASS	Atlas-SNP
TNN	63923	hgsc.bcm.edu	37	1	175097864	175097864	+	Silent	SNP	G	G	A	rs12022593	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	91	47	81	0	0.516484	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
ZC3HAV1	56829	hgsc.bcm.edu	37	7	138740037	138740037	+	Missense_Mutation	SNP	G	G	C	rs2297236	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	38	38	46	0	1	0	G|0.451;C|0.549	0.549	strong	ZC3HAV1,NS,carcinoma,0,2	ZC3HAV1	75	2	NM_020119	exon10	c.C2101G	p.Q701E	CTGGCTGATGGCT	.	PASS	Atlas-SNP
YEATS2	55689	hgsc.bcm.edu	37	3	183476685	183476685	+	Missense_Mutation	SNP	G	G	A	rs262993	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	330	137	367	0	0.415152	0	G|0.576;A|0.424	0.424	strong	YEATS2,NS,carcinoma,-1,1	YEATS2	111	1	NM_018023	exon13	c.G1588A	p.V530I	TCTCAGGTCTCCC	.	PASS	Atlas-SNP
DEGS2	123099	hgsc.bcm.edu	37	14	100615961	100615961	+	Missense_Mutation	SNP	C	C	T	rs4905937	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	41	26	27	0	0.634146	0	C|0.864;T|0.136	0.136	strong	.	DEGS2	25	.	NM_206918	exon2	c.G169A	p.A57T	AGCAGGCCAGCAT	.	PASS	Atlas-SNP
GFRA1	2674	hgsc.bcm.edu	37	10	117849353	117849353	+	Missense_Mutation	SNP	T	T	C	rs2072276	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	33	11	27	0	0.333333	0	T|0.878;G|0.015	.	strong	.	GFRA1	107	.	NM_005264	exon9	c.A1096G	p.T366A	TGGTAGTGGCAGT	.	PASS	Atlas-SNP
BRCA2	675	hgsc.bcm.edu	37	13	32929232	32929232	+	Silent	SNP	A	A	G	rs1799955	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	91	49	121	0	0.538462	0	A|0.772;G|0.228	0.228	strong	.	BRCA2	812	.	NM_000059	exon14	c.A7242G	p.S2414S	TAAATCACATTTT	.	PASS	Atlas-SNP
CNTN6	27255	hgsc.bcm.edu	37	3	1418753	1418753	+	Silent	SNP	G	G	A	rs17038365	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	43	115	0	0.494253	0	G|0.918;A|0.082	0.082	strong	.	CNTN6	245	.	NM_014461	exon17	c.G2160A	p.T720T	CATTACGTGGGAG	.	PASS	Atlas-SNP
AP3D1	8943	hgsc.bcm.edu	37	19	2138654	2138654	+	Silent	SNP	T	T	G	rs25672	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	102	102	73	0	1	0	T|0.695;G|0.304;N|0.000;A|0.000	0.304	strong	.	AP3D1	81	.	NM_001261826	exon2	c.A156C	p.I52I	CACCGCTATGTTG	.	PASS	Atlas-SNP
TSHZ1	10194	hgsc.bcm.edu	37	18	72998524	72998524	+	Missense_Mutation	SNP	C	C	T	rs200266026		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	98	35	131	0	0.357143	0	.	.	weak	.	TSHZ1	104	.	NM_005786	exon2	c.C1027T	p.P343S	GCGAACCCGTACG	.	PASS	Atlas-SNP
PHLDB3	653583	hgsc.bcm.edu	37	19	43990795	43990795	+	Missense_Mutation	SNP	G	G	A	rs117243018	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	43	18	56	0	0.418605	0	G|0.984;A|0.016	0.016	strong	.	PHLDB3	30	.	NM_198850	exon12	c.C1394T	p.A465V	GCCATGGCCTGCT	.	PASS	Atlas-SNP
EP400	57634	hgsc.bcm.edu	37	12	132562126	132562126	+	Missense_Mutation	SNP	G	G	A	rs73164912	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	65	38	69	0	0.584615	0	G|0.875;A|0.125	0.125	strong	.	EP400	370	.	NM_015409	exon53	c.G9280A	p.A3094T	GTGCCCGCCAGCT	.	PASS	Atlas-SNP
SH3PXD2A	9644	hgsc.bcm.edu	37	10	105363289	105363289	+	Silent	SNP	T	T	C	rs3740471	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	66	34	74	0	0.515152	0	T|0.835;C|0.165	0.165	strong	.	SH3PXD2A	90	.	NM_014631	exon14	c.A1602G	p.A534A	GCCGAATGCAGGG	.	PASS	Atlas-SNP
ZNF91	7644	hgsc.bcm.edu	37	19	23542291	23542291	+	Missense_Mutation	SNP	G	G	C	rs385750	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	19	7	28	0	0.368421	0	G|0.713;C|0.287	0.287	strong	.	ZNF91	349	.	NM_003430	exon4	c.C3490G	p.L1164V	AAAGTAGTGGGAT	.	PASS	Atlas-SNP
EAPP	55837	hgsc.bcm.edu	37	14	34985658	34985658	+	Missense_Mutation	SNP	C	C	T	rs17856037	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	212	94	241	0	0.443396	0	C|0.950;T|0.050	0.050	strong	.	EAPP	28	.	NM_018453	exon6	c.G716A	p.R239Q	TCTTCCCGGTTAG	.	PASS	Atlas-SNP
FAM160B1	57700	hgsc.bcm.edu	37	10	116602805	116602805	+	Silent	SNP	A	A	G	rs17092491	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	143	73	166	0	0.51049	0	A|0.908;G|0.092	0.092	strong	.	FAM160B1	107	.	NM_020940	exon6	c.A636G	p.E212E	AGAGGAACTATCT	.	PASS	Atlas-SNP
GPR133	283383	hgsc.bcm.edu	37	12	131475607	131475607	+	Missense_Mutation	SNP	C	C	A	rs137909892	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	144	75	134	0	0.520833	0	C|0.997;A|0.003	0.003	strong	.	GPR133	136	.	NM_198827	exon7	c.C794A	p.S265Y	TGACATCCACAGC	.	PASS	Atlas-SNP
KIF2B	84643	hgsc.bcm.edu	37	17	51901244	51901244	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	27	96	0	0.313953	0	.	.	none	.	KIF2B	254	.	NM_032559	exon1	c.G850A	p.A284T	TTCACCGCCCAGC	.	PASS	Atlas-SNP
CDHR1	92211	hgsc.bcm.edu	37	10	85960395	85960395	+	Silent	SNP	A	A	G	rs4933975	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	212	109	218	2	0.514151	0.00917431	A|0.487;G|0.513	0.513	strong	CDHR1,NS,carcinoma,+2,1	CDHR1	122	1	NM_001171971	exon6	c.A477G	p.A159A	CCATGCAGTGGAC	.	scavenged	Atlas-SNP
RNF111	54778	hgsc.bcm.edu	37	15	59368167	59368167	+	Silent	SNP	G	G	A	rs7178935	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	64	35	63	0	0.546875	0	G|0.595;A|0.405	0.405	strong	.	RNF111	179	.	NM_017610	exon7	c.G1701A	p.V567V	GCCAGTGGACCTG	.	PASS	Atlas-SNP
C9orf89	84270	hgsc.bcm.edu	37	9	95869981	95869981	+	Silent	SNP	G	G	A	rs74414352	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	34	85	0	0.435897	0	G|0.997;A|0.003	0.003	strong	.	C9orf89	12	.	NM_032310	exon2	c.G33A	p.V11V	CCTGGTGCAGGAC	.	PASS	Atlas-SNP
PDXDC1	23042	hgsc.bcm.edu	37	16	15111218	15111218	+	Missense_Mutation	SNP	C	C	T	rs75456399		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	144	12	180	0	0.0833333	0	.	.	weak	.	PDXDC1	59	.	NM_015027	exon11	c.C902T	p.P301L	CTGGCCCGTGGCT	.	PASS	Atlas-SNP
GABBR2	9568	hgsc.bcm.edu	37	9	101068580	101068580	+	Silent	SNP	G	G	A	rs2304389	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	208	116	210	1	0.557692	0.0047619	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
LAMB1	3912	hgsc.bcm.edu	37	7	107615506	107615506	+	Silent	SNP	C	C	T	rs11770141	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	23	13	43	0	0.565217	0	C|0.903;T|0.097	0.097	strong	.	LAMB1	185	.	NM_002291	exon12	c.G1407A	p.G469G	AGGATTCCCTCCA	.	PASS	Atlas-SNP
NAGK	55577	hgsc.bcm.edu	37	2	71304738	71304738	+	Silent	SNP	G	G	A	rs1043701	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	53	106	0	0.546392	0	G|0.935;A|0.065	0.065	strong	.	NAGK	34	.	NM_017567	exon9	c.G954A	p.V318V	CTCTGTGTGGAAG	.	PASS	Atlas-SNP
FSTL5	56884	hgsc.bcm.edu	37	4	162680603	162680603	+	Silent	SNP	A	A	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	210	52	239	0	0.247619	0	.	.	none	.	FSTL5	207	.	NM_020116	exon6	c.T687A	p.A229A	CTTGTCAGCATTA	.	PASS	Atlas-SNP
LEPREL1	55214	hgsc.bcm.edu	37	3	189712010	189712010	+	Silent	SNP	G	G	A	rs1719600	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	57	27	70	0	0.473684	0	G|0.812;A|0.188	0.188	strong	.	LEPREL1	95	.	NM_018192	exon3	c.C696T	p.H232H	TTCGAAGTGCCTG	.	PASS	Atlas-SNP
SOCS5	9655	hgsc.bcm.edu	37	2	46986716	46986716	+	Silent	SNP	C	C	G	rs41489952	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	323	249	159	0	0.770898	0	C|0.935;G|0.065	0.065	strong	.	SOCS5	62	.	NM_144949	exon2	c.C1047G	p.T349T	CCATACCCATGTT	.	PASS	Atlas-SNP
ZNF721	170960	hgsc.bcm.edu	37	4	437831	437831	+	Missense_Mutation	SNP	C	C	T	rs72501950	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	44	74	0	0.536585	0	C|0.855;T|0.145	0.145	strong	.	ZNF721	205	.	NM_133474	exon3	c.C425A	p.S142Y	TTGCCACGTTCTT	.	PASS	Atlas-SNP
RNASET2	8635	hgsc.bcm.edu	37	6	167344583	167344583	+	Silent	SNP	A	A	G	rs13213697	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	40	80	0	0.512821	0	A|0.780;G|0.220	0.220	strong	.	RNASET2	18	.	NM_003730	exon8	c.T516C	p.L172L	TCTGGCAAGGGCA	.	PASS	Atlas-SNP
NSD1	64324	hgsc.bcm.edu	37	5	176638506	176638506	+	Missense_Mutation	SNP	G	G	C	rs28932179	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	144	67	136	0	0.465278	0	G|0.975;C|0.025	0.025	strong	NSD1_ENST00000439151,NS,carcinoma,-2,2	NSD1	416	2	NM_022455	exon5	c.G3106C	p.A1036P	TTTTCAGCCCAAA	.	PASS	Atlas-SNP
CCR8	1237	hgsc.bcm.edu	37	3	39374151	39374151	+	Missense_Mutation	SNP	C	C	T	rs144913149	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	354	180	416	0	0.508475	0	C|0.999;T|0.001	0.001	strong	.	CCR8	34	.	NM_005201	exon2	c.C329T	p.S110F	TGGTGTCTGGCTT	.	PASS	Atlas-SNP
CALML5	51806	hgsc.bcm.edu	37	10	5541230	5541230	+	Missense_Mutation	SNP	T	T	C	rs11546426	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	83	37	95	0	0.445783	0	T|0.677;C|0.323;A|0.000	0.323	strong	.	CALML5	25	.	NM_017422	exon1	c.A172G	p.S58G	CGTCGCTGTCAAC	.	PASS	Atlas-SNP
BSCL2	26580	hgsc.bcm.edu	37	11	62458275	62458275	+	Missense_Mutation	SNP	T	T	C	rs6856	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	47	10	65	0	0.212766	0	T|0.825;C|0.175	0.175	strong	.	BSCL2	35	.	NM_001130702	exon8	c.A803G	p.K268R	GGGATCTTCAGGG	.	PASS	Atlas-SNP
KRT27	342574	hgsc.bcm.edu	37	17	38938591	38938591	+	Missense_Mutation	SNP	C	C	G	rs2469826	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	62	28	70	0	0.451613	0	C|0.685;G|0.315	0.315	strong	KRT27,NS,carcinoma,0,1	KRT27	41	1	NM_181537	exon1	c.G155C	p.S52T	GATGAGCTGCCCC	.	PASS	Atlas-SNP
TGIF1	7050	hgsc.bcm.edu	37	18	3457695	3457695	+	Silent	SNP	C	C	T	rs2229335	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	90	47	102	0	0.522222	0	C|0.955;T|0.045	0.045	strong	.	TGIF1	41	.	NM_170695	exon3	c.C963T	p.V321V	GTCGGTCGGTGTG	.	PASS	Atlas-SNP
OTUD4	54726	hgsc.bcm.edu	37	4	146058966	146058966	+	Silent	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	239	3	261	1	0.0125523	0.00383142	.	.	none	OTUD4_ENST00000447906,NS,malignant_melanoma,0,2	OTUD4	120	2	NM_001102653	exon21	c.C2766T	p.S922S	TTTCAGGCTTTGA	.	scavenged	Atlas-SNP
PSG8	440533	hgsc.bcm.edu	37	19	43262267	43262267	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	90	39	95	0	0.433333	0	.	.	none	.	PSG8	101	.	NM_001130167	exon3	c.A596G	p.N199S	GTCCTGTTGGTTT	.	PASS	Atlas-SNP
MED24	9862	hgsc.bcm.edu	37	17	38175866	38175866	+	Silent	SNP	G	G	A	rs11555254	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	123	63	128	0	0.512195	0	G|0.850;A|0.150	0.150	strong	.	MED24	89	.	NM_014815	exon26	c.C2886T	p.S962S	GGGGCTGGACATG	.	PASS	Atlas-SNP
S1PR5	53637	hgsc.bcm.edu	37	19	10624838	10624838	+	Missense_Mutation	SNP	C	C	T	rs150461309	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	63	30	80	0	0.47619	0	C|0.997;T|0.003	0.003	strong	.	S1PR5	33	.	NM_030760	exon2	c.G850A	p.V284I	GGAGTACAGGACA	.	PASS	Atlas-SNP
GRK4	2868	hgsc.bcm.edu	37	4	2990499	2990499	+	Missense_Mutation	SNP	G	G	T	rs2960306	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	60	60	81	0	1	0	G|0.638;T|0.362	0.362	strong	.	GRK4	72	.	NM_182982	exon3	c.G194T	p.R65L	GAAGACGTCTCTT	.	PASS	Atlas-SNP
MIOX	55586	hgsc.bcm.edu	37	22	50926768	50926768	+	Silent	SNP	C	C	T	rs2232883	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	96	37	86	0	0.385417	0	C|0.878;T|0.122	0.122	strong	.	MIOX	21	.	NM_017584	exon5	c.C405T	p.P135P	GGAGCCCCAGGTA	.	PASS	Atlas-SNP
ZNF419	79744	hgsc.bcm.edu	37	19	58002859	58002859	+	Silent	SNP	T	T	C	rs62126198	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	225	12	216	0	0.0533333	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
YWHAE	7531	hgsc.bcm.edu	37	17	1265285	1265285	+	Silent	SNP	C	C	T	rs34137556	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	65	37	71	0	0.569231	0	C|0.981;T|0.019	0.019	strong	.	YWHAE	50	.	NM_006761	exon3	c.G282A	p.K94K	GATTAACTTTAGC	.	PASS	Atlas-SNP
TRIM49C	642612	hgsc.bcm.edu	37	11	89768577	89768577	+	Silent	SNP	C	C	T	rs61903674	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	369	101	322	0	0.273713	0	.	.	weak	.	TRIM49C	48	.	NM_001195234	exon3	c.C198T	p.T66T	CAAAACCAACATT	.	PASS	Atlas-SNP
KIF17	57576	hgsc.bcm.edu	37	1	21044151	21044151	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	13	6	13	0	0.461538	0	.	.	none	.	KIF17	130	.	NM_001122819	exon1	c.C49T	p.Q17X	CCCGCTGGTTCAT	.	PASS	Atlas-SNP
MLC1	23209	hgsc.bcm.edu	37	22	50502491	50502491	+	Missense_Mutation	SNP	T	T	C	rs11568188	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	56	12	136	1	0.214286	0.00735294	T|0.905;C|0.095	0.095	strong	MLC1,rectum,carcinoma,0,2	MLC1	48	2	NM_015166	exon11	c.A1031G	p.N344S	GGGCCGTTCTGGG	.	scavenged	Atlas-SNP
PLEK	5341	hgsc.bcm.edu	37	2	68592496	68592496	+	Missense_Mutation	SNP	C	C	T	rs17035364	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	106	33	111	0	0.311321	0	C|0.952;T|0.048	0.048	strong	.	PLEK	64	.	NM_002664	exon1	c.C13T	p.R5W	CCAAAGCGGATCA	.	PASS	Atlas-SNP
HIST1H1B	3009	hgsc.bcm.edu	37	6	27835272	27835272	+	Silent	SNP	T	T	C	rs200948	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	63	30	94	0	0.47619	0	T|0.896;C|0.104	0.104	strong	.	HIST1H1B	54	.	NM_005322	exon1	c.A36G	p.P12P	CGGCGCTGGGGTG	.	PASS	Atlas-SNP
PLA2G4C	8605	hgsc.bcm.edu	37	19	48558286	48558286	+	Silent	SNP	G	G	A	rs2307281	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	76	44	92	0	0.578947	0	G|0.854;A|0.146	0.146	strong	.	PLA2G4C	76	.	NM_001159322	exon15	c.C1308T	p.D436D	GCAGTAGTCAGTG	.	PASS	Atlas-SNP
PCDH15	65217	hgsc.bcm.edu	37	10	55955485	55955485	+	Silent	SNP	A	A	G	rs7921598	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	48	127	0	0.521739	0	A|0.756;G|0.244	0.244	strong	.	PCDH15	1715	.	NM_001142763	exon12	c.T1278C	p.T426T	AGGTGAAGTCAAA	.	PASS	Atlas-SNP
TRIM66	9866	hgsc.bcm.edu	37	11	8668082	8668082	+	Missense_Mutation	SNP	C	C	T	rs61741649	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	410	341	352	0	0.831707	0	C|0.963;T|0.037	0.037	strong	.	TRIM66	45	.	NM_014818	exon6	c.G434A	p.R145K	ACCTTCCTATGCT	.	PASS	Atlas-SNP
TRPC1	7220	hgsc.bcm.edu	37	3	142523349	142523349	+	Silent	SNP	G	G	A	rs3821647	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	232	108	220	0	0.465517	0	G|0.806;A|0.194	0.194	strong	TRPC1,NS,carcinoma,0,1	TRPC1	82	1	NM_001251845	exon12	c.G2031A	p.T677T	ATGTACGTTACCT	.	PASS	Atlas-SNP
JAK1	3716	hgsc.bcm.edu	37	1	65311214	65311214	+	Silent	SNP	G	G	C	rs3737139	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	153	73	165	0	0.477124	0	G|0.958;C|0.042	0.042	strong	.	JAK1	209	.	NM_002227	exon15	c.C2097G	p.A699A	GGCACTGGCCAGC	.	PASS	Atlas-SNP
CLEC18C	283971	hgsc.bcm.edu	37	16	70211370	70211370	+	Missense_Mutation	SNP	C	C	G	rs3869428		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	545	98	529	0	0.179817	0	.	.	weak	CLEC18C,rectum,carcinoma,0,1	CLEC18C	15	1	NM_173619	exon3	c.C443G	p.T148S	CCTGCACCCACTA	.	scavenged	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195507915	195507915	+	Silent	SNP	T	T	C	rs71635073	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	203	55	157	0	0.270936	0	C|1.000;|0.000	1.000	weak	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.A10536G	p.S3512S	GGATGCTGAGGAA	.	PASS	Atlas-SNP
ME3	10873	hgsc.bcm.edu	37	11	86267714	86267714	+	Silent	SNP	C	C	A	rs12287767	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	93	23	118	0	0.247312	0	C|0.774;A|0.226	0.226	strong	.	ME3	70	.	NM_006680	exon4	c.G348T	p.R116R	CTCGTTCCGGTCT	.	PASS	Atlas-SNP
LRRIQ1	84125	hgsc.bcm.edu	37	12	85438499	85438499	+	Missense_Mutation	SNP	G	G	A	rs3765044	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	206	101	244	0	0.490291	0	G|0.796;A|0.204	0.204	strong	.	LRRIQ1	512	.	NM_001079910	exon4	c.G248A	p.C83Y	TAGGCTGTAGTTA	.	PASS	Atlas-SNP
CPAMD8	27151	hgsc.bcm.edu	37	19	17100550	17100550	+	Missense_Mutation	SNP	A	A	T	rs61744414	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	68	29	103	0	0.426471	0	A|0.967;T|0.033	0.033	strong	.	CPAMD8	192	.	NM_015692	exon13	c.T1439A	p.V480E	GCCCCCACAGGCT	.	PASS	Atlas-SNP
KRTAP4-8	728224	hgsc.bcm.edu	37	17	39254133	39254133	+	Missense_Mutation	SNP	G	G	T	rs200462175		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	40	4	50	0	0.1	0	.	.	weak	.	KRTAP4-8	57	.	NM_031960	exon1	c.C204A	p.S68R	ACAGCAGCTGGGG	.	PASS	Atlas-SNP
RPGRIP1	57096	hgsc.bcm.edu	37	14	21770681	21770681	+	Silent	SNP	A	A	G	rs17792599	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	49	111	0	0.569767	0	A|0.857;G|0.142	0.142	strong	.	RPGRIP1	213	.	NM_020366	exon4	c.A525G	p.P175P	CCCTCCATCGTTT	.	PASS	Atlas-SNP
ULK4	54986	hgsc.bcm.edu	37	3	41831203	41831203	+	Missense_Mutation	SNP	C	C	T	rs17215589	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	93	46	97	0	0.494624	0	C|0.898;T|0.102	0.102	strong	.	ULK4	150	.	NM_017886	exon21	c.G2143A	p.A715T	TGGCAGCGAATAA	.	PASS	Atlas-SNP
KRTAP5-5	439915	hgsc.bcm.edu	37	11	1651625	1651625	+	Silent	SNP	G	G	A	rs200756510	byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	56	17	65	0	0.303571	0	G|0.988;A|0.011	0.011	strong	KRTAP5-5,NS,carcinoma,+2,1	KRTAP5-5	86	1	NM_001001480	exon1	c.G555A	p.Q185Q	CTGCCAGTCCAGC	.	PASS	Atlas-SNP
NEB	4703	hgsc.bcm.edu	37	2	152389991	152389991	+	Silent	SNP	A	A	G	rs114218081	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	102	46	127	0	0.45098	0	A|0.979;G|0.021	0.021	strong	.	NEB	1697	.	NM_001271208	exon144	c.T21487C	p.L7163L	CAGTCAACATATC	.	PASS	Atlas-SNP
C6orf223	221416	hgsc.bcm.edu	37	6	43968814	43968814	+	Missense_Mutation	SNP	A	A	G	rs2295333	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	42	90	0	0.56	0	A|0.833;G|0.167	0.167	strong	.	C6orf223	14	.	NM_001171992	exon2	c.A185G	p.Q62R	AGTGGCAAGACTT	.	PASS	Atlas-SNP
IQCF1	132141	hgsc.bcm.edu	37	3	51929183	51929183	+	Missense_Mutation	SNP	C	C	T	rs11927897	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	51	111	0	0.6	0	C|0.968;T|0.032	0.032	strong	.	IQCF1	26	.	NM_152397	exon4	c.G341A	p.R114Q	GCCTGCCGCCTCT	.	PASS	Atlas-SNP
ARFRP1	10139	hgsc.bcm.edu	37	20	62331989	62331989	+	Silent	SNP	T	T	G	rs1048665	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	76	35	70	0	0.460526	0	T|0.790;G|0.200;C|0.001;A|0.009	0.200	strong	.	ARFRP1	17	.	NM_001134758	exon7	c.A483C	p.R161R	GCAATCTCGCCTG	.	PASS	Atlas-SNP
PTH1R	5745	hgsc.bcm.edu	37	3	46939575	46939575	+	Silent	SNP	C	C	A	rs143863124	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	119	56	112	0	0.470588	0	C|0.996;A|0.004	0.004	strong	.	PTH1R	49	.	NM_001184744	exon6	c.C436A	p.R146R	GCCTACCGACGCT	.	PASS	Atlas-SNP
ATF6	22926	hgsc.bcm.edu	37	1	161751741	161751741	+	Missense_Mutation	SNP	A	A	G	rs1058405	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	56	18	68	0	0.321429	0	A|0.793;G|0.207	0.207	strong	.	ATF6	84	.	NM_007348	exon3	c.A199G	p.M67V	GATTTGATGCCTT	.	PASS	Atlas-SNP
MTTP	4547	hgsc.bcm.edu	37	4	100503136	100503136	+	Missense_Mutation	SNP	C	C	G	rs141736123	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	151	70	163	0	0.463576	0	C|0.989;G|0.010;T|0.000	0.010	strong	.	MTTP	127	.	NM_000253	exon3	c.C136G	p.R46G	CTTGATCGGGGCA	.	PASS	Atlas-SNP
ALMS1	7840	hgsc.bcm.edu	37	2	73680508	73680508	+	Missense_Mutation	SNP	G	G	C	rs6546839	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	66	66	77	0	1	0	G|0.687;C|0.313	0.313	strong	.	ALMS1	384	.	NM_015120	exon8	c.G6851C	p.R2284P	TTGCCCGTTTCAG	.	PASS	Atlas-SNP
TPX2	22974	hgsc.bcm.edu	37	20	30381700	30381700	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	158	38	184	0	0.240506	0	.	.	none	.	TPX2	61	.	NM_012112	exon14	c.G1559A	p.G520E	ATTATGGGGTGCC	.	PASS	Atlas-SNP
PCDHGA12	26025	hgsc.bcm.edu	37	5	140810773	140810773	+	Silent	SNP	G	G	A	rs17097300	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	50	25	52	0	0.5	0	G|0.959;A|0.041	0.041	strong	.	PCDHGA12	271	.	NM_032094	exon1	c.G447A	p.E149E	CACTGAGATGCGG	.	PASS	Atlas-SNP
CDRT15L2	256223	hgsc.bcm.edu	37	17	20483255	20483255	+	Missense_Mutation	SNP	G	G	A	rs150637113	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	292	140	334	0	0.479452	0	G|0.986;A|0.014	0.014	strong	.	CDRT15L2	5	.	NM_001190790	exon1	c.G199A	p.G67R	CCATCGGGGCTGC	.	PASS	Atlas-SNP
KANK2	25959	hgsc.bcm.edu	37	19	11304498	11304498	+	Silent	SNP	C	C	T	rs755238	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	46	18	41	0	0.391304	0	C|0.934;T|0.066	0.066	strong	KANK2,NS,carcinoma,0,1	KANK2	47	1	NM_015493	exon2	c.G258A	p.S86S	GCACAGCGACTCA	.	PASS	Atlas-SNP
ZNF701	55762	hgsc.bcm.edu	37	19	53086598	53086598	+	Missense_Mutation	SNP	G	G	A	rs3745102	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	111	110	135	0	0.990991	0	G|0.686;A|0.314	0.314	strong	.	ZNF701	44	.	NM_001172655	exon5	c.G1484A	p.R495H	GTCATCGTAGACT	.	PASS	Atlas-SNP
KCNS3	3790	hgsc.bcm.edu	37	2	18113508	18113508	+	Silent	SNP	G	G	A	rs3747516	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	145	61	113	0	0.42069	0	G|0.744;A|0.256	0.256	strong	.	KCNS3	85	.	NM_002252	exon3	c.G1233A	p.K411K	TTCCAAGTACTAC	.	PASS	Atlas-SNP
ABCA13	154664	hgsc.bcm.edu	37	7	48311658	48311658	+	Missense_Mutation	SNP	G	G	A	rs17547816	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	31	22	78	0	0.709677	0	G|0.965;A|0.035	0.035	strong	.	ABCA13	1192	.	NM_152701	exon17	c.G2395A	p.E799K	GGCAACGAAGTGA	.	PASS	Atlas-SNP
SUSD1	64420	hgsc.bcm.edu	37	9	114804173	114804173	+	Silent	SNP	G	G	A	rs3849117	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	96	49	122	0	0.510417	0	G|0.943;A|0.057	0.057	strong	.	SUSD1	51	.	NM_022486	exon16	c.C2217T	p.L739L	GAATGTGAGAATG	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	17	8	10	0	0.470588	0	G|0.804;T|0.196	0.196	strong	.	RNF39	27	.	NM_025236	exon4	c.C911A	p.A304E	TCGTCCGCATCCT	.	PASS	Atlas-SNP
ADAMTS7	11173	hgsc.bcm.edu	37	15	79064143	79064143	+	Silent	SNP	C	C	G	rs11635870	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	49	63	0	0.569767	0	C|0.715;G|0.285	0.285	strong	.	ADAMTS7	142	.	NM_014272	exon15	c.G2160C	p.A720A	TGCGCCCGCTGGG	.	PASS	Atlas-SNP
ZNF417	147687	hgsc.bcm.edu	37	19	58420162	58420162	+	Missense_Mutation	SNP	T	T	C	rs61735221	byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	215	97	239	0	0.451163	0	T|0.053;C|0.947	0.947	strong	.	ZNF417	44	.	NM_152475	exon3	c.A1484G	p.N495S	CATTCATTGCATT	.	PASS	Atlas-SNP
MPHOSPH9	10198	hgsc.bcm.edu	37	12	123705962	123705962	+	Missense_Mutation	SNP	C	C	T	rs36121382	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	150	72	152	0	0.48	0	C|0.942;T|0.058	0.058	strong	.	MPHOSPH9	75	.	NM_022782	exon1	c.G373A	p.G125S	TTTCACCAAGAAA	.	PASS	Atlas-SNP
HNRNPH3	3189	hgsc.bcm.edu	37	10	70101417	70101417	+	Missense_Mutation	SNP	G	G	C	rs16925347	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	83	41	116	0	0.493976	0	G|0.943;C|0.057	0.057	strong	.	HNRNPH3	33	.	NM_012207	exon8	c.G851C	p.G284A	TGGGAGGCTACGG	.	PASS	Atlas-SNP
PRKAR1B	5575	hgsc.bcm.edu	37	7	590199	590199	+	Silent	SNP	A	A	G	rs11545042	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	35	10	56	0	0.285714	0	A|0.826;G|0.174	0.174	strong	.	PRKAR1B	32	.	NM_001164760	exon11	c.T1014C	p.T338T	CACGACAGTGGCC	.	PASS	Atlas-SNP
LAMA2	3908	hgsc.bcm.edu	37	6	129571272	129571272	+	Missense_Mutation	SNP	G	G	A	rs36044314	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	53	12	101	0	0.226415	0	G|0.987;A|0.013	0.013	strong	.	LAMA2	481	.	NM_000426	exon13	c.G1798A	p.G600R	GTAGGAGGACAGT	.	PASS	Atlas-SNP
PPFIA4	8497	hgsc.bcm.edu	37	1	203044777	203044777	+	Missense_Mutation	SNP	G	G	A	rs12130501	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	26	12	13	0	0.461538	0	G|0.992;A|0.008	0.008	strong	PPFIA4_ENST00000272198,colon,carcinoma,-1,2	PPFIA4	139	2	NM_015053	exon16	c.G1948A	p.G650S	GGTCGCGGCGGCA	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29910622	29910622	+	Silent	SNP	C	C	T	rs199501996	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	141	19	105	0	0.134752	0	C|0.998;T|0.002	0.002	strong	HLA-A,NS,carcinoma,0,4	HLA-A	89	4	NM_001242758	exon2	c.C162T	p.D54D	GGACGACACGCAG	.	scavenged	Atlas-SNP
ANO7	50636	hgsc.bcm.edu	37	2	242151585	242151585	+	Silent	SNP	C	C	T	rs7593101	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	123	66	124	0	0.536585	0	C|0.787;T|0.213	0.213	strong	.	ANO7	136	.	NM_001001891	exon16	c.C1800T	p.Y600Y	CTTCTACTCCTCA	.	PASS	Atlas-SNP
MYPOP	339344	hgsc.bcm.edu	37	19	46394187	46394187	+	Silent	SNP	C	C	T	rs62111265	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	19	13	24	0	0.684211	0	C|0.872;G|0.000;T|0.128	0.128	strong	.	MYPOP	23	.	NM_001012643	exon3	c.G894A	p.L298L	TCCTGGCAGAAGG	.	PASS	Atlas-SNP
MCPH1	79648	hgsc.bcm.edu	37	8	6338306	6338306	+	Missense_Mutation	SNP	C	C	A	rs12674488	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	80	13	90	0	0.1625	0	C|0.850;A|0.150	0.150	strong	.	MCPH1	65	.	NM_024596	exon11	c.C2045A	p.T682N	GTGAGACCACGAC	.	PASS	Atlas-SNP
C6orf70	55780	hgsc.bcm.edu	37	6	170176648	170176648	+	Missense_Mutation	SNP	A	A	G	rs4716346	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	44	13	80	0	0.295455	0	A|0.706;G|0.294	0.294	strong	.	C6orf70	63	.	NM_018341	exon16	c.A1618G	p.S540G	AGCATCAGCGAAC	.	PASS	Atlas-SNP
CEP170B	283638	hgsc.bcm.edu	37	14	105350178	105350178	+	Silent	SNP	C	C	T	rs45449696	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	29	57	0	0.408451	0	C|0.760;T|0.240	0.240	strong	.	.	.	.	NM_001112726	exon9	c.C1062T	p.H354H	CAAGCACGAGGAC	.	PASS	Atlas-SNP
PKD1L1	168507	hgsc.bcm.edu	37	7	47869038	47869038	+	Silent	SNP	T	T	C	rs7788583	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	36	20	62	0	0.555556	0	T|0.785;C|0.215	0.215	strong	PKD1L1,NS,carcinoma,0,1	PKD1L1	328	1	NM_138295	exon44	c.A6720G	p.A2240A	CTCGCCTGCACAG	.	PASS	Atlas-SNP
WFDC10A	140832	hgsc.bcm.edu	37	20	44259549	44259549	+	Silent	SNP	G	G	A	rs2272961	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	122	64	142	0	0.52459	0	G|0.807;A|0.193	0.193	strong	.	WFDC10A	7	.	NM_080753	exon2	c.G132A	p.Q44Q	GCAGCAGCCTAAA	.	PASS	Atlas-SNP
AMZ1	155185	hgsc.bcm.edu	37	7	2752330	2752330	+	Missense_Mutation	SNP	C	C	T	rs111981479	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	115	87	158	0	0.756522	0	C|0.990;T|0.010	0.010	strong	.	AMZ1	41	.	NM_133463	exon7	c.C1315T	p.R439C	CTCGACCGCTGGG	.	PASS	Atlas-SNP
SVIL	6840	hgsc.bcm.edu	37	10	29839798	29839798	+	Silent	SNP	A	A	G	rs17834991	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	30	111	0	0.4	0	A|0.839;G|0.161;T|0.000	0.161	strong	SVIL,NS,carcinoma,0,1	SVIL	226	1	NM_003174	exon8	c.T555C	p.Y185Y	GAGGGCATAGTCC	.	PASS	Atlas-SNP
NTAN1	123803	hgsc.bcm.edu	37	16	15131962	15131962	+	Missense_Mutation	SNP	A	A	G	rs1135999	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	109	76	178	1	0.697248	0.00561798	A|0.707;G|0.293	0.293	strong	.	NTAN1	21	.	NM_173474	exon10	c.T859C	p.S287P	TTCCAGAAAACAG	.	PASS	Atlas-SNP
GABRG3	2567	hgsc.bcm.edu	37	15	27772676	27772676	+	Silent	SNP	C	C	T	rs140679	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	122	58	128	0	0.47541	0	C|0.472;T|0.528	0.528	strong	.	GABRG3	115	.	NM_033223	exon8	c.C963T	p.T321T	TGTGACCGTGTGC	.	PASS	Atlas-SNP
C7	730	hgsc.bcm.edu	37	5	40964852	40964852	+	Missense_Mutation	SNP	A	A	C	rs13157656	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	203	110	206	0	0.541872	0	A|0.817;C|0.182	0.182	strong	.	C7	136	.	NM_000587	exon14	c.A1759C	p.T587P	GAAGGTACAATGT	.	PASS	Atlas-SNP
CALHM1	255022	hgsc.bcm.edu	37	10	105218254	105218254	+	Silent	SNP	C	C	T	rs4918016	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	142	75	135	0	0.528169	0	C|0.702;T|0.298	0.298	strong	.	CALHM1	33	.	NM_001001412	exon1	c.G255A	p.P85P	GCCCAGCGGCCGC	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29910607	29910607	+	Silent	SNP	G	G	C	rs72555397		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	115	16	83	0	0.13913	0	.	.	weak	HLA-A,NS,carcinoma,0,5	HLA-A	89	5	NM_001242758	exon2	c.G147C	p.V49V	CGCCGTGGGCTAC	.	scavenged	Atlas-SNP
HTT	3064	hgsc.bcm.edu	37	4	3227419	3227419	+	Silent	SNP	A	A	G	rs362273	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	174	83	186	0	0.477012	0	A|0.737;G|0.263	0.263	strong	HTT,caecum,carcinoma,0,1	HTT	221	1	NM_002111	exon57	c.A7797G	p.L2599L	GCTGCTACAGATC	.	PASS	Atlas-SNP
HSPA4	3308	hgsc.bcm.edu	37	5	132412424	132412424	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	109	19	166	0	0.174312	0	.	.	none	.	HSPA4	68	.	NM_002154	exon7	c.T742C	p.F248L	GAAGAATTTGGGA	.	PASS	Atlas-SNP
ZFP64	55734	hgsc.bcm.edu	37	20	50769379	50769379	+	Missense_Mutation	SNP	C	C	T	rs3746414	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	83	43	89	0	0.518072	0	C|0.848;T|0.152	0.152	strong	.	ZFP64	240	.	NM_018197	exon6	c.G1352A	p.S451N	CTCTCACTGTACT	.	PASS	Atlas-SNP
PECR	55825	hgsc.bcm.edu	37	2	216908679	216908679	+	Silent	SNP	C	C	T	rs2303842	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	156	68	156	0	0.435897	0	C|0.838;T|0.161	0.161	strong	PECR,NS,carcinoma,0,1	PECR	22	1	NM_018441	exon7	c.G774A	p.S258S	ATCCACCGACTGT	.	PASS	Atlas-SNP
IDO2	169355	hgsc.bcm.edu	37	8	39840234	39840234	+	Missense_Mutation	SNP	A	A	G	rs4736794	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	59	38	92	0	0.644068	0	A|0.845;G|0.155	0.155	strong	.	IDO2	78	.	NM_194294	exon5	c.A418G	p.I140V	CCTCCTATCCTGG	.	PASS	Atlas-SNP
TRIM11	81559	hgsc.bcm.edu	37	1	228589861	228589861	+	Missense_Mutation	SNP	G	G	A	rs143926476		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	132	31	143	0	0.234848	0	G|1.000;A|0.000	0.000	weak	.	TRIM11	38	.	NM_145214	exon2	c.C410T	p.A137V	AGCTTCGCCTGCG	.	PASS	Atlas-SNP
SLC5A8	160728	hgsc.bcm.edu	37	12	101561940	101561940	+	Silent	SNP	A	A	T	rs9634221	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	120	63	139	0	0.525	0	A|0.847;T|0.153	0.153	strong	.	SLC5A8	102	.	NM_145913	exon11	c.T1254A	p.G418G	AACCATACCAAAT	.	PASS	Atlas-SNP
LARGE	9215	hgsc.bcm.edu	37	22	34022284	34022284	+	Silent	SNP	G	G	A	rs86487	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	35	91	0	0.479452	0	G|0.597;A|0.403	0.403	strong	LARGE,NS,carcinoma,-2,1	LARGE	98	1	NM_004737	exon5	c.C435T	p.A145A	GTATCCGGCGCAG	.	PASS	Atlas-SNP
MUSK	4593	hgsc.bcm.edu	37	9	113449489	113449489	+	Missense_Mutation	SNP	C	C	T	rs35142681	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	157	157	212	0	1	0	C|0.983;T|0.017	0.017	strong	.	MUSK	112	.	NM_001166281	exon3	c.C299T	p.T100M	GCTGCACGGCCAA	.	PASS	Atlas-SNP
PCDHB16	57717	hgsc.bcm.edu	37	5	140564214	140564214	+	Silent	SNP	T	T	C	rs61739446	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	22	58	0	0.37931	0	T|0.863;C|0.137	0.137	strong	.	PCDHB16	159	.	NM_020957	exon1	c.T2080C	p.L694L	GTGGCGTTGGCCT	.	PASS	Atlas-SNP
FAS	355	hgsc.bcm.edu	37	10	90771767	90771767	+	Missense_Mutation	SNP	G	G	A	rs56006128	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	54	27	83	0	0.5	0	G|0.999;A|0.001	0.001	strong	.	FAS	47	.	NM_152872	exon7	c.G580A	p.E194K	AGAAAGGAAGTAC	.	PASS	Atlas-SNP
CDH2	1000	hgsc.bcm.edu	37	18	25593740	25593740	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	131	5	166	0	0.0381679	0	.	.	none	CDH2,NS,carcinoma,-1,1	CDH2	194	1	NM_001792	exon3	c.C306A	p.F102L	TATCAGGAACTTG	.	scavenged	Atlas-SNP
CATSPER3	347732	hgsc.bcm.edu	37	5	134343661	134343661	+	Silent	SNP	C	C	T	rs10044000	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	126	58	129	0	0.460317	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
AFAP1L1	134265	hgsc.bcm.edu	37	5	148680717	148680717	+	Missense_Mutation	SNP	G	G	A	rs61734415	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	35	99	0	0.5	0	G|0.972;A|0.028	0.028	strong	AFAP1L1,NS,carcinoma,+1,1	AFAP1L1	86	1	NM_001146337	exon4	c.G251A	p.R84Q	ACCTTCGGGACAT	.	PASS	Atlas-SNP
CABLES2	81928	hgsc.bcm.edu	37	20	60966374	60966374	+	Silent	SNP	G	G	C	rs13042761	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	61	27	68	0	0.442623	0	G|0.891;C|0.109	0.109	strong	.	CABLES2	30	.	NM_031215	exon9	c.C1227G	p.G409G	GCAGGCGCCAGCG	.	PASS	Atlas-SNP
MLC1	23209	hgsc.bcm.edu	37	22	50515273	50515273	+	Silent	SNP	G	G	A	rs6010165	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	53	26	65	0	0.490566	0	G|0.884;A|0.116	0.116	strong	.	MLC1	48	.	NM_015166	exon7	c.C594T	p.Y198Y	TACTGAGTAAGAT	.	PASS	Atlas-SNP
C5orf60	285679	hgsc.bcm.edu	37	5	179071836	179071836	+	Silent	SNP	C	C	T	rs4990391	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	150	149	248	0	0.993333	0	C|0.848;T|0.152	0.152	strong	C5orf60,colon,carcinoma,0,1	C5orf60	24	1	NM_001142306	exon1	c.G186A	p.P62P	TGAGGACGGCTCC	.	PASS	Atlas-SNP
DUSP2	1844	hgsc.bcm.edu	37	2	96810609	96810609	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	80	26	66	0	0.325	0	.	.	none	.	DUSP2	20	.	NM_004418	exon2	c.G401A	p.G134D	TGGAAGCCGTCGA	.	PASS	Atlas-SNP
AHNAK	79026	hgsc.bcm.edu	37	11	62284888	62284888	+	Silent	SNP	G	G	A	rs11555628	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	126	21	139	0	0.166667	0	G|0.966;C|0.000;A|0.034	0.034	strong	.	AHNAK	532	.	NM_001620	exon5	c.C17001T	p.T5667T	AGAGAAGGTAAAT	.	PASS	Atlas-SNP
SERGEF	26297	hgsc.bcm.edu	37	11	17981047	17981047	+	Silent	SNP	C	C	T	rs211146	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	44	44	96	0	1	0	C|0.326;T|0.674	0.674	strong	.	SERGEF	38	.	NM_012139	exon9	c.G981A	p.S327S	CGGAGACGAAGGC	.	PASS	Atlas-SNP
TMPRSS4	56649	hgsc.bcm.edu	37	11	117979606	117979606	+	Missense_Mutation	SNP	G	G	C	rs45441097	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	63	42	53	0	0.666667	0	G|0.997;C|0.003	0.003	strong	.	TMPRSS4	46	.	NM_019894	exon7	c.G578C	p.C193S	TGCACTGTCTTGG	.	PASS	Atlas-SNP
TES	26136	hgsc.bcm.edu	37	7	115897392	115897392	+	Silent	SNP	G	G	C	rs4710	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	158	158	161	0	1	0	T|0.000;G|0.669;C|0.331	0.331	strong	TES_ENST00000257721,colon,carcinoma,+1,2	TES	68	2	NM_015641	exon7	c.G1122C	p.R374R	GCAGCGGGTGACC	.	PASS	Atlas-SNP
DEF8	54849	hgsc.bcm.edu	37	16	90015960	90015960	+	Silent	SNP	G	G	C	rs6500462	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	132	33	102	0	0.25	0	G|0.947;C|0.053	0.053	strong	.	DEF8	28	.	NM_207514	exon2	c.G87C	p.G29G	CACCGGGGTGACT	.	PASS	Atlas-SNP
BRDT	676	hgsc.bcm.edu	37	1	92442695	92442695	+	Missense_Mutation	SNP	A	A	C	rs1156281	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	102	50	124	0	0.490196	0	A|0.865;C|0.135	0.135	strong	.	BRDT	133	.	NM_001242806	exon6	c.A726C	p.K242N	AGAAAAATCAGTG	.	PASS	Atlas-SNP
PCDHB3	56132	hgsc.bcm.edu	37	5	140480852	140480852	+	Missense_Mutation	SNP	G	G	A	rs12515688	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	61	25	78	0	0.409836	0	G|0.822;A|0.178	0.178	strong	.	PCDHB3	208	.	NM_018937	exon1	c.G619A	p.E207K	CAGCCGGAACTCA	.	PASS	Atlas-SNP
CCL14	6358	hgsc.bcm.edu	37	17	34313674	34313674	+	Silent	SNP	G	G	A	rs113937434	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	119	61	107	0	0.512605	0	G|0.977;A|0.023	0.023	strong	.	CCL14	22	.	NM_032962	exon1	c.C12T	p.S4S	AGCCACGGAGATC	.	PASS	Atlas-SNP
BCOR	54880	hgsc.bcm.edu	37	X	39932949	39932949	+	Silent	SNP	G	G	A	rs17145653	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	74	73	119	1	0.986486	0.00840336	0|0.004;A|0.006	0.006	strong	.	BCOR	351	.	NM_001123385	exon4	c.C1650T	p.T550T	AGCATCGGTGCCG	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	138	31	143	0	0.224638	0	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	.	PASS	Atlas-SNP
GPR113	165082	hgsc.bcm.edu	37	2	26536694	26536694	+	Missense_Mutation	SNP	C	C	T	rs2052937	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	152	150	139	0	0.986842	0	C|0.313;T|0.687	0.687	strong	.	GPR113	134	.	NM_001145168	exon8	c.G1210A	p.A404T	CACAAGCGTACGT	.	PASS	Atlas-SNP
TXNDC2	84203	hgsc.bcm.edu	37	18	9887857	9887857	+	Missense_Mutation	SNP	G	G	A	rs17732496	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	112	55	136	0	0.491071	0	G|0.887;A|0.113	0.113	strong	.	TXNDC2	168	.	NM_001098529	exon2	c.G1381A	p.A461T	TTTGAGGCATCAC	.	PASS	Atlas-SNP
CHAT	1103	hgsc.bcm.edu	37	10	50824619	50824619	+	Missense_Mutation	SNP	G	G	A	rs3810950	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	46	22	63	0	0.478261	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
FHAD1	114827	hgsc.bcm.edu	37	1	15723843	15723843	+	Silent	SNP	G	G	A	rs2294490	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	74	74	98	0	1	0	G|0.663;A|0.337	0.337	strong	.	FHAD1	78	.	NM_052929	exon31	c.G4173A	p.L1391L	GATGCTGAGGAAA	.	PASS	Atlas-SNP
ACAN	176	hgsc.bcm.edu	37	15	89415247	89415247	+	Missense_Mutation	SNP	C	C	G	rs3817428	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	140	76	122	1	0.542857	0.00819672	C|0.854;G|0.146	0.146	strong	ACAN,NS,carcinoma,0,1	ACAN	220	1	NM_013227	exon15	c.C7119G	p.D2373E	CCAAGACTACCAG	.	scavenged	Atlas-SNP
RNF213	57674	hgsc.bcm.edu	37	17	78261730	78261730	+	Silent	SNP	G	G	A	rs17853714	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	105	63	109	0	0.6	0	G|0.861;A|0.139	0.139	strong	.	RNF213	766	.	NM_001256071	exon4	c.G378A	p.P126P	AAACCCGTGGCCT	.	PASS	Atlas-SNP
GPR114	221188	hgsc.bcm.edu	37	16	57601792	57601792	+	Silent	SNP	C	C	T	rs9937918	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	51	59	0	0.68	0	C|0.625;T|0.375	0.375	strong	.	GPR114	52	.	NM_153837	exon9	c.C846T	p.R282R	AACACGCATCCAC	.	PASS	Atlas-SNP
THBS1	7057	hgsc.bcm.edu	37	15	39880358	39880358	+	Silent	SNP	C	C	T	rs2228261	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	103	59	118	0	0.572816	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
ARSD	414	hgsc.bcm.edu	37	X	2836084	2836084	+	Silent	SNP	C	C	G	rs73632973	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	84	10	91	0	0.119048	0	C|0.928;G|0.072	0.072	strong	.	ARSD	47	.	NM_001669	exon5	c.G624C	p.A208A	CCCCAGCGCCAGG	.	PASS	Atlas-SNP
PTPRG	5793	hgsc.bcm.edu	37	3	62278938	62278938	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	196	2	218	0	0.0102041	0	.	.	none	PTPRG,NS,carcinoma,-1,1	PTPRG	153	1	NM_002841	exon30	c.G4294A	p.A1432T	CTTATTGCAGATG	.	scavenged	Atlas-SNP
ITGB1	3688	hgsc.bcm.edu	37	10	33214802	33214802	+	Silent	SNP	A	A	G	rs2298141	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	80	39	107	0	0.4875	0	A|0.852;G|0.148	0.148	strong	.	ITGB1	156	.	NM_002211	exon6	c.T783C	p.C261C	TACTCCACAAACT	.	PASS	Atlas-SNP
TRAIP	10293	hgsc.bcm.edu	37	3	49866584	49866584	+	Silent	SNP	T	T	G	rs35129566	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	121	69	155	0	0.570248	0	T|0.809;G|0.191	0.191	strong	.	TRAIP	47	.	NM_005879	exon15	c.A1362C	p.T454T	AGGCACTGTCTTC	.	PASS	Atlas-SNP
C10orf10	11067	hgsc.bcm.edu	37	10	45473317	45473317	+	Silent	SNP	C	C	T	rs3740094	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	43	24	50	0	0.55814	0	C|0.872;T|0.128	0.128	strong	.	C10orf10	6	.	NM_007021	exon2	c.G162A	p.L54L	CTTGTCCAGCACA	.	PASS	Atlas-SNP
LRPPRC	10128	hgsc.bcm.edu	37	2	44201376	44201376	+	Silent	SNP	T	T	C	rs4953042	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	708	549	396	2	0.775424	0.00505051	T|0.840;C|0.160	0.160	strong	.	LRPPRC	105	.	NM_133259	exon9	c.A1068G	p.Q356Q	TAAAATTTGCAAC	.	PASS	Atlas-SNP
CCDC18	343099	hgsc.bcm.edu	37	1	93676478	93676478	+	Missense_Mutation	SNP	A	A	C	rs76148185	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	153	80	176	0	0.522876	0	A|0.982;C|0.018	0.018	strong	.	CCDC18	93	.	NM_206886	exon10	c.A1329C	p.E443D	TTCGGAATTGAGG	.	PASS	Atlas-SNP
PCYOX1L	78991	hgsc.bcm.edu	37	5	148747902	148747902	+	Missense_Mutation	SNP	G	G	C	rs4705336	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	141	70	163	1	0.496454	0.00613497	G|0.877;C|0.123	0.123	strong	PCYOX1L,NS,carcinoma,0,1	PCYOX1L	32	1	NM_024028	exon6	c.G1170C	p.E390D	CCAGGAGGCAGCT	.	scavenged	Atlas-SNP
KRTAP4-6	81871	hgsc.bcm.edu	37	17	39296412	39296412	+	Missense_Mutation	SNP	T	T	A	rs200470462		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	59	8	64	1	0.135593	0.015625	.	.	weak	KRTAP4-6,NS,carcinoma,0,2	KRTAP4-6	46	2	NM_030976	exon1	c.A328T	p.S110C	AGATGCTGCAGCT	.	scavenged	Atlas-SNP
DHX33	56919	hgsc.bcm.edu	37	17	5356913	5356913	+	Silent	SNP	C	C	T	rs16954697	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	98	45	156	0	0.459184	0	C|0.819;N|0.001	.	strong	.	DHX33	41	.	NM_020162	exon8	c.G1383A	p.S461S	TGGCTTCGACATG	.	PASS	Atlas-SNP
TBC1D1	23216	hgsc.bcm.edu	37	4	38022219	38022219	+	Missense_Mutation	SNP	G	G	A	rs112261209	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	250	115	235	0	0.46	0	G|0.992;A|0.008	0.008	strong	.	TBC1D1	94	.	NM_015173	exon5	c.G980A	p.R327K	GCATCAGACACGT	.	PASS	Atlas-SNP
DCHS2	54798	hgsc.bcm.edu	37	4	155287535	155287535	+	Missense_Mutation	SNP	T	T	C	rs10017772	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	177	80	177	0	0.451977	0	C|0.446;N|0.000	0.446	strong	.	DCHS2	594	.	NM_001142552	exon3	c.A2303G	p.H768R	ACAGGATGATTAT	.	PASS	Atlas-SNP
ENG	2022	hgsc.bcm.edu	37	9	130616621	130616621	+	Missense_Mutation	SNP	G	G	A	rs35400405	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	117	61	102	0	0.521368	0	G|0.950;A|0.050	0.050	strong	.	ENG	44	.	NM_001114753	exon1	c.C14T	p.T5M	GGGAGCGTGCCGC	.	PASS	Atlas-SNP
NPC1L1	29881	hgsc.bcm.edu	37	7	44579180	44579180	+	Silent	SNP	G	G	C	rs2072183	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	73	128	0	0.722772	0	G|0.762;C|0.238;A|0.000	0.238	strong	.	NPC1L1	141	.	NM_001101648	exon2	c.C816G	p.L272L	GGAGTCGAGGGCC	.	PASS	Atlas-SNP
WWP2	11060	hgsc.bcm.edu	37	16	69967897	69967897	+	Silent	SNP	T	T	C	rs2270841	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	180	179	187	0	0.994444	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
ZFP64	55734	hgsc.bcm.edu	37	20	50769549	50769549	+	Silent	SNP	A	A	G	rs3746413	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	34	67	0	0.492754	0	A|0.821;G|0.179	0.179	strong	.	ZFP64	240	.	NM_018197	exon6	c.T1182C	p.H394H	GTCCCCATGGAAC	.	PASS	Atlas-SNP
MMS22L	253714	hgsc.bcm.edu	37	6	97613299	97613299	+	Missense_Mutation	SNP	G	G	A	rs10484830	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	30	110	0	0.384615	0	G|0.898;A|0.102	0.102	strong	.	MMS22L	102	.	NM_198468	exon21	c.C3044T	p.P1015L	GCATTCGGATTTT	.	PASS	Atlas-SNP
KIAA1683	80726	hgsc.bcm.edu	37	19	18375563	18375563	+	Silent	SNP	G	G	A	rs12608744	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	50	29	75	0	0.58	0	G|0.789;A|0.211	0.211	strong	.	KIAA1683	190	.	NM_001145304	exon3	c.C2787T	p.P929P	GCTCTGGGGCAGG	.	PASS	Atlas-SNP
CUTC	51076	hgsc.bcm.edu	37	10	101502968	101502968	+	Silent	SNP	A	A	G	rs3740076	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	255	114	321	0	0.447059	0	A|0.931;G|0.069	0.069	strong	.	CUTC	32	.	NM_015960	exon4	c.A252G	p.P84P	TCGGCCACGGGGA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195507077	195507077	+	Missense_Mutation	SNP	G	G	A	rs76343663	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	7	22	3	0.0853659	0.136364	G|0.991;A|0.009	0.009	strong	MUC4_ENST00000463781,NS,carcinoma,+1,1	MUC4	1505	1	NM_018406	exon2	c.C11374T	p.P3792S	GAAGAGGGGTGGT	.	scavenged	Atlas-SNP
OR51B4	79339	hgsc.bcm.edu	37	11	5322737	5322737	+	Missense_Mutation	SNP	A	A	G	rs10837771	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	213	156	216	1	0.732394	0.00462963	A|0.589;G|0.411	0.411	strong	.	OR51B4	64	.	NM_033179	exon1	c.T440C	p.M147T	CCTCTCATCAGTA	.	PASS	Atlas-SNP
LTBP1	4052	hgsc.bcm.edu	37	2	33623567	33623567	+	Silent	SNP	G	G	A	rs138835287	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	107	55	138	0	0.514019	0	G|0.999;A|0.001	0.001	strong	LTBP1_ENST00000407925,NS,carcinoma,0,3	LTBP1	317	3	NM_206943	exon34	c.G5121A	p.P1707P	CACTCCGTTGAAT	.	PASS	Atlas-SNP
DDX19A	55308	hgsc.bcm.edu	37	16	70395387	70395387	+	Silent	SNP	C	C	T	rs1134074	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	60	39	45	0	0.65	0	C|0.732;T|0.268	0.268	strong	.	DDX19A	39	.	NM_018332	exon5	c.C360T	p.N120N	AGAGAACGCATTA	.	PASS	Atlas-SNP
SPATA31E1	286234	hgsc.bcm.edu	37	9	90503451	90503451	+	Missense_Mutation	SNP	G	G	A	rs11142017	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	106	47	122	0	0.443396	0	G|0.532;A|0.468	0.468	strong	.	.	.	.	NM_178828	exon4	c.G4049A	p.R1350H	ACTTCCGCGCCCA	.	PASS	Atlas-SNP
NPC1L1	29881	hgsc.bcm.edu	37	7	44553238	44553238	+	Silent	SNP	A	A	G	rs217434	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	39	34	54	0	0.871795	0	A|0.838;G|0.162	0.162	strong	NPC1L1,right_lower_lobe,carcinoma,-2,1	NPC1L1	141	1	NM_013389	exon20	c.T3888C	p.V1296V	CGGGTTAACGTCA	.	PASS	Atlas-SNP
ELSPBP1	64100	hgsc.bcm.edu	37	19	48519205	48519205	+	Silent	SNP	C	C	T	rs34647554	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	77	41	98	0	0.532468	0	C|0.902;T|0.098	0.098	strong	.	ELSPBP1	29	.	NM_022142	exon4	c.C264T	p.C88C	CAGCTGCATCTCC	.	PASS	Atlas-SNP
PCNT	5116	hgsc.bcm.edu	37	21	47860110	47860110	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	35	12	29	0	0.342857	0	.	.	none	.	PCNT	283	.	NM_006031	exon42	c.G9388A	p.V3130I	AGCAATGTCAAGG	.	PASS	Atlas-SNP
CCDC66	285331	hgsc.bcm.edu	37	3	56628031	56628031	+	Missense_Mutation	SNP	G	G	A	rs7637449	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	120	120	165	0	1	0	G|0.660;A|0.340	0.340	strong	.	CCDC66	145	.	NM_001141947	exon10	c.G1379A	p.R460Q	ACAGACGACGACA	.	PASS	Atlas-SNP
MYO9B	4650	hgsc.bcm.edu	37	19	17305440	17305440	+	Silent	SNP	T	T	C	rs1064305	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	93	42	104	0	0.451613	0	T|0.392;C|0.608	0.608	strong	.	MYO9B	264	.	NM_001130065	exon22	c.T3204C	p.G1068G	AGCAGGTGCTGAG	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	153	153	283	0	1	0	A|0.517;0|0.025	.	strong	.	GPR112	459	.	NM_153834	exon6	c.A828G	p.I276M	ACCTATATTTGCA	.	PASS	Atlas-SNP
OR10AD1	121275	hgsc.bcm.edu	37	12	48597064	48597064	+	Silent	SNP	A	A	G	rs17224828	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	41	25	48	0	0.609756	0	A|0.939;G|0.061	0.061	strong	.	OR10AD1	24	.	NM_001004134	exon1	c.T12C	p.N4N	GCTGCCATTCCTT	.	PASS	Atlas-SNP
ENGASE	64772	hgsc.bcm.edu	37	17	77079576	77079576	+	Silent	SNP	A	A	G	rs61756761	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	120	59	131	1	0.491667	0.00763359	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	.	scavenged	Atlas-SNP
AMZ1	155185	hgsc.bcm.edu	37	7	2752456	2752456	+	Nonsense_Mutation	SNP	C	C	T	rs145687592	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	100	21	74	0	0.21	0	C|0.998;T|0.002	0.002	strong	.	AMZ1	41	.	NM_133463	exon7	c.C1441T	p.R481X	AGTGCCCGAAAAC	.	PASS	Atlas-SNP
CCL3	6348	hgsc.bcm.edu	37	17	34416537	34416537	+	Silent	SNP	G	G	A	rs1130371	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	321	166	288	0	0.517134	0	G|0.795;A|0.205	0.205	strong	.	CCL3	8	.	NM_002983	exon2	c.C180T	p.P60P	GACACCGGGCTTG	.	PASS	Atlas-SNP
MCPH1	79648	hgsc.bcm.edu	37	8	6478986	6478986	+	Silent	SNP	C	C	T	rs2912010	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	25	24	47	0	0.96	0	C|0.558;T|0.442	0.442	strong	.	MCPH1	65	.	NM_024596	exon13	c.C2226T	p.S742S	CCGAAGCGAGTGC	.	PASS	Atlas-SNP
NLRP5	126206	hgsc.bcm.edu	37	19	56569629	56569629	+	Missense_Mutation	SNP	C	C	G	rs12462795	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	153	74	195	0	0.48366	0	C|0.827;G|0.173	0.173	strong	.	NLRP5	217	.	NM_153447	exon14	c.C3323G	p.S1108C	TGACTTCTGATTG	.	PASS	Atlas-SNP
AGAP11	119385	hgsc.bcm.edu	37	10	88768657	88768657	+	Silent	SNP	C	C	T	rs1745901	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	335	142	397	1	0.423881	0.00251889	C|0.222;T|0.778	0.778	strong	.	.	.	.	NM_133447	exon12	c.C648T	p.D216D	TTCAGACATCGGG	.	PASS	Atlas-SNP
GSTP1	2950	hgsc.bcm.edu	37	11	67353970	67353970	+	Silent	SNP	T	T	C	rs4891	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	51	14	98	0	0.27451	0	T|0.688;C|0.312	0.312	strong	.	GSTP1	21	.	NM_000852	exon7	c.T555C	p.S185S	CCTCAGTGCCCGG	.	PASS	Atlas-SNP
OR10AD1	121275	hgsc.bcm.edu	37	12	48596579	48596579	+	Missense_Mutation	SNP	C	C	T	rs17224674	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	139	55	138	0	0.395683	0	C|0.954;T|0.046	0.046	strong	.	OR10AD1	24	.	NM_001004134	exon1	c.G497A	p.R166Q	GGCTCTCGGAATG	.	PASS	Atlas-SNP
MYH11	4629	hgsc.bcm.edu	37	16	15839034	15839034	+	Silent	SNP	G	G	A	rs1050113	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	60	12	55	0	0.2	0	T|0.000;G|0.726;C|0.000;A|0.274	0.274	strong	MYH11_ENST00000396324,NS,carcinoma,-2,4	MYH11	520	4	NM_001040114	exon21	c.C2493T	p.A831A	GTAGGCGGCGCAG	.	PASS	Atlas-SNP
PPP6R2	9701	hgsc.bcm.edu	37	22	50877166	50877166	+	Silent	SNP	G	G	C	rs4824131	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	56	30	64	0	0.535714	0	G|0.367;C|0.633	0.633	strong	.	PPP6R2	71	.	NM_001242898	exon19	c.G2103C	p.A701A	GGAAGCGCCCCCT	.	PASS	Atlas-SNP
AMPD1	270	hgsc.bcm.edu	37	1	115221116	115221116	+	Missense_Mutation	SNP	C	C	A	rs61752478	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	77	40	127	0	0.519481	0	C|0.997;A|0.003	0.003	strong	.	AMPD1	223	.	NM_000036	exon8	c.G1029T	p.M343I	CTGGTTCATGCAA	.	PASS	Atlas-SNP
PDCD6IP	10015	hgsc.bcm.edu	37	3	33893987	33893987	+	Missense_Mutation	SNP	A	A	G	rs9813017	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	176	79	190	0	0.448864	0	A|0.901;G|0.099	0.099	strong	.	PDCD6IP	62	.	NM_001162429	exon13	c.A1664G	p.N555S	TTGTAAATGTCTT	.	PASS	Atlas-SNP
IZUMO1	284359	hgsc.bcm.edu	37	19	49244219	49244219	+	Silent	SNP	C	C	A	rs2307018	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	104	54	126	0	0.519231	0	C|0.585;A|0.415	0.415	strong	.	IZUMO1	30	.	NM_182575	exon10	c.G999T	p.A333A	CTCGGCCGCTCCA	.	PASS	Atlas-SNP
ITPRIPL1	150771	hgsc.bcm.edu	37	2	96993757	96993757	+	Missense_Mutation	SNP	C	C	T	rs2279105	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	116	50	148	0	0.431034	0	C|0.705;T|0.295	0.295	strong	.	ITPRIPL1	58	.	NM_178495	exon1	c.C1412T	p.T471M	CCCTCACGGACTG	.	PASS	Atlas-SNP
SUN1	23353	hgsc.bcm.edu	37	7	883105	883105	+	Silent	SNP	C	C	T	rs113652875	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	23	88	0	0.328571	0	C|0.969;T|0.031	0.031	strong	.	SUN1	157	.	NM_001171945	exon7	c.C669T	p.P223P	GCACCCCGCGGCC	.	PASS	Atlas-SNP
ZSCAN9	7746	hgsc.bcm.edu	37	6	28195521	28195521	+	Silent	SNP	A	A	G	rs12197427	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	160	77	200	0	0.48125	0	A|0.971;G|0.029	0.029	strong	ZNF193,NS,carcinoma,+2,1	.	.	1	NM_006299	exon3	c.A474G	p.L158L	GCCTCTAGCAGAG	.	PASS	Atlas-SNP
UGT2A1	10941	hgsc.bcm.edu	37	4	70455231	70455231	+	Silent	SNP	G	G	A	rs41292305	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	131	46	143	0	0.351145	0	G|0.973;A|0.027	0.027	strong	UGT2A1_ENST00000457664,colon,carcinoma,-1,2	UGT2A1	131	2	NM_001252274	exon7	c.C1941T	p.L647L	CCAGGTGAGGTCA	.	PASS	Atlas-SNP
MYH10	4628	hgsc.bcm.edu	37	17	8416901	8416901	+	Silent	SNP	C	C	T	rs11374	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	39	75	0	0.557143	0	A|0.000;C|0.606;G|0.000;T|0.394	0.394	strong	MYH10,NS,carcinoma,0,1	MYH10	148	1	NM_001256012	exon23	c.G2700A	p.T900T	CACCTTCGTCTGC	.	PASS	Atlas-SNP
C6orf223	221416	hgsc.bcm.edu	37	6	43970827	43970827	+	Silent	SNP	G	G	A	rs2295334	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	102	49	82	0	0.480392	0	G|0.927;A|0.073	0.073	strong	.	C6orf223	14	.	NM_153246	exon4	c.G693A	p.A231A	ATCCGCGGCGCTC	.	PASS	Atlas-SNP
SLC45A1	50651	hgsc.bcm.edu	37	1	8390888	8390888	+	Silent	SNP	G	G	A	rs2289731	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	61	31	55	0	0.508197	0	G|0.636;A|0.364	0.364	strong	SLC45A1,NS,carcinoma,0,2	SLC45A1	85	2	NM_001080397	exon4	c.G1335A	p.P445P	TAAGCCGAGGTCA	.	PASS	Atlas-SNP
C1QTNF1	114897	hgsc.bcm.edu	37	17	77040185	77040185	+	Silent	SNP	G	G	C	rs4789853	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	29	17	46	0	0.586207	0	G|0.616;C|0.384	0.384	strong	.	C1QTNF1	62	.	NM_030968	exon2	c.G135C	p.S45S	GCCGTCGCCTCCG	.	PASS	Atlas-SNP
ACOT11	26027	hgsc.bcm.edu	37	1	55060251	55060251	+	Missense_Mutation	SNP	C	C	T	rs2304306	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	135	56	148	0	0.414815	0	C|0.950;T|0.050	0.050	strong	.	ACOT11	105	.	NM_147161	exon6	c.C494T	p.P165L	TCACGCCGCGGAC	.	PASS	Atlas-SNP
FCGR3A	2214	hgsc.bcm.edu	37	1	161518286	161518286	+	Missense_Mutation	SNP	C	C	T	rs428888	bycluster;byfrequency;by2hit2allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	428	83	714	0	0.193925	0	C|0.667;T|0.333	0.333	strong	FCGR3A,colon,carcinoma,+2,1	FCGR3A	38	1	NM_000569	exon3	c.G352A	p.D118N	TGTCGTCGACTGT	.	scavenged	Atlas-SNP
PCDHB8	56128	hgsc.bcm.edu	37	5	140559849	140559849	+	Missense_Mutation	SNP	G	G	A	rs17096961	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	98	59	101	0	0.602041	0	G|0.827;A|0.173	0.173	strong	.	PCDHB8	199	.	NM_019120	exon1	c.G2234A	p.S745N	CCGGGAGCCTGTC	.	PASS	Atlas-SNP
PLD1	5337	hgsc.bcm.edu	37	3	171404478	171404478	+	Missense_Mutation	SNP	C	C	A	rs2290480	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	186	71	202	0	0.38172	0	C|0.841;A|0.159	0.159	strong	PLD1,NS,carcinoma,0,2	PLD1	134	2	NM_002662	exon16	c.G1864T	p.A622S	TACCAGCATGAGG	.	PASS	Atlas-SNP
AZI1	22994	hgsc.bcm.edu	37	17	79170576	79170576	+	Silent	SNP	C	C	T	rs1542961	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	110	110	92	1	1	0.0108696	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	.	scavenged	Atlas-SNP
GPR75-ASB3	100302652	hgsc.bcm.edu	37	2	53955850	53955850	+	Silent	SNP	C	C	T	rs17521008	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	120	94	66	0	0.783333	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
GRIN3B	116444	hgsc.bcm.edu	37	19	1003172	1003172	+	Missense_Mutation	SNP	C	C	T	rs2240154	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	66	66	46	1	1	0.0217391	C|0.842;T|0.158	0.158	strong	GRIN3B,colon,carcinoma,-1,1	GRIN3B	46	1	NM_138690	exon2	c.C470T	p.T157M	TGGAGACGCTGCT	.	scavenged	Atlas-SNP
MAP1A	4130	hgsc.bcm.edu	37	15	43818115	43818115	+	Missense_Mutation	SNP	G	G	A	rs145659671	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	83	53	54	1	0.638554	0.0185185	G|0.992;A|0.008	0.008	strong	MAP1A,NS,carcinoma,0,1	MAP1A	189	1	NM_002373	exon4	c.G4444A	p.D1482N	CAAAAGGACAGGG	.	scavenged	Atlas-SNP
ACER3	55331	hgsc.bcm.edu	37	11	76637680	76637680	+	Silent	SNP	G	G	A	rs4479014	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	111	15	103	0	0.135135	0	G|0.422;A|0.578	0.578	strong	.	ACER3	19	.	NM_018367	exon2	c.G183A	p.K61K	GGAAAAGCGGTAC	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	94	55	108	0	0.585106	0	C|0.742;G|0.258	0.258	strong	.	FRMD4B	90	.	NM_015123	exon6	c.G519C	p.E173D	TTCGCTCTCTACT	.	PASS	Atlas-SNP
GRIN3A	116443	hgsc.bcm.edu	37	9	104449098	104449098	+	Missense_Mutation	SNP	C	C	T	rs10989591	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	36	95	0	0.507042	0	C|0.652;T|0.348	0.348	strong	.	GRIN3A	186	.	NM_133445	exon2	c.G1084A	p.V362M	CCTCCACATTCTG	.	PASS	Atlas-SNP
RNF139	11236	hgsc.bcm.edu	37	8	125498547	125498547	+	Silent	SNP	C	C	T	rs3812471	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	81	81	121	0	1	0	C|0.445;T|0.555	0.555	strong	.	RNF139	57	.	NM_007218	exon2	c.C657T	p.Y219Y	AATTTACGGATTA	.	PASS	Atlas-SNP
KRTAP4-8	728224	hgsc.bcm.edu	37	17	39253815	39253815	+	Silent	SNP	G	G	A	rs77163010	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	118	55	139	0	0.466102	0	G|0.983;A|0.017	0.017	strong	.	KRTAP4-8	57	.	NM_031960	exon1	c.C522T	p.C174C	GCGGGGGCAGGTG	.	PASS	Atlas-SNP
CPQ	10404	hgsc.bcm.edu	37	8	98041698	98041698	+	Silent	SNP	C	C	T	rs113729124	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	19	109	0	0.206522	0	C|0.993;G|0.000;T|0.007	0.007	strong	.	.	.	.	NM_016134	exon6	c.C1029T	p.A343A	TGGTGCCTTCCAG	.	PASS	Atlas-SNP
PABPC4L	132430	hgsc.bcm.edu	37	4	135121601	135121601	+	Missense_Mutation	SNP	C	C	T	rs10009368	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	156	154	181	0	0.987179	0	C|0.348;T|0.652	0.652	strong	.	PABPC4L	60	.	NM_001114734	exon2	c.G748A	p.V250I	TGTAAACATTGGT	.	PASS	Atlas-SNP
ZNF259	8882	hgsc.bcm.edu	37	11	116655600	116655600	+	Missense_Mutation	SNP	G	G	A	rs35120633	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	206	53	227	0	0.257282	0	G|0.948;A|0.052	0.052	strong	.	ZNF259	27	.	NM_003904	exon8	c.C791T	p.A264V	GCGGGGGCATTGC	.	PASS	Atlas-SNP
C9orf114	51490	hgsc.bcm.edu	37	9	131586374	131586374	+	Silent	SNP	G	G	A	rs7033070	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	81	47	78	0	0.580247	0	G|0.671;A|0.329	0.329	strong	C9orf114,NS,carcinoma,0,1	C9orf114	28	1	NM_016390	exon10	c.C891T	p.A297A	GGCAGAGGCCACA	.	PASS	Atlas-SNP
MAP1A	4130	hgsc.bcm.edu	37	15	43820423	43820423	+	Missense_Mutation	SNP	C	C	T	rs28438815	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	21	54	0	0.304348	0	C|0.977;T|0.023	0.023	strong	.	MAP1A	189	.	NM_002373	exon4	c.C6752T	p.A2251V	GACCTGCCTCACC	.	PASS	Atlas-SNP
PTGS1	5742	hgsc.bcm.edu	37	9	125154660	125154660	+	Missense_Mutation	SNP	C	C	T	rs200295924		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	230	57	272	0	0.247826	0	.	.	weak	.	PTGS1	84	.	NM_000962	exon11	c.C1637T	p.P546L	GGAAGCCGAGCAC	.	PASS	Atlas-SNP
CHFR	55743	hgsc.bcm.edu	37	12	133423662	133423662	+	Missense_Mutation	SNP	C	C	T	rs2306536	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	42	29	65	0	0.690476	0	C|0.795;T|0.205	0.205	strong	CHFR_ENST00000432561,colon,carcinoma,0,2	CHFR	83	2	NM_001161344	exon15	c.G1738A	p.V580M	GAGCCACGAGGCT	.	PASS	Atlas-SNP
ZNF682	91120	hgsc.bcm.edu	37	19	20117685	20117685	+	Missense_Mutation	SNP	G	G	A	rs2075090	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	35	16	51	0	0.457143	0	G|0.895;A|0.105	0.105	strong	.	ZNF682	51	.	NM_033196	exon4	c.C626T	p.T209I	TTAAAGGTTTTGC	.	PASS	Atlas-SNP
CHRD	8646	hgsc.bcm.edu	37	3	184099378	184099378	+	Silent	SNP	C	C	A	rs35929225	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	81	47	66	0	0.580247	0	C|0.808;A|0.192	0.192	strong	.	CHRD	149	.	NM_003741	exon4	c.C477A	p.G159G	GCCAGGCGCTGAG	.	PASS	Atlas-SNP
DCAF12	25853	hgsc.bcm.edu	37	9	34125258	34125258	+	Silent	SNP	C	C	G	rs61735450	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	65	32	74	0	0.492308	0	C|0.969;G|0.031	0.031	strong	.	DCAF12	37	.	NM_015397	exon2	c.G96C	p.S32S	GTGAAGCGAGTGA	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100681211	100681211	+	Missense_Mutation	SNP	G	G	C	rs147094151	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	36	68	0	0.521739	0	G|0.968;C|0.032	0.032	strong	.	MUC17	804	.	NM_001040105	exon3	c.G6514C	p.V2172L	ACCACAGTGGTGG	.	PASS	Atlas-SNP
CC2D1B	200014	hgsc.bcm.edu	37	1	52822722	52822722	+	Missense_Mutation	SNP	G	G	A	rs201266966	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	173	84	164	0	0.485549	0	G|0.997;A|0.003	0.003	weak	CC2D1B,NS,carcinoma,0,1	CC2D1B	73	1	NM_032449	exon16	c.C1847T	p.A616V	TCCTCCGCCTTCT	.	PASS	Atlas-SNP
IL11	3589	hgsc.bcm.edu	37	19	55879872	55879872	+	Silent	SNP	C	C	T	rs1126757	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	145	77	166	0	0.531034	0	C|0.636;T|0.364	0.364	strong	.	IL11	16	.	NM_000641	exon3	c.G246A	p.A82A	TGCCCCCGCACTC	.	PASS	Atlas-SNP
FAM129A	116496	hgsc.bcm.edu	37	1	184801065	184801065	+	Silent	SNP	T	T	C	rs487675	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	94	93	143	0	0.989362	0	T|0.682;C|0.318	0.318	strong	FAM129A,colon,carcinoma,0,1	FAM129A	98	1	NM_052966	exon6	c.A633G	p.Q211Q	AAAGGCTTGGGCT	.	PASS	Atlas-SNP
ZFHX4	79776	hgsc.bcm.edu	37	8	77765865	77765865	+	Silent	SNP	C	C	T	rs2728455	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	90	90	94	0	1	0	C|0.867;T|0.133	0.133	strong	.	ZFHX4	878	.	NM_024721	exon10	c.C6708T	p.Y2236Y	TGACTACCAGCTT	.	PASS	Atlas-SNP
NSUN2	54888	hgsc.bcm.edu	37	5	6600064	6600064	+	Missense_Mutation	SNP	G	G	T	rs61744358	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	41	25	62	0	0.609756	0	C|0.000;G|0.932;T|0.067	0.067	strong	NSUN2,colon,carcinoma,0,1	NSUN2	82	1	NM_017755	exon19	c.C2279A	p.P760Q	CCCGCCGGGTCAC	.	PASS	Atlas-SNP
PIAS4	51588	hgsc.bcm.edu	37	19	4037723	4037723	+	Silent	SNP	G	G	A	rs140558761	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	80	43	53	0	0.5375	0	G|0.998;A|0.002	0.002	strong	.	PIAS4	40	.	NM_015897	exon11	c.G1383A	p.P461P	GAAGCCGGGCGCC	.	PASS	Atlas-SNP
SLFN14	342618	hgsc.bcm.edu	37	17	33881631	33881631	+	Missense_Mutation	SNP	T	T	C	rs321612	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	107	56	140	0	0.523364	0	C|0.651;N|0.000	0.651	strong	.	SLFN14	43	.	NM_001129820	exon2	c.A1153G	p.K385E	TAAATTTGTGGAC	.	PASS	Atlas-SNP
NOS2	4843	hgsc.bcm.edu	37	17	26125743	26125743	+	Silent	SNP	G	G	A	rs3730014	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	118	67	157	0	0.567797	0	G|0.988;A|0.012	0.012	strong	.	NOS2	113	.	NM_000625	exon2	c.C93T	p.A31A	ACAGGGGGCTTTC	.	PASS	Atlas-SNP
PLCD1	5333	hgsc.bcm.edu	37	3	38051941	38051941	+	Silent	SNP	T	T	C	rs9857730	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	172	84	144	0	0.488372	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
METTL21B	25895	hgsc.bcm.edu	37	12	58174306	58174306	+	Silent	SNP	T	T	C	rs923829	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	60	29	55	0	0.483333	0	T|0.672;C|0.328	0.328	strong	.	METTL21B	16	.	NM_015433	exon3	c.T558C	p.H186H	GGAGCATGGGACA	.	PASS	Atlas-SNP
FTSJD1	55783	hgsc.bcm.edu	37	16	71319539	71319539	+	Silent	SNP	C	C	T	rs3826247	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	161	161	172	0	1	0	C|0.460;T|0.540	0.540	strong	.	FTSJD1	70	.	NM_018348	exon3	c.G285A	p.A95A	TTTCCCCGCTTTA	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105418170	105418170	+	Silent	SNP	G	G	C	rs200879546	byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	126	18	45	0	0.142857	0	G|0.993;C|0.007	0.007	strong	AHNAK2_ENST00000333244,NS,carcinoma,0,2	AHNAK2	719	2	NM_138420	exon7	c.C3618G	p.L1206L	GGTCTTGAGGTCC	.	scavenged	Atlas-SNP
CACNA1C	775	hgsc.bcm.edu	37	12	2791132	2791132	+	Missense_Mutation	SNP	A	A	G	rs10774053	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	41	41	48	0	1	0	A|0.230;G|0.770	0.770	strong	.	CACNA1C	1023	.	NM_199460	exon45	c.A5605G	p.M1869V	GTTCCGATGTGTG	.	PASS	Atlas-SNP
AP2B1	163	hgsc.bcm.edu	37	17	33998802	33998802	+	Silent	SNP	G	G	C	rs1049379	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	34	76	0	0.465753	0	G|0.518;C|0.482	0.482	strong	.	AP2B1	70	.	NM_001030006	exon16	c.G2061C	p.V687V	ATCGGTGCCTGCA	.	PASS	Atlas-SNP
APLF	200558	hgsc.bcm.edu	37	2	68753240	68753240	+	Missense_Mutation	SNP	T	T	A	rs35002937	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	135	79	174	1	0.585185	0.00574713	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
MUC5B	727897	hgsc.bcm.edu	37	11	1264772	1264772	+	Missense_Mutation	SNP	T	T	C	rs2943500	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	324	8	222	2	0.0246914	0.00900901	.	.	weak	MUC5B,NS,neuroblastoma,0,3	MUC5B	473	3	NM_002458	exon31	c.T6662C	p.I2221T	CGGGCATCTTGGG	.	scavenged	Atlas-SNP
DENND4A	10260	hgsc.bcm.edu	37	15	65994733	65994733	+	Silent	SNP	C	C	T	rs17810074	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	237	130	234	0	0.548523	0	C|0.761;T|0.239	0.239	strong	.	DENND4A	217	.	NM_001144823	exon17	c.G2340A	p.V780V	GACTTTCACATAA	.	PASS	Atlas-SNP
TBXAS1	6916	hgsc.bcm.edu	37	7	139706915	139706915	+	Missense_Mutation	SNP	G	G	A	rs3735354	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	184	88	194	0	0.478261	0	G|0.998;A|0.002	0.002	strong	.	TBXAS1	121	.	NM_001166253	exon11	c.G1300A	p.E434K	AGCCTCGAGGAAG	.	PASS	Atlas-SNP
SLC17A3	10786	hgsc.bcm.edu	37	6	25850845	25850845	+	Missense_Mutation	SNP	C	C	T	rs56027330	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	62	30	54	0	0.483871	0	C|0.910;T|0.090	0.090	strong	SLC17A3,NS,carcinoma,+1,1	SLC17A3	95	1	NM_001098486	exon8	c.G835A	p.G279R	AAGACCCGACCTG	.	PASS	Atlas-SNP
MYO9B	4650	hgsc.bcm.edu	37	19	17283657	17283657	+	Silent	SNP	C	C	T	rs2279006	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	47	16	34	0	0.340426	0	C|0.845;T|0.155	0.155	strong	.	MYO9B	264	.	NM_001130065	exon13	c.C2025T	p.I675I	GCTCATCGGCATG	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	112	47	132	0	0.419643	0	T|0.669;A|0.331	0.331	strong	.	CCDC109B	47	.	NM_017918	exon3	c.T188A	p.I63N	CAGTTATTTATAG	.	PASS	Atlas-SNP
NAT10	55226	hgsc.bcm.edu	37	11	34130342	34130342	+	Silent	SNP	A	A	G	rs11552143	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	162	125	191	0	0.771605	0	A|0.913;G|0.087	0.087	strong	.	NAT10	78	.	NM_024662	exon3	c.A162G	p.S54S	GCCTTCAGTGCTG	.	PASS	Atlas-SNP
KPRP	448834	hgsc.bcm.edu	37	1	152732567	152732567	+	Missense_Mutation	SNP	G	G	A	rs16834461	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	163	75	232	0	0.460123	0	G|0.798;A|0.202	0.202	strong	.	KPRP	152	.	NM_001025231	exon2	c.G503A	p.R168H	GAGGGCGTCCTGC	.	PASS	Atlas-SNP
SIRT3	23410	hgsc.bcm.edu	37	11	233212	233212	+	Silent	SNP	C	C	A	rs11555236	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	81	66	89	0	0.814815	0	C|0.849;A|0.151	0.151	strong	.	SIRT3	28	.	NM_012239	exon3	c.G477T	p.S159S	CCCCGGCGATCTG	.	PASS	Atlas-SNP
LILRB3	11025	hgsc.bcm.edu	37	19	54724457	54724457	+	Missense_Mutation	SNP	T	T	C	rs1052995	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	57	31	151	0	0.54386	0	T|1.000;|0.000	.	strong	.	LILRB3	67	.	NM_006864	exon6	c.A1199G	p.Y400C	GAGCTGTATGAGC	.	PASS	Atlas-SNP
CCDC110	256309	hgsc.bcm.edu	37	4	186381165	186381165	+	Silent	SNP	G	G	A	rs7699724	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	135	50	162	0	0.37037	0	G|0.547;A|0.453	0.453	strong	.	CCDC110	78	.	NM_152775	exon6	c.C576T	p.D192D	CAAGATGTCAGAA	.	PASS	Atlas-SNP
DHX38	9785	hgsc.bcm.edu	37	16	72130815	72130815	+	Silent	SNP	C	C	A	rs1050362	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	113	36	91	0	0.318584	0	C|0.529;A|0.471	0.471	strong	DHX38,right_upper_lobe,carcinoma,-2,2	DHX38	91	2	NM_014003	exon3	c.C418A	p.R140R	GAGCGGCGGGAAC	.	PASS	Atlas-SNP
NUP210L	91181	hgsc.bcm.edu	37	1	153982536	153982536	+	Missense_Mutation	SNP	C	C	T	rs199611847	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	67	29	58	0	0.432836	0	.	.	weak	.	NUP210L	181	.	NM_001159484	exon35	c.G4842A	p.M1614I	GCACAGCATGAGG	.	PASS	Atlas-SNP
ANKMY1	51281	hgsc.bcm.edu	37	2	241463639	241463639	+	Missense_Mutation	SNP	C	C	T	rs3796119	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	80	33	102	1	0.4125	0.00980392	C|0.990;T|0.010	0.010	strong	ANKMY1_ENST00000361678,NS,carcinoma,+2,2	ANKMY1	112	2	NM_016552	exon7	c.G1228A	p.E410K	CGCCCTCGTGGCT	.	scavenged	Atlas-SNP
UGT2B11	10720	hgsc.bcm.edu	37	4	70080139	70080139	+	Missense_Mutation	SNP	C	C	T	rs7688262	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	393	157	557	1	0.399491	0.00179533	C|0.886;T|0.114	0.114	strong	UGT2B11,NS,carcinoma,-1,2	UGT2B11	92	2	NM_001073	exon1	c.G302A	p.R101Q	TCTTTTCGAATGT	.	PASS	Atlas-SNP
ZNF91	7644	hgsc.bcm.edu	37	19	23543834	23543834	+	Silent	SNP	C	C	T	rs7255296	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	49	18	53	0	0.367347	0	C|0.854;T|0.146	0.146	strong	.	ZNF91	349	.	NM_003430	exon4	c.G1947A	p.K649K	AATTCTCTTATGT	.	PASS	Atlas-SNP
KIFC1	3833	hgsc.bcm.edu	37	6	33374015	33374015	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	120	52	119	0	0.433333	0	.	.	none	.	KIFC1	47	.	NM_002263	exon8	c.G1579A	p.A527T	GCTGTGGCCCGCA	.	PASS	Atlas-SNP
GIMAP8	155038	hgsc.bcm.edu	37	7	150164155	150164155	+	Silent	SNP	T	T	C	rs61748320	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	138	54	169	0	0.391304	0	T|0.985;C|0.015	0.015	strong	.	GIMAP8	136	.	NM_175571	exon2	c.T369C	p.A123A	TGGAGCTGAAGCC	.	PASS	Atlas-SNP
WBSCR28	135886	hgsc.bcm.edu	37	7	73279413	73279413	+	Missense_Mutation	SNP	C	C	T	rs118088869	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	107	65	126	0	0.607477	0	C|0.983;T|0.017	0.017	strong	.	WBSCR28	24	.	NM_182504	exon2	c.C163T	p.R55W	GAGGCCCGGGGGT	.	PASS	Atlas-SNP
SLC22A24	283238	hgsc.bcm.edu	37	11	62848445	62848445	+	Silent	SNP	A	A	G	rs11231340	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	129	33	132	1	0.255814	0.00757576	A|0.539;G|0.460	0.460	strong	SLC22A24_ENST00000417740,NS,carcinoma,0,1	SLC22A24	31	1	NM_001136506	exon9	c.T1545C	p.L515L	TTCTGGAAGGAGG	.	scavenged	Atlas-SNP
BPIFB4	149954	hgsc.bcm.edu	37	20	31678534	31678534	+	Silent	SNP	T	T	C	rs2070326	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	121	50	119	0	0.413223	0	T|0.784;C|0.216	0.216	strong	.	.	.	.	NM_182519	exon8	c.T1072C	p.L358L	GGGATATTGGGAA	.	PASS	Atlas-SNP
MEPE	56955	hgsc.bcm.edu	37	4	88766969	88766969	+	Missense_Mutation	SNP	A	A	G	rs61731014	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	33	13	50	0	0.393939	0	A|0.983;G|0.017	0.017	strong	.	MEPE	86	.	NM_020203	exon4	c.A949G	p.I317V	AATACCATTGGAA	.	PASS	Atlas-SNP
FASN	2194	hgsc.bcm.edu	37	17	80045086	80045086	+	Silent	SNP	G	G	C	rs4485435	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	83	40	91	0	0.481928	0	G|0.762;C|0.238	0.238	strong	.	FASN	154	.	NM_004104	exon21	c.C3267G	p.A1089A	GCCTCCGGCCACT	.	PASS	Atlas-SNP
STOX2	56977	hgsc.bcm.edu	37	4	184931818	184931818	+	Silent	SNP	G	G	A	rs4861597	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	228	120	208	0	0.526316	0	G|0.583;A|0.417	0.417	strong	.	STOX2	142	.	NM_020225	exon3	c.G1827A	p.T609T	TGAGACGGTGCTC	.	PASS	Atlas-SNP
NAV2	89797	hgsc.bcm.edu	37	11	19970501	19970501	+	Silent	SNP	T	T	C	rs11025335	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	109	21	135	0	0.192661	0	T|0.792;C|0.208	0.208	strong	.	NAV2	255	.	NM_001244963	exon11	c.T2589C	p.H863H	CTGCCATGTGGAC	.	PASS	Atlas-SNP
MUC6	4588	hgsc.bcm.edu	37	11	1016849	1016849	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	1074	35	758	23	0.0325885	0.030343	.	.	none	MUC6_ENST00000421673,NS,carcinoma,0,2	MUC6	408	2	NM_005961	exon31	c.G5952C	p.M1984I	TGCAGTCATAGGA	.	scavenged	Atlas-SNP
P2RY8	286530	hgsc.bcm.edu	37	X	1584817	1584817	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	68	27	84	0	0.397059	0	.	.	none	.	P2RY8	53	.	NM_178129	exon2	c.G635A	p.C212Y	GTGTAACAAGCCA	.	PASS	Atlas-SNP
OR5D16	390144	hgsc.bcm.edu	37	11	55606818	55606818	+	Silent	SNP	C	C	T	rs11231253	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	219	43	254	0	0.196347	0	C|0.619;T|0.381	0.381	strong	OR5D16,NS,adenoma,0,1	OR5D16	94	1	NM_001005496	exon1	c.C591T	p.S197S	TCTCAGCCAGTTG	.	PASS	Atlas-SNP
HDLBP	3069	hgsc.bcm.edu	37	2	242179134	242179134	+	Silent	SNP	G	G	A	rs10153800	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	42	105	0	0.456522	0	G|0.800;A|0.200	0.200	strong	.	HDLBP	118	.	NM_005336	exon19	c.C2493T	p.G831G	CACCCCGCCATAC	.	PASS	Atlas-SNP
SYT16	83851	hgsc.bcm.edu	37	14	62463214	62463214	+	Silent	SNP	C	C	T	rs1889806	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	41	66	0	0.5	0	C|0.433;T|0.567	0.567	strong	SYT16,NS,carcinoma,+2,1	SYT16	144	1	NM_031914	exon1	c.C477T	p.D159D	CTTTGACAGCCAG	.	PASS	Atlas-SNP
BRCA2	675	hgsc.bcm.edu	37	13	32911888	32911888	+	Silent	SNP	A	A	G	rs1801406	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	63	63	92	0	1	0	A|0.722;G|0.278	0.278	strong	.	BRCA2	812	.	NM_000059	exon11	c.A3396G	p.K1132K	TAGAAAACCAAGC	.	PASS	Atlas-SNP
SCIN	85477	hgsc.bcm.edu	37	7	12610451	12610451	+	Silent	SNP	G	G	A	rs76096341	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	112	30	149	0	0.267857	0	G|0.970;A|0.030	0.030	strong	.	SCIN	105	.	NM_001112706	exon1	c.G39A	p.A13A	CCGGGCGGGCAAG	.	PASS	Atlas-SNP
AP3B1	8546	hgsc.bcm.edu	37	5	77473165	77473165	+	Silent	SNP	A	A	G	rs4532349	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	149	103	116	0	0.691275	0	A|0.832;G|0.168	0.168	strong	AP3B1,colon,carcinoma,0,1	AP3B1	94	1	NM_003664	exon9	c.T1038C	p.N346N	CTACCTATTGCTA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195509879	195509879	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	131	13	122	0	0.0992366	0	.	.	none	MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	NM_018406	exon2	c.T8572C	p.S2858P	CTGTGGACACTGA	.	PASS	Atlas-SNP
FUNDC1	139341	hgsc.bcm.edu	37	X	44401295	44401295	+	Silent	SNP	T	T	G	rs41298452	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	207	205	309	2	0.990338	0.00647249	T|0.917;G|0.083	0.083	strong	.	FUNDC1	15	.	NM_173794	exon2	c.A81C	p.A27A	TCTTCTTGCATAC	.	PASS	Atlas-SNP
STPG2	285555	hgsc.bcm.edu	37	4	98893476	98893476	+	Silent	SNP	C	C	T	rs783959	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	198	196	261	2	0.989899	0.00766284	C|0.581;T|0.419	0.419	strong	C4orf37,NS,carcinoma,0,2	.	.	2	NM_174952	exon7	c.G888A	p.S296S	CTGAACCGAGAAG	.	scavenged	Atlas-SNP
BCL2L14	79370	hgsc.bcm.edu	37	12	12247616	12247616	+	Silent	SNP	T	T	C	rs11054683	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	195	77	246	0	0.394872	0	T|0.781;C|0.219	0.219	strong	.	BCL2L14	47	.	NM_138723	exon5	c.T697C	p.L233L	AAGGCTTTGATGG	.	PASS	Atlas-SNP
SLC7A10	56301	hgsc.bcm.edu	37	19	33700281	33700281	+	Silent	SNP	C	C	A	rs2303094	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	39	74	0	0.565217	0	C|0.956;A|0.044	0.044	strong	SLC7A10,NS,carcinoma,0,1	SLC7A10	43	1	NM_019849	exon10	c.G1374T	p.T458T	CACCCCCGTAAGG	.	PASS	Atlas-SNP
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057958	46057958	+	Silent	SNP	C	C	T	rs4818951	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	195	192	194	0	0.984615	0	C|0.368;T|0.632	0.632	strong	.	KRTAP10-10	37	.	NM_181688	exon1	c.C624T	p.S208S	CCCCTCCTGCGGT	.	PASS	Atlas-SNP
OR10C1	442194	hgsc.bcm.edu	37	6	29408528	29408528	+	Missense_Mutation	SNP	A	A	G	rs2074464	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	155	68	176	0	0.43871	0	T|0.005;G|0.594;A|0.401	0.594	strong	.	OR10C1	58	.	NM_013941	exon1	c.A736G	p.M246V	CTGATCATGGTCT	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	155	86	154	0	0.554839	0	A|0.864;T|0.136	0.136	strong	.	DSG1	176	.	NM_001942	exon15	c.A2522T	p.Y841F	AGTCTTACACCAC	.	PASS	Atlas-SNP
CHGA	1113	hgsc.bcm.edu	37	14	93398849	93398849	+	Missense_Mutation	SNP	G	G	A	rs9658664	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	45	20	60	0	0.444444	0	G|0.992;A|0.008	0.008	strong	.	CHGA	32	.	NM_001275	exon7	c.G943A	p.G315S	CCGCAAGGCCTCT	.	PASS	Atlas-SNP
ROCK2	9475	hgsc.bcm.edu	37	2	11359120	11359120	+	Missense_Mutation	SNP	G	G	T	rs2230774	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	301	119	296	1	0.395349	0.00337838	T|0.320;G|0.373;C|0.181;N|0.000;A|0.127	0.320	strong	ROCK2_ENST00000315872,NS,carcinoma,0,1	ROCK2	224	1	NM_004850	exon10	c.C1292A	p.T431N	GAATCAGTTTCTC	.	PASS	Atlas-SNP
BTBD16	118663	hgsc.bcm.edu	37	10	124096041	124096041	+	Silent	SNP	T	T	C	rs1129973	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	74	30	120	1	0.405405	0.00833333	T|0.621;C|0.379	0.379	strong	BTBD16,NS,lymphoid_neoplasm,0,1	BTBD16	44	1	NM_144587	exon15	c.T1296C	p.S432S	TCCCTCTGCGGTC	.	scavenged	Atlas-SNP
CEP192	55125	hgsc.bcm.edu	37	18	13068132	13068132	+	Missense_Mutation	SNP	T	T	C	rs578208	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	53	29	74	0	0.54717	0	A|0.001;C|0.718	0.718	strong	.	CEP192	340	.	NM_032142	exon23	c.T4654C	p.S1552P	AAGGAATCCGTCC	.	PASS	Atlas-SNP
SLC9C1	285335	hgsc.bcm.edu	37	3	111981849	111981849	+	Silent	SNP	C	C	T	rs9860819	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	269	269	354	0	1	0	C|0.400;T|0.600	0.600	strong	.	.	.	.	NM_183061	exon10	c.G1119A	p.K373K	CATCCCCTTCATT	.	PASS	Atlas-SNP
LILRA6	79168	hgsc.bcm.edu	37	19	54746380	54746380	+	Missense_Mutation	SNP	C	C	T	rs150628522	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	199	62	274	0	0.311558	0	C|0.795;T|0.205	0.205	strong	LILRA6,NS,carcinoma,0,2	LILRA6	75	2	NM_024318	exon2	c.G61A	p.V21M	CCTGCACGCGGGT	.	scavenged	Atlas-SNP
LAMA1	284217	hgsc.bcm.edu	37	18	7049171	7049171	+	Missense_Mutation	SNP	C	C	T	rs140718292	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	104	50	109	1	0.480769	0.00917431	C|0.993;T|0.007	0.007	strong	LAMA1,scalp,carcinoma,-1,1	LAMA1	458	1	NM_005559	exon5	c.G674A	p.R225H	CGAAGGCGAATAT	.	scavenged	Atlas-SNP
OR10H2	26538	hgsc.bcm.edu	37	19	15838972	15838972	+	Missense_Mutation	SNP	T	T	A	rs61733719	byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	203	83	140	1	0.408867	0.00714286	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	.	scavenged	Atlas-SNP
XPC	7508	hgsc.bcm.edu	37	3	14199887	14199887	+	Missense_Mutation	SNP	G	G	A	rs2228000	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	53	26	69	0	0.490566	0	G|0.772;A|0.228	0.228	strong	XPC,caecum,carcinoma,+1,1	XPC	60	1	NM_004628	exon9	c.C1496T	p.A499V	GATGCCGCTGGCA	.	PASS	Atlas-SNP
OR52E2	119678	hgsc.bcm.edu	37	11	5080234	5080234	+	Silent	SNP	T	T	C	rs2445333	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	74	126	0	0.762887	0	T|0.698;C|0.302	0.302	strong	.	OR52E2	63	.	NM_001005164	exon1	c.A624G	p.L208L	AAACACTAGATTA	.	PASS	Atlas-SNP
CAMKV	79012	hgsc.bcm.edu	37	3	49898273	49898273	+	Silent	SNP	A	A	G	rs2681781	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	98	66	145	0	0.673469	0	A|0.515;G|0.485	0.485	strong	.	CAMKV	84	.	NM_024046	exon8	c.T651C	p.N217N	AGGTGGATTGCCT	.	PASS	Atlas-SNP
TUBG1	7283	hgsc.bcm.edu	37	17	40766546	40766546	+	Silent	SNP	C	C	G	rs80029012	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	184	69	246	0	0.375	0	G|1.000;|0.000	1.000	weak	.	TUBG1	25	.	NM_001070	exon10	c.C1029G	p.R343R	GGAACGCAAGTTG	.	PASS	Atlas-SNP
ADI1	55256	hgsc.bcm.edu	37	2	3504687	3504687	+	Silent	SNP	A	A	G	rs9950	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	198	198	152	1	1	0.00657895	A|0.473;G|0.527	0.527	strong	ADI1,NS,carcinoma,0,1	ADI1	12	1	NM_018269	exon3	c.T318C	p.D106D	CCTCACATCGAAG	.	PASS	Atlas-SNP
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32497900	32497900	+	Splice_Site	SNP	A	A	G	rs78612727	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	14	123	0	0.162791	0	A|0.994;G|0.006	0.006	strong	.	HLA-DRB5	31	.	NM_002125	exon2	c.100+2T>C	.	GCACTTACGTCGG	.	PASS	Atlas-SNP
PYGB	5834	hgsc.bcm.edu	37	20	25259006	25259006	+	Missense_Mutation	SNP	G	G	T	rs2228976	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	107	52	104	0	0.485981	0	G|0.833;T|0.167	0.167	strong	PYGB,NS,carcinoma,0,2	PYGB	84	2	NM_002862	exon8	c.G907T	p.A303S	GTGGCCGCCACGC	.	PASS	Atlas-SNP
KIAA0368	23392	hgsc.bcm.edu	37	9	114174384	114174384	+	Silent	SNP	C	C	T	rs16916079	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	67	29	92	0	0.432836	0	C|0.943;T|0.057	0.057	strong	KIAA0368,NS,carcinoma,0,1	KIAA0368	144	1	NM_001080398	exon22	c.G2658A	p.A886A	AAACAACGCTGCC	.	PASS	Atlas-SNP
ANKRD22	118932	hgsc.bcm.edu	37	10	90585819	90585819	+	Silent	SNP	G	G	A	rs7893917	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	35	52	0	0.5	0	G|0.659;A|0.341	0.341	strong	.	ANKRD22	23	.	NM_144590	exon4	c.C375T	p.G125G	TTCGACGCCAGCA	.	PASS	Atlas-SNP
PRKD1	5587	hgsc.bcm.edu	37	14	30046511	30046511	+	Missense_Mutation	SNP	T	T	C	rs45582934	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	255	108	306	1	0.423529	0.00326797	T|0.992;C|0.008	0.008	strong	.	PRKD1	316	.	NM_002742	exon18	c.A2672G	p.H891R	TCACTGTGGCTAG	.	PASS	Atlas-SNP
PKHD1L1	93035	hgsc.bcm.edu	37	8	110420384	110420384	+	Silent	SNP	T	T	C	rs13254245	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	90	66	139	0	0.733333	0	T|0.689;C|0.311	0.311	strong	.	PKHD1L1	522	.	NM_177531	exon18	c.T1920C	p.N640N	ACTGAATTGGGAT	.	PASS	Atlas-SNP
RNF32	140545	hgsc.bcm.edu	37	7	156469179	156469179	+	Missense_Mutation	SNP	C	C	T	rs2302146	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	40	118	0	0.571429	0	C|0.600;T|0.400	0.400	strong	.	RNF32	77	.	NM_001184996	exon9	c.C919T	p.R307C	GGTCAGCGCGTGG	.	PASS	Atlas-SNP
TESPA1	9840	hgsc.bcm.edu	37	12	55368291	55368291	+	Missense_Mutation	SNP	C	C	T	rs62623446	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	108	58	97	0	0.537037	0	C|0.968;T|0.032	0.032	strong	.	.	.	.	NM_001098815	exon2	c.G56A	p.R19H	CTCTGACGGAGCC	.	PASS	Atlas-SNP
C12orf40	283461	hgsc.bcm.edu	37	12	40085906	40085906	+	Missense_Mutation	SNP	A	A	T	rs73270414	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	122	52	144	0	0.42623	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
COL11A2	1302	hgsc.bcm.edu	37	6	33144243	33144243	+	Silent	SNP	T	T	A	rs1799908	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	67	66	70	0	0.985075	0	T|0.527;A|0.473	0.473	strong	COL11A2,NS,carcinoma,0,2	COL11A2	124	2	NM_080680	exon27	c.A2136T	p.G712G	TAGAGGTCCCTGA	.	PASS	Atlas-SNP
FMN2	56776	hgsc.bcm.edu	37	1	240492734	240492734	+	Missense_Mutation	SNP	G	G	A	rs3795677	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	224	115	266	0	0.513393	0	G|0.684;A|0.316	0.316	strong	FMN2,NS,carcinoma,+1,1	FMN2	451	1	NM_020066	exon10	c.G4403A	p.R1468H	CAATTCGTCGCAA	.	PASS	Atlas-SNP
SLFN11	91607	hgsc.bcm.edu	37	17	33680807	33680807	+	Silent	SNP	G	G	A	rs9897352	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	133	89	166	0	0.669173	0	G|0.234;A|0.766	0.766	strong	SLFN11,NS,carcinoma,0,1	SLFN11	112	1	NM_152270	exon4	c.C1470T	p.T490T	AAAGGCGGTGCGA	.	scavenged	Atlas-SNP
C15orf32	145858	hgsc.bcm.edu	37	15	93015427	93015427	+	Missense_Mutation	SNP	G	G	A	rs1455773	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	53	73	0	0.609195	0	G|0.616;N|0.000	.	strong	.	C15orf32	22	.	NM_153040	exon1	c.G49A	p.A17T	CACCCGGCTGACC	.	PASS	Atlas-SNP
ELSPBP1	64100	hgsc.bcm.edu	37	19	48519158	48519158	+	Missense_Mutation	SNP	C	C	T	rs34129198	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	38	88	0	0.463415	0	C|0.837;T|0.163	0.163	strong	.	ELSPBP1	29	.	NM_022142	exon4	c.C217T	p.R73C	TACCCACGCTGTA	.	PASS	Atlas-SNP
PLEKHD1	400224	hgsc.bcm.edu	37	14	69995112	69995112	+	Silent	SNP	G	G	A	rs55727771	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	64	62	86	0	0.96875	0	G|0.895;A|0.105	0.105	strong	.	PLEKHD1	24	.	NM_001161498	exon13	c.G1497A	p.S499S	CCCCTCGGCACTC	.	PASS	Atlas-SNP
C5orf55	116349	hgsc.bcm.edu	37	5	442586	442586	+	Missense_Mutation	SNP	G	G	C	rs10035612	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	27	14	34	0	0.518519	0	G|0.925;C|0.075	0.075	strong	.	C5orf55	11	.	NM_138464	exon1	c.C352G	p.R118G	AGGACCGGCCCTC	.	PASS	Atlas-SNP
ECE2	9718	hgsc.bcm.edu	37	3	183996068	183996068	+	Silent	SNP	C	C	T	rs3752904	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	132	66	164	0	0.5	0	C|0.451;T|0.549	0.549	strong	.	ECE2	303	.	NM_014693	exon6	c.C1071T	p.A357A	CAGTGCCGACTCT	.	PASS	Atlas-SNP
HCFC1R1	54985	hgsc.bcm.edu	37	16	3073240	3073240	+	Missense_Mutation	SNP	G	G	T	rs10508	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	67	50	55	1	0.746269	0.0181818	G|0.817;T|0.183	0.183	strong	HCFC1R1_ENST00000248089,NS,carcinoma,0,2	HCFC1R1	17	2	NM_017885	exon3	c.C275A	p.P92Q	CTGAGTGGGGGCA	.	scavenged	Atlas-SNP
FPR3	2359	hgsc.bcm.edu	37	19	52327784	52327784	+	Silent	SNP	C	C	T	rs3752125	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	320	133	350	0	0.415625	0	C|0.753;T|0.247	0.247	strong	.	FPR3	66	.	NM_002030	exon2	c.C783T	p.G261G	AATTGGCATTCTA	.	PASS	Atlas-SNP
SRGAP3	9901	hgsc.bcm.edu	37	3	9099989	9099989	+	Silent	SNP	A	A	G	rs61747289	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	177	75	244	0	0.423729	0	A|0.967;G|0.033	0.033	strong	.	SRGAP3	146	.	NM_014850	exon7	c.T969C	p.N323N	GACTTGATTGCAC	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	350	349	320	0	0.997143	0	C|0.375;G|0.625	0.625	strong	.	C2orf16	357	.	NM_032266	exon1	c.C1964G	p.T655S	CATGTACTCAAGT	.	PASS	Atlas-SNP
DGKB	1607	hgsc.bcm.edu	37	7	14217673	14217673	+	Silent	SNP	G	G	A	rs6966154	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	37	29	35	0	0.783784	0	G|0.720;A|0.280	0.280	strong	.	DGKB	166	.	NM_145695	exon23	c.C2229T	p.C743C	GCAGGAGCACTGA	.	PASS	Atlas-SNP
ARMC12	221481	hgsc.bcm.edu	37	6	35705892	35705892	+	Silent	SNP	T	T	C	rs2817041	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	76	76	61	0	1	0	T|0.216;C|0.784	0.784	strong	.	.	.	.	NM_145028	exon2	c.T333C	p.Y111Y	TGAGTATGCCAAG	.	PASS	Atlas-SNP
DNHD1	144132	hgsc.bcm.edu	37	11	6588228	6588228	+	Missense_Mutation	SNP	G	G	A	rs10769699	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	175	174	137	1	0.994286	0.00729927	G|0.727;A|0.273	0.273	strong	.	DNHD1	198	.	NM_144666	exon36	c.G11489A	p.R3830H	AGCTGCGTGCTCA	.	PASS	Atlas-SNP
MED14	9282	hgsc.bcm.edu	37	X	40573157	40573157	+	Silent	SNP	G	G	A	rs6520683	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	171	169	219	0	0.988304	0	G|0.693;A|0.307	0.307	strong	.	MED14	108	.	NM_004229	exon5	c.C525T	p.D175D	AATTTTGTCCTGC	.	PASS	Atlas-SNP
PIGR	5284	hgsc.bcm.edu	37	1	207109116	207109116	+	Missense_Mutation	SNP	C	C	T	rs2275531	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	76	29	86	0	0.381579	0	C|0.639;T|0.361	0.361	strong	PIGR,NS,carcinoma,0,1	PIGR	98	1	NM_002644	exon5	c.G1093A	p.G365S	CAGAGCCTCCTGC	.	PASS	Atlas-SNP
INSL3	3640	hgsc.bcm.edu	37	19	17932190	17932190	+	Silent	SNP	T	T	C	rs1047233	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	16	7	7	0	0.4375	0	T|0.715;G|0.000;C|0.284;A|0.000	0.284	strong	INSL3,NS,carcinoma,0,1	INSL3	8	1	NM_005543	exon1	c.A126G	p.L42L	GCGCACTAGCGCG	.	PASS	Atlas-SNP
ADAMTS7	11173	hgsc.bcm.edu	37	15	79064080	79064080	+	Silent	SNP	G	G	A	rs11635931	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	34	44	0	0.492754	0	G|0.721;A|0.279	0.279	strong	.	ADAMTS7	142	.	NM_014272	exon15	c.C2223T	p.S741S	GTCCTCGCTCCGC	.	PASS	Atlas-SNP
ADPRH	141	hgsc.bcm.edu	37	3	119305379	119305379	+	Silent	SNP	T	T	A	rs25676	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	54	89	0	0.627907	0	T|0.650;A|0.350	0.350	strong	.	ADPRH	33	.	NM_001125	exon4	c.T546A	p.A182A	CTATGCTGTGAAT	.	PASS	Atlas-SNP
ACTR1B	10120	hgsc.bcm.edu	37	2	98275354	98275354	+	Missense_Mutation	SNP	G	G	A	rs11692435	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	55	28	85	0	0.509091	0	G|0.950;A|0.050	0.050	strong	ACTR1B,NS,adenoma,0,1	ACTR1B	34	1	NM_005735	exon5	c.C428T	p.A143V	AGCACAGCCTGCA	.	PASS	Atlas-SNP
DHDH	27294	hgsc.bcm.edu	37	19	49438363	49438363	+	Missense_Mutation	SNP	G	G	A	rs2270941	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	19	6	6	0	0.315789	0	G|0.533;A|0.467	0.467	strong	DHDH,NS,carcinoma,0,1	DHDH	35	1	NM_014475	exon2	c.G197A	p.S66N	ACCCGAGCGTGGG	.	PASS	Atlas-SNP
ACAP1	9744	hgsc.bcm.edu	37	17	7254315	7254315	+	Missense_Mutation	SNP	G	G	A	rs35985803	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	115	63	98	0	0.547826	0	G|0.944;A|0.056	0.056	strong	.	ACAP1	66	.	NM_014716	exon21	c.G2119A	p.A707T	GGGCAGGCAGGTA	.	PASS	Atlas-SNP
LTBP2	4053	hgsc.bcm.edu	37	14	75019002	75019002	+	Silent	SNP	C	C	T	rs61738025	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	80	38	105	0	0.475	0	C|0.928;T|0.072	0.072	strong	.	LTBP2	158	.	NM_000428	exon6	c.G1287A	p.L429L	GATAGGCAGGTGG	.	PASS	Atlas-SNP
ZNF469	84627	hgsc.bcm.edu	37	16	88494603	88494603	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	66	115	0	0.653465	0	.	.	none	.	ZNF469	121	.	NM_001127464	exon1	c.G725T	p.S242I	AGAATAGCTTCCC	.	PASS	Atlas-SNP
DSG3	1830	hgsc.bcm.edu	37	18	29056063	29056063	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	67	16	89	0	0.238806	0	.	.	none	.	DSG3	172	.	NM_001944	exon16	c.C2840T	p.S947F	AACCTTCCACTGC	.	PASS	Atlas-SNP
DSPP	1834	hgsc.bcm.edu	37	4	88537035	88537035	+	Missense_Mutation	SNP	A	A	G	rs202210195	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	94	34	73	0	0.361702	0	.	.	weak	DSPP,NS,carcinoma,-1,1	DSPP	174	1	NM_014208	exon5	c.A3221G	p.D1074G	GCAGTGACAGCAG	.	PASS	Atlas-SNP
B3GALNT2	148789	hgsc.bcm.edu	37	1	235652513	235652513	+	Silent	SNP	T	T	C	rs291396	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	59	35	63	0	0.59322	0	T|0.416;C|0.584	0.584	strong	.	B3GALNT2	36	.	NM_152490	exon3	c.A321G	p.E107E	AGGATCTTCCCTG	.	PASS	Atlas-SNP
MAP1A	4130	hgsc.bcm.edu	37	15	43817406	43817406	+	Silent	SNP	T	T	C	rs480108	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	138	41	118	0	0.297101	0	T|0.539;C|0.461	0.461	strong	.	MAP1A	189	.	NM_002373	exon4	c.T3735C	p.D1245D	CGAGGATACCTCT	.	PASS	Atlas-SNP
HELT	391723	hgsc.bcm.edu	37	4	185940952	185940952	+	Missense_Mutation	SNP	C	C	G	rs1078461	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	171	78	167	0	0.45614	0	C|0.898;G|0.102	0.102	strong	.	HELT	34	.	NM_001029887	exon3	c.C439G	p.L147V	CAGTACCTGAGAG	.	PASS	Atlas-SNP
PYGB	5834	hgsc.bcm.edu	37	20	25260931	25260931	+	Silent	SNP	A	A	G	rs2227890	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	152	72	152	0	0.473684	0	A|0.513;G|0.487	0.487	strong	PYGB,NS,carcinoma,0,1	PYGB	84	1	NM_002862	exon10	c.A1122G	p.A374A	CTGTGCATACACC	.	PASS	Atlas-SNP
OR10AD1	121275	hgsc.bcm.edu	37	12	48596890	48596890	+	Silent	SNP	G	G	A	rs17823193	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	152	82	192	0	0.539474	0	G|0.939;A|0.061	0.061	strong	.	OR10AD1	24	.	NM_001004134	exon1	c.C186T	p.F62F	GAGGAAGAAGTAC	.	PASS	Atlas-SNP
HLA-G	3135	hgsc.bcm.edu	37	6	29795636	29795636	+	Silent	SNP	G	G	A	rs1630223	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	143	132	141	0	0.923077	0	G|0.509;A|0.491	0.491	strong	.	HLA-G	90	.	NM_002127	exon2	c.G15A	p.A5A	CATGGCGCCCCGA	.	PASS	Atlas-SNP
FAM149A	25854	hgsc.bcm.edu	37	4	187078819	187078819	+	Silent	SNP	C	C	G	rs2276923	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	49	17	58	0	0.346939	0	C|0.839;G|0.161	0.161	strong	.	FAM149A	52	.	NM_001006655	exon7	c.C675G	p.S225S	CCCGTCCGGACAC	.	PASS	Atlas-SNP
SCN10A	6336	hgsc.bcm.edu	37	3	38739416	38739416	+	Silent	SNP	C	C	T	rs145313578	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	165	80	166	2	0.484848	0.0120482	C|0.999;T|0.001	0.001	strong	SCN10A,NS,carcinoma,-1,2	SCN10A	359	2	NM_006514	exon27	c.G5295A	p.S1765S	AAAGTCCGAGAGA	.	scavenged	Atlas-SNP
KIAA1147	57189	hgsc.bcm.edu	37	7	141362558	141362558	+	Silent	SNP	G	G	T	rs375569681		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	62	37	66	0	0.596774	0	.	.	weak	.	KIAA1147	32	.	NM_001080392	exon9	c.C1266A	p.G422G	GCCCATGCCCCGG	.	PASS	Atlas-SNP
MYO18A	399687	hgsc.bcm.edu	37	17	27424316	27424316	+	Silent	SNP	G	G	A	rs8067806	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	50	12	49	0	0.24	0	G|0.745;A|0.255	0.255	strong	.	MYO18A	217	.	NM_078471	exon27	c.C4155T	p.T1385T	TTTCTTGGTGAAG	.	PASS	Atlas-SNP
TAAR6	319100	hgsc.bcm.edu	37	6	132892332	132892332	+	Missense_Mutation	SNP	G	G	A	rs8192625	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	93	61	137	0	0.655914	0	G|0.930;A|0.070	0.070	strong	.	TAAR6	68	.	NM_175067	exon1	c.G872A	p.C291Y	CTGCCTGTATTTA	.	PASS	Atlas-SNP
MINK1	50488	hgsc.bcm.edu	37	17	4797910	4797910	+	Missense_Mutation	SNP	G	G	A	rs79940062	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	95	40	103	0	0.421053	0	G|0.993;A|0.007	0.007	strong	.	MINK1	110	.	NM_153827	exon24	c.G2899A	p.D967N	AGTGGGGACAGCA	.	PASS	Atlas-SNP
CD83	9308	hgsc.bcm.edu	37	6	14131804	14131804	+	Silent	SNP	G	G	A	rs7743206	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	89	40	137	0	0.449438	0	G|0.859;A|0.141	0.141	strong	.	CD83	23	.	NM_004233	exon3	c.G207A	p.R69R	CCTCAGGGGACAG	.	PASS	Atlas-SNP
GPRIN2	9721	hgsc.bcm.edu	37	10	46999863	46999863	+	Missense_Mutation	SNP	C	C	G	rs4445576	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	106	22	100	0	0.207547	0	C|0.822;G|0.178	0.178	strong	GPRIN2,NS,carcinoma,0,3	GPRIN2	94	3	NM_014696	exon3	c.C983G	p.S328C	AGGCATCCCCGCT	.	PASS	Atlas-SNP
SMCHD1	23347	hgsc.bcm.edu	37	18	2724930	2724930	+	Missense_Mutation	SNP	A	A	T	rs633422	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	27	11	42	0	0.407407	0	A|0.748;T|0.252	0.252	strong	.	SMCHD1	88	.	NM_015295	exon21	c.A2637T	p.K879N	AACCAAAGGACCA	.	PASS	Atlas-SNP
HTR3D	200909	hgsc.bcm.edu	37	3	183756702	183756702	+	Missense_Mutation	SNP	G	G	A	rs6789754	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	154	72	171	0	0.467532	0	G|0.341;A|0.659	0.659	strong	.	HTR3D	65	.	NM_001163646	exon8	c.G1304A	p.R435H	TCTTCCGCCTCTA	.	PASS	Atlas-SNP
STAMBPL1	57559	hgsc.bcm.edu	37	10	90673047	90673047	+	Missense_Mutation	SNP	G	G	A	rs34270879	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	177	81	145	0	0.457627	0	G|0.970;A|0.030	0.030	strong	.	STAMBPL1	63	.	NM_020799	exon6	c.G610A	p.E204K	CTGTCAGAGCAGA	.	PASS	Atlas-SNP
MGME1	92667	hgsc.bcm.edu	37	20	17968923	17968923	+	Silent	SNP	T	T	C	rs28455091	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	89	42	127	0	0.47191	0	T|0.732;C|0.268	0.268	strong	.	.	.	.	NM_052865	exon4	c.T846C	p.D282D	CCATGATACCAAC	.	PASS	Atlas-SNP
PRRC2C	23215	hgsc.bcm.edu	37	1	171557600	171557600	+	Missense_Mutation	SNP	A	A	G	rs2421847	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	148	59	176	0	0.398649	0	A|0.977;G|0.023	0.023	strong	.	.	.	.	NM_015172	exon33	c.A8149G	p.T2717A	CCTGCCACTGTGA	.	PASS	Atlas-SNP
PRMT10	90826	hgsc.bcm.edu	37	4	148560210	148560210	+	Silent	SNP	G	G	A	rs34852471	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	84	39	124	0	0.464286	0	G|0.976;A|0.024	0.024	strong	.	PRMT10	68	.	NM_138364	exon11	c.C2223T	p.D741D	GGATAGGTCCAAA	.	PASS	Atlas-SNP
NRCAM	4897	hgsc.bcm.edu	37	7	107834613	107834613	+	Missense_Mutation	SNP	G	G	C	rs6958498	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	195	193	281	0	0.989744	0	G|0.295;C|0.705	0.705	strong	.	NRCAM	267	.	NM_001037132	exon14	c.C1633G	p.P545A	ATGTAGGATCTGA	.	PASS	Atlas-SNP
CAMKV	79012	hgsc.bcm.edu	37	3	49899795	49899795	+	Silent	SNP	G	G	A	rs3796386	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	116	66	151	0	0.568965	0	G|0.650;A|0.350	0.350	strong	.	CAMKV	84	.	NM_024046	exon2	c.C27T	p.G9G	CTTGTCGCCCAGA	.	PASS	Atlas-SNP
SLC6A17	388662	hgsc.bcm.edu	37	1	110709720	110709720	+	Missense_Mutation	SNP	G	G	A	rs12737742	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	90	44	88	0	0.488889	0	A|0.305;C|0.000;G|0.695	0.305	strong	.	SLC6A17	86	.	NM_001010898	exon2	c.G169A	p.A57T	CTGGATGCAGAGG	.	PASS	Atlas-SNP
NSD1	64324	hgsc.bcm.edu	37	5	176637471	176637471	+	Missense_Mutation	SNP	G	G	A	rs28932177	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	185	69	174	0	0.372973	0	G|0.983;A|0.017	0.017	strong	.	NSD1	416	.	NM_022455	exon5	c.G2071A	p.A691T	TTTGCTGCCACAA	.	PASS	Atlas-SNP
MED12L	116931	hgsc.bcm.edu	37	3	151090424	151090424	+	Missense_Mutation	SNP	G	G	A	rs3732765	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	41	122	0	0.5	0	G|0.766;A|0.234	0.234	strong	MED12L,NS,carcinoma,0,1	MED12L	271	1	NM_053002	exon25	c.G3629A	p.R1210Q	GTTTGCGATGTGA	.	PASS	Atlas-SNP
NR0B1	190	hgsc.bcm.edu	37	X	30326983	30326983	+	Silent	SNP	C	C	T	rs2269345	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	56	55	52	0	0.982143	0	C|0.621;T|0.379	0.379	strong	.	NR0B1	61	.	NM_000475	exon1	c.G498A	p.R166R	CCCTGGCCGTGCC	.	PASS	Atlas-SNP
KRT37	8688	hgsc.bcm.edu	37	17	39580660	39580660	+	Missense_Mutation	SNP	T	T	C	rs9916724	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	117	60	158	0	0.512821	0	T|0.619;C|0.381	0.381	strong	.	KRT37	61	.	NM_003770	exon1	c.A116G	p.N39S	GCAGCATTGGCCT	.	PASS	Atlas-SNP
ALMS1	7840	hgsc.bcm.edu	37	2	73829372	73829372	+	Silent	SNP	C	C	T	rs1052162	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	187	184	287	0	0.983957	0	C|0.663;T|0.337	0.337	strong	.	ALMS1	384	.	NM_015120	exon20	c.C12172T	p.L4058L	AAGCGCCTGAAGT	.	PASS	Atlas-SNP
SLFN11	91607	hgsc.bcm.edu	37	17	33680811	33680811	+	Missense_Mutation	SNP	C	C	A	rs9898983	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	122	42	149	1	0.344262	0.00671141	C|0.694;A|0.306	0.306	strong	SLFN11,NS,carcinoma,0,2	SLFN11	112	2	NM_152270	exon4	c.G1466T	p.R489L	GCGGTGCGAGTGC	.	scavenged	Atlas-SNP
DAAM2	23500	hgsc.bcm.edu	37	6	39864730	39864730	+	Silent	SNP	C	C	T	rs3008815	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	49	29	48	0	0.591837	0	C|0.551;T|0.449	0.449	strong	.	DAAM2	101	.	NM_015345	exon20	c.C2484T	p.I828I	CAAGATCGCTGAC	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	63	11	79	0	0.174603	0	C|0.846;A|0.154	0.154	strong	.	LPL	78	.	NM_000237	exon8	c.C1164A	p.T388T	TAAGACCTACTCC	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	60	60	64	0	1	0	G|0.661;A|0.339	0.339	strong	.	TRAPPC10	109	.	NM_003274	exon14	c.G2176A	p.V726M	GCCCACGTGCTGA	.	PASS	Atlas-SNP
MRPS30	10884	hgsc.bcm.edu	37	5	44809162	44809162	+	Missense_Mutation	SNP	G	G	C	rs3747479	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	40	82	3	0.533333	0.0365854	A|0.000;C|0.396;G|0.604	0.396	strong	MRPS30_ENST00000507110,NS,carcinoma,0,4	MRPS30	90	4	NM_016640	exon1	c.G98C	p.C33S	CGACCTGCCAAGA	.	scavenged	Atlas-SNP
KIF17	57576	hgsc.bcm.edu	37	1	21044161	21044161	+	Silent	SNP	A	A	G	rs601329	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	11	11	13	0	1	0	A|0.268;G|0.732	0.732	strong	.	KIF17	130	.	NM_001122819	exon1	c.T39C	p.R13R	CATGGGACGGCAG	.	PASS	Atlas-SNP
FERMT3	83706	hgsc.bcm.edu	37	11	63979162	63979162	+	Silent	SNP	C	C	T	rs17851033	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	90	65	101	0	0.722222	0	C|0.944;T|0.056	0.056	strong	.	FERMT3	51	.	NM_031471	exon6	c.C729T	p.A243A	CAAGGCCGGGGAC	.	PASS	Atlas-SNP
C4A	720	hgsc.bcm.edu	37	6	31963559	31963559	+	Silent	SNP	A	A	G	rs2258218	bycluster;byfrequency;by2hit2allele;byhapmap	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	230	10	1276	19	0.0434783	0.0148903	A|0.500;G|0.500	0.500	strong	C4B,right_upper_lobe,carcinoma,0,2	C4A	15	2	NM_007293	exon25	c.G3218G	p.G1073G	CACGGGACAGCAG	.	scavenged	Atlas-SNP
MAG	4099	hgsc.bcm.edu	37	19	35793589	35793589	+	Silent	SNP	C	C	T	rs1126770	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	28	44	0	0.482759	0	C|0.728;T|0.272	0.272	strong	.	MAG	172	.	NM_080600	exon7	c.C1209T	p.T403T	GGCCACCGCCTTC	.	PASS	Atlas-SNP
SPTBN4	57731	hgsc.bcm.edu	37	19	41038574	41038574	+	Missense_Mutation	SNP	G	G	A	rs814501	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	80	38	76	0	0.475	0	G|0.572;A|0.428	0.428	strong	.	SPTBN4	213	.	NM_020971	exon19	c.G3991A	p.G1331S	CGGGATGGCACGC	.	PASS	Atlas-SNP
LCE3D	84648	hgsc.bcm.edu	37	1	152552285	152552285	+	Missense_Mutation	SNP	C	C	A	rs61745411		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	140	63	154	1	0.45	0.00649351	C|0.986;A|0.014	0.014	weak	LCE3D,NS,carcinoma,0,1	LCE3D	28	1	NM_032563	exon2	c.G128T	p.G43V	CCACAGCCCCCAG	.	scavenged	Atlas-SNP
MAML3	55534	hgsc.bcm.edu	37	4	140640703	140640703	+	Missense_Mutation	SNP	G	G	T	rs61747885	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	65	31	60	0	0.476923	0	G|0.877;T|0.123	0.123	strong	.	MAML3	192	.	NM_018717	exon6	c.C3179A	p.P1060H	GCTGGGGGCTGGC	.	PASS	Atlas-SNP
HIST1H1C	3006	hgsc.bcm.edu	37	6	26056277	26056277	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	127	36	153	0	0.283465	0	.	.	none	.	HIST1H1C	80	.	NM_005319	exon1	c.A380C	p.K127T	TTAGGTTTGGTTC	.	PASS	Atlas-SNP
CELA2A	63036	hgsc.bcm.edu	37	1	15789297	15789297	+	Silent	SNP	A	A	C	rs55772743		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	155	151	190	2	0.974194	0.0105263	.	.	weak	CELA2A,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	CELA2A	32	1	NM_033440	exon4	c.A297C	p.A99A	GCTGGCAGTCAGT	.	scavenged	Atlas-SNP
NUP210L	91181	hgsc.bcm.edu	37	1	154031134	154031134	+	Missense_Mutation	SNP	C	C	A	rs201928881	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	66	32	95	0	0.484848	0	.	.	weak	.	NUP210L	181	.	NM_001159484	exon21	c.G2886T	p.E962D	ATAGACCTCCAAG	.	PASS	Atlas-SNP
UGT2B11	10720	hgsc.bcm.edu	37	4	70079975	70079975	+	Missense_Mutation	SNP	A	A	G	rs7697037	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	317	160	405	0	0.504732	0	A|0.840;G|0.160	0.160	strong	.	UGT2B11	92	.	NM_001073	exon1	c.T466C	p.C156R	CACCACAGGGAAA	.	PASS	Atlas-SNP
F5	2153	hgsc.bcm.edu	37	1	169521849	169521849	+	Silent	SNP	T	T	C	rs6035	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	202	101	209	1	0.5	0.00478469	T|0.917;C|0.083	0.083	strong	.	F5	301	.	NM_000130	exon8	c.A1242G	p.K414K	ATCTTCTTTCATA	.	PASS	Atlas-SNP
TRIM39	56658	hgsc.bcm.edu	37	6	30297529	30297529	+	Silent	SNP	T	T	C	rs2057727	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	120	58	155	0	0.483333	0	T|0.696;C|0.304	0.304	strong	.	TRIM39	56	.	NM_172016	exon3	c.T435C	p.D145D	GGACGATGCTACA	.	PASS	Atlas-SNP
DAB2	1601	hgsc.bcm.edu	37	5	39381618	39381618	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	123	43	88	0	0.349593	0	.	.	none	.	DAB2	124	.	NM_001343	exon11	c.C1442T	p.P481L	GGGTTGGGCTGCA	.	PASS	Atlas-SNP
KRTAP4-9	100132386	hgsc.bcm.edu	37	17	39262122	39262122	+	Missense_Mutation	SNP	G	G	A	rs188946528	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	42	12	51	0	0.285714	0	G|0.972;A|0.028	0.028	strong	KRTAP4-9_ENST00000377734,NS,carcinoma,+1,2	KRTAP4-9	110	2	NM_001146041	exon1	c.G482A	p.R161H	GCTGCCGCCCCTC	.	PASS	Atlas-SNP
TXLNB	167838	hgsc.bcm.edu	37	6	139581461	139581461	+	Silent	SNP	C	C	T	rs6904970	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	80	25	110	0	0.3125	0	C|0.915;T|0.085	0.085	strong	.	TXLNB	96	.	NM_153235	exon6	c.G996A	p.K332K	ATATTCCTTTTCT	.	PASS	Atlas-SNP
C1QTNF2	114898	hgsc.bcm.edu	37	5	159776637	159776637	+	Silent	SNP	C	C	T	rs10053189	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	65	28	70	0	0.430769	0	C|0.626;T|0.374	0.374	strong	.	C1QTNF2	33	.	NM_031908	exon3	c.G531A	p.K177K	CTCCCCCTTCTTG	.	PASS	Atlas-SNP
MFAP3	4238	hgsc.bcm.edu	37	5	153429459	153429459	+	Silent	SNP	T	T	C	rs690592	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	170	73	158	0	0.429412	0	T|0.355;C|0.645	0.645	strong	.	MFAP3	20	.	NM_005927	exon2	c.T177C	p.D59D	TGATGATGTCATC	.	PASS	Atlas-SNP
RNF213	57674	hgsc.bcm.edu	37	17	78263514	78263514	+	Silent	SNP	G	G	A	rs17853713	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	49	102	0	0.485149	0	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	.	PASS	Atlas-SNP
SLC35G6	643664	hgsc.bcm.edu	37	17	7386217	7386217	+	Missense_Mutation	SNP	T	T	C	rs200349946	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	148	38	164	0	0.256757	0	T|0.734;C|0.266	0.266	strong	POLR2A_ENST00000412468,NS,carcinoma,0,3	.	.	3	NM_001102614	exon2	c.T914C	p.V305A	AGACTGTGGCACC	.	scavenged	Atlas-SNP
BTN2A1	11120	hgsc.bcm.edu	37	6	26463575	26463575	+	Missense_Mutation	SNP	G	G	T	rs13195402	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	61	29	64	0	0.47541	0	G|0.952;T|0.048	0.048	strong	.	BTN2A1	118	.	NM_001197234	exon4	c.G534T	p.W178C	AGTGTGGAGGGAC	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	122	70	107	0	0.57377	0	C|0.721;G|0.279	0.279	strong	.	RAPGEF3	98	.	NM_001098531	exon2	c.G46C	p.A16P	CCACAGCCAGGCC	.	PASS	Atlas-SNP
KRT9	3857	hgsc.bcm.edu	37	17	39727894	39727894	+	Silent	SNP	A	A	G	rs115965791	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	37	81	0	0.493333	0	A|0.995;G|0.005	0.005	strong	.	KRT9	78	.	NM_000226	exon1	c.T351C	p.G117G	AGAACCACCACCA	.	PASS	Atlas-SNP
STAG1	10274	hgsc.bcm.edu	37	3	136088038	136088038	+	Silent	SNP	G	G	A	rs9860801	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	142	61	124	0	0.429577	0	G|0.655;A|0.344	0.344	strong	.	STAG1	135	.	NM_005862	exon24	c.C2457T	p.F819F	TGGATTGAACACC	.	PASS	Atlas-SNP
CAV3	859	hgsc.bcm.edu	37	3	8775589	8775589	+	Silent	SNP	C	C	T	rs1974763	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	98	56	115	0	0.571429	0	C|0.925;T|0.075	0.075	strong	.	CAV3	20	.	NM_033337	exon1	c.C27T	p.L9L	AGATCTCGAGGCC	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29910801	29910801	+	Missense_Mutation	SNP	C	C	A	rs1136692	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	98	177	0	0.970297	0	A|0.278;C|0.722	0.278	strong	.	HLA-A	89	.	NM_001242758	exon2	c.C341A	p.A114D	GCGAGGCCGGTGA	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179479245	179479245	+	Silent	SNP	C	C	T	rs72677244	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	123	66	173	0	0.536585	0	C|0.941;T|0.059	0.059	strong	.	TTN	18412	.	NM_001267550	exon261	c.G48996A	p.E16332E	CACAGCCTCAATG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195512343	195512343	+	Silent	SNP	G	G	A	rs113457754	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	95	20	68	0	0.210526	0	G|0.500;A|0.500	0.500	weak	MUC4_ENST00000463781,NS,carcinoma,0,4	MUC4	1505	4	NM_018406	exon2	c.C6108T	p.T2036T	AGTATCGGTGACA	.	PASS	Atlas-SNP
KRT84	3890	hgsc.bcm.edu	37	12	52777578	52777578	+	Missense_Mutation	SNP	C	C	T	rs1613931	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	91	46	116	0	0.505495	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
ZNF30	90075	hgsc.bcm.edu	37	19	35435589	35435589	+	Silent	SNP	C	C	T	rs3761066	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	46	31	63	0	0.673913	0	C|0.747;T|0.253	0.253	strong	.	ZNF30	44	.	NM_001099438	exon5	c.C1722T	p.C574C	GGAATGCGGGAAG	.	PASS	Atlas-SNP
CLCN2	1181	hgsc.bcm.edu	37	3	184075047	184075047	+	Silent	SNP	A	A	G	rs2228291	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	38	22	49	0	0.578947	0	A|0.659;G|0.341	0.341	strong	.	CLCN2	74	.	NM_001171087	exon9	c.T906C	p.I302I	GGCTGTAATAGTC	.	PASS	Atlas-SNP
USH2A	7399	hgsc.bcm.edu	37	1	215956140	215956140	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	30	125	0	0.309278	0	.	.	none	.	USH2A	1168	.	NM_206933	exon53	c.A10525C	p.K3509Q	CTATTTTGGTCCA	.	PASS	Atlas-SNP
BNIPL	149428	hgsc.bcm.edu	37	1	151015564	151015564	+	Missense_Mutation	SNP	G	G	A	rs61751620	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	184	98	207	0	0.532609	0	G|0.985;A|0.015	0.015	strong	.	BNIPL	45	.	NM_138278	exon5	c.G566A	p.R189H	AGCAGCGCGTAGA	.	PASS	Atlas-SNP
LRP1	4035	hgsc.bcm.edu	37	12	57597023	57597023	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	89	25	112	0	0.280899	0	.	.	none	LRP1,bladder,carcinoma,-1,1	LRP1	428	1	NM_002332	exon69	c.C10771T	p.R3591C	GCGGGGCGCTGGA	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	167	77	231	0	0.461078	0	T|0.432;G|0.002	0.432	strong	.	KIAA0226L	63	.	NM_025113	exon3	c.G454A	p.G152R	AAATCCCAGGGCT	.	PASS	Atlas-SNP
OTOP1	133060	hgsc.bcm.edu	37	4	4199760	4199760	+	Silent	SNP	G	G	A	rs17697262	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	94	41	146	1	0.43617	0.00684932	G|0.855;A|0.145	0.145	strong	OTOP1,NS,carcinoma,-2,1	OTOP1	118	1	NM_177998	exon5	c.C801T	p.I267I	GTAGTAGATCCCG	.	scavenged	Atlas-SNP
CA6	765	hgsc.bcm.edu	37	1	9009444	9009444	+	Missense_Mutation	SNP	A	A	C	rs2274328	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	110	55	86	0	0.5	0	A|0.488;C|0.511	0.511	strong	CA6_ENST00000319474,brain,glioma,0,2	CA6	47	2	NM_001270500	exon2	c.A202C	p.M68L	CTCAATATGACAG	.	PASS	Atlas-SNP
KATNB1	10300	hgsc.bcm.edu	37	16	57787027	57787027	+	Silent	SNP	C	C	T	rs12922275	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	59	41	0	0.842857	0	C|0.918;T|0.082	0.082	strong	.	KATNB1	35	.	NM_005886	exon11	c.C894T	p.Y298Y	CTCCTACGTGGTG	.	PASS	Atlas-SNP
STON1	11037	hgsc.bcm.edu	37	2	48808882	48808882	+	Silent	SNP	T	T	A	rs3749144	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	196	43	117	0	0.219388	0	T|0.678;A|0.322	0.322	strong	.	STON1	100	.	NM_001198595	exon3	c.T1110A	p.P370P	TGAACCTGACATA	.	PASS	Atlas-SNP
ACBD5	91452	hgsc.bcm.edu	37	10	27508758	27508758	+	Silent	SNP	T	T	C	rs10764690	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	114	114	159	1	1	0.00628931	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
ITGA8	8516	hgsc.bcm.edu	37	10	15649698	15649698	+	Missense_Mutation	SNP	T	T	G	rs9333269	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	127	59	143	0	0.464567	0	T|0.949;G|0.051	0.051	strong	ITGA8,NS,carcinoma,0,1	ITGA8	230	1	NM_003638	exon17	c.A1742C	p.Q581P	AAATCCTGGCACT	.	PASS	Atlas-SNP
CCIN	881	hgsc.bcm.edu	37	9	36171092	36171092	+	Silent	SNP	G	G	A	rs61735202	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	53	22	79	0	0.415094	0	G|0.975;A|0.025	0.025	strong	.	CCIN	56	.	NM_005893	exon1	c.G1593A	p.G531G	ATGTGGGGGTGTC	.	PASS	Atlas-SNP
CHRM3	1131	hgsc.bcm.edu	37	1	240070855	240070855	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	123	32	138	0	0.260163	0	.	.	none	.	CHRM3	118	.	NM_000740	exon5	c.C104G	p.T35S	CCGTCACTCATTT	.	PASS	Atlas-SNP
CCPG1	9236	hgsc.bcm.edu	37	15	55653031	55653031	+	Silent	SNP	A	A	G	rs501231	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	122	61	115	0	0.5	0	A|0.518;G|0.482	0.482	strong	CCPG1,NS,carcinoma,0,1	CCPG1	74	1	NM_020739	exon8	c.T940C	p.L314L	TCTCCAAGGATAC	.	PASS	Atlas-SNP
OAF	220323	hgsc.bcm.edu	37	11	120099791	120099791	+	Silent	SNP	C	C	T	rs2465654	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	99	75	138	0	0.757576	0	C|0.869;T|0.131	0.131	strong	.	OAF	12	.	NM_178507	exon4	c.C762T	p.F254F	CAGCTTCGACTTC	.	PASS	Atlas-SNP
PMS1	5378	hgsc.bcm.edu	37	2	190728798	190728798	+	Missense_Mutation	SNP	A	A	G	rs201205478	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	186	85	155	0	0.456989	0	.	.	weak	.	PMS1	78	.	NM_000534	exon10	c.A2186G	p.N729S	TCCACAATCTCAG	.	PASS	Atlas-SNP
POM121L12	285877	hgsc.bcm.edu	37	7	53103371	53103371	+	Missense_Mutation	SNP	G	G	T	rs72598684	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	48	24	40	0	0.5	0	G|0.715;T|0.285	0.285	strong	.	POM121L12	146	.	NM_182595	exon1	c.G7T	p.A3S	ATGGGCGCTGCAG	.	PASS	Atlas-SNP
EPS8L2	64787	hgsc.bcm.edu	37	11	720197	720197	+	Silent	SNP	C	C	T	rs3087546	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	202	45	173	0	0.222772	0	C|0.473;T|0.527	0.527	strong	EPS8L2,rectum,carcinoma,0,1	EPS8L2	42	1	NM_022772	exon5	c.C301T	p.L101L	CAGTCGCTGCGGC	.	PASS	Atlas-SNP
SGK2	10110	hgsc.bcm.edu	37	20	42199296	42199296	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	4	77	0	0.045977	0	.	.	none	.	SGK2	50	.	NM_016276	exon6	c.C580T	p.P194S	CTGGAGCCCCGGG	.	PASS	Atlas-SNP
TTC21B	79809	hgsc.bcm.edu	37	2	166771842	166771842	+	Silent	SNP	A	A	G	rs138449110		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	37	74	0	0.430233	0	A|1.000;G|0.000	0.000	weak	.	TTC21B	130	.	NM_024753	exon15	c.T2007C	p.D669D	TTCAATATCTCCT	.	PASS	Atlas-SNP
ARHGAP21	57584	hgsc.bcm.edu	37	10	24889664	24889664	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	194	38	214	0	0.195876	0	.	.	none	.	ARHGAP21	185	.	NM_020824	exon14	c.G3043A	p.D1015N	CACAGTCGGACGT	.	PASS	Atlas-SNP
MYBBP1A	10514	hgsc.bcm.edu	37	17	4446457	4446457	+	Silent	SNP	G	G	A	rs751670	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	5	5	6	0	1	0	G|0.812;A|0.188	0.188	strong	.	MYBBP1A	69	.	NM_014520	exon20	c.C2643T	p.H881H	CAGGTGGTGCCTG	.	PASS	Atlas-SNP
KRTAP4-6	81871	hgsc.bcm.edu	37	17	39296167	39296167	+	Silent	SNP	A	A	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	132	5	122	1	0.0378788	0.00819672	.	.	none	KRTAP4-6,bladder,carcinoma,0,9	KRTAP4-6	46	9	NM_030976	exon1	c.T573C	p.I191I	GGTGGAAATGACA	.	scavenged	Atlas-SNP
CROCC	9696	hgsc.bcm.edu	37	1	17265507	17265507	+	Missense_Mutation	SNP	C	C	T	rs201951425	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	9	5	3	0	0.555556	0	C|0.983;T|0.017	0.017	strong	CROCC,NS,carcinoma,0,1	CROCC	185	1	NM_014675	exon12	c.C1478T	p.P493L	GGACCCCGTCCCC	.	scavenged	Atlas-SNP
SYNE1	23345	hgsc.bcm.edu	37	6	152671865	152671865	+	Missense_Mutation	SNP	T	T	G	rs13210127	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	161	110	299	0	0.68323	0	T|0.963;G|0.037	0.037	strong	.	SYNE1	3227	.	NM_182961	exon71	c.A11621C	p.K3874T	ACTGACTTTACTG	.	PASS	Atlas-SNP
OTOP1	133060	hgsc.bcm.edu	37	4	4199261	4199261	+	Missense_Mutation	SNP	C	C	T	rs11736799	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	68	33	92	0	0.485294	0	C|0.980;T|0.020	0.020	strong	.	OTOP1	118	.	NM_177998	exon5	c.G1300A	p.V434M	TCTCCACGATCGC	.	PASS	Atlas-SNP
IQCE	23288	hgsc.bcm.edu	37	7	2649686	2649686	+	Missense_Mutation	SNP	C	C	T	rs368687600		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	95	73	96	0	0.768421	0	.	.	weak	.	IQCE	66	.	NM_152558	exon22	c.C1978T	p.P660S	CCCTCTCCCTCAG	.	PASS	Atlas-SNP
ZNF85	7639	hgsc.bcm.edu	37	19	21131728	21131728	+	Silent	SNP	A	A	G	rs12972502	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	67	66	93	0	0.985075	0	A|0.919;G|0.081	0.081	strong	.	ZNF85	72	.	NM_001256171	exon5	c.A498G	p.Q166Q	TAACCAATGTCTC	.	PASS	Atlas-SNP
TMEM8A	58986	hgsc.bcm.edu	37	16	427784	427784	+	Silent	SNP	G	G	A	rs11641742	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	136	136	178	0	1	0	G|0.455;A|0.545	0.545	strong	.	TMEM8A	49	.	NM_021259	exon2	c.C186T	p.Y62Y	ACTGCCGTACCAG	.	PASS	Atlas-SNP
OR10H4	126541	hgsc.bcm.edu	37	19	16060248	16060248	+	Missense_Mutation	SNP	A	A	G	rs16980822	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	190	104	200	0	0.547368	0	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
MYO18B	84700	hgsc.bcm.edu	37	22	26388337	26388337	+	Silent	SNP	C	C	T	rs916425	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	64	28	62	0	0.4375	0	C|0.866;T|0.134	0.134	strong	.	MYO18B	322	.	NM_032608	exon40	c.C6165T	p.Y2055Y	GAAGTACGTGGAG	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105415577	105415577	+	Silent	SNP	G	G	A	rs375265904		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	55	8	1	0	0.145455	0	.	.	weak	AHNAK2_ENST00000333244,NS,carcinoma,0,1	AHNAK2	719	1	NM_138420	exon7	c.C6211T	p.L2071L	TGGGCAGGTGCCC	.	scavenged	Atlas-SNP
TBC1D1	23216	hgsc.bcm.edu	37	4	38016395	38016395	+	Missense_Mutation	SNP	T	T	G	rs10501	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	38	13	40	0	0.342105	0	T|0.448;G|0.552	0.552	strong	TBC1D1,NS,carcinoma,0,1	TBC1D1	94	1	NM_015173	exon3	c.T683G	p.V228G	AGCCTGTGCGCAG	.	PASS	Atlas-SNP
FMN2	56776	hgsc.bcm.edu	37	1	240256822	240256822	+	Silent	SNP	C	C	A	rs10926124	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	13	8	9	0	0.615385	0	C|0.617;A|0.383	0.383	strong	FMN2,NS,carcinoma,+1,1	FMN2	451	1	NM_020066	exon1	c.C1413A	p.A471A	CCGGGCCGACGGC	.	scavenged	Atlas-SNP
KANK2	25959	hgsc.bcm.edu	37	19	11303554	11303554	+	Missense_Mutation	SNP	A	A	G	rs17616661	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	176	81	212	0	0.460227	0	A|0.936;G|0.064	0.064	strong	.	KANK2	47	.	NM_015493	exon2	c.T1202C	p.M401T	TTCACCATATGGA	.	PASS	Atlas-SNP
UMODL1	89766	hgsc.bcm.edu	37	21	43557698	43557698	+	Missense_Mutation	SNP	A	A	C	rs3819142	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	146	96	128	0	0.657534	0	A|0.810;C|0.190	0.190	strong	.	UMODL1	186	.	NM_173568	exon21	c.A4309C	p.N1437H	CAGTCCAACAACT	.	PASS	Atlas-SNP
POLD3	10714	hgsc.bcm.edu	37	11	74329615	74329615	+	Silent	SNP	T	T	C	rs4944052	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	129	128	133	0	0.992248	0	T|0.602;C|0.398	0.398	strong	POLD3,NS,carcinoma,0,1	POLD3	87	1	NM_006591	exon6	c.T426C	p.P142P	CGTCCCTAGAGCT	.	PASS	Atlas-SNP
ANKRD32	84250	hgsc.bcm.edu	37	5	93987532	93987532	+	Missense_Mutation	SNP	C	C	A	rs6891545	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	77	76	95	0	0.987013	0	C|0.778;A|0.222	0.222	strong	.	ANKRD32	117	.	NM_032290	exon7	c.C864A	p.S288R	TGGAAGCCATACA	.	PASS	Atlas-SNP
DUSP15	128853	hgsc.bcm.edu	37	20	30452782	30452782	+	Silent	SNP	C	C	T	rs4911536	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	118	118	153	0	1	0	C|0.733;T|0.267	0.267	strong	DUSP15,NS,carcinoma,0,1	DUSP15	28	1	NM_080611	exon4	c.G162A	p.P54P	AGCGACCGGGATG	.	PASS	Atlas-SNP
RSF1	51773	hgsc.bcm.edu	37	11	77378388	77378388	+	Silent	SNP	T	T	C	rs4945197	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	94	79	139	0	0.840426	0	T|0.813;C|0.187	0.187	strong	RSF1,NS,carcinoma,0,1	RSF1	105	1	NM_016578	exon16	c.A3900G	p.L1300L	CCGGTGTAGCCGT	.	PASS	Atlas-SNP
SLC12A6	9990	hgsc.bcm.edu	37	15	34542872	34542872	+	Silent	SNP	C	C	G	rs17236798	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	220	108	263	0	0.490909	0	C|0.822;G|0.178	0.178	strong	.	SLC12A6	205	.	NM_133647	exon11	c.G1551C	p.P517P	ACCAATCGGAATA	.	PASS	Atlas-SNP
SMARCA5	8467	hgsc.bcm.edu	37	4	144471249	144471249	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	66	14	61	0	0.212121	0	.	.	none	.	SMARCA5	73	.	NM_003601	exon23	c.A3085G	p.K1029E	GGACCAAAGCCTT	.	PASS	Atlas-SNP
DHDH	27294	hgsc.bcm.edu	37	19	49445774	49445774	+	Nonsense_Mutation	SNP	C	C	T	rs10423255	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	50	84	0	0.543478	0	C|0.938;T|0.062	0.062	strong	.	DHDH	35	.	NM_014475	exon5	c.C697T	p.Q233X	ACCGTGCAGCTCT	.	PASS	Atlas-SNP
GABRB1	2560	hgsc.bcm.edu	37	4	47408709	47408709	+	Silent	SNP	A	A	G	rs6289	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	135	56	192	0	0.414815	0	A|0.721;G|0.279	0.279	strong	.	GABRB1	107	.	NM_000812	exon8	c.A846G	p.T282T	CACGACAGTGCTT	.	PASS	Atlas-SNP
DOPEY2	9980	hgsc.bcm.edu	37	21	37661405	37661405	+	Missense_Mutation	SNP	G	G	A	rs3827183	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	218	132	197	0	0.605505	0	G|0.873;A|0.127	0.127	strong	DOPEY2,NS,carcinoma,0,1	DOPEY2	184	1	NM_005128	exon35	c.G6416A	p.G2139E	CAGTGGGGGAGAT	.	PASS	Atlas-SNP
ANXA10	11199	hgsc.bcm.edu	37	4	169098914	169098914	+	Silent	SNP	A	A	G	rs477897	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	152	86	175	0	0.565789	0	A|0.841;G|0.159	0.159	strong	.	ANXA10	44	.	NM_007193	exon7	c.A504G	p.T168T	ATATACAGACCCT	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29910761	29910761	+	Missense_Mutation	SNP	G	G	A	rs1136688	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	142	140	227	0	0.985915	0	A|0.386;G|0.614	0.386	strong	.	HLA-A	89	.	NM_001242758	exon2	c.G301A	p.D101N	CGAGTGGACCTGG	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105417894	105417894	+	Missense_Mutation	SNP	C	C	G	rs2819440	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	84	83	0	0	0.988095	.	C|0.249;G|0.751	0.751	strong	.	AHNAK2	719	.	NM_138420	exon7	c.G3894C	p.M1298I	GGCCTGCATGTCC	.	PASS	Atlas-SNP
UHRF1BP1	54887	hgsc.bcm.edu	37	6	34826663	34826663	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	130	32	133	0	0.246154	0	.	.	none	.	UHRF1BP1	102	.	NM_017754	exon14	c.G2530A	p.V844M	AAGGAGGTGCTGC	.	PASS	Atlas-SNP
NAV2	89797	hgsc.bcm.edu	37	11	20112417	20112417	+	Silent	SNP	A	A	C	rs2243624	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	76	13	61	0	0.171053	0	A|0.618;C|0.382	0.382	strong	.	NAV2	255	.	NM_001244963	exon29	c.A5682C	p.S1894S	AATTTCAGAATGC	.	PASS	Atlas-SNP
RNF32	140545	hgsc.bcm.edu	37	7	156469133	156469133	+	Missense_Mutation	SNP	C	C	G	rs2302147	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	74	44	104	0	0.594595	0	C|0.601;G|0.399	0.399	strong	.	RNF32	77	.	NM_001184996	exon9	c.C873G	p.H291Q	GACCCACGAGTGC	.	PASS	Atlas-SNP
PRPH	5630	hgsc.bcm.edu	37	12	49689009	49689009	+	Missense_Mutation	SNP	G	G	A	rs57451017	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	135	67	104	0	0.496296	0	G|0.986;A|0.014	0.014	strong	.	PRPH	26	.	NM_006262	exon1	c.G26A	p.R9Q	GCCTCCGGGCCGG	.	PASS	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	137	61	162	0	0.445255	0	T|0.535;C|0.464	0.464	strong	.	TBC1D13	27	.	NM_018201	exon8	c.T569C	p.V190A	ACTCTGTGCCATC	.	PASS	Atlas-SNP
ACAN	176	hgsc.bcm.edu	37	15	89400080	89400080	+	Missense_Mutation	SNP	A	A	G	rs35546357	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	53	28	80	0	0.528302	0	A|0.983;G|0.017	0.017	strong	.	ACAN	220	.	NM_001135	exon12	c.A4264G	p.T1422A	GAGACTACTGCCC	.	PASS	Atlas-SNP
TBC1D9B	23061	hgsc.bcm.edu	37	5	179290845	179290845	+	Missense_Mutation	SNP	T	T	G	rs30386	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	138	138	116	1	1	0.00862069	T|0.501;G|0.499	0.499	strong	.	TBC1D9B	157	.	NM_198868	exon22	c.A3356C	p.K1119T	GGGGCTTTTCCGA	.	PASS	Atlas-SNP
XPO5	57510	hgsc.bcm.edu	37	6	43514382	43514382	+	Silent	SNP	A	A	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	98	43	142	0	0.438776	0	.	.	none	XPO5,NS,carcinoma,-1,1	XPO5	79	1	NM_020750	exon20	c.T2268C	p.S756S	ATTTCCACTGGAT	.	PASS	Atlas-SNP
MYO7A	4647	hgsc.bcm.edu	37	11	76912636	76912636	+	Missense_Mutation	SNP	A	A	T	rs2276288	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	71	75	0	1	0	A|0.422;T|0.578	0.578	strong	.	MYO7A	164	.	NM_000260	exon36	c.A4996T	p.S1666C	ACCGACAGTGTGT	.	PASS	Atlas-SNP
DSP	1832	hgsc.bcm.edu	37	6	7584617	7584617	+	Silent	SNP	C	C	T	rs2076300	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	143	84	126	0	0.587413	0	C|0.732;T|0.268	0.268	strong	DSP,NS,carcinoma,0,1	DSP	306	1	NM_004415	exon24	c.C7122T	p.T2374T	CGCAACCGGGGGG	.	PASS	Atlas-SNP
ADAMTS7	11173	hgsc.bcm.edu	37	15	79058090	79058090	+	Missense_Mutation	SNP	A	A	G	rs2929158	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	10	72	0	0.103093	0	A|0.897;G|0.103	0.103	strong	ADAMTS7,rectum,carcinoma,0,1	ADAMTS7	142	1	NM_014272	exon19	c.T4163C	p.V1388A	TCAGGGACTCTGT	.	scavenged	Atlas-SNP
HAO1	54363	hgsc.bcm.edu	37	20	7894999	7894999	+	Silent	SNP	C	C	T	rs373499154	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	160	2	171	0	0.0125	0	.	.	weak	HAO1,colon,carcinoma,0,1	HAO1	71	1	NM_017545	exon3	c.G357A	p.A119A	AGCTTCCGCCACT	.	scavenged	Atlas-SNP
LILRB3	11025	hgsc.bcm.edu	37	19	54723030	54723030	+	Missense_Mutation	SNP	C	C	A	rs61734493	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	27	87	0	0.465517	0	C|0.956;A|0.044	0.044	strong	.	LILRB3	67	.	NM_006864	exon8	c.G1394T	p.R465L	TGACGTCGGAGGA	.	PASS	Atlas-SNP
CHGB	1114	hgsc.bcm.edu	37	20	5903932	5903932	+	Missense_Mutation	SNP	G	G	T	rs142841879	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	23	12	28	0	0.521739	0	G|0.997;T|0.003	0.003	strong	.	CHGB	112	.	NM_001819	exon4	c.G1142T	p.W381L	AGAGTTGGGATGA	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	70	78	0	1	0	A|0.493;G|0.507	0.507	strong	.	OR52J3	77	.	NM_001001916	exon1	c.A906G	p.E302E	TCGAGAACGAGTG	.	PASS	Atlas-SNP
FRZB	2487	hgsc.bcm.edu	37	2	183731193	183731193	+	Missense_Mutation	SNP	C	C	A	rs36077496	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	37	22	28	0	0.594595	0	C|0.973;A|0.027	0.027	strong	.	FRZB	42	.	NM_001463	exon1	c.G88T	p.A30S	CCCGAGCCCCGGG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195511556	195511556	+	Missense_Mutation	SNP	T	T	A	rs79961534	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	39	19	100	0	0.487179	0	T|0.996;A|0.004	0.004	weak	MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	NM_018406	exon2	c.A6895T	p.T2299S	GACCTGTGGATGC	.	PASS	Atlas-SNP
DISC1	27185	hgsc.bcm.edu	37	1	232144887	232144887	+	Missense_Mutation	SNP	A	A	G	rs821617	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	22	12	20	0	0.545455	0	A|0.764;G|0.236	0.236	strong	.	DISC1	207	.	NM_001164538	exon11	c.A2399G	p.K800R	TTGGGAAGGCTTC	.	PASS	Atlas-SNP
MBD3L3	653657	hgsc.bcm.edu	37	19	7056537	7056537	+	Silent	SNP	G	G	A	rs201991311	byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	139	22	107	0	0.158273	0	G|0.975;A|0.025	0.025	strong	MBD3L3,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	MBD3L3	12	1	NM_001164425	exon2	c.C423T	p.P141P	AGGGGTGGGCTCA	.	scavenged	Atlas-SNP
C1orf65	164127	hgsc.bcm.edu	37	1	223566859	223566859	+	Silent	SNP	T	T	C	rs111306873	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	17	10	31	0	0.588235	0	T|0.930;C|0.070	0.070	strong	.	C1orf65	71	.	NM_152610	exon1	c.T42C	p.D14D	CCGGGATCTCTGG	.	PASS	Atlas-SNP
RFC2	5982	hgsc.bcm.edu	37	7	73663362	73663362	+	Silent	SNP	T	T	C	rs1805395	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	35	19	48	0	0.542857	0	T|0.971;C|0.029	0.029	strong	.	RFC2	27	.	NM_181471	exon4	c.A312G	p.E104E	ATTGAGTTCCAAC	.	PASS	Atlas-SNP
LRRC8C	84230	hgsc.bcm.edu	37	1	90179532	90179532	+	Missense_Mutation	SNP	A	A	G	rs12032393	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	48	21	42	0	0.4375	0	A|0.869;G|0.131	0.131	strong	.	LRRC8C	73	.	NM_032270	exon3	c.A1403G	p.N468S	TAGACAATCTTCA	.	PASS	Atlas-SNP
EML2	24139	hgsc.bcm.edu	37	19	46127999	46127999	+	Silent	SNP	C	C	T	rs36013288	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	34	85	1	0.472222	0.0117647	C|0.993;T|0.007	0.007	strong	EML2,NS,carcinoma,-1,1	EML2	64	1	NM_001193268	exon12	c.G1422A	p.G474G	GAGGTTCCCCCCA	.	scavenged	Atlas-SNP
PCDHB7	56129	hgsc.bcm.edu	37	5	140552558	140552558	+	Silent	SNP	T	T	C	rs17096945	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	121	65	150	0	0.53719	0	T|0.860;C|0.140	0.140	strong	PCDHB7,NS,carcinoma,-2,1	PCDHB7	231	1	NM_018940	exon1	c.T142C	p.L48L	ACCAACTTGGCAA	.	PASS	Atlas-SNP
GJA9	81025	hgsc.bcm.edu	37	1	39340282	39340282	+	Missense_Mutation	SNP	C	C	T	rs880303	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	81	47	92	0	0.580247	0	C|0.662;N|0.000	.	strong	.	GJA9	55	.	NM_030772	exon2	c.G1489A	p.V497I	ACACTACGTGATT	.	PASS	Atlas-SNP
CATSPERD	257062	hgsc.bcm.edu	37	19	5748257	5748257	+	Missense_Mutation	SNP	A	A	G	rs139627891	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	79	35	108	0	0.443038	0	A|0.989;G|0.011	0.011	strong	.	.	.	.	NM_152784	exon10	c.A895G	p.I299V	CACAACATTGCTG	.	PASS	Atlas-SNP
LRGUK	136332	hgsc.bcm.edu	37	7	133812351	133812351	+	Silent	SNP	T	T	C	rs61732215	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	147	73	139	0	0.496599	0	T|0.945;C|0.055	0.055	strong	.	LRGUK	113	.	NM_144648	exon1	c.T231C	p.D77D	CGGAGATGAGGAC	.	PASS	Atlas-SNP
NRBF2	29982	hgsc.bcm.edu	37	10	64913517	64913517	+	Missense_Mutation	SNP	G	G	A	rs145813277	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	180	26	196	0	0.144444	0	G|0.998;A|0.002	0.002	strong	NRBF2,trunk,malignant_melanoma,0,1	NRBF2	18	1	NM_030759	exon4	c.G403A	p.D135N	ATCTTTGACAGGG	.	scavenged	Atlas-SNP
RPAP1	26015	hgsc.bcm.edu	37	15	41819466	41819466	+	Missense_Mutation	SNP	G	G	A	rs35981448	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	74	37	91	0	0.5	0	G|0.996;A|0.004	0.004	strong	.	RPAP1	111	.	NM_015540	exon13	c.C1645T	p.R549C	CGTAGCGCAGCCG	.	PASS	Atlas-SNP
DIP2A	23181	hgsc.bcm.edu	37	21	47910523	47910523	+	Silent	SNP	A	A	G	rs7279002	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	194	74	161	0	0.381443	0	A|0.634;G|0.366	0.366	strong	.	DIP2A	332	.	NM_206891	exon3	c.A174G	p.P58P	AGACCCATCTCTG	.	PASS	Atlas-SNP
MSL1	339287	hgsc.bcm.edu	37	17	38282624	38282624	+	Silent	SNP	C	C	T	rs28526298	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	100	47	121	0	0.47	0	C|0.938;T|0.062	0.062	strong	.	MSL1	21	.	NM_001012241	exon3	c.C168T	p.P56P	CAAGCCCTTCTCA	.	PASS	Atlas-SNP
LINGO1	84894	hgsc.bcm.edu	37	15	77907145	77907145	+	Silent	SNP	G	G	A	rs3743481	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	152	86	140	0	0.565789	0	G|0.496;A|0.504	0.504	strong	LINGO1,rectum,carcinoma,0,1	LINGO1	76	1	NM_032808	exon2	c.C1104T	p.S368S	CGGGTTGGAGTCC	.	PASS	Atlas-SNP
HTR1B	3351	hgsc.bcm.edu	37	6	78172260	78172260	+	Silent	SNP	C	C	G	rs6296	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	49	25	83	0	0.510204	0	C|0.709;G|0.291	0.291	strong	.	HTR1B	55	.	NM_000863	exon1	c.G861C	p.V287V	TTGGTTCACATAC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195507226	195507226	+	Missense_Mutation	SNP	A	A	G	rs201269328	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	76	66	65	9	0.868421	0.138462	A|0.001;G|0.999	0.999	weak	MUC4_ENST00000463781,NS,carcinoma,-1,2	MUC4	1505	2	NM_018406	exon2	c.T11225C	p.V3742A	GGGGTGACGTGAC	.	scavenged	Atlas-SNP
LRP1	4035	hgsc.bcm.edu	37	12	57550588	57550588	+	Silent	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	47	5	57	0	0.106383	0	.	.	none	.	LRP1	428	.	NM_002332	exon10	c.G1446A	p.Q482Q	CGACCAGTATGGG	.	PASS	Atlas-SNP
GPAT2	150763	hgsc.bcm.edu	37	2	96688916	96688916	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	264	29	339	1	0.109848	0.00294985	.	.	none	GPAT2,NS,carcinoma,+1,1	GPAT2	46	1	NM_207328	exon19	c.C2087T	p.P696L	AGCAGCGGGCTGA	.	scavenged	Atlas-SNP
SLC29A3	55315	hgsc.bcm.edu	37	10	73082563	73082563	+	Missense_Mutation	SNP	A	A	G	rs2277257	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	121	60	129	0	0.495868	0	A|0.527;G|0.473	0.473	strong	.	SLC29A3	51	.	NM_018344	exon2	c.A52G	p.R18G	ACCTACAGAACCA	.	PASS	Atlas-SNP
CDH6	1004	hgsc.bcm.edu	37	5	31317952	31317952	+	Silent	SNP	T	T	C	rs2229575	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	68	67	74	0	0.985294	0	T|0.595;C|0.405	0.405	strong	.	CDH6	175	.	NM_004932	exon11	c.T1803C	p.H601H	CTGCCATGCGGAG	.	PASS	Atlas-SNP
SFSWAP	6433	hgsc.bcm.edu	37	12	132250712	132250712	+	Silent	SNP	G	G	C	rs1051233	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	41	18	40	0	0.439024	0	G|0.840;C|0.160	0.160	strong	.	SFSWAP	69	.	NM_001261411	exon13	c.G2001C	p.L667L	AAAGCTGGCCCAG	.	PASS	Atlas-SNP
GATC	283459	hgsc.bcm.edu	37	12	120884328	120884328	+	Silent	SNP	C	C	T	rs2235217	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	61	38	70	0	0.622951	0	C|0.744;T|0.256	0.256	strong	.	GATC	12	.	NM_176818	exon1	c.C45T	p.G15G	TCTGGGCGGGCGC	.	PASS	Atlas-SNP
ORAI1	84876	hgsc.bcm.edu	37	12	122079348	122079348	+	Silent	SNP	T	T	C	rs3741597	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	112	45	134	0	0.401786	0	T|0.942;C|0.058	0.058	strong	.	ORAI1	66	.	NM_032790	exon2	c.T711C	p.A237A	GGCAGCTGCCATC	.	PASS	Atlas-SNP
ACTL7B	10880	hgsc.bcm.edu	37	9	111618209	111618209	+	Missense_Mutation	SNP	A	A	G	rs17728850	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	41	10	52	0	0.243902	0	A|0.915;G|0.085	0.085	strong	.	ACTL7B	57	.	NM_006686	exon1	c.T2C	p.M1T	GTCGCCATCTGCC	.	PASS	Atlas-SNP
ATXN1	6310	hgsc.bcm.edu	37	6	16327897	16327897	+	Missense_Mutation	SNP	C	C	A	rs184327938	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	51	19	48	0	0.372549	0	C|0.926;A|0.074	0.074	strong	ATXN1,NS,carcinoma,0,3	ATXN1	117	3	NM_001128164	exon7	c.G645T	p.Q215H	CTGCTGCTGCTGC	.	PASS	Atlas-SNP
CDKL4	344387	hgsc.bcm.edu	37	2	39440541	39440541	+	Silent	SNP	G	G	A	rs375514414		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	328	67	173	0	0.204268	0	.	.	weak	CDKL4,NS,carcinoma,0,1	CDKL4	30	1	NM_001009565	exon3	c.C363T	p.N121N	ACTTACGTTATGT	.	PASS	Atlas-SNP
HPS1	3257	hgsc.bcm.edu	37	10	100189568	100189568	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	63	33	93	0	0.52381	0	.	.	none	.	HPS1	65	.	NM_000195	exon9	c.G847T	p.G283W	TCCCCCCAGTTGG	.	PASS	Atlas-SNP
ZNF750	79755	hgsc.bcm.edu	37	17	80789628	80789628	+	Missense_Mutation	SNP	T	T	C	rs8074277	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	144	56	169	0	0.388889	0	T|0.855;C|0.145	0.145	strong	ZNF750,NS,adenoma,0,1	ZNF750	60	1	NM_024702	exon2	c.A703G	p.M235V	GGTGCATGTAAGG	.	PASS	Atlas-SNP
KRT17	3872	hgsc.bcm.edu	37	17	39777895	39777895	+	Nonsense_Mutation	SNP	T	T	A	rs146900210	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	347	172	307	1	0.495677	0.00325733	T|1.000;A|0.000	0.000	strong	.	KRT17	57	.	NM_000422	exon4	c.A784T	p.K262X	CCATCTTCTCATA	.	PASS	Atlas-SNP
ZSCAN1	284312	hgsc.bcm.edu	37	19	58549366	58549366	+	Silent	SNP	C	C	G	rs159870	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	18	6	9	0	0.333333	0	C|0.331;G|0.669	0.669	strong	.	ZSCAN1	102	.	NM_182572	exon3	c.C162G	p.L54L	GCACCTCGCGCTG	.	PASS	Atlas-SNP
PANX2	56666	hgsc.bcm.edu	37	22	50615556	50615556	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	181	4	163	0	0.0220994	0	.	.	none	PANX2_ENST00000395842,colon,carcinoma,0,2	PANX2	69	2	NM_052839	exon2	c.G415A	p.A139T	GTGCCCGCGCTGG	.	scavenged	Atlas-SNP
PPP1R26	9858	hgsc.bcm.edu	37	9	138377657	138377657	+	Missense_Mutation	SNP	T	T	C	rs1808998	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	22	14	34	0	0.636364	0	T|0.653;C|0.347	0.347	strong	.	.	.	.	NM_014811	exon4	c.T1301C	p.M434T	AGACCATGGACCC	.	PASS	Atlas-SNP
IDI2	91734	hgsc.bcm.edu	37	10	1065458	1065458	+	Silent	SNP	C	C	T	rs17851563	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	52	29	39	0	0.557692	0	C|0.978;T|0.022	0.022	strong	IDI2,caecum,carcinoma,0,1	IDI2	20	1	NM_033261	exon5	c.G683A	p.X228X	GCCTCTCACACTC	.	PASS	Atlas-SNP
FBLIM1	54751	hgsc.bcm.edu	37	1	16095031	16095031	+	Silent	SNP	G	G	A	rs140170023	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	120	55	123	0	0.458333	0	G|0.989;A|0.011	0.011	strong	.	FBLIM1	46	.	NM_001024215	exon4	c.G447A	p.A149A	CCCAGCGGAGGGA	.	PASS	Atlas-SNP
LAMA4	3910	hgsc.bcm.edu	37	6	112435912	112435912	+	Silent	SNP	A	A	T	rs1050353	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	115	57	128	0	0.495652	0	A|0.701;T|0.299	0.299	strong	.	LAMA4	227	.	NM_001105206	exon37	c.T5160A	p.V1720V	GGGTGTAACTGAG	.	PASS	Atlas-SNP
OR7A10	390892	hgsc.bcm.edu	37	19	14951898	14951898	+	Silent	SNP	G	G	T	rs3752195	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	53	28	73	0	0.528302	0	G|0.787;T|0.213	0.213	strong	OR7A10,NS,carcinoma,-2,1	OR7A10	33	1	NM_001005190	exon1	c.C792A	p.A264A	GTGGGTGGCAGCA	.	PASS	Atlas-SNP
CETN3	1070	hgsc.bcm.edu	37	5	89703535	89703535	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	332	122	342	0	0.36747	0	.	.	none	.	CETN3	16	.	NM_004365	exon2	c.T134G	p.I45R	TAATCTATTGCTT	.	PASS	Atlas-SNP
ARHGAP26	23092	hgsc.bcm.edu	37	5	142254679	142254679	+	Silent	SNP	A	A	G	rs185200	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	91	44	141	0	0.483516	0	A|0.466;G|0.534	0.534	strong	.	ARHGAP26	57	.	NM_015071	exon3	c.A255G	p.R85R	AGCAAGATCTTTG	.	PASS	Atlas-SNP
PKN1	5585	hgsc.bcm.edu	37	19	14582539	14582539	+	Silent	SNP	C	C	T	rs8598	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	22	17	19	0	0.772727	0	C|0.867;T|0.133	0.133	strong	.	PKN1	99	.	NM_213560	exon22	c.C2790T	p.L930L	GCCCCTCACAGCC	.	PASS	Atlas-SNP
C9orf129	445577	hgsc.bcm.edu	37	9	96080699	96080699	+	Missense_Mutation	SNP	C	C	T	rs36081907	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	34	65	0	0.478873	0	C|0.886;T|0.114	0.114	strong	.	C9orf129	18	.	NM_001098808	exon5	c.G572A	p.R191H	GAGAGACGGCGGG	.	PASS	Atlas-SNP
NEIL3	55247	hgsc.bcm.edu	37	4	178262683	178262683	+	Silent	SNP	T	T	C	rs17676249	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	53	25	51	0	0.471698	0	T|0.826;C|0.174	0.174	strong	.	NEIL3	89	.	NM_018248	exon6	c.T756C	p.P252P	GCGTCCTAATTGT	.	PASS	Atlas-SNP
APH1B	83464	hgsc.bcm.edu	37	15	63569902	63569902	+	Missense_Mutation	SNP	C	C	T	rs117618017	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	130	85	75	0	0.653846	0	C|0.915;T|0.085	0.085	strong	APH1B,NS,lymphoid_neoplasm,0,3	APH1B	27	3	NM_001145646	exon1	c.C80T	p.T27I	TCGCCACCGAGCC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195507323	195507323	+	Missense_Mutation	SNP	T	T	C	rs201618076		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	96	13	80	1	0.135417	0.0125	.	.	weak	MUC4_ENST00000463781,uveal_tract,malignant_melanoma,0,1	MUC4	1505	1	NM_018406	exon2	c.A11128G	p.T3710A	GGGTGGTGTGACC	.	scavenged	Atlas-SNP
TRIM51	84767	hgsc.bcm.edu	37	11	55653164	55653164	+	Missense_Mutation	SNP	G	G	A	rs10897403	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	62	15	118	0	0.241935	0	G|0.613;A|0.387	0.387	strong	.	.	.	.	NM_032681	exon2	c.G260A	p.S87N	TCCTTAGCTCTGA	.	PASS	Atlas-SNP
CACNA1I	8911	hgsc.bcm.edu	37	22	40057273	40057273	+	Silent	SNP	T	T	C	rs136852	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	59	37	66	0	0.627119	0	T|0.284;C|0.716	0.716	strong	.	CACNA1I	264	.	NM_021096	exon16	c.T2859C	p.S953S	GAGCAGTGTCATG	.	PASS	Atlas-SNP
OR1L8	138881	hgsc.bcm.edu	37	9	125330240	125330240	+	Missense_Mutation	SNP	T	T	G	rs72751258	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	114	66	132	0	0.578947	0	T|0.989;G|0.011	0.011	strong	.	OR1L8	90	.	NM_001004454	exon1	c.A517C	p.N173H	TAACATTGGAGTC	.	PASS	Atlas-SNP
NFXL1	152518	hgsc.bcm.edu	37	4	47901476	47901476	+	Missense_Mutation	SNP	G	G	A	rs12651301	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	138	72	174	0	0.521739	0	G|0.647;A|0.353	0.353	strong	.	NFXL1	79	.	NM_152995	exon6	c.C737T	p.P246L	AGCCACGGATCTA	.	PASS	Atlas-SNP
HIST1H2BG	8339	hgsc.bcm.edu	37	6	26216656	26216656	+	Silent	SNP	T	T	C	rs41266811	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	115	58	111	0	0.504348	0	T|0.903;C|0.097	0.097	strong	.	HIST1H2BG	25	.	NM_003518	exon1	c.A216G	p.E72E	GATGCGTTCGAAG	.	PASS	Atlas-SNP
OR5L1	219437	hgsc.bcm.edu	37	11	55579102	55579102	+	Missense_Mutation	SNP	C	C	T	rs34961497	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	167	103	121	0	0.616766	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
OR51F1	256892	hgsc.bcm.edu	37	11	4790268	4790268	+	Missense_Mutation	SNP	C	C	A	rs1030726	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	118	13	90	0	0.110169	0	C|0.712;A|0.288	0.288	strong	.	OR51F1	60	.	NM_001004752	exon1	c.G880T	p.D294Y	CACTGTCGATGAT	.	PASS	Atlas-SNP
CLASRP	11129	hgsc.bcm.edu	37	19	45563695	45563695	+	Silent	SNP	G	G	A	rs147776329	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	33	89	0	0.383721	0	G|0.991;A|0.009	0.009	strong	.	CLASRP	44	.	NM_007056	exon9	c.G759A	p.K253K	TGCCAAGGCTCTT	.	PASS	Atlas-SNP
OPLAH	26873	hgsc.bcm.edu	37	8	145114924	145114924	+	Silent	SNP	G	G	C	rs7003860	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	61	59	76	0	0.967213	0	G|0.894;C|0.106	0.106	strong	.	OPLAH	78	.	NM_017570	exon2	c.C12G	p.P4P	GCCCTCGGGGCTG	.	PASS	Atlas-SNP
DTHD1	401124	hgsc.bcm.edu	37	4	36310049	36310049	+	Missense_Mutation	SNP	C	C	T	rs12507599	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	67	37	112	0	0.552239	0	C|0.725;T|0.275	0.275	strong	.	DTHD1	63	.	NM_001170700	exon6	c.C1654T	p.R552C	CCATCTCGTCATT	.	PASS	Atlas-SNP
VPRBP	9730	hgsc.bcm.edu	37	3	51458204	51458204	+	Silent	SNP	G	G	A	rs150385433	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	121	69	153	0	0.570248	0	G|0.995;A|0.005	0.005	strong	.	VPRBP	107	.	NM_014703	exon14	c.C2061T	p.S687S	CAGTAAGGACAGG	.	PASS	Atlas-SNP
CD70	970	hgsc.bcm.edu	37	19	6586268	6586268	+	Silent	SNP	G	G	A	rs1862511	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	106	105	131	0	0.990566	0	G|0.695;A|0.305	0.305	strong	.	CD70	24	.	NM_001252	exon3	c.C345T	p.C115C	GGAGGAGCAGATG	.	PASS	Atlas-SNP
STT3A	3703	hgsc.bcm.edu	37	11	125478126	125478126	+	Silent	SNP	C	C	T	rs149906495		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	96	2	127	0	0.0208333	0	C|1.000;T|0.000	0.000	weak	STT3A,NS,carcinoma,0,1	STT3A	52	1	NM_152713	exon9	c.C903T	p.S301S	CCGGAGCGTCATC	.	scavenged	Atlas-SNP
CETN3	1070	hgsc.bcm.edu	37	5	89703641	89703641	+	Missense_Mutation	SNP	C	C	G	rs4873	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	138	64	167	0	0.463768	0	C|0.804;G|0.196	0.196	strong	.	CETN3	16	.	NM_004365	exon2	c.G28C	p.V10L	CCACTACAAGCTC	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	88	49	106	0	0.556818	0	A|0.786;N|0.000	.	strong	.	ATAD5	150	.	NM_024857	exon2	c.A103T	p.T35S	ACATCTACCTGCA	.	PASS	Atlas-SNP
SIPA1L2	57568	hgsc.bcm.edu	37	1	232574921	232574921	+	Missense_Mutation	SNP	T	T	C	rs2275307	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	64	27	86	0	0.421875	0	T|0.688;C|0.311	0.311	strong	.	SIPA1L2	218	.	NM_020808	exon13	c.A3964G	p.T1322A	AGATGGTGGACGC	.	PASS	Atlas-SNP
SOGA1	140710	hgsc.bcm.edu	37	20	35443768	35443768	+	Missense_Mutation	SNP	G	G	A	rs201600310		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	36	96	0	0.439024	0	G|0.998;A|0.002	0.002	weak	.	SOGA1	136	.	NM_080627	exon5	c.C2077T	p.R693W	GCAGCCGGAAGTC	.	PASS	Atlas-SNP
KIAA1549	57670	hgsc.bcm.edu	37	7	138545996	138545996	+	Silent	SNP	G	G	A	rs12707399	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	40	17	72	0	0.425	0	G|0.913;A|0.087	0.087	strong	.	KIAA1549	314	.	NM_020910	exon16	c.C5136T	p.P1712P	GACTCCGGGGCCT	.	PASS	Atlas-SNP
DDX27	55661	hgsc.bcm.edu	37	20	47859217	47859217	+	Missense_Mutation	SNP	G	G	A	rs1130146	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	126	67	104	0	0.531746	0	G|0.716;A|0.284	0.284	strong	.	DDX27	74	.	NM_017895	exon19	c.G2296A	p.G766S	CGAGCTGGGTAGG	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	47	140	0	0.484536	0	C|0.539;G|0.461	0.461	strong	.	C10orf113	32	.	NM_001010896	exon2	c.G328C	p.D110H	CTGGATCTGGTTC	.	PASS	Atlas-SNP
ARAP3	64411	hgsc.bcm.edu	37	5	141033870	141033870	+	Missense_Mutation	SNP	T	T	G	rs61749636	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	167	81	165	0	0.48503	0	T|0.952;G|0.048	0.048	strong	ARAP3,colon,carcinoma,+2,4	ARAP3	139	4	NM_022481	exon33	c.A4282C	p.T1428P	CCCGTGTGGTGGA	.	PASS	Atlas-SNP
CCM2	83605	hgsc.bcm.edu	37	7	45077978	45077978	+	Missense_Mutation	SNP	G	G	A	rs2107732	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	57	17	85	0	0.298246	0	G|0.938;A|0.062	0.062	strong	.	CCM2	42	.	NM_001029835	exon2	c.G220A	p.V74I	GAGCGCGTCGAGC	.	PASS	Atlas-SNP
ZNF185	7739	hgsc.bcm.edu	37	X	152083059	152083059	+	Missense_Mutation	SNP	G	G	A	rs6526142	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	69	131	0	0.985714	0	G|0.750;A|0.250	0.250	strong	.	ZNF185	92	.	NM_001178109	exon1	c.G26A	p.R9H	GAGGCCGCACCAA	.	PASS	Atlas-SNP
ZNF679	168417	hgsc.bcm.edu	37	7	63726678	63726678	+	Missense_Mutation	SNP	T	T	A	rs1830036	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	32	8	45	0	0.25	0	T|0.900;A|0.100	0.100	strong	.	ZNF679	80	.	NM_153363	exon5	c.T667A	p.C223S	TTCAACTGCTCTT	.	PASS	Atlas-SNP
MFI2	4241	hgsc.bcm.edu	37	3	196743130	196743130	+	Silent	SNP	T	T	C	rs6779362	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	76	34	110	0	0.447368	0	T|0.686;C|0.314	0.314	strong	MFI2,NS,carcinoma,0,1	MFI2	88	1	NM_005929	exon8	c.A1011G	p.T337T	GGTCTGTGTGGCG	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	122	51	130	0	0.418033	0	A|0.796;G|0.204	0.204	strong	.	NPPA	14	.	NM_006172	exon3	c.T454C	p.X152R	ATCTTCAGTACTG	.	PASS	Atlas-SNP
PODXL	5420	hgsc.bcm.edu	37	7	131194255	131194255	+	Missense_Mutation	SNP	G	G	C	rs35893129	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	178	95	185	0	0.533708	0	G|0.949;C|0.051	0.051	strong	.	PODXL	53	.	NM_001018111	exon4	c.C892G	p.P298A	TCGTGGGCTGCAC	.	PASS	Atlas-SNP
ZKSCAN4	387032	hgsc.bcm.edu	37	6	28219661	28219661	+	Missense_Mutation	SNP	G	G	A	rs9986596	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	48	34	73	0	0.708333	0	G|0.842;A|0.158	0.158	strong	.	ZKSCAN4	42	.	NM_019110	exon1	c.C98T	p.S33F	AAGGCGGAGGCTT	.	PASS	Atlas-SNP
GK5	256356	hgsc.bcm.edu	37	3	141884493	141884493	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	303	148	396	0	0.488449	0	.	.	none	GK5,NS,carcinoma,+1,1	GK5	45	1	NM_001039547	exon16	c.C1561T	p.R521C	TGGAGCGTTTCAC	.	PASS	Atlas-SNP
CRISPLD2	83716	hgsc.bcm.edu	37	16	84906098	84906098	+	Missense_Mutation	SNP	C	C	G	rs721005	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	338	337	286	0	0.997041	0	C|0.539;G|0.461	0.461	strong	CRISPLD2,NS,carcinoma,0,1	CRISPLD2	36	1	NM_031476	exon9	c.C965G	p.T322S	TTGGAACTCTGTT	.	PASS	Atlas-SNP
C2orf16	84226	hgsc.bcm.edu	37	2	27802805	27802805	+	Silent	SNP	A	A	G	rs3811644	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	200	78	164	0	0.39	0	A|0.811;G|0.189	0.189	strong	.	C2orf16	357	.	NM_032266	exon1	c.A3366G	p.L1122L	CTGCCTACAGTGT	.	PASS	Atlas-SNP
MYOF	26509	hgsc.bcm.edu	37	10	95095792	95095792	+	Silent	SNP	A	A	G	rs79155397	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	114	50	119	0	0.438596	0	A|0.936;G|0.064	0.064	strong	.	MYOF	177	.	NM_013451	exon41	c.T4449C	p.C1483C	TAGTTCACAATTA	.	PASS	Atlas-SNP
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057422	46057422	+	Missense_Mutation	SNP	T	T	A	rs112205018	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	84	16	116	0	0.190476	0	T|0.742;A|0.258	0.258	strong	KRTAP10-10,caecum,carcinoma,0,1	KRTAP10-10	37	1	NM_181688	exon1	c.T88A	p.C30S	GAGCCCTGCTGCT	.	PASS	Atlas-SNP
MAGEC3	139081	hgsc.bcm.edu	37	X	140983103	140983103	+	Silent	SNP	C	C	T	rs176025	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	150	148	201	1	0.986667	0.00497512	C|0.685;T|0.315	0.315	strong	.	MAGEC3	228	.	NM_138702	exon5	c.C958T	p.L320L	CTTGCACTGTGGG	.	PASS	Atlas-SNP
SIGLEC6	946	hgsc.bcm.edu	37	19	52033158	52033158	+	Missense_Mutation	SNP	C	C	T	rs35931837	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	109	44	105	0	0.40367	0	C|0.914;T|0.086	0.086	strong	SIGLEC6_ENST00000425629,NS,carcinoma,+2,2	SIGLEC6	142	2	NM_001177548	exon5	c.G865A	p.G289S	GGTTGCCGTCAGC	.	PASS	Atlas-SNP
MTUS1	57509	hgsc.bcm.edu	37	8	17611886	17611886	+	Silent	SNP	G	G	A	rs2979788	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	139	139	219	0	1	0	G|0.311;A|0.689	0.689	strong	.	MTUS1	144	.	NM_001001924	exon2	c.C1431T	p.P477P	TAAACTGGGTTTA	.	PASS	Atlas-SNP
TSHZ3	57616	hgsc.bcm.edu	37	19	31769763	31769763	+	Silent	SNP	G	G	A	rs12461253	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	89	43	107	0	0.483146	0	G|0.689;A|0.311	0.311	strong	.	TSHZ3	549	.	NM_020856	exon2	c.C936T	p.V312V	GGCGGCGACAGGA	.	PASS	Atlas-SNP
PDE4DIP	9659	hgsc.bcm.edu	37	1	144922523	144922523	+	Missense_Mutation	SNP	C	C	T	rs2455994	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	160	34	229	0	0.2125	0	C|0.738;T|0.262	0.262	strong	.	PDE4DIP	817	.	NM_001002811	exon3	c.G1373A	p.R458H	ACCTCACGTTCCC	.	PASS	Atlas-SNP
BCAT2	587	hgsc.bcm.edu	37	19	49309776	49309776	+	Missense_Mutation	SNP	G	G	C	rs117048185	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	45	86	0	0.529412	0	G|0.990;C|0.010	0.010	strong	.	BCAT2	35	.	NM_001190	exon3	c.C298G	p.Q100E	CCACCTGCAGGGA	.	PASS	Atlas-SNP
RPTN	126638	hgsc.bcm.edu	37	1	152129100	152129100	+	Missense_Mutation	SNP	C	C	T	rs200003389	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	179	32	273	1	0.178771	0.003663	C|0.966;T|0.034	0.034	strong	RPTN,NS,carcinoma,0,1	RPTN	123	1	NM_001122965	exon3	c.G475A	p.G159S	ACTGACCATGGTG	.	scavenged	Atlas-SNP
TET1	80312	hgsc.bcm.edu	37	10	70405539	70405539	+	Missense_Mutation	SNP	A	A	G	rs71483917	alternate_allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	157	69	180	0	0.43949	0	ATA|0.500;GTG|0.500	.	alt	.	TET1	255	.	NM_030625	exon4	c.A3053G	p.N1018S	ACACCAATAAAAG	.	PASS	Atlas-SNP
LILRB3	11025	hgsc.bcm.edu	37	19	54722275	54722275	+	Silent	SNP	G	G	A	rs56528424		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	144	65	173	0	0.451389	0	.	.	weak	.	LILRB3	67	.	NM_006864	exon11	c.C1548T	p.A516A	CTTCACGGCAGCA	.	PASS	Atlas-SNP
DCPS	28960	hgsc.bcm.edu	37	11	126174164	126174164	+	Silent	SNP	C	C	T	rs695029	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	80	63	98	0	0.7875	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
C4orf17	84103	hgsc.bcm.edu	37	4	100443800	100443800	+	Missense_Mutation	SNP	G	G	A	rs17029087	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	40	107	0	0.434783	0	G|0.780;A|0.220	0.220	strong	.	C4orf17	42	.	NM_032149	exon3	c.G271A	p.E91K	GTCCAGGAGAGCC	.	PASS	Atlas-SNP
THOC5	8563	hgsc.bcm.edu	37	22	29913272	29913272	+	Missense_Mutation	SNP	C	C	T	rs737976	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	169	77	205	0	0.455621	0	C|0.516;T|0.484	0.484	strong	.	THOC5	58	.	NM_001002878	exon17	c.G1573A	p.V525I	GGGCAACTGTCAC	.	PASS	Atlas-SNP
LMO2	4005	hgsc.bcm.edu	37	11	33881016	33881016	+	Silent	SNP	T	T	C	rs3740617	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	145	145	196	1	1	0.00510204	A|0.005;C|0.553	0.553	strong	LMO2,NS,carcinoma,-2,2	LMO2	21	2	NM_005574	exon6	c.A570G	p.K190K	GGCGCATTTGAAA	.	PASS	Atlas-SNP
SLC4A5	57835	hgsc.bcm.edu	37	2	74460685	74460685	+	Silent	SNP	C	C	T	rs3796109	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	28	12	25	0	0.428571	0	C|0.917;T|0.083	0.083	strong	.	SLC4A5	215	.	NM_021196	exon18	c.G2439A	p.T813T	AGGCCGCGTTGGC	.	PASS	Atlas-SNP
NCOA6	23054	hgsc.bcm.edu	37	20	33328372	33328372	+	Silent	SNP	C	C	T	rs141863711		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	45	16	56	0	0.355556	0	C|1.000;T|0.000	0.000	weak	.	NCOA6	219	.	NM_014071	exon11	c.G5688A	p.P1896P	AGTGCCCGGGCCC	.	PASS	Atlas-SNP
ZNF217	7764	hgsc.bcm.edu	37	20	52192417	52192417	+	Silent	SNP	C	C	T	rs45439395	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	99	55	106	0	0.555556	0	C|0.997;T|0.003	0.003	strong	.	ZNF217	227	.	NM_006526	exon3	c.G2886A	p.P962P	CTGCGACGGATAC	.	PASS	Atlas-SNP
WDR33	55339	hgsc.bcm.edu	37	2	128522207	128522207	+	Missense_Mutation	SNP	C	C	T	rs17534123	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	294	145	383	0	0.493197	0	C|0.943;T|0.057	0.057	strong	.	WDR33	136	.	NM_001006622	exon6	c.G821A	p.R274Q	TGATACCGGGACA	.	PASS	Atlas-SNP
DPYSL4	10570	hgsc.bcm.edu	37	10	134017388	134017388	+	Silent	SNP	C	C	G	rs1052556	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	169	85	153	0	0.502959	0	C|0.865;G|0.135	0.135	strong	.	DPYSL4	91	.	NM_006426	exon13	c.C1584G	p.V528V	CTCCGTCCCTCCT	.	PASS	Atlas-SNP
ZNF735	730291	hgsc.bcm.edu	37	7	63680401	63680401	+	Silent	SNP	C	C	T	rs10258764	bycluster;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	15	10	20	0	0.666667	0	C|0.910;T|0.090	0.090	strong	.	.	.	.	NM_001159524	exon4	c.C972T	p.P324P	GAAACCCTACACA	.	PASS	Atlas-SNP
PLA2R1	22925	hgsc.bcm.edu	37	2	160885418	160885418	+	Missense_Mutation	SNP	G	G	C	rs35771982	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	244	116	277	0	0.47541	0	G|0.655;C|0.345	0.345	strong	.	PLA2R1	153	.	NM_001195641	exon5	c.C898G	p.H300D	CAGCGTGTTCATC	.	PASS	Atlas-SNP
OR5L1	219437	hgsc.bcm.edu	37	11	55579801	55579801	+	Missense_Mutation	SNP	T	T	C	rs12790505	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	98	75	82	0	0.765306	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
MC1R	4157	hgsc.bcm.edu	37	16	89985950	89985950	+	Missense_Mutation	SNP	C	C	T	rs34158934	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	115	67	114	0	0.582609	0	C|0.995;T|0.005	0.005	strong	.	MC1R	20	.	NM_002386	exon1	c.C284T	p.T95M	TGGAGACGGCCGT	.	PASS	Atlas-SNP
PITPNM3	83394	hgsc.bcm.edu	37	17	6406883	6406883	+	Missense_Mutation	SNP	C	C	T	rs3809835	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	25	10	19	0	0.4	0	C|0.696;T|0.304	0.304	strong	.	PITPNM3	91	.	NM_031220	exon4	c.G238A	p.A80T	ACGGCGCGGTCCC	.	PASS	Atlas-SNP
PTBP1	5725	hgsc.bcm.edu	37	19	804396	804396	+	Silent	SNP	C	C	T	rs3180287	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	31	31	42	0	1	0	C|0.862;G|0.000;T|0.138	0.138	strong	.	PTBP1	43	.	NM_031990	exon5	c.C393T	p.S131S	GTTCTCCAACCAC	.	PASS	Atlas-SNP
A2ML1	144568	hgsc.bcm.edu	37	12	8995756	8995756	+	Silent	SNP	A	A	G	rs7308106	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	55	27	50	0	0.490909	0	A|0.939;G|0.061	0.061	strong	.	A2ML1	199	.	NM_144670	exon12	c.A1275G	p.V425V	CTTAGTATATAAT	.	PASS	Atlas-SNP
CBR3	874	hgsc.bcm.edu	37	21	37507769	37507769	+	Silent	SNP	C	C	T	rs881712	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	132	70	108	0	0.530303	0	C|0.666;T|0.334	0.334	strong	.	CBR3	11	.	NM_001236	exon1	c.C279T	p.V93V	GGCCGTCGCCTTC	.	PASS	Atlas-SNP
LILRA4	23547	hgsc.bcm.edu	37	19	54848741	54848741	+	Silent	SNP	T	T	C	rs12985462	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	164	77	205	0	0.469512	0	T|0.855;C|0.145	0.145	strong	LILRA4,NS,carcinoma,0,1	LILRA4	91	1	NM_012276	exon5	c.A882G	p.R294R	GTAGCATCTGTAC	.	PASS	Atlas-SNP
RGS3	5998	hgsc.bcm.edu	37	9	116356776	116356776	+	Silent	SNP	C	C	T	rs61749208	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	151	81	137	0	0.536424	0	C|0.933;G|0.000;T|0.067	0.067	strong	.	RGS3	251	.	NM_144488	exon23	c.C3147T	p.P1049P	CCCTCCCGCGGGC	.	PASS	Atlas-SNP
TPRX1	284355	hgsc.bcm.edu	37	19	48305602	48305602	+	Silent	SNP	C	C	T	rs147608412	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	26	7	20	0	0.269231	0	C|0.943;T|0.057	0.057	strong	TPRX1,NS,carcinoma,-1,1	TPRX1	46	1	NM_198479	exon2	c.G666A	p.P222P	TGGGATCGGGCCT	.	PASS	Atlas-SNP
PTOV1	53635	hgsc.bcm.edu	37	19	50358133	50358133	+	Silent	SNP	T	T	G	rs75478119	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	110	109	152	1	0.990909	0.00657895	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
FAT1	2195	hgsc.bcm.edu	37	4	187531022	187531022	+	Missense_Mutation	SNP	A	A	G	rs28647489	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	170	80	165	2	0.470588	0.0121212	A|0.797;G|0.203	0.203	strong	FAT1,NS,carcinoma,0,2	FAT1	500	2	NM_005245	exon15	c.T10001C	p.V3334A	CTGAACACAGGGG	.	scavenged	Atlas-SNP
VPS13C	54832	hgsc.bcm.edu	37	15	62202482	62202482	+	Missense_Mutation	SNP	C	C	T	rs10851704	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	46	46	60	0	1	0	C|0.476;T|0.524	0.524	strong	.	VPS13C	506	.	NM_020821	exon64	c.G8738A	p.S2913N	GACAAACTTTCTG	.	PASS	Atlas-SNP
TSPYL4	23270	hgsc.bcm.edu	37	6	116575116	116575116	+	Missense_Mutation	SNP	G	G	T	rs17524614	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	104	104	112	0	1	0	G|0.876;T|0.124	0.124	strong	.	TSPYL4	18	.	NM_021648	exon1	c.C56A	p.A19D	GGAGCAGCCAGGC	.	PASS	Atlas-SNP
ZNF142	7701	hgsc.bcm.edu	37	2	219513782	219513782	+	Silent	SNP	T	T	C	rs4674322	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	49	21	57	0	0.428571	0	T|0.861;C|0.139	0.139	strong	.	ZNF142	190	.	NM_001105537	exon6	c.A849G	p.P283P	GGGTAATGGCTCT	.	PASS	Atlas-SNP
ADAM33	80332	hgsc.bcm.edu	37	20	3652365	3652365	+	Missense_Mutation	SNP	T	T	C	rs55687415	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	53	22	66	0	0.415094	0	T|0.992;C|0.008	0.008	strong	.	ADAM33	76	.	NM_025220	exon16	c.A1768G	p.M590V	GCACCATGTGCGG	.	PASS	Atlas-SNP
CISD3	284106	hgsc.bcm.edu	37	17	36889559	36889559	+	Missense_Mutation	SNP	C	C	T	rs2879097	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	76	33	81	0	0.434211	0	C|0.849;T|0.151	0.151	strong	.	CISD3	12	.	NM_001136498	exon4	c.C235T	p.R79C	TTCCAACGCACTG	.	PASS	Atlas-SNP
LMNA	4000	hgsc.bcm.edu	37	1	156084760	156084760	+	Silent	SNP	C	C	T	rs11549668	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	25	20	31	0	0.8	0	C|0.991;T|0.009	0.009	strong	.	LMNA	31	.	NM_170707	exon1	c.C51T	p.S17S	GGCCAGCTCCACT	.	PASS	Atlas-SNP
SOX5	6660	hgsc.bcm.edu	37	12	23687354	23687354	+	Silent	SNP	G	G	A	rs61756181	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	80	35	83	0	0.4375	0	G|0.977;A|0.023	0.023	strong	.	SOX5	134	.	NM_006940	exon15	c.C2091T	p.S697S	AGACACGCTTGAG	.	PASS	Atlas-SNP
C7	730	hgsc.bcm.edu	37	5	40964885	40964885	+	Missense_Mutation	SNP	A	A	T	rs60714178	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	230	113	220	0	0.491304	0	A|0.902;T|0.098	0.098	strong	.	C7	136	.	NM_000587	exon14	c.A1792T	p.T598S	GTGTACACTTGCA	.	PASS	Atlas-SNP
MAP7D1	55700	hgsc.bcm.edu	37	1	36636774	36636774	+	Silent	SNP	G	G	A	rs139650826	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	39	72	0	0.47561	0	G|0.992;A|0.008	0.008	strong	.	MAP7D1	62	.	NM_018067	exon2	c.G249A	p.Q83Q	CCCGCAGGAAGAG	.	PASS	Atlas-SNP
APCDD1	147495	hgsc.bcm.edu	37	18	10471764	10471764	+	Silent	SNP	C	C	T	rs3748414	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	51	29	58	0	0.568627	0	T|0.102;G|0.000;C|0.898	0.102	strong	.	APCDD1	57	.	NM_153000	exon3	c.C480T	p.A160A	GGTGGCCGAGAAG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195507925	195507925	+	Missense_Mutation	SNP	C	C	T	rs71635074	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	186	36	143	0	0.193548	0	T|1.000;|0.000	1.000	weak	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.G10526A	p.G3509D	GAAGCGCCGGTGA	.	PASS	Atlas-SNP
NAT2	10	hgsc.bcm.edu	37	8	18258370	18258370	+	Missense_Mutation	SNP	G	G	A	rs1799931	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	13	82	0	0.173333	0	G|0.949;A|0.051	0.051	strong	.	NAT2	34	.	NM_000015	exon2	c.G857A	p.G286E	GTGATGGATCCCT	.	PASS	Atlas-SNP
C1orf27	54953	hgsc.bcm.edu	37	1	186363119	186363119	+	Missense_Mutation	SNP	C	C	G	rs12084264	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	214	211	273	0	0.985981	0	C|0.756;G|0.244	0.244	strong	C1orf27_ENST00000287859,NS,carcinoma,0,2	C1orf27	41	2	NM_017847	exon9	c.C752G	p.S251C	GTCATTCTTTTGA	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	37	17	70	0	0.459459	0	A|0.750;G|0.250	0.250	strong	.	SERPINA5	69	.	NM_000624	exon3	c.A313G	p.K105E	TCAGAGAAGGAGC	.	PASS	Atlas-SNP
OR5H2	79310	hgsc.bcm.edu	37	3	98002429	98002429	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	137	39	169	0	0.284672	0	.	.	none	OR5H2,NS,carcinoma,0,1	OR5H2	63	1	NM_001005482	exon1	c.A698T	p.K233M	TAAAAAAGAAGTC	.	PASS	Atlas-SNP
NOS1AP	9722	hgsc.bcm.edu	37	1	162335256	162335256	+	Silent	SNP	C	C	T	rs348624	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	89	34	78	0	0.382022	0	C|0.779;T|0.221	0.221	strong	.	NOS1AP	139	.	NM_014697	exon9	c.C1002T	p.R334R	GGCTCGCGTGCAT	.	PASS	Atlas-SNP
MYOF	26509	hgsc.bcm.edu	37	10	95082894	95082894	+	Silent	SNP	G	G	A	rs35527060	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	163	82	226	0	0.503067	0	G|0.960;A|0.040	0.040	strong	MYOF,caecum,carcinoma,-1,1	MYOF	177	1	NM_013451	exon48	c.C5397T	p.D1799D	GATAACGTCCTTG	.	PASS	Atlas-SNP
CHST4	10164	hgsc.bcm.edu	37	16	71570847	71570847	+	Missense_Mutation	SNP	G	G	A	rs148657245	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	205	131	181	0	0.639024	0	G|0.993;A|0.007	0.007	strong	.	CHST4	47	.	NM_001166395	exon2	c.G267A	p.M89I	CTGGATGCTGCAC	.	PASS	Atlas-SNP
HIBADH	11112	hgsc.bcm.edu	37	7	27702390	27702390	+	Silent	SNP	C	C	A	rs11550134	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	50	39	45	0	0.78	0	C|0.727;A|0.273	0.273	strong	.	HIBADH	28	.	NM_152740	exon1	c.G18T	p.R6R	GAGGAGCCGTAAG	.	PASS	Atlas-SNP
KRTAP12-4	386684	hgsc.bcm.edu	37	21	46074202	46074202	+	Silent	SNP	A	A	G	rs9984726	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	148	148	167	0	1	0	A|0.264;G|0.736	0.736	strong	.	KRTAP12-4	10	.	NM_198698	exon1	c.T330C	p.T110T	GCAGCCAGTGGGG	.	PASS	Atlas-SNP
HLA-C	3107	hgsc.bcm.edu	37	6	31238995	31238995	+	Silent	SNP	G	G	A	rs41553316	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	149	48	125	0	0.322148	0	G|0.972;A|0.028	0.028	strong	.	HLA-C	92	.	NM_002117	exon3	c.C474T	p.T158T	CGCGGCGGTCCAG	.	PASS	Atlas-SNP
NOD1	10392	hgsc.bcm.edu	37	7	30492550	30492550	+	Silent	SNP	G	G	A	rs72551114	byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	66	21	91	0	0.318182	0	G|0.895;A|0.105	0.105	strong	.	NOD1	79	.	NM_006092	exon6	c.C483T	p.D161D	GATGGTGTCCATG	.	PASS	Atlas-SNP
DNAH1	25981	hgsc.bcm.edu	37	3	52391735	52391735	+	Silent	SNP	A	A	C	rs11714402	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	142	72	144	1	0.507042	0.00694444	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
NME8	51314	hgsc.bcm.edu	37	7	37934146	37934146	+	Missense_Mutation	SNP	T	T	C	rs56128139	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	242	190	268	0	0.785124	0	T|0.761;C|0.239	0.239	strong	.	.	.	.	NM_016616	exon16	c.T1478C	p.I493T	AGCAAATAGAGAA	.	PASS	Atlas-SNP
MICA	100507436	hgsc.bcm.edu	37	6	31380194	31380194	+	Missense_Mutation	SNP	T	T	C	rs41554412	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	44	24	98	0	0.545455	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
KLHDC7B	113730	hgsc.bcm.edu	37	22	50988062	50988062	+	Silent	SNP	G	G	T	rs140519	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	38	57	0	0.542857	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
SFRP2	6423	hgsc.bcm.edu	37	4	154709854	154709854	+	Missense_Mutation	SNP	G	G	A	rs4643790	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	110	50	91	0	0.454545	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
SIGLEC12	89858	hgsc.bcm.edu	37	19	52001485	52001485	+	Missense_Mutation	SNP	G	G	A	rs11668530	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	42	42	66	0	1	0	G|0.640;A|0.360	0.360	strong	.	SIGLEC12	243	.	NM_053003	exon5	c.C1192T	p.H398Y	CAAGGTGCAGGGA	.	PASS	Atlas-SNP
MYH7B	57644	hgsc.bcm.edu	37	20	33565755	33565755	+	Missense_Mutation	SNP	G	G	A	rs11906160	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	28	9	22	0	0.321429	0	G|0.858;A|0.142	0.142	strong	.	MYH7B	145	.	NM_020884	exon5	c.G73A	p.A25T	TGGGCCGCCTTGA	.	PASS	Atlas-SNP
ACTR3C	653857	hgsc.bcm.edu	37	7	149983565	149983565	+	Missense_Mutation	SNP	T	T	C	rs76400975		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	120	30	201	0	0.25	0	T|0.500;C|0.500	0.500	weak	Q9C0K3_HUMAN,NS,carcinoma,0,1	.	.	1	NM_001164459	exon5	c.A362G	p.Q121R	CACTTCTGGGGAT	.	scavenged	Atlas-SNP
GDPGP1	390637	hgsc.bcm.edu	37	15	90785060	90785060	+	Missense_Mutation	SNP	C	C	T	rs10153004	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	180	74	138	0	0.411111	0	C|0.835;T|0.165	0.165	strong	.	.	.	.	NM_001013657	exon4	c.C920T	p.T307I	CCCTCACAGGGGT	.	PASS	Atlas-SNP
STON1	11037	hgsc.bcm.edu	37	2	48808898	48808898	+	Silent	SNP	C	C	T	rs3749145	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	226	53	127	0	0.234513	0	C|0.681;T|0.319	0.319	strong	.	STON1	100	.	NM_001198595	exon3	c.C1126T	p.L376L	CAGATGCTGAAGT	.	PASS	Atlas-SNP
MFHAS1	9258	hgsc.bcm.edu	37	8	8749318	8749318	+	Silent	SNP	A	A	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	36	17	42	0	0.472222	0	.	.	none	.	MFHAS1	58	.	NM_004225	exon1	c.T1251C	p.H417H	AGCCTTATGCCCC	.	PASS	Atlas-SNP
PKHD1	5314	hgsc.bcm.edu	37	6	51914956	51914956	+	Missense_Mutation	SNP	G	G	A	rs9370096	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	108	108	109	0	1	0	G|0.620;A|0.380	0.380	strong	.	PKHD1	927	.	NM_170724	exon22	c.C2278T	p.R760C	CTTACCGTGCAGT	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29910731	29910731	+	Missense_Mutation	SNP	G	G	A	rs79361534	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	179	108	274	0	0.603352	0	A|0.124;G|0.876	0.124	strong	.	HLA-A	89	.	NM_001242758	exon2	c.G271A	p.V91M	CGGAATGTGAAGG	.	PASS	Atlas-SNP
RNF17	56163	hgsc.bcm.edu	37	13	25440318	25440318	+	Missense_Mutation	SNP	G	G	A	rs9507425	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	227	103	274	0	0.453745	0	G|0.778;A|0.222	0.222	strong	.	RNF17	259	.	NM_031277	exon30	c.G4138A	p.E1380K	GAAGAGGAACAAT	.	PASS	Atlas-SNP
KRTAP10-9	386676	hgsc.bcm.edu	37	21	46047857	46047857	+	Missense_Mutation	SNP	C	C	T	rs9980129	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	185	183	139	0	0.989189	0	C|0.352;T|0.648	0.648	strong	.	KRTAP10-9	24	.	NM_198690	exon1	c.C769T	p.R257C	TCCTCCCGCCAGC	.	PASS	Atlas-SNP
SLC16A9	220963	hgsc.bcm.edu	37	10	61414176	61414176	+	Missense_Mutation	SNP	G	G	A	rs56370926	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	49	21	54	0	0.428571	0	G|0.965;A|0.035	0.035	strong	.	SLC16A9	58	.	NM_194298	exon5	c.C608T	p.A203V	TCTGGAGCTATTT	.	PASS	Atlas-SNP
CYP4F2	8529	hgsc.bcm.edu	37	19	16006413	16006413	+	Silent	SNP	G	G	A	rs3093114	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	33	21	28	0	0.636364	0	G|0.861;A|0.139	0.139	strong	.	CYP4F2	97	.	NM_001082	exon3	c.C246T	p.A82A	GTAGGTGGCCACC	.	PASS	Atlas-SNP
MYH9	4627	hgsc.bcm.edu	37	22	36684354	36684354	+	Missense_Mutation	SNP	T	T	C	rs2269529	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	89	42	110	0	0.47191	0	T|0.784;C|0.216	0.216	strong	.	MYH9	225	.	NM_002473	exon34	c.A4876G	p.I1626V	AGTCGATGTGCGC	.	PASS	Atlas-SNP
WDR25	79446	hgsc.bcm.edu	37	14	100996337	100996337	+	Missense_Mutation	SNP	G	G	A	rs144754220		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	91	20	98	0	0.21978	0	G|1.000;A|0.000	0.000	weak	.	WDR25	37	.	NM_001161476	exon7	c.G1594A	p.A532T	GTCCTCGCCACCT	.	PASS	Atlas-SNP
DNMT1	1786	hgsc.bcm.edu	37	19	10265725	10265725	+	Silent	SNP	G	G	A	rs75443147	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	45	27	64	0	0.6	0	G|0.997;A|0.003	0.003	strong	.	DNMT1	148	.	NM_001130823	exon20	c.C1500T	p.A500A	GTATTCGGCAAAT	.	PASS	Atlas-SNP
ACRV1	56	hgsc.bcm.edu	37	11	125547869	125547869	+	Missense_Mutation	SNP	C	C	T	rs34788353	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	180	118	200	1	0.655556	0.005	C|0.924;T|0.076	0.076	strong	.	ACRV1	21	.	NM_001612	exon2	c.G376A	p.G126R	GTTCTCCGGAGAG	.	PASS	Atlas-SNP
POM121L12	285877	hgsc.bcm.edu	37	7	53104078	53104078	+	Silent	SNP	G	G	A	rs72598686	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	61	35	64	0	0.57377	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
ICAM3	3385	hgsc.bcm.edu	37	19	10449358	10449358	+	Missense_Mutation	SNP	T	T	C	rs7258015	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	129	47	140	2	0.364341	0.0142857	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	.	scavenged	Atlas-SNP
PEX14	5195	hgsc.bcm.edu	37	1	10596341	10596341	+	Silent	SNP	C	C	T	rs12375	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	181	86	218	0	0.475138	0	C|0.770;T|0.230	0.230	strong	.	PEX14	40	.	NM_004565	exon3	c.C156T	p.F52F	AGCATTCCTAAAG	.	PASS	Atlas-SNP
IL4I1	259307	hgsc.bcm.edu	37	19	50393269	50393269	+	Silent	SNP	A	A	G	rs56359967	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	34	16	45	0	0.470588	0	A|0.881;G|0.119	0.119	strong	.	IL4I1	50	.	NM_172374	exon10	c.T1428C	p.F476F	TACCACAAAGCCA	.	PASS	Atlas-SNP
RPS14	6208	hgsc.bcm.edu	37	5	149826526	149826526	+	Silent	SNP	C	C	T	rs4841	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	54	23	53	0	0.425926	0	T|0.198;G|0.151;C|0.606;A|0.044	0.198	strong	.	RPS14	11	.	NM_001025071	exon3	c.G150A	p.K50K	GGTTTCCCTGGGG	.	PASS	Atlas-SNP
C5orf47	133491	hgsc.bcm.edu	37	5	173426709	173426709	+	Missense_Mutation	SNP	G	G	T	rs56138314	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	125	51	157	0	0.408	0	G|0.971;T|0.029	0.029	strong	C5orf47,NS,carcinoma,-1,1	C5orf47	14	1	NM_001144954	exon3	c.G418T	p.V140L	GTTTTAGTATGGA	.	PASS	Atlas-SNP
SLC28A1	9154	hgsc.bcm.edu	37	15	85478729	85478729	+	Missense_Mutation	SNP	G	G	A	rs2242046	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	74	73	54	0	0.986486	0	G|0.690;A|0.310	0.310	strong	.	SLC28A1	118	.	NM_004213	exon15	c.G1561A	p.D521N	GTCGGCGACAGGA	.	PASS	Atlas-SNP
BRD7	29117	hgsc.bcm.edu	37	16	50368663	50368663	+	Silent	SNP	G	G	A	rs1062348	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	127	78	114	0	0.614173	0	G|0.826;A|0.174	0.174	strong	.	BRD7	61	.	NM_013263	exon7	c.C846T	p.A282A	TGCTTCGGCATCT	.	PASS	Atlas-SNP
STK31	56164	hgsc.bcm.edu	37	7	23751736	23751736	+	Silent	SNP	A	A	G	rs7779633	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	150	109	188	1	0.726667	0.00531915	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
PCDHGC5	56097	hgsc.bcm.edu	37	5	140870516	140870516	+	Missense_Mutation	SNP	A	A	G	rs2074912	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	64	64	91	0	1	0	A|0.821;G|0.179	0.179	strong	.	PCDHGC5	199	.	NM_018929	exon1	c.A1709G	p.D570G	GGCCAGACTGGGA	.	PASS	Atlas-SNP
IQGAP2	10788	hgsc.bcm.edu	37	5	75948650	75948650	+	Missense_Mutation	SNP	A	A	G	rs2431363	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	122	122	128	0	1	0	G|0.459;N|0.000	0.459	strong	.	IQGAP2	186	.	NM_006633	exon18	c.A2170G	p.I724V	GATTCTATTGTGA	.	PASS	Atlas-SNP
GPAM	57678	hgsc.bcm.edu	37	10	113926224	113926224	+	Missense_Mutation	SNP	A	A	G	rs35019520	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	108	38	108	0	0.351852	0	A|0.990;G|0.010	0.010	strong	.	GPAM	68	.	NM_001244949	exon12	c.T1157C	p.I386T	ATTCTAATAACAC	.	PASS	Atlas-SNP
NDUFA9	4704	hgsc.bcm.edu	37	12	4768290	4768290	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	67	30	101	0	0.447761	0	.	.	none	.	NDUFA9	45	.	NM_005002	exon5	c.G499A	p.V167I	ATTCATGTTTCAC	.	PASS	Atlas-SNP
BAIAP3	8938	hgsc.bcm.edu	37	16	1389222	1389222	+	Silent	SNP	C	C	T	rs61742684	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	43	42	41	0	0.976744	0	C|0.973;T|0.027	0.027	strong	.	BAIAP3	88	.	NM_003933	exon4	c.C382T	p.L128L	CTCGGCCTGAGAG	.	PASS	Atlas-SNP
GLB1L	79411	hgsc.bcm.edu	37	2	220101974	220101974	+	Silent	SNP	A	A	G	rs61733623	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	149	80	169	1	0.536913	0.00591716	A|0.990;G|0.010	0.010	strong	GLB1L,colon,carcinoma,-1,1	GLB1L	52	1	NM_024506	exon17	c.T1785C	p.P595P	TCCCCTAGGAAAC	.	scavenged	Atlas-SNP
RAD54B	25788	hgsc.bcm.edu	37	8	95423464	95423464	+	Silent	SNP	A	A	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	240	111	259	0	0.4625	0	.	.	none	.	RAD54B	88	.	NM_012415	exon4	c.T384C	p.V128V	CCAAACAACACTG	.	PASS	Atlas-SNP
ACTN1	87	hgsc.bcm.edu	37	14	69352230	69352230	+	Silent	SNP	G	G	A	rs15993	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	28	95	0	0.373333	0	G|0.811;A|0.189	0.189	strong	.	ACTN1	77	.	NM_001102	exon12	c.C1297T	p.L433L	TGAGCAGGGCCTT	.	PASS	Atlas-SNP
TRIOBP	11078	hgsc.bcm.edu	37	22	38122122	38122122	+	Missense_Mutation	SNP	T	T	C	rs5756795	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	47	26	55	0	0.553191	0	T|0.609;C|0.391	0.391	strong	.	TRIOBP	262	.	NM_001039141	exon7	c.T3559C	p.F1187L	TCCCTCTTCTTCC	.	PASS	Atlas-SNP
FHAD1	114827	hgsc.bcm.edu	37	1	15616139	15616139	+	Missense_Mutation	SNP	G	G	A	rs486557	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	68	32	79	0	0.470588	0	G|0.777;A|0.223	0.223	strong	.	FHAD1	78	.	NM_052929	exon4	c.G545A	p.R182H	ACGCCCGCAAGCC	.	PASS	Atlas-SNP
IQGAP2	10788	hgsc.bcm.edu	37	5	75932965	75932965	+	Missense_Mutation	SNP	G	G	C	rs2455230	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	85	119	0	1	0	G|0.436;C|0.563	0.563	strong	IQGAP2,NS,carcinoma,0,1	IQGAP2	186	1	NM_006633	exon16	c.G1887C	p.L629F	ATGCTTGTATAAA	.	PASS	Atlas-SNP
DEFB129	140881	hgsc.bcm.edu	37	20	210061	210061	+	Silent	SNP	G	G	A	rs13045643	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	70	73	0	1	0	G|0.710;A|0.289	0.289	strong	DEFB129,NS,carcinoma,0,1	DEFB129	24	1	NM_080831	exon2	c.G201A	p.L67L	CTACCTGCAATAT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195505838	195505838	+	Missense_Mutation	SNP	G	G	C	rs59101491	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	116	6	72	3	0.0517241	0.0416667	.	.	weak	MUC4_ENST00000463781,NS,carcinoma,+2,19	MUC4	1505	19	NM_018406	exon2	c.C12613G	p.H4205D	TGGCGTGACCTGT	.	scavenged	Atlas-SNP
EXT1	2131	hgsc.bcm.edu	37	8	118819578	118819578	+	Silent	SNP	C	C	T	rs7837891	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	99	116	1	0.980198	0.00862069	C|0.659;T|0.341	0.341	strong	.	EXT1	98	.	NM_000127	exon9	c.G1761A	p.E587E	AATCCTCTCAGGG	.	PASS	Atlas-SNP
FAM151A	338094	hgsc.bcm.edu	37	1	55075122	55075122	+	Missense_Mutation	SNP	C	C	G	rs11206394	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	34	77	0	0.472222	0	C|0.901;G|0.099	0.099	strong	.	FAM151A	58	.	NM_176782	exon8	c.G1577C	p.G526A	AGCCTGCCTATGG	.	PASS	Atlas-SNP
ABCC3	8714	hgsc.bcm.edu	37	17	48745345	48745345	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	115	3	152	0	0.026087	0	.	.	none	ABCC3,caecum,carcinoma,+1,1	ABCC3	138	1	NM_003786	exon13	c.C1757T	p.P586L	TGCTGCCCCAGTT	.	scavenged	Atlas-SNP
PLCH2	9651	hgsc.bcm.edu	37	1	2430617	2430617	+	Silent	SNP	C	C	T	rs2296442	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	100	186	0	0.990099	0	C|0.593;T|0.407	0.407	strong	.	PLCH2	131	.	NM_014638	exon19	c.C2529T	p.I843I	TCCCATCGGGCGT	.	PASS	Atlas-SNP
VIPR2	7434	hgsc.bcm.edu	37	7	158828692	158828692	+	Missense_Mutation	SNP	C	C	T	rs145308657	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	56	29	68	0	0.517857	0	C|1.000;T|0.000	0.000	weak	.	VIPR2	53	.	NM_003382	exon8	c.G760A	p.V254I	TGCAGACGGTGGG	.	PASS	Atlas-SNP
PLCD4	84812	hgsc.bcm.edu	37	2	219492952	219492952	+	Missense_Mutation	SNP	C	C	T	rs61733653	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	80	45	107	0	0.5625	0	C|0.994;T|0.006	0.006	strong	.	PLCD4	51	.	NM_032726	exon7	c.C973T	p.R325W	TATATACGGTGCA	.	PASS	Atlas-SNP
OR7A17	26333	hgsc.bcm.edu	37	19	14992031	14992031	+	Missense_Mutation	SNP	A	A	G	rs10405129	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	28	82	0	0.482759	0	A|0.747;G|0.253	0.253	strong	.	OR7A17	37	.	NM_030901	exon1	c.T137C	p.I46T	GCCAGGATGATGA	.	PASS	Atlas-SNP
PSME4	23198	hgsc.bcm.edu	37	2	54115904	54115904	+	Silent	SNP	A	A	G	rs805400	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	199	147	91	0	0.738693	0	A|0.711;G|0.289	0.289	strong	.	PSME4	247	.	NM_014614	exon38	c.T4342C	p.L1448L	ATTCCAACAGCAG	.	PASS	Atlas-SNP
YEATS2	55689	hgsc.bcm.edu	37	3	183521939	183521939	+	Silent	SNP	C	C	T	rs34612765	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	89	36	106	0	0.404494	0	C|0.962;T|0.038	0.038	strong	.	YEATS2	111	.	NM_018023	exon27	c.C3747T	p.S1249S	GGACTCCATCGAG	.	PASS	Atlas-SNP
ADCK4	79934	hgsc.bcm.edu	37	19	41209477	41209477	+	Silent	SNP	C	C	T	rs11538385	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	96	53	106	1	0.552083	0.00943396	C|0.773;T|0.227	0.227	strong	ADCK4_ENST00000324464,colon,carcinoma,-1,6	ADCK4	92	6	NM_024876	exon9	c.G768A	p.A256A	GAGTACCGCCAGC	.	scavenged	Atlas-SNP
SLC13A3	64849	hgsc.bcm.edu	37	20	45242269	45242269	+	Silent	SNP	G	G	C	rs2273024	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	106	55	122	0	0.518868	0	G|0.680;C|0.320	0.320	strong	.	SLC13A3	88	.	NM_022829	exon2	c.C207G	p.L69L	GGGGAAGAGGACG	.	PASS	Atlas-SNP
RRP12	23223	hgsc.bcm.edu	37	10	99141205	99141205	+	Silent	SNP	A	A	G	rs2275089	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	161	94	157	0	0.583851	0	A|0.622;G|0.378	0.378	strong	.	RRP12	97	.	NM_015179	exon12	c.T1356C	p.A452A	AATGTCAGCCATG	.	PASS	Atlas-SNP
CPAMD8	27151	hgsc.bcm.edu	37	19	17100552	17100552	+	Silent	SNP	A	A	G	rs1973093	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	68	103	0	0.985507	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
C20orf96	140680	hgsc.bcm.edu	37	20	256727	256727	+	Missense_Mutation	SNP	T	T	A	rs3827147	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	39	107	0	0.402062	0	T|0.339;A|0.661	0.661	strong	.	C20orf96	28	.	NM_153269	exon10	c.A913T	p.I305F	CAATAATCTGAGA	.	PASS	Atlas-SNP
TRIM21	6737	hgsc.bcm.edu	37	11	4411241	4411241	+	Silent	SNP	C	C	T	rs926101	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	90	13	110	0	0.144444	0	C|0.811;T|0.189	0.189	strong	.	TRIM21	45	.	NM_003141	exon2	c.G399A	p.Q133Q	GTACTCCTGTGCA	.	PASS	Atlas-SNP
ZFP64	55734	hgsc.bcm.edu	37	20	50803573	50803573	+	Silent	SNP	G	G	A	rs34351592	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	31	80	0	0.449275	0	G|0.864;A|0.136	0.136	strong	.	ZFP64	240	.	NM_018197	exon2	c.C84T	p.P28P	GATGTCGGGAGTC	.	PASS	Atlas-SNP
GYS2	2998	hgsc.bcm.edu	37	12	21713402	21713402	+	Missense_Mutation	SNP	T	T	C	rs2306180	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	116	115	177	1	0.991379	0.00564972	C|0.742;N|0.000	0.742	strong	.	GYS2	110	.	NM_021957	exon8	c.A1087G	p.M363V	ACACCATCACTGT	.	PASS	Atlas-SNP
USP36	57602	hgsc.bcm.edu	37	17	76814782	76814782	+	Silent	SNP	G	G	A	rs35273233	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	148	66	152	0	0.445946	0	G|0.848;A|0.152	0.152	strong	.	USP36	243	.	NM_025090	exon10	c.C990T	p.R330R	GGCAAAGCGCTTG	.	PASS	Atlas-SNP
GSPT1	2935	hgsc.bcm.edu	37	16	11981487	11981487	+	Silent	SNP	G	G	A	rs3752426	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	207	156	209	0	0.753623	0	G|0.830;A|0.170	0.170	strong	.	GSPT1	71	.	NM_002094	exon7	c.C897T	p.G299G	CTTGTGGCCAGGG	.	PASS	Atlas-SNP
C8A	731	hgsc.bcm.edu	37	1	57340727	57340727	+	Missense_Mutation	SNP	C	C	A	rs652785	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	30	80	0	0.434783	0	C|0.671;N|0.000	.	strong	.	C8A	103	.	NM_000562	exon3	c.C277A	p.Q93K	GTAAGGCAAGCAC	.	PASS	Atlas-SNP
PDE4DIP	9659	hgsc.bcm.edu	37	1	144854645	144854645	+	Silent	SNP	T	T	C	rs143461294	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	210	31	206	0	0.147619	0	T|0.999;C|0.001	0.001	strong	.	PDE4DIP	817	.	NM_014644	exon42	c.A6825G	p.T2275T	CCTTTCTGTTGAT	.	PASS	Atlas-SNP
DLST	1743	hgsc.bcm.edu	37	14	75367807	75367807	+	Silent	SNP	C	C	T	rs20578	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	172	85	239	0	0.494186	0	C|0.690;T|0.310	0.310	strong	.	DLST	42	.	NM_001933	exon14	c.C1098T	p.G366G	GGATGGCGGTACC	.	PASS	Atlas-SNP
TPX2	22974	hgsc.bcm.edu	37	20	30382315	30382315	+	Silent	SNP	A	A	G	rs3203770	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	37	79	0	0.506849	0	A|0.722;G|0.278	0.278	strong	.	TPX2	61	.	NM_012112	exon15	c.A1797G	p.R599R	TGACAGAAGAGGT	.	PASS	Atlas-SNP
STXBP5L	9515	hgsc.bcm.edu	37	3	120976051	120976051	+	Missense_Mutation	SNP	C	C	G	rs17249244	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	62	32	67	0	0.516129	0	C|0.880;G|0.120	0.120	strong	.	STXBP5L	159	.	NM_014980	exon17	c.C1703G	p.T568S	TTATTACCCCTGA	.	PASS	Atlas-SNP
EFCAB4B	84766	hgsc.bcm.edu	37	12	3788145	3788145	+	Missense_Mutation	SNP	C	C	T	rs242018	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	102	51	107	0	0.5	0	C|0.763;T|0.237	0.237	strong	.	EFCAB4B	100	.	NM_001144958	exon6	c.G460A	p.E154K	CATCTTCGCCCAT	.	PASS	Atlas-SNP
ZFAT	57623	hgsc.bcm.edu	37	8	135614972	135614972	+	Silent	SNP	A	A	G	rs3739422	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	108	105	142	0	0.972222	0	A|0.643;G|0.357	0.357	strong	.	ZFAT	265	.	NM_020863	exon6	c.T990C	p.Y330Y	CGAGCAATAGTCG	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	112	112	181	0	1	0	0|0.014;G|0.475	0.475	strong	.	LONRF3	138	.	NM_001031855	exon10	c.A2034G	p.A678A	GCAAGCATCATTG	.	PASS	Atlas-SNP
KRTAP3-2	83897	hgsc.bcm.edu	37	17	39156027	39156027	+	Missense_Mutation	SNP	G	G	A	rs3829598	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	118	55	131	0	0.466102	0	G|0.865;A|0.135	0.135	strong	.	KRTAP3-2	11	.	NM_031959	exon1	c.C79T	p.R27C	CACAGCGGCAGGA	.	PASS	Atlas-SNP
LRRC56	115399	hgsc.bcm.edu	37	11	551235	551235	+	Silent	SNP	G	G	A	rs35537971	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	229	174	205	0	0.759825	0	G|0.835;A|0.165	0.165	strong	.	LRRC56	23	.	NM_198075	exon9	c.G729A	p.P243P	CCCCCCGCGGCTG	.	PASS	Atlas-SNP
UGT2B7	7364	hgsc.bcm.edu	37	4	69972949	69972949	+	Silent	SNP	C	C	G	rs4292394	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	106	44	153	0	0.415094	0	C|0.420;G|0.580	0.580	strong	.	UGT2B7	79	.	NM_001074	exon4	c.C1059G	p.L353L	TCGGCTCTACAAG	.	PASS	Atlas-SNP
KCNIP4	80333	hgsc.bcm.edu	37	4	20852244	20852244	+	Silent	SNP	A	A	G	rs3765122	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	47	21	55	0	0.446809	0	A|0.672;G|0.328	0.328	strong	.	KCNIP4	85	.	NM_025221	exon2	c.T150C	p.P50P	GGCTTCAGGCCGA	.	PASS	Atlas-SNP
OR2T3	343173	hgsc.bcm.edu	37	1	248637381	248637381	+	Missense_Mutation	SNP	G	G	A	rs139789199	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	491	51	482	0	0.10387	0	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	.	scavenged	Atlas-SNP
TPH2	121278	hgsc.bcm.edu	37	12	72372862	72372862	+	Silent	SNP	A	A	G	rs7305115	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	57	57	58	0	1	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
TRPC4AP	26133	hgsc.bcm.edu	37	20	33657126	33657126	+	Silent	SNP	G	G	A	rs1998233	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	227	226	316	1	0.995595	0.00316456	G|0.223;A|0.777	0.777	strong	.	TRPC4AP	64	.	NM_199368	exon3	c.C387T	p.Y129Y	AAAAATGTAAGTA	.	PASS	Atlas-SNP
MYC	4609	hgsc.bcm.edu	37	8	128750540	128750540	+	Missense_Mutation	SNP	A	A	G	rs4645959	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	47	34	72	0	0.723404	0	A|0.974;G|0.026	0.026	strong	.	MYC	168	.	NM_002467	exon2	c.A77G	p.N26S	ACAGGAACTATGA	.	PASS	Atlas-SNP
PFDN1	5201	hgsc.bcm.edu	37	5	139680027	139680027	+	Silent	SNP	A	A	G	rs145830713	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	291	151	312	0	0.5189	0	A|0.989;G|0.011	0.011	strong	.	PFDN1	10	.	NM_002622	exon2	c.T174C	p.T58T	CATGTTAGTCTCA	.	PASS	Atlas-SNP
USP48	84196	hgsc.bcm.edu	37	1	22033020	22033020	+	Silent	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	199	63	198	0	0.316583	0	.	.	none	USP48,colon,carcinoma,0,1	USP48	91	1	NM_032236	exon17	c.G2151A	p.K717K	AGAAGTCTTTTGC	.	PASS	Atlas-SNP
PGLYRP2	114770	hgsc.bcm.edu	37	19	15587185	15587185	+	Missense_Mutation	SNP	C	C	T	rs733731	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	175	80	222	0	0.457143	0	C|0.637;T|0.363	0.363	strong	PGLYRP2_ENST00000292609,NS,carcinoma,0,4	PGLYRP2	116	4	NM_052890	exon2	c.G296A	p.R99Q	TCATGTCGGGCCA	.	PASS	Atlas-SNP
FBXO38	81545	hgsc.bcm.edu	37	5	147805120	147805120	+	Missense_Mutation	SNP	T	T	C	rs10043775	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	107	52	129	0	0.485981	0	T|0.734;C|0.266	0.266	strong	FBXO38,NS,carcinoma,0,1	FBXO38	115	1	NM_001271723	exon14	c.T1774C	p.S592P	CCAACCTCAATTA	.	PASS	Atlas-SNP
TM6SF2	53345	hgsc.bcm.edu	37	19	19380996	19380996	+	Silent	SNP	G	G	T	rs2074300	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	114	114	116	0	1	0	G|0.794;T|0.206	0.206	strong	.	TM6SF2	39	.	NM_001001524	exon4	c.C387A	p.G129G	GATGGCGCCGGCC	.	PASS	Atlas-SNP
TAP2	6891	hgsc.bcm.edu	37	6	32800412	32800412	+	Missense_Mutation	SNP	C	C	T	rs1800454	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	111	33	168	0	0.297297	0	C|0.860;T|0.140	0.140	strong	TAP2_ENST00000458336,NS,carcinoma,0,4	TAP2	98	4	NM_018833	exon6	c.G1135A	p.V379I	TCCTTACGAGCAG	.	PASS	Atlas-SNP
FAT3	120114	hgsc.bcm.edu	37	11	92088524	92088524	+	Silent	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	102	32	114	0	0.313726	0	.	.	none	.	FAT3	1822	.	NM_001008781	exon1	c.C3246T	p.I1082I	CTCCATCAGGGAT	.	PASS	Atlas-SNP
DTX1	1840	hgsc.bcm.edu	37	12	113496151	113496151	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	79	13	83	0	0.164557	0	.	.	none	.	DTX1	83	.	NM_004416	exon1	c.C154G	p.L52V	AACGTGCTGAAGG	.	PASS	Atlas-SNP
KIAA1614	57710	hgsc.bcm.edu	37	1	180886216	180886216	+	Missense_Mutation	SNP	C	C	T	rs77695365	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	108	56	143	0	0.518519	0	C|0.955;T|0.045	0.045	strong	.	KIAA1614	75	.	NM_020950	exon2	c.C977T	p.S326F	CTCCATCCTGGGA	.	PASS	Atlas-SNP
PLCB4	5332	hgsc.bcm.edu	37	20	9288522	9288522	+	Missense_Mutation	SNP	G	G	A	rs6077510	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	64	36	92	0	0.5625	0	G|0.505;A|0.495	0.495	strong	.	PLCB4	204	.	NM_182797	exon2	c.G61A	p.A21T	GAAGGAGCAGTTT	.	PASS	Atlas-SNP
SLC9C2	284525	hgsc.bcm.edu	37	1	173472465	173472465	+	Missense_Mutation	SNP	G	G	A	rs72709309	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	122	69	134	0	0.565574	0	G|0.973;A|0.027	0.027	strong	.	.	.	.	NM_178527	exon27	c.C3311T	p.A1104V	ACTGAGGCTAACC	.	PASS	Atlas-SNP
EAF1	85403	hgsc.bcm.edu	37	3	15476011	15476011	+	Silent	SNP	C	C	G	rs1563415	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	34	101	0	0.414634	0	C|0.796;G|0.204	0.204	strong	.	EAF1	16	.	NM_033083	exon4	c.C492G	p.P164P	TAACCCCTCACCT	.	PASS	Atlas-SNP
ZNF880	400713	hgsc.bcm.edu	37	19	52887437	52887437	+	Missense_Mutation	SNP	A	A	C	rs8104812	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	67	67	93	0	1	0	A|0.655;C|0.345	0.345	strong	.	ZNF880	45	.	NM_001145434	exon4	c.A604C	p.N202H	GCTAACAATCAAG	.	PASS	Atlas-SNP
LRPPRC	10128	hgsc.bcm.edu	37	2	44201315	44201315	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	550	65	342	0	0.118182	0	.	.	none	.	LRPPRC	105	.	NM_133259	exon9	c.T1129A	p.L377I	GTTGTAAAAAGAA	.	PASS	Atlas-SNP
PRLHR	2834	hgsc.bcm.edu	37	10	120353843	120353843	+	Missense_Mutation	SNP	G	G	A	rs8192524	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	18	9	22	0	0.5	0	G|0.968;A|0.032	0.032	strong	.	PRLHR	41	.	NM_004248	exon2	c.C914T	p.P305L	GCGTGGGGGTCGA	.	PASS	Atlas-SNP
PTBP2	58155	hgsc.bcm.edu	37	1	97272456	97272456	+	Silent	SNP	A	A	G	rs6699932	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	81	80	124	0	0.987654	0	A|0.707;G|0.293	0.293	strong	.	PTBP2	62	.	NM_021190	exon11	c.A1113G	p.L371L	GATTTTATACAAT	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	122	122	122	0	1	0	T|0.663;A|0.337	0.337	strong	.	.	.	.	NM_001080479	exon35	c.T4920A	p.H1640Q	TTTCCATGAAAGC	.	PASS	Atlas-SNP
DCLRE1C	64421	hgsc.bcm.edu	37	10	14987181	14987181	+	Missense_Mutation	SNP	C	C	A	rs138077101	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	117	53	138	0	0.452991	0	C|1.000;A|0.000	0.000	strong	.	DCLRE1C	136	.	NM_001033855	exon3	c.G169T	p.V57F	GATAAACCTTCAA	.	PASS	Atlas-SNP
COL5A1	1289	hgsc.bcm.edu	37	9	137619195	137619195	+	Silent	SNP	C	C	T	rs3124299	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	108	58	104	0	0.537037	0	C|0.665;T|0.335	0.335	strong	.	COL5A1	323	.	NM_000093	exon5	c.C738T	p.T246T	TGACACCGCAGTA	.	PASS	Atlas-SNP
CEACAM6	4680	hgsc.bcm.edu	37	19	42260569	42260569	+	Silent	SNP	G	G	A	rs55738855		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	131	75	151	0	0.572519	0	.	.	weak	CEACAM6,NS,carcinoma,0,1	CEACAM6	52	1	NM_002483	exon2	c.G126A	p.P42P	CACGCCGTTCAAT	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	94	44	114	0	0.468085	0	T|0.866;C|0.134	0.134	strong	.	REV1	100	.	NM_001037872	exon6	c.A1118G	p.N373S	AGGGTATTGACAA	.	PASS	Atlas-SNP
TBL3	10607	hgsc.bcm.edu	37	16	2025678	2025678	+	Silent	SNP	C	C	A	rs17602	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	46	37	31	0	0.804348	0	C|0.921;A|0.079	0.079	strong	.	TBL3	54	.	NM_006453	exon10	c.C954A	p.L318L	GTTGCTCTACGAG	.	PASS	Atlas-SNP
GDF15	9518	hgsc.bcm.edu	37	19	18499151	18499151	+	Silent	SNP	C	C	T	rs1059022	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	120	74	134	0	0.616667	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
KLHL3	26249	hgsc.bcm.edu	37	5	136969793	136969793	+	Silent	SNP	C	C	T	rs2301708	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	65	35	74	0	0.538462	0	C|0.814;T|0.186	0.186	strong	KLHL3,NS,carcinoma,0,1	KLHL3	54	1	NM_017415	exon12	c.G1383A	p.E461E	GTACTGCTCCACA	.	PASS	Atlas-SNP
INSR	3643	hgsc.bcm.edu	37	19	7150532	7150532	+	Missense_Mutation	SNP	G	G	A	rs143523271	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	51	21	51	0	0.411765	0	G|0.999;A|0.001	0.001	strong	.	INSR	265	.	NM_000208	exon11	c.C2243T	p.S748L	GTGCCTGAAGAGG	.	PASS	Atlas-SNP
HLA-C	3107	hgsc.bcm.edu	37	6	31238925	31238925	+	Missense_Mutation	SNP	C	C	T	rs141142418	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	174	49	146	0	0.281609	0	C|0.971;T|0.029	0.029	strong	.	HLA-C	92	.	NM_002117	exon3	c.G544A	p.A182T	GGTAGGCTCTCAG	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	39	12	66	0	0.307692	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
EXO1	9156	hgsc.bcm.edu	37	1	242035438	242035438	+	Missense_Mutation	SNP	G	G	A	rs4149965	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	223	109	286	0	0.488789	0	G|0.851;A|0.149	0.149	strong	EXO1,caecum,carcinoma,0,2	EXO1	103	2	NM_006027	exon10	c.G1372A	p.V458M	TCTGAAGTGTTTG	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	94	48	80	0	0.510638	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
PARL	55486	hgsc.bcm.edu	37	3	183551309	183551309	+	Silent	SNP	C	C	T	rs140027735	alternate_allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	249	79	272	0	0.317269	0	C|1.000;A|0.000	.	alt	PARL,NS,carcinoma,-2,1	PARL	32	1	NM_018622	exon9	c.G999A	p.A333A	ATGTGCCGCATGA	.	PASS	Atlas-SNP
SIPA1	6494	hgsc.bcm.edu	37	11	65408937	65408937	+	Missense_Mutation	SNP	C	C	T	rs3741378	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	35	72	0	0.603448	0	C|0.800;T|0.200	0.200	strong	.	SIPA1	45	.	NM_006747	exon2	c.C545T	p.S182F	CAGCATCCCCACC	.	PASS	Atlas-SNP
SLC16A7	9194	hgsc.bcm.edu	37	12	60168491	60168491	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	209	44	257	0	0.210526	0	.	.	none	.	SLC16A7	82	.	NM_001270622	exon5	c.T415G	p.F139V	AAATACTTCTATA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195512531	195512531	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	134	6	63	1	0.0447761	0.015873	.	.	none	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.G5920A	p.A1974T	AGGAAGCGTCGGT	.	scavenged	Atlas-SNP
FERMT1	55612	hgsc.bcm.edu	37	20	6069723	6069723	+	Silent	SNP	G	G	A	rs35413391	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	28	76	0	0.394366	0	G|0.949;A|0.051	0.051	strong	.	FERMT1	106	.	NM_017671	exon10	c.C1153T	p.L385L	TTGGTAGTAACTT	.	PASS	Atlas-SNP
ANO1	55107	hgsc.bcm.edu	37	11	70007770	70007770	+	Missense_Mutation	SNP	T	T	C	rs2186797	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	212	39	256	0	0.183962	0	T|0.969;C|0.031	0.031	strong	.	ANO1	156	.	NM_018043	exon18	c.T1823C	p.F608S	TGATCTTCAAGGC	.	PASS	Atlas-SNP
TTC30A	92104	hgsc.bcm.edu	37	2	178482771	178482771	+	Missense_Mutation	SNP	C	C	T	rs59353759	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	166	81	161	0	0.487952	0	C|0.974;T|0.026	0.026	strong	.	TTC30A	60	.	NM_152275	exon1	c.G659A	p.R220H	TGCTGGCGGATGC	.	PASS	Atlas-SNP
NKTR	4820	hgsc.bcm.edu	37	3	42679497	42679497	+	Silent	SNP	C	C	T	rs35890296	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	50	108	0	0.49505	0	C|0.823;T|0.177	0.177	strong	.	NKTR	116	.	NM_005385	exon13	c.C2301T	p.S767S	AAATAGCGTTTCA	.	PASS	Atlas-SNP
BOD1	91272	hgsc.bcm.edu	37	5	173036257	173036257	+	Silent	SNP	A	A	G	rs77014290	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	197	17	146	1	0.0862944	0.00684932	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	.	scavenged	Atlas-SNP
MTSS1	9788	hgsc.bcm.edu	37	8	125568485	125568485	+	Silent	SNP	C	C	T	rs145509745		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	131	68	149	0	0.519084	0	C|1.000;T|0.000	0.000	weak	.	MTSS1	79	.	NM_014751	exon12	c.G1392A	p.S464S	GGCAGCCGATACA	.	PASS	Atlas-SNP
DDX60L	91351	hgsc.bcm.edu	37	4	169299528	169299528	+	Missense_Mutation	SNP	T	T	C	rs13110927	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	152	151	185	0	0.993421	0	T|0.533;C|0.467	0.467	strong	.	DDX60L	116	.	NM_001012967	exon33	c.A4462G	p.N1488D	TTAAATTAGCATT	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	44	20	65	0	0.454545	0	A|0.818;G|0.182	0.182	strong	.	PCDHB11	162	.	NM_018931	exon1	c.A11G	p.Q4R	AGAACCAAGGGAC	.	PASS	Atlas-SNP
TRIM27	5987	hgsc.bcm.edu	37	6	28891176	28891176	+	Silent	SNP	T	T	C	rs2230683	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	45	19	64	0	0.422222	0	T|0.950;C|0.050	0.050	strong	.	TRIM27	26	.	NM_006510	exon1	c.A234G	p.V78V	CTGCTTTACCAGT	.	PASS	Atlas-SNP
NRCAM	4897	hgsc.bcm.edu	37	7	107849908	107849908	+	Silent	SNP	G	G	A	rs1269621	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	108	106	157	0	0.981481	0	G|0.434;A|0.566	0.566	strong	.	NRCAM	267	.	NM_001037132	exon9	c.C1032T	p.N344N	TAATGCGTTTTTT	.	PASS	Atlas-SNP
TLN2	83660	hgsc.bcm.edu	37	15	63111778	63111778	+	Missense_Mutation	SNP	G	G	A	rs138463845	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	49	29	45	2	0.591837	0.0444444	G|0.995;A|0.005	0.005	strong	TLN2,NS,carcinoma,-2,2	TLN2	253	2	NM_015059	exon50	c.G6835A	p.G2279S	GTCGCCGGCGCTG	.	scavenged	Atlas-SNP
PRF1	5551	hgsc.bcm.edu	37	10	72360457	72360457	+	Missense_Mutation	SNP	G	G	A	rs151232299	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	239	91	252	0	0.380753	0	G|1.000;A|0.000	0.000	weak	PRF1,right_upper_lobe,carcinoma,+2,1	PRF1	64	1	NM_001083116	exon2	c.C202T	p.R68W	CGGGCCGCAGGAA	.	PASS	Atlas-SNP
MPHOSPH10	10199	hgsc.bcm.edu	37	2	71360282	71360282	+	Missense_Mutation	SNP	G	G	A	rs13010513	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	108	59	115	0	0.546296	0	G|0.825;A|0.175	0.175	strong	.	MPHOSPH10	81	.	NM_005791	exon2	c.G344A	p.R115H	AGGAACGTGAAGA	.	PASS	Atlas-SNP
KCNQ1	3784	hgsc.bcm.edu	37	11	2869188	2869188	+	Silent	SNP	C	C	T	rs11601907	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	124	33	111	0	0.266129	0	C|0.892;T|0.108	0.108	strong	.	KCNQ1	60	.	NM_000218	exon16	c.C1986T	p.Y662Y	CACCTACGAGCAG	.	PASS	Atlas-SNP
EDDM3A	10876	hgsc.bcm.edu	37	14	21215923	21215923	+	Missense_Mutation	SNP	G	G	T	rs34552133	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	146	74	178	0	0.506849	0	T|0.100;G|0.900;A|0.000	0.100	strong	.	EDDM3A	15	.	NM_006683	exon2	c.G184T	p.G62C	CTGAAAGGCAAGA	.	PASS	Atlas-SNP
BAI2	576	hgsc.bcm.edu	37	1	32221612	32221612	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	121	54	171	0	0.446281	0	.	.	none	.	BAI2	128	.	NM_001703	exon4	c.G826A	p.E276K	TCATCTCGGTTGT	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	213	111	228	0	0.521127	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
INSR	3643	hgsc.bcm.edu	37	19	7125519	7125519	+	Silent	SNP	G	G	A	rs1799815	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	45	25	81	0	0.555556	0	G|0.956;A|0.044	0.044	strong	.	INSR	265	.	NM_000208	exon17	c.C3033T	p.Y1011Y	CGGCACGTACACA	.	PASS	Atlas-SNP
MUC6	4588	hgsc.bcm.edu	37	11	1017974	1017974	+	Missense_Mutation	SNP	C	C	G	rs200353019	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	440	34	357	11	0.0772727	0.0308123	.	.	weak	MUC6_ENST00000421673,colon,carcinoma,0,2	MUC6	408	2	NM_005961	exon31	c.G4827C	p.Q1609H	TGTGGTCTGAGGG	.	scavenged	Atlas-SNP
LPPR3	0	hgsc.bcm.edu	37	19	814680	814680	+	Silent	SNP	G	G	T	rs56944467	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	23	14	38	0	0.608696	0	G|0.886;T|0.114	0.114	strong	.	.	.	.	NM_024888	exon6	c.C669A	p.A223A	GTGAGGGGCCGGA	.	PASS	Atlas-SNP
GNAT2	2780	hgsc.bcm.edu	37	1	110148974	110148974	+	Silent	SNP	C	C	T	rs1799875	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	202	89	209	0	0.440594	0	C|0.630;T|0.370	0.370	strong	.	GNAT2	31	.	NM_005272	exon5	c.G546A	p.T182T	GATGCCCGTGGTT	.	PASS	Atlas-SNP
BAG5	9529	hgsc.bcm.edu	37	14	104028270	104028270	+	Silent	SNP	T	T	C	rs7148456	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	187	89	227	0	0.475936	0	T|0.730;C|0.270	0.270	strong	.	BAG5	47	.	NM_001015049	exon1	c.A75G	p.P25P	CCACAATGGCCTA	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105417396	105417396	+	Missense_Mutation	SNP	C	C	G	rs144323040	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	74	0	0	0.986667	.	C|0.975;G|0.025	0.025	strong	.	AHNAK2	719	.	NM_138420	exon7	c.G4392C	p.E1464D	TGGGGCCTCGACA	.	PASS	Atlas-SNP
ADAMTS18	170692	hgsc.bcm.edu	37	16	77328895	77328895	+	Silent	SNP	C	C	T	rs12935229	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	196	89	121	0	0.454082	0	C|0.890;T|0.110	0.110	strong	.	ADAMTS18	270	.	NM_199355	exon19	c.G2931A	p.V977V	TGTGCTCACTGGA	.	PASS	Atlas-SNP
CNTN2	6900	hgsc.bcm.edu	37	1	205031116	205031116	+	Missense_Mutation	SNP	C	C	T	rs2229866	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	65	34	71	0	0.523077	0	C|0.586;T|0.414	0.414	strong	.	CNTN2	116	.	NM_005076	exon9	c.C1097T	p.P366L	GGGAGCCTCTGGC	.	PASS	Atlas-SNP
COL6A5	256076	hgsc.bcm.edu	37	3	130098349	130098349	+	Silent	SNP	G	G	A	rs16845861	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	119	61	123	0	0.512605	0	G|0.632;A|0.368	0.368	strong	COL6A5,colon,carcinoma,+1,1	COL6A5	205	1	NM_153264	exon4	c.G756A	p.R252R	TTTAAGGCATCTT	.	PASS	Atlas-SNP
DYNC2H1	79659	hgsc.bcm.edu	37	11	102980324	102980324	+	Silent	SNP	C	C	T	rs17301028	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	55	62	0	0.763889	0	C|0.950;T|0.050	0.050	strong	.	DYNC2H1	246	.	NM_001377	exon1	c.C21T	p.D7D	TGCGGACGTTCGG	.	PASS	Atlas-SNP
WDR52	55779	hgsc.bcm.edu	37	3	113146130	113146130	+	Missense_Mutation	SNP	T	T	C	rs59722850	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	221	116	248	0	0.524887	0	T|0.784;C|0.216	0.216	strong	.	WDR52	151	.	NM_001164496	exon3	c.A157G	p.K53E	CCCCTTTGGTAAA	.	PASS	Atlas-SNP
NOXO1	124056	hgsc.bcm.edu	37	16	2030127	2030127	+	Missense_Mutation	SNP	G	G	A	rs61729118	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	89	76	76	0	0.853933	0	G|0.928;A|0.072	0.072	strong	.	NOXO1	13	.	NM_172168	exon5	c.C472T	p.L158F	TGGAGAGGCGGCC	.	PASS	Atlas-SNP
ADAMTSL3	57188	hgsc.bcm.edu	37	15	84539619	84539619	+	Missense_Mutation	SNP	C	C	G	rs4144691	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	29	29	34	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
PRKAR2B	5577	hgsc.bcm.edu	37	7	106799997	106799997	+	Silent	SNP	G	G	A	rs257376	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	38	103	0	0.463415	0	G|0.497;A|0.503	0.503	strong	.	PRKAR2B	34	.	NM_002736	exon11	c.G1227A	p.T409T	TGGAACGAACATG	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	29	81	0	0.337209	0	G|0.669;A|0.331	0.331	strong	.	MAP1A	189	.	NM_002373	exon4	c.G4381A	p.D1461N	CAAAAGGATACAG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195507717	195507717	+	Silent	SNP	G	G	T	rs376353447	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	39	76	0	0.423913	0	.	.	weak	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.C10734A	p.S3578S	ACCTGTGGATACT	.	PASS	Atlas-SNP
ZNF554	115196	hgsc.bcm.edu	37	19	2833802	2833802	+	Missense_Mutation	SNP	A	A	G	rs867168	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	37	101	0	0.506849	0	A|0.773;G|0.227	0.227	strong	.	ZNF554	47	.	NM_001102651	exon5	c.A569G	p.E190G	AGTTAGAGGACAG	.	PASS	Atlas-SNP
UNC13A	23025	hgsc.bcm.edu	37	19	17716896	17716896	+	Silent	SNP	G	G	T	rs3746198	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	24	15	22	0	0.625	0	G|0.909;T|0.091	0.091	strong	.	UNC13A	299	.	NM_001080421	exon42	c.C5079A	p.S1693S	CTCGGCGGAGCGC	.	PASS	Atlas-SNP
KIAA0930	23313	hgsc.bcm.edu	37	22	45608215	45608215	+	Nonsense_Mutation	SNP	G	G	A	rs150665432	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	47	123	0	0.552941	0	G|0.996;A|0.004	0.004	strong	.	KIAA0930	43	.	NM_015264	exon1	c.C10T	p.Q4X	CAGCCTGAGAGCC	.	PASS	Atlas-SNP
FAT2	2196	hgsc.bcm.edu	37	5	150930205	150930205	+	Silent	SNP	C	C	T	rs35489594	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	134	60	142	0	0.447761	0	C|0.995;T|0.005	0.005	strong	.	FAT2	465	.	NM_001447	exon7	c.G4524A	p.T1508T	TCCCACCGTTACC	.	PASS	Atlas-SNP
LTN1	26046	hgsc.bcm.edu	37	21	30339234	30339234	+	Missense_Mutation	SNP	T	T	C	rs61735768	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	95	30	81	0	0.315789	0	T|0.880;C|0.120	0.120	strong	LTN1,NS,carcinoma,0,1	LTN1	141	1	NM_015565	exon10	c.A1717G	p.S573G	ATGAGCTCTTCGG	.	PASS	Atlas-SNP
MYH8	4626	hgsc.bcm.edu	37	17	10304500	10304500	+	Silent	SNP	C	C	T	rs3744553	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	93	41	129	0	0.44086	0	C|0.949;T|0.051	0.051	strong	.	MYH8	346	.	NM_002472	exon25	c.G3117A	p.G1039G	CAGAGACCCTTCA	.	PASS	Atlas-SNP
LIMK1	3984	hgsc.bcm.edu	37	7	73520264	73520264	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	16	81	0	0.205128	0	.	.	none	.	LIMK1	55	.	NM_002314	exon6	c.T668C	p.I223T	ACCGGATCTTGGA	.	PASS	Atlas-SNP
THEG	51298	hgsc.bcm.edu	37	19	372689	372689	+	Missense_Mutation	SNP	G	G	A	rs35119230	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	164	74	150	0	0.451219	0	G|0.976;A|0.024	0.024	strong	.	THEG	58	.	NM_016585	exon5	c.C577T	p.R193C	CCACGCGGCGGGA	.	PASS	Atlas-SNP
SPOCK1	6695	hgsc.bcm.edu	37	5	136834138	136834138	+	Missense_Mutation	SNP	T	T	C	rs111393448	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	40	23	43	0	0.575	0	T|0.991;C|0.009	0.009	strong	.	SPOCK1	58	.	NM_004598	exon2	c.A110G	p.N37S	AGGAAATTGCCGT	.	PASS	Atlas-SNP
SYNE1	23345	hgsc.bcm.edu	37	6	152708310	152708310	+	Missense_Mutation	SNP	G	G	A	rs214950	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	145	49	207	0	0.337931	0	G|0.776;A|0.224	0.224	strong	.	SYNE1	3227	.	NM_033071	exon54	c.C8405T	p.A2802V	GACTTCGCAATTA	.	PASS	Atlas-SNP
CCDC79	283847	hgsc.bcm.edu	37	16	66812797	66812797	+	Silent	SNP	C	C	T	rs363162	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	108	108	104	0	1	0	C|0.441;T|0.559	0.559	strong	.	CCDC79	32	.	NM_001136505	exon10	c.G822A	p.T274T	AGTCTTCGTCACA	.	PASS	Atlas-SNP
CXXC5	51523	hgsc.bcm.edu	37	5	139060486	139060486	+	Silent	SNP	G	G	A	rs356445	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	16	6	21	0	0.375	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
CYP2C9	1559	hgsc.bcm.edu	37	10	96702047	96702047	+	Missense_Mutation	SNP	C	C	T	rs41400645		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	137	67	174	0	0.489051	0	C|1.000;|0.000	.	weak	.	CYP2C9	82	.	NM_000771	exon3	c.C430T	p.R144C	GAGGACCGTGTTC	.	PASS	Atlas-SNP
SLC22A23	63027	hgsc.bcm.edu	37	6	3273457	3273457	+	Silent	SNP	A	A	G	rs9503518	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	124	67	73	0	0.540323	0	A|0.899;G|0.101	0.101	strong	.	SLC22A23	89	.	NM_015482	exon10	c.T1893C	p.S631S	CCCGTTAGAAATG	.	PASS	Atlas-SNP
CEACAM8	1088	hgsc.bcm.edu	37	19	43093033	43093033	+	Silent	SNP	G	G	A	rs35599593	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	301	153	339	0	0.508306	0	G|0.969;A|0.031	0.031	strong	.	CEACAM8	44	.	NM_001816	exon4	c.C861T	p.P287P	GATGTTGGGGATA	.	PASS	Atlas-SNP
NBPF10	100132406	hgsc.bcm.edu	37	1	145302704	145302704	+	Missense_Mutation	SNP	A	A	G	rs61814645		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	16	9	53	2	0.5625	0.0377358	G|1.000;|0.000	1.000	weak	NBPF10_ENST00000369338,NS,neuroblastoma,0,2	NBPF10	221	2	NM_001039703	exon8	c.A1142G	p.K381R	AGTTAAAGGAGAA	.	scavenged	Atlas-SNP
ZNF512	84450	hgsc.bcm.edu	37	2	27838058	27838058	+	Silent	SNP	C	C	A	rs11127071	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	158	157	163	0	0.993671	0	C|0.399;A|0.601	0.601	strong	.	ZNF512	54	.	NM_032434	exon11	c.C1155A	p.L385L	AGGGCTCCCTACC	.	PASS	Atlas-SNP
AP1G1	164	hgsc.bcm.edu	37	16	71773190	71773190	+	Missense_Mutation	SNP	G	G	T	rs904763	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	202	115	124	0	0.569307	0	G|0.820;T|0.180	0.180	strong	.	AP1G1	83	.	NM_001030007	exon21	c.C2063A	p.P688H	AAGAAGGGGGGCT	.	PASS	Atlas-SNP
PTPRN2	5799	hgsc.bcm.edu	37	7	157929370	157929370	+	Missense_Mutation	SNP	C	C	T	rs55645575	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	88	32	99	0	0.363636	0	C|0.989;T|0.011	0.011	strong	.	PTPRN2	243	.	NM_130843	exon8	c.G1150A	p.D384N	CATCGTCGTCCTG	.	PASS	Atlas-SNP
ZBBX	79740	hgsc.bcm.edu	37	3	167051726	167051726	+	Silent	SNP	A	A	G	rs10936530	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	119	56	148	0	0.470588	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
SLC24A2	25769	hgsc.bcm.edu	37	9	19786217	19786217	+	Silent	SNP	G	G	A	rs1536517	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	79	30	85	0	0.379747	0	G|0.882;A|0.118	0.118	strong	SLC24A2,NS,carcinoma,0,1	SLC24A2	93	1	NM_001193288	exon1	c.C648T	p.I216I	AAAGAGGATGTTG	.	PASS	Atlas-SNP
TNS1	7145	hgsc.bcm.edu	37	2	218695102	218695102	+	Missense_Mutation	SNP	G	G	A	rs3796028	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	34	64	0	0.586207	0	G|0.646;A|0.354	0.354	strong	.	TNS1	251	.	NM_022648	exon21	c.C3010T	p.R1004W	GGATCCGTCTTCT	.	PASS	Atlas-SNP
FAT4	79633	hgsc.bcm.edu	37	4	126402890	126402890	+	Silent	SNP	G	G	A	rs6824160	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	90	37	111	0	0.411111	0	G|0.890;A|0.110	0.110	strong	.	FAT4	1752	.	NM_024582	exon15	c.G12813A	p.V4271V	TACTGTGAAGGTG	.	PASS	Atlas-SNP
NOP14	8602	hgsc.bcm.edu	37	4	2951804	2951804	+	Missense_Mutation	SNP	A	A	G	rs2515960	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	202	199	256	1	0.985148	0.00390625	A|0.537;G|0.463	0.463	strong	.	NOP14	69	.	NM_003703	exon8	c.T1139C	p.L380S	AGGTCCAAGTGGC	.	PASS	Atlas-SNP
OSCP1	127700	hgsc.bcm.edu	37	1	36889005	36889005	+	Silent	SNP	G	G	A	rs16822954	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	66	34	78	0	0.515152	0	G|0.890;A|0.110	0.110	strong	.	OSCP1	48	.	NM_145047	exon5	c.C579T	p.S193S	AGGCCCGGACACC	.	PASS	Atlas-SNP
ARHGEF5	7984	hgsc.bcm.edu	37	7	144062222	144062222	+	Silent	SNP	G	G	A	rs201478085		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	151	27	165	0	0.178808	0	G|0.995;A|0.005	0.005	weak	ARHGEF5,NS,carcinoma,+2,2	ARHGEF5	73	2	NM_005435	exon2	c.G2460A	p.P820P	TTTGCCGCAGCCC	.	scavenged	Atlas-SNP
LRP1B	53353	hgsc.bcm.edu	37	2	141259283	141259283	+	Silent	SNP	G	G	A	rs35296183	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	32	46	0	0.444444	0	G|0.847;A|0.153	0.153	strong	.	LRP1B	1315	.	NM_018557	exon55	c.C8823T	p.D2941D	TTGACAGTCTTGA	.	PASS	Atlas-SNP
PLCB3	5331	hgsc.bcm.edu	37	11	64026685	64026685	+	Silent	SNP	C	C	T	rs28395882	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	10	3	13	0	0.3	0	C|0.817;T|0.183	0.183	strong	PLCB3,NS,carcinoma,0,1	PLCB3	103	1	NM_000932	exon13	c.C1494T	p.S498S	GAGCTCCGCGGCC	.	scavenged	Atlas-SNP
PRR11	55771	hgsc.bcm.edu	37	17	57247133	57247133	+	Missense_Mutation	SNP	G	G	A	rs145780567	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	47	101	0	0.546512	0	G|0.994;A|0.006	0.006	strong	PRR11,NS,carcinoma,+1,1	PRR11	36	1	NM_018304	exon2	c.G20A	p.R7Q	AACAACGAAGACG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195506990	195506990	+	Missense_Mutation	SNP	C	C	G	rs200783894	byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	59	10	70	5	0.169492	0.0714286	C|0.746;G|0.253	0.253	strong	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.G11461C	p.D3821H	TGGTGTCACCTGT	.	scavenged	Atlas-SNP
PRKCQ	5588	hgsc.bcm.edu	37	10	6498723	6498723	+	Silent	SNP	G	G	A	rs11258943	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	121	53	163	0	0.438017	0	G|0.837;A|0.163	0.163	strong	.	PRKCQ	113	.	NM_006257	exon15	c.C1560T	p.I520I	ATCCGCGATCTTG	.	PASS	Atlas-SNP
CHI3L2	1117	hgsc.bcm.edu	37	1	111783982	111783982	+	Silent	SNP	C	C	A	rs13721	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	80	80	76	0	1	0	A|0.280;C|0.697;T|0.022	0.280	strong	.	CHI3L2	38	.	NM_004000	exon9	c.C952A	p.R318R	ATCACGCGGCTCC	.	PASS	Atlas-SNP
PDZD8	118987	hgsc.bcm.edu	37	10	119043295	119043295	+	Silent	SNP	C	C	T	rs41314485	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	131	70	129	0	0.534351	0	C|0.993;T|0.007	0.007	strong	.	PDZD8	85	.	NM_173791	exon5	c.G2949A	p.E983E	ACAGACCTCCGTG	.	PASS	Atlas-SNP
INPP5F	22876	hgsc.bcm.edu	37	10	121551581	121551581	+	Silent	SNP	A	A	C	rs2289306	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	99	47	152	2	0.474747	0.0131579	A|0.616;C|0.384	0.384	strong	INPP5F_ENST00000369081,NS,carcinoma,0,1	INPP5F	112	1	NM_001243195	exon5	c.A645C	p.A215A	GTTTGCACTTGGG	.	scavenged	Atlas-SNP
OR9G9	504191	hgsc.bcm.edu	37	11	56468258	56468258	+	Missense_Mutation	SNP	C	C	T	rs78340277	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	227	85	257	0	0.374449	0	C|0.987;T|0.013	0.013	strong	.	.	.	.	NM_001013358	exon1	c.C395T	p.A132V	TTTATGCCCAGGC	.	PASS	Atlas-SNP
CACNA1C	775	hgsc.bcm.edu	37	12	2794937	2794937	+	Missense_Mutation	SNP	C	C	T	rs201777030		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	118	16	110	2	0.135593	0.0181818	.	.	weak	Q6YL47_HUMAN,trunk,malignant_melanoma,0,3	CACNA1C	1023	3	NM_199460	exon47	c.C5858T	p.T1953M	AACTGACGCTCCC	.	scavenged	Atlas-SNP
PKD1L2	114780	hgsc.bcm.edu	37	16	81249954	81249954	+	Missense_Mutation	SNP	T	T	A	rs7191351	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	95	95	83	0	1	0	A|0.526;N|0.001	0.526	strong	.	PKD1L2	361	.	NM_001076780	exon2	c.A359T	p.Q120L	GCGGCCTGCCCTC	.	PASS	Atlas-SNP
FAM208B	54906	hgsc.bcm.edu	37	10	5803349	5803349	+	Silent	SNP	A	A	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	120	28	119	0	0.233333	0	.	.	none	C10orf18,NS,carcinoma,+2,2	.	.	2	NM_017782	exon19	c.A7089C	p.R2363R	CTCTCGATCATCA	.	PASS	Atlas-SNP
PADI6	353238	hgsc.bcm.edu	37	1	17708528	17708528	+	Missense_Mutation	SNP	G	G	A	rs61766772	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	128	59	141	0	0.460938	0	G|0.963;A|0.037	0.037	strong	.	PADI6	51	.	NM_207421	exon6	c.G620A	p.R207Q	AATATCGGCTAGT	.	PASS	Atlas-SNP
FAM205A	259308	hgsc.bcm.edu	37	9	34726821	34726821	+	Missense_Mutation	SNP	A	A	C	rs117956208	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	90	53	116	0	0.588889	0	A|0.987;C|0.013	0.013	strong	.	FAM205A	45	.	NM_001141917	exon4	c.T416G	p.L139R	ATCTCTAGGCAAG	.	PASS	Atlas-SNP
MPC2	25874	hgsc.bcm.edu	37	1	167893759	167893759	+	Silent	SNP	G	G	A	rs9618	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	102	102	160	1	1	0.00625	G|0.609;A|0.391	0.391	strong	BRP44,caecum,carcinoma,0,1	.	.	1	NM_001143674	exon3	c.C126T	p.F42F	CCAGAAGAAAACT	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	59	58	70	0	0.983051	0	G|0.728;T|0.272	0.272	strong	.	CASC1	146	.	NM_001082972	exon4	c.C289A	p.R97S	TCAAACGGGCTTC	.	PASS	Atlas-SNP
CCDC92	80212	hgsc.bcm.edu	37	12	124427306	124427306	+	Missense_Mutation	SNP	T	T	A	rs11057401	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	131	62	118	0	0.473282	0	T|0.710;A|0.290	0.290	strong	CCDC92,colon,carcinoma,0,1	CCDC92	18	1	NM_025140	exon4	c.A208T	p.S70C	CCGAACTTTTGAC	.	PASS	Atlas-SNP
SLFN11	91607	hgsc.bcm.edu	37	17	33690466	33690466	+	Missense_Mutation	SNP	C	C	A	rs12453150	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	62	33	92	0	0.532258	0	C|0.564;A|0.436	0.436	strong	.	SLFN11	112	.	NM_152270	exon2	c.G361T	p.V121F	GCTTGACAGAGCG	.	PASS	Atlas-SNP
OXNAD1	92106	hgsc.bcm.edu	37	3	16327855	16327855	+	Missense_Mutation	SNP	T	T	G	rs842274	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	142	141	183	0	0.992958	0	T|0.589;G|0.405	0.405	strong	.	OXNAD1	31	.	NM_138381	exon5	c.T190G	p.S64A	ATTGTGTCAGCAG	.	PASS	Atlas-SNP
AMELX	265	hgsc.bcm.edu	37	X	11316742	11316742	+	Silent	SNP	C	C	T	rs2106416	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	68	68	88	0	1	0	C|0.765;T|0.235	0.235	strong	.	AMELX	31	.	NM_182680	exon6	c.C261T	p.H87H	ACAGCACCCCCCG	.	PASS	Atlas-SNP
XRN1	54464	hgsc.bcm.edu	37	3	142123841	142123841	+	Silent	SNP	C	C	T	rs2306700	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	275	140	339	0	0.509091	0	C|0.867;T|0.133	0.133	strong	.	XRN1	138	.	NM_001042604	exon16	c.G1791A	p.E597E	TAGGCACTCACTA	.	PASS	Atlas-SNP
KANSL1	284058	hgsc.bcm.edu	37	17	44248499	44248499	+	Silent	SNP	G	G	C	rs2240758	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	41	207	0	0.476744	0	G|0.432;C|0.568	0.568	strong	KIAA1267,NS,carcinoma,-1,3	.	.	3	NM_001193466	exon2	c.C1011G	p.S337S	TCTCAAGGATTCC	.	PASS	Atlas-SNP
KRTAP10-9	386676	hgsc.bcm.edu	37	21	46047633	46047633	+	Missense_Mutation	SNP	A	A	G	rs8127342	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	164	164	124	0	1	0	A|0.343;G|0.657	0.657	strong	.	KRTAP10-9	24	.	NM_198690	exon1	c.A545G	p.Y182C	AGTCCTACTGTGT	.	PASS	Atlas-SNP
DFFB	1677	hgsc.bcm.edu	37	1	3800242	3800242	+	Silent	SNP	A	A	G	rs3205087	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	95	94	147	0	0.989474	0	A|0.607;G|0.393	0.393	strong	.	DFFB	30	.	NM_004402	exon7	c.A954G	p.P318P	TGACCCAAGCAGA	.	PASS	Atlas-SNP
ING4	51147	hgsc.bcm.edu	37	12	6760367	6760367	+	Silent	SNP	C	C	T	rs76327967	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	110	45	131	0	0.409091	0	C|0.923;T|0.077	0.077	strong	.	ING4	31	.	NM_001127582	exon8	c.G744A	p.K248K	CTATTTCTTCTTC	.	PASS	Atlas-SNP
CHD5	26038	hgsc.bcm.edu	37	1	6202245	6202245	+	Silent	SNP	G	G	A	rs2273032	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	100	37	158	0	0.37	0	G|0.879;N|0.001	.	strong	CHD5_ENST00000262450,NS,carcinoma,0,1	CHD5	267	1	NM_015557	exon15	c.C2379T	p.N793N	AAACTCGTTCTCC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195508982	195508982	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	49	4	36	1	0.0816327	0.0277778	.	.	none	MUC4_ENST00000463781,NS,malignant_melanoma,0,2	MUC4	1505	2	NM_018406	exon2	c.G9469A	p.D3157N	AAGTGTCGGTGAC	.	scavenged	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	89	89	80	0	1	0	C|0.506;G|0.494	0.494	strong	.	.	.	.	NM_001271428	exon10	c.G1034C	p.S345T	CTGCTACTTTTCT	.	PASS	Atlas-SNP
GFM2	84340	hgsc.bcm.edu	37	5	74037386	74037386	+	Missense_Mutation	SNP	T	T	A	rs16872235	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	274	161	328	1	0.587591	0.00304878	T|0.878;A|0.122	0.122	strong	.	GFM2	38	.	NM_032380	exon11	c.A898T	p.S300C	TCTCACTAAATTC	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	37	102	0	0.402174	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
ASB11	140456	hgsc.bcm.edu	37	X	15332558	15332558	+	Silent	SNP	A	A	G	rs5935944	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	85	100	0	1	0	A|0.680;0|0.003	.	strong	.	ASB11	79	.	NM_001012428	exon1	c.T51C	p.R17R	TCTGATACGTTCT	.	PASS	Atlas-SNP
COL4A1	1282	hgsc.bcm.edu	37	13	110827580	110827580	+	Silent	SNP	C	C	T	rs874204	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	104	53	128	0	0.509615	0	C|0.658;A|0.001	.	strong	.	COL4A1	372	.	NM_001845	exon37	c.G3183A	p.G1061G	TCGCAGCCCTGGG	.	PASS	Atlas-SNP
SMCR9	140776	hgsc.bcm.edu	37	17	17326363	17326363	+	Missense_Mutation	SNP	G	G	A	rs35590625	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	15	6	11	0	0.4	0	G|0.747;A|0.253	0.253	strong	.	.	.	.	NM_001243312	exon3	c.G178A	p.V60I	TTGAGTGTTCTTC	.	PASS	Atlas-SNP
C4orf17	84103	hgsc.bcm.edu	37	4	100443782	100443782	+	Missense_Mutation	SNP	T	T	C	rs13119384	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	90	90	110	0	1	0	T|0.458;C|0.542	0.542	strong	.	C4orf17	42	.	NM_032149	exon3	c.T253C	p.S85P	TACCCCTCCAGCA	.	PASS	Atlas-SNP
PIGW	284098	hgsc.bcm.edu	37	17	34893655	34893655	+	Missense_Mutation	SNP	C	C	G	rs61755368	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	114	57	125	0	0.5	0	C|0.995;G|0.005	0.005	strong	.	PIGW	50	.	NM_178517	exon2	c.C705G	p.H235Q	AGTTCACTGGAAC	.	PASS	Atlas-SNP
ZNF816	125893	hgsc.bcm.edu	37	19	53454543	53454543	+	Missense_Mutation	SNP	G	G	A	rs11084210	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	66	34	86	0	0.515152	0	A|0.112;C|0.000;G|0.888	0.112	strong	.	ZNF816	73	.	NM_001202457	exon4	c.C485T	p.S162L	AGATGCGAATGAA	.	PASS	Atlas-SNP
FAM214A	56204	hgsc.bcm.edu	37	15	52901284	52901284	+	Silent	SNP	T	T	C	rs58018557	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	83	51	78	0	0.614458	0	T|0.652;C|0.348	0.348	strong	.	.	.	.	NM_019600	exon6	c.A1827G	p.S609S	GGAAGTTGATAAA	.	PASS	Atlas-SNP
S100PBP	64766	hgsc.bcm.edu	37	1	33292008	33292008	+	Missense_Mutation	SNP	G	G	A	rs61739743	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	36	110	0	0.439024	0	G|0.990;A|0.010	0.010	strong	.	S100PBP	31	.	NM_001256121	exon3	c.G308A	p.S103N	CGTACAGCCTGGG	.	PASS	Atlas-SNP
KIAA1967	57805	hgsc.bcm.edu	37	8	22463623	22463623	+	Silent	SNP	C	C	T	rs7843828	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	98	74	104	0	0.755102	0	C|0.705;T|0.295	0.295	strong	KIAA1967,colon,carcinoma,+1,1	KIAA1967	72	1	NM_021174	exon3	c.C84T	p.G28G	TCTGGGCCCTCCT	.	PASS	Atlas-SNP
SPTA1	6708	hgsc.bcm.edu	37	1	158624528	158624528	+	Missense_Mutation	SNP	G	G	T	rs35948326	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	45	25	80	0	0.555556	0	G|0.972;T|0.028	0.028	strong	SPTA1,NS,carcinoma,-1,1	SPTA1	720	1	NM_003126	exon21	c.C2909A	p.A970D	GGTGCAGCCTGTT	.	PASS	Atlas-SNP
SLCO1A2	6579	hgsc.bcm.edu	37	12	21457434	21457434	+	Missense_Mutation	SNP	T	T	G	rs11568563	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	169	82	231	0	0.485207	0	T|0.964;G|0.036	0.036	strong	SLCO1A2,lymph_node,lymphoid_neoplasm,0,1	SLCO1A2	107	1	NM_134431	exon7	c.A516C	p.E172D	GGGAGTTTCACCC	.	PASS	Atlas-SNP
ICAM1	3383	hgsc.bcm.edu	37	19	10395248	10395248	+	Silent	SNP	C	C	T	rs13306429	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	62	28	74	0	0.451613	0	C|0.994;T|0.006	0.006	strong	.	ICAM1	32	.	NM_000201	exon5	c.C1095T	p.N365N	GGACAACGGGCGC	.	PASS	Atlas-SNP
IGFN1	91156	hgsc.bcm.edu	37	1	201163305	201163305	+	Missense_Mutation	SNP	C	C	A	rs189690117	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	116	116	123	0	1	0	C|0.999;A|0.001	0.001	strong	.	IGFN1	220	.	NM_001164586	exon3	c.C31A	p.P11T	CACATCCCTGGAG	.	PASS	Atlas-SNP
PCDHB6	56130	hgsc.bcm.edu	37	5	140531374	140531374	+	Silent	SNP	T	T	C	rs17844437	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	167	70	171	0	0.419162	0	T|0.924;C|0.076	0.076	strong	.	PCDHB6	161	.	NM_018939	exon1	c.T1536C	p.F512F	CCTGTTTGCCCTC	.	PASS	Atlas-SNP
C1orf65	164127	hgsc.bcm.edu	37	1	223567808	223567808	+	Missense_Mutation	SNP	C	C	T	rs6682552	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	115	54	110	0	0.469565	0	C|0.933;T|0.067	0.067	strong	.	C1orf65	71	.	NM_152610	exon1	c.C991T	p.R331W	GGCCTGCGGCGGG	.	PASS	Atlas-SNP
KRT28	162605	hgsc.bcm.edu	37	17	38955991	38955991	+	Missense_Mutation	SNP	C	C	T	rs7209228	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	42	13	69	0	0.309524	0	C|0.859;T|0.141	0.141	strong	.	KRT28	65	.	NM_181535	exon1	c.G155A	p.G52D	CCCAAGCCCCCTC	.	PASS	Atlas-SNP
KRT32	3882	hgsc.bcm.edu	37	17	39622068	39622068	+	Missense_Mutation	SNP	G	G	T	rs2071561	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	121	121	120	0	1	0	G|0.553;T|0.445	0.445	strong	.	KRT32	57	.	NM_002278	exon3	c.C665A	p.S222Y	TTCAGGGACTCAA	.	PASS	Atlas-SNP
NFIX	4784	hgsc.bcm.edu	37	19	13183882	13183882	+	Nonsense_Mutation	SNP	C	C	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	105	27	120	0	0.257143	0	.	.	none	.	NFIX	61	.	NM_001271043	exon3	c.C605G	p.S202X	ATAGTTCAAACCA	.	PASS	Atlas-SNP
ETS2	2114	hgsc.bcm.edu	37	21	40191431	40191431	+	Silent	SNP	T	T	G	rs457705	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	62	62	68	1	1	0.0147059	T|0.298;G|0.702	0.702	strong	ETS2_ENST00000360214,NS,carcinoma,0,2	ETS2	87	2	NM_001256295	exon9	c.T1236G	p.T412T	AGGGACTCCCAAA	.	scavenged	Atlas-SNP
SLC24A2	25769	hgsc.bcm.edu	37	9	19622268	19622268	+	Silent	SNP	T	T	C	rs4977308	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	36	98	0	0.514286	0	T|0.231;C|0.769	0.769	strong	.	SLC24A2	93	.	NM_001193288	exon2	c.A960G	p.P320P	TAGAGTTGGTTCA	.	PASS	Atlas-SNP
TUBG2	27175	hgsc.bcm.edu	37	17	40811919	40811919	+	Silent	SNP	A	A	G	rs525911	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	229	83	282	0	0.362445	0	A|0.485;G|0.515	0.515	strong	.	TUBG2	43	.	NM_016437	exon2	c.A117G	p.E39E	GGAGGAATTCGCC	.	PASS	Atlas-SNP
ABI3BP	25890	hgsc.bcm.edu	37	3	100617668	100617668	+	Silent	SNP	G	G	T	rs34999788	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	67	22	92	0	0.328358	0	G|0.913;T|0.087	0.087	strong	.	ABI3BP	305	.	NM_015429	exon4	c.C420A	p.S140S	ACCCCAGGACAGG	.	PASS	Atlas-SNP
HLA-DPB1	3115	hgsc.bcm.edu	37	6	33053609	33053609	+	Missense_Mutation	SNP	G	G	A	rs11551421	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	90	46	80	0	0.511111	0	G|0.913;A|0.087	0.087	strong	.	HLA-DPB1	28	.	NM_002121	exon4	c.G700A	p.V234M	GGCTTCGTGCTGG	.	PASS	Atlas-SNP
HELZ2	85441	hgsc.bcm.edu	37	20	62191937	62191937	+	Silent	SNP	G	G	A	rs11551685	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	61	33	73	0	0.540984	0	G|0.842;A|0.158	0.158	strong	.	.	.	.	NM_001037335	exon17	c.C7395T	p.C2465C	GACAGGGCAGCTC	.	PASS	Atlas-SNP
LGR6	59352	hgsc.bcm.edu	37	1	202183308	202183308	+	Missense_Mutation	SNP	C	C	T	rs10920362	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	107	57	106	0	0.53271	0	C|0.563;T|0.437	0.437	strong	.	LGR6	102	.	NM_001017404	exon1	c.C26T	p.S9L	GCCGCTCAGCGAG	.	PASS	Atlas-SNP
CCRL2	9034	hgsc.bcm.edu	37	3	46450297	46450297	+	Missense_Mutation	SNP	A	A	G	rs3204850	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	234	111	219	0	0.474359	0	A|0.948;G|0.052	0.052	strong	.	CCRL2	23	.	NM_001130910	exon2	c.A763G	p.I255V	TTTGCCATAATGG	.	PASS	Atlas-SNP
NCAPH2	29781	hgsc.bcm.edu	37	22	50960682	50960682	+	Splice_Site	SNP	C	C	T	rs140524	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	37	71	1	0.493333	0.0140845	C|0.810;T|0.190	0.190	strong	NCAPH2,NS,carcinoma,0,1	NCAPH2	69	1	NM_001185011	exon14	c.1233+2C>T	.	GGGAGGCAAGTCC	.	scavenged	Atlas-SNP
TYK2	7297	hgsc.bcm.edu	37	19	10477206	10477206	+	Silent	SNP	G	G	A	rs280523	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	134	51	142	0	0.380597	0	G|0.905;A|0.095	0.095	strong	.	TYK2	126	.	NM_003331	exon6	c.C516T	p.T172T	CTCCTCGGTCGAC	.	PASS	Atlas-SNP
KIF18B	146909	hgsc.bcm.edu	37	17	43008970	43008970	+	Missense_Mutation	SNP	T	T	C	rs17546822	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	37	111	0	0.425287	0	T|0.964;C|0.036	0.036	strong	.	KIF18B	63	.	NM_001264573	exon11	c.A1553G	p.Q518R	ACCTACTGCTTAG	.	PASS	Atlas-SNP
NOL9	79707	hgsc.bcm.edu	37	1	6585956	6585956	+	Silent	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	251	4	246	0	0.0159363	0	.	.	none	NOL9,bladder,carcinoma,0,1	NOL9	49	1	NM_024654	exon12	c.G2067A	p.E689E	TGGTTTCTCTTTA	.	scavenged	Atlas-SNP
KIAA1755	85449	hgsc.bcm.edu	37	20	36869516	36869516	+	Missense_Mutation	SNP	C	C	A	rs1205434	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	66	34	65	0	0.515152	0	C|0.710;A|0.290	0.290	strong	.	KIAA1755	145	.	NM_001029864	exon3	c.G1017T	p.K339N	TTCTGGCTTTGTG	.	PASS	Atlas-SNP
MTHFR	4524	hgsc.bcm.edu	37	1	11863057	11863057	+	Silent	SNP	G	G	A	rs2066470	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	112	65	122	0	0.580357	0	G|0.910;A|0.090	0.090	strong	.	MTHFR	65	.	NM_005957	exon2	c.C117T	p.P39P	CCGCTCGGGGTCC	.	PASS	Atlas-SNP
PDS5A	23244	hgsc.bcm.edu	37	4	39921942	39921942	+	Silent	SNP	A	A	G	rs28449663	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	173	72	205	0	0.416185	0	A|0.598;G|0.402	0.402	strong	PDS5A_ENST00000503396,NS,carcinoma,0,2	PDS5A	114	2	NM_001100399	exon7	c.T732C	p.A244A	TACATTAGCAATG	.	PASS	Atlas-SNP
NEK9	91754	hgsc.bcm.edu	37	14	75590846	75590846	+	Silent	SNP	A	A	T	rs175449	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	139	77	134	0	0.553957	0	A|0.436;T|0.564	0.564	strong	.	NEK9	64	.	NM_033116	exon2	c.T300A	p.I100I	AATAACAATCTCA	.	PASS	Atlas-SNP
CYP4F2	8529	hgsc.bcm.edu	37	19	16008257	16008257	+	Silent	SNP	T	T	C	rs3093106	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	155	78	169	0	0.503226	0	T|0.799;C|0.201	0.201	strong	.	CYP4F2	97	.	NM_001082	exon2	c.A165G	p.P55P	CCGTCTTGGGGGT	.	PASS	Atlas-SNP
HLA-DOB	3112	hgsc.bcm.edu	37	6	32781554	32781554	+	Missense_Mutation	SNP	G	G	A	rs2070121	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	33	187	0	0.326733	0	G|0.912;A|0.088	0.088	strong	.	HLA-DOB	17	.	NM_002120	exon4	c.C700T	p.L234F	GCCCAAGTAGGAA	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	24	73	0	0.347826	0	A|0.607;T|0.393	0.393	strong	.	SLC30A5	54	.	NM_022902	exon14	c.A1800T	p.T600T	AGATACACTTGGC	.	PASS	Atlas-SNP
OVCH1	341350	hgsc.bcm.edu	37	12	29648275	29648275	+	Missense_Mutation	SNP	G	G	A	rs10843438	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	186	86	251	0	0.462366	0	G|0.534;A|0.466	0.466	strong	OVCH1,NS,carcinoma,+1,1	OVCH1	195	1	NM_183378	exon4	c.C397T	p.R133C	ATTCACGGCTGTT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195507242	195507242	+	Missense_Mutation	SNP	C	C	A	rs112808291	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	83	28	71	0	0.337349	0	A|1.000;|0.000	1.000	weak	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.G11209T	p.A3737S	TGGATGCTGAGGA	.	PASS	Atlas-SNP
C8orf74	203076	hgsc.bcm.edu	37	8	10532188	10532188	+	Silent	SNP	T	T	C	rs61729951	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	137	105	144	0	0.766423	0	T|0.992;C|0.008	0.008	strong	.	C8orf74	28	.	NM_001040032	exon2	c.T81C	p.L27L	GAGGCTTCTGAAC	.	PASS	Atlas-SNP
FAR1	84188	hgsc.bcm.edu	37	11	13743325	13743325	+	Silent	SNP	A	A	G	rs34341612	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	49	32	70	0	0.653061	0	A|0.990;G|0.010	0.010	strong	.	FAR1	40	.	NM_032228	exon10	c.A1176G	p.E392E	TCTTGAATATTTC	.	PASS	Atlas-SNP
UGT1A8	54576	hgsc.bcm.edu	37	2	234527118	234527118	+	Silent	SNP	A	A	G	rs1042605	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	154	79	171	0	0.512987	0	A|0.856;G|0.144	0.144	strong	.	UGT1A8	69	.	NM_019076	exon1	c.A765G	p.T255T	GCGAACAGACTTT	.	PASS	Atlas-SNP
ESYT2	57488	hgsc.bcm.edu	37	7	158528254	158528254	+	Silent	SNP	G	G	A	rs34974906	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	66	25	82	0	0.378788	0	G|0.884;A|0.116	0.116	strong	ESYT2,NS,malignant_melanoma,0,3	ESYT2	70	3	NM_020728	exon20	c.C2526T	p.L842L	AACGTCGAGCGTT	.	PASS	Atlas-SNP
STOX1	219736	hgsc.bcm.edu	37	10	70641785	70641785	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	160	73	175	0	0.45625	0	.	.	none	.	STOX1	75	.	NM_001130160	exon2	c.T382C	p.C128R	CTTTGCTGTGCTA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195511668	195511668	+	Silent	SNP	G	G	A	rs3107748	bycluster;byfrequency;by2hit2allele;byhapmap	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	117	29	127	0	0.247863	0	G|0.762;A|0.238	0.238	strong	MUC4_ENST00000463781,NS,carcinoma,0,5	MUC4	1505	5	NM_018406	exon2	c.C6783T	p.D2261D	GGAAGCGTCGGTG	.	PASS	Atlas-SNP
KRT86	3892	hgsc.bcm.edu	37	12	52695787	52695787	+	Silent	SNP	C	C	T	rs112261068	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	17	15	5	0	0.882353	0	C|0.873;T|0.127	0.127	strong	.	KRT86	33	.	NM_002284	exon1	c.C87T	p.A29A	CACCGCCGCCCCC	.	PASS	Atlas-SNP
MSRB2	22921	hgsc.bcm.edu	37	10	23408278	23408278	+	Silent	SNP	C	C	T	rs7427	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	132	60	114	0	0.454545	0	C|0.746;T|0.254	0.254	strong	.	MSRB2	21	.	NM_012228	exon4	c.C342T	p.S114S	GTTTTCCGAGGCT	.	PASS	Atlas-SNP
COL6A3	1293	hgsc.bcm.edu	37	2	238249630	238249630	+	Silent	SNP	C	C	T	rs4433949	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	195	93	206	0	0.476923	0	C|0.625;T|0.375	0.375	strong	.	COL6A3	608	.	NM_004369	exon38	c.G7929A	p.A2643A	CAGGTACGCTATG	.	PASS	Atlas-SNP
DIAPH3	81624	hgsc.bcm.edu	37	13	60413550	60413550	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	52	10	68	0	0.192308	0	.	.	none	.	DIAPH3	139	.	NM_001042517	exon23	c.C2770A	p.Q924K	CCATCTGCCTCAA	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	175	86	236	0	0.491429	0	G|0.818;T|0.182	0.182	strong	.	DENND5B	114	.	NM_144973	exon5	c.C1459A	p.H487N	CACAATGCAGTTT	.	PASS	Atlas-SNP
KIF4A	24137	hgsc.bcm.edu	37	X	69573639	69573639	+	Silent	SNP	C	C	T	rs1199429	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	175	175	238	0	1	0	0|0.003;T|0.145	0.145	strong	.	KIF4A	118	.	NM_012310	exon15	c.C1656T	p.P552P	GCAGCCCATTCAG	.	PASS	Atlas-SNP
MCM3	4172	hgsc.bcm.edu	37	6	52129484	52129484	+	Missense_Mutation	SNP	C	C	T	rs2230240	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	113	62	115	0	0.548673	0	C|0.841;T|0.159	0.159	strong	.	MCM3	63	.	NM_002388	exon17	c.G2464A	p.E822K	GCTCTTCGCTGTC	.	PASS	Atlas-SNP
UGT1A7	54577	hgsc.bcm.edu	37	2	234590970	234590970	+	Missense_Mutation	SNP	T	T	G	rs76359435	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	23	115	0	0.319444	0	.	.	weak	.	UGT1A7	74	.	NM_019077	exon1	c.T387G	p.N129K	GTTTAATGACCGA	.	PASS	Atlas-SNP
OR4X1	390113	hgsc.bcm.edu	37	11	48286234	48286234	+	Silent	SNP	A	A	G	rs61732322	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	224	49	199	0	0.21875	0	A|0.962;G|0.038	0.038	strong	.	OR4X1	75	.	NM_001004726	exon1	c.A822G	p.T274T	TTATACAGTGGTC	.	PASS	Atlas-SNP
C17orf74	201243	hgsc.bcm.edu	37	17	7330290	7330290	+	Missense_Mutation	SNP	C	C	T	rs78371599	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	128	75	115	0	0.585938	0	C|0.968;T|0.032	0.032	strong	.	C17orf74	56	.	NM_175734	exon3	c.C980T	p.S327L	CTGCCTCGGTGTC	.	PASS	Atlas-SNP
IL17REL	400935	hgsc.bcm.edu	37	22	50439194	50439194	+	Missense_Mutation	SNP	C	C	T	rs9617090	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	94	50	98	0	0.531915	0	C|0.696;T|0.304	0.304	strong	.	IL17REL	21	.	NM_001001694	exon5	c.G208A	p.G70R	GCCCCCCCTGCTG	.	PASS	Atlas-SNP
GATC	283459	hgsc.bcm.edu	37	12	120884291	120884291	+	Missense_Mutation	SNP	C	C	T	rs17431446	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	31	83	0	0.378049	0	C|0.963;T|0.037	0.037	strong	.	GATC	12	.	NM_176818	exon1	c.C8T	p.S3L	TGTGGTCGCGGTT	.	PASS	Atlas-SNP
GCAT	23464	hgsc.bcm.edu	37	22	38204089	38204089	+	Missense_Mutation	SNP	C	C	T	rs710187	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	88	52	74	0	0.590909	0	C|0.420;T|0.580	0.580	strong	GCAT,NS,carcinoma,0,1	GCAT	27	1	NM_001171690	exon1	c.C115T	p.R39C	GGCATCCGCGGAG	.	PASS	Atlas-SNP
SLC12A7	10723	hgsc.bcm.edu	37	5	1073802	1073802	+	Silent	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	131	3	160	0	0.0229008	0	.	.	none	SLC12A7,caecum,carcinoma,-1,1	SLC12A7	97	1	NM_006598	exon17	c.G2187A	p.S729S	CAGCACCGAGCCC	.	scavenged	Atlas-SNP
HS3ST3A1	9955	hgsc.bcm.edu	37	17	13399616	13399616	+	Silent	SNP	A	A	T	rs62057033	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	287	95	381	1	0.33101	0.00262467	A|0.615;T|0.385	0.385	strong	.	HS3ST3A1	39	.	NM_006042	exon2	c.T1119A	p.P373P	GATCTCAGGATGG	.	PASS	Atlas-SNP
ZBTB3	79842	hgsc.bcm.edu	37	11	62521475	62521475	+	Silent	SNP	T	T	C	rs72929471	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	93	14	113	0	0.150538	0	T|0.821;C|0.179	0.179	strong	.	ZBTB3	47	.	NM_024784	exon1	c.A60G	p.R20R	TCTTTTTCGCTCC	.	PASS	Atlas-SNP
TTLL4	9654	hgsc.bcm.edu	37	2	219602819	219602819	+	Silent	SNP	G	G	A	rs3731876	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	36	36	64	0	1	0	G|0.459;A|0.541	0.541	strong	.	TTLL4	96	.	NM_014640	exon3	c.G420A	p.P140P	GAGCCCGTCAGAA	.	PASS	Atlas-SNP
PCDHB8	56128	hgsc.bcm.edu	37	5	140559058	140559058	+	Silent	SNP	G	G	A	rs61741789	byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	261	41	228	0	0.157088	0	G|0.680;A|0.320	0.320	strong	.	PCDHB8	199	.	NM_019120	exon1	c.G1443A	p.S481S	AGACTCGGGCACC	.	PASS	Atlas-SNP
TGM7	116179	hgsc.bcm.edu	37	15	43569097	43569097	+	Missense_Mutation	SNP	C	C	T	rs146833656	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	84	63	69	0	0.75	0	C|0.992;T|0.008	0.008	strong	.	TGM7	86	.	NM_052955	exon12	c.G1936A	p.E646K	TTCCTTCCAGCAC	.	PASS	Atlas-SNP
SLC9C1	285335	hgsc.bcm.edu	37	3	111918215	111918215	+	Missense_Mutation	SNP	C	C	T	rs28516377	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	66	66	68	0	1	0	C|0.725;T|0.275	0.275	strong	SLC9A10,NS,carcinoma,0,1	.	.	1	NM_183061	exon20	c.G2476A	p.G826S	TTAAGCCAAAAGC	.	PASS	Atlas-SNP
PAK2	5062	hgsc.bcm.edu	37	3	196530022	196530022	+	Silent	SNP	C	C	T	rs115224945	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	66	4	75	3	0.0606061	0.04	C|0.986;T|0.015	0.015	strong	PAK2_ENST00000327134,rectum,carcinoma,0,2	PAK2	113	2	NM_002577	exon4	c.C423T	p.S141S	TCTGAGCTTTACT	.	scavenged	Atlas-SNP
ZCCHC3	85364	hgsc.bcm.edu	37	20	278806	278806	+	Silent	SNP	C	C	T	rs1057189	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	38	18	37	0	0.473684	0	C|0.780;T|0.220	0.220	strong	.	ZCCHC3	20	.	NM_033089	exon1	c.C579T	p.S193S	GCGCTCCATCGGC	.	PASS	Atlas-SNP
OR11H4	390442	hgsc.bcm.edu	37	14	20711852	20711852	+	Missense_Mutation	SNP	C	C	G	rs17277270	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	88	47	138	0	0.534091	0	C|0.896;G|0.104	0.104	strong	.	OR11H4	63	.	NM_001004479	exon1	c.C902G	p.T301S	TCTATACTCTTCG	.	PASS	Atlas-SNP
SNAPC4	6621	hgsc.bcm.edu	37	9	139276407	139276407	+	Missense_Mutation	SNP	C	C	T	rs34569521	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	136	57	187	0	0.419118	0	C|0.942;T|0.058	0.058	strong	.	SNAPC4	82	.	NM_003086	exon17	c.G2186A	p.R729Q	CAGCGCCGCTGCC	.	PASS	Atlas-SNP
SLC30A5	64924	hgsc.bcm.edu	37	5	68417643	68417643	+	Silent	SNP	C	C	T	rs164578	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	249	92	271	0	0.369478	0	C|0.589;T|0.411	0.411	strong	.	SLC30A5	54	.	NM_022902	exon13	c.C1692T	p.H564H	TTCACACCATATG	.	PASS	Atlas-SNP
FAM135A	57579	hgsc.bcm.edu	37	6	71238105	71238105	+	Missense_Mutation	SNP	A	A	G	rs2747701	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	149	83	143	0	0.557047	0	A|0.647;G|0.353	0.353	strong	.	FAM135A	181	.	NM_001162529	exon14	c.A3725G	p.D1242G	AAGAGGATGGTTC	.	PASS	Atlas-SNP
ZNF714	148206	hgsc.bcm.edu	37	19	21300964	21300964	+	Silent	SNP	T	T	C	rs111456417	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	13	13	23	0	1	0	T|0.935;C|0.065	0.065	strong	.	ZNF714	121	.	NM_182515	exon5	c.T1494C	p.H498H	TAAACATAGGAAA	.	PASS	Atlas-SNP
TMEM44	93109	hgsc.bcm.edu	37	3	194353875	194353875	+	Missense_Mutation	SNP	G	G	T	rs1675955	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	165	70	74	0	0.424242	0	G|0.652;T|0.348	0.348	strong	.	TMEM44	42	.	NM_138399	exon1	c.C70A	p.H24N	CGCGGTGGCGGGC	.	PASS	Atlas-SNP
TDG	6996	hgsc.bcm.edu	37	12	104380734	104380734	+	Missense_Mutation	SNP	G	G	A	rs2888805	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	55	10	35	0	0.181818	0	G|0.908;A|0.092	0.092	strong	.	TDG	43	.	NM_003211	exon10	c.G1099A	p.V367M	GAGAGCGTGGAGT	.	PASS	Atlas-SNP
SSC5D	284297	hgsc.bcm.edu	37	19	56002329	56002329	+	Silent	SNP	C	C	T	rs4801305	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	164	72	136	0	0.439024	0	C|0.947;T|0.053	0.053	strong	.	SSC5D	65	.	NM_001195267	exon6	c.C777T	p.P259P	AGGGCCCGTGTGG	.	PASS	Atlas-SNP
TPST2	8459	hgsc.bcm.edu	37	22	26936897	26936897	+	Silent	SNP	G	G	A	rs12169509	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	37	81	0	0.435294	0	G|0.823;A|0.177	0.177	strong	.	TPST2	23	.	NM_001008566	exon3	c.C700T	p.L234L	CAGGCAGGCACTT	.	PASS	Atlas-SNP
MORC1	27136	hgsc.bcm.edu	37	3	108719470	108719470	+	Silent	SNP	C	C	G	rs3762698	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	118	58	148	0	0.491525	0	C|0.734;G|0.266	0.266	strong	.	MORC1	211	.	NM_014429	exon21	c.G2121C	p.L707L	AAAGTTCAGACTC	.	PASS	Atlas-SNP
XDH	7498	hgsc.bcm.edu	37	2	31589847	31589847	+	Silent	SNP	G	G	A	rs2295475	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	104	52	83	0	0.5	0	G|0.765;A|0.235	0.235	strong	.	XDH	191	.	NM_000379	exon21	c.C2211T	p.I737I	GCCACCGATGTAT	.	PASS	Atlas-SNP
CPA1	1357	hgsc.bcm.edu	37	7	130023561	130023561	+	Missense_Mutation	SNP	G	G	A	rs34474469	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	119	59	123	0	0.495798	0	G|0.979;A|0.021	0.021	strong	.	CPA1	73	.	NM_001868	exon6	c.G622A	p.A208T	TTCACCGCCATTC	.	PASS	Atlas-SNP
DZIP1	22873	hgsc.bcm.edu	37	13	96293759	96293759	+	Silent	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	102	2	124	0	0.0196078	0	.	.	none	DZIP1_ENST00000347108,NS,neuroblastoma,-2,2	DZIP1	195	2	NM_014934	exon5	c.G387A	p.E129E	CAAGTACTCGATG	.	scavenged	Atlas-SNP
LACTB	114294	hgsc.bcm.edu	37	15	63419699	63419699	+	Missense_Mutation	SNP	A	A	C	rs34536322	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	132	72	171	0	0.545455	0	A|0.971;C|0.029	0.029	strong	.	LACTB	29	.	NM_171846	exon4	c.A763C	p.K255Q	GAAGGCAAAAGTA	.	PASS	Atlas-SNP
ZNF485	220992	hgsc.bcm.edu	37	10	44112245	44112245	+	Missense_Mutation	SNP	G	G	A	rs12354886	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	79	43	75	0	0.544304	0	G|0.786;A|0.214	0.214	strong	.	ZNF485	102	.	NM_145312	exon5	c.G754A	p.A252T	GCCTTCGCTCAGA	.	PASS	Atlas-SNP
RPP40	10799	hgsc.bcm.edu	37	6	4995464	4995464	+	Missense_Mutation	SNP	C	C	T	rs12332997	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	80	21	74	0	0.2625	0	C|0.966;T|0.034	0.034	strong	RPP40,colon,carcinoma,0,1	RPP40	36	1	NM_006638	exon8	c.G940A	p.V314I	CTTGAACGGACAG	.	PASS	Atlas-SNP
TRIM31	11074	hgsc.bcm.edu	37	6	30078330	30078330	+	Silent	SNP	C	C	T	rs2239529	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	116	62	158	0	0.534483	0	C|0.907;T|0.093	0.093	strong	TRIM31,trunk,malignant_melanoma,-2,2	TRIM31	40	2	NM_007028	exon4	c.G639A	p.A213A	TTTCCCCGCTTCC	.	PASS	Atlas-SNP
SLC27A2	11001	hgsc.bcm.edu	37	15	50474900	50474900	+	Silent	SNP	C	C	T	rs34490804	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	99	36	76	0	0.363636	0	C|0.905;T|0.095	0.095	strong	.	SLC27A2	50	.	NM_003645	exon1	c.C276T	p.A92A	AGTGGCCCGGGCG	.	PASS	Atlas-SNP
AURKA	6790	hgsc.bcm.edu	37	20	54961541	54961541	+	Missense_Mutation	SNP	A	A	T	rs2273535	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	40	113	0	0.45977	0	A|0.773;T|0.227	0.227	strong	.	AURKA	42	.	NM_198437	exon3	c.T91A	p.F31I	AAGGAAATTGCTG	.	PASS	Atlas-SNP
KIDINS220	57498	hgsc.bcm.edu	37	2	8917015	8917015	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	160	2	140	0	0.0125	0	.	.	none	KIDINS220,caecum,carcinoma,0,1	KIDINS220	136	1	NM_020738	exon21	c.A2711G	p.Y904C	CTTCGGTAAGTGT	.	scavenged	Atlas-SNP
KLHL12	59349	hgsc.bcm.edu	37	1	202888947	202888947	+	Silent	SNP	T	T	C	rs3182429	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	135	54	175	0	0.4	0	T|0.778;C|0.222	0.222	strong	.	KLHL12	50	.	NM_021633	exon3	c.A285G	p.T95T	ATGTACTGTTTCT	.	PASS	Atlas-SNP
ALKBH2	121642	hgsc.bcm.edu	37	12	109527872	109527872	+	Missense_Mutation	SNP	T	T	C	rs139644396	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	40	90	0	0.512821	0	T|0.985;C|0.015	0.015	strong	.	ALKBH2	16	.	NM_001001655	exon3	c.A421G	p.I141V	CCCGGATGCGCTC	.	PASS	Atlas-SNP
TSSK2	23617	hgsc.bcm.edu	37	22	19119545	19119545	+	Silent	SNP	C	C	T	rs45604134	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	74	42	111	0	0.567568	0	C|0.846;T|0.154	0.154	strong	.	TSSK2	29	.	NM_053006	exon1	c.C633T	p.C211C	GGTCTGCGGCTCC	.	PASS	Atlas-SNP
SNF8	11267	hgsc.bcm.edu	37	17	47007963	47007963	+	Silent	SNP	C	C	T	rs2270576	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	41	15	39	0	0.365854	0	C|0.747;T|0.253	0.253	strong	.	SNF8	15	.	NM_007241	exon8	c.G651A	p.L217L	TTCCTTCAGCAGG	.	PASS	Atlas-SNP
C11orf16	56673	hgsc.bcm.edu	37	11	8947586	8947586	+	Missense_Mutation	SNP	C	C	G	rs11042127	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	96	13	77	0	0.135417	0	C|0.787;G|0.213	0.213	strong	.	C11orf16	43	.	NM_020643	exon5	c.G628C	p.V210L	ACTGGACCCCACC	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1266537	1266537	+	Silent	SNP	G	G	T	rs199659189	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	393	23	327	1	0.0585242	0.0030581	G|0.790;T|0.211	0.211	strong	MUC5B,NS,carcinoma,0,2	MUC5B	473	2	NM_002458	exon31	c.G8427T	p.L2809L	AGCCCTGTCCAGC	.	scavenged	Atlas-SNP
AMOTL2	51421	hgsc.bcm.edu	37	3	134077470	134077470	+	Missense_Mutation	SNP	C	C	G	rs1353776	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	51	24	66	0	0.470588	0	C|0.254;G|0.746	0.746	strong	.	AMOTL2	52	.	NM_016201	exon9	c.G2196C	p.E732D	GGGGCCCTCAGTC	.	PASS	Atlas-SNP
SOCS1	8651	hgsc.bcm.edu	37	16	11348810	11348810	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	17	11	12	0	0.647059	0	.	.	none	SOCS1,lymph_node,lymphoid_neoplasm,+2,1	SOCS1	84	1	NM_003745	exon2	c.G526A	p.E176K	ACAGCTCCTGCAG	.	PASS	Atlas-SNP
PKD1L1	168507	hgsc.bcm.edu	37	7	47921682	47921682	+	Silent	SNP	A	A	T	rs10951936	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	84	21	121	0	0.25	0	A|0.721;T|0.279	0.279	strong	.	PKD1L1	328	.	NM_138295	exon20	c.T3267A	p.A1089A	GTCCTTAGCTAGG	.	PASS	Atlas-SNP
UTRN	7402	hgsc.bcm.edu	37	6	144852201	144852201	+	Missense_Mutation	SNP	G	G	A	rs12204734	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	121	120	220	0	0.991736	0	G|0.871;A|0.129	0.129	strong	.	UTRN	327	.	NM_007124	exon41	c.G5920A	p.A1974T	GACAGGGCAATGG	.	PASS	Atlas-SNP
PHLDB3	653583	hgsc.bcm.edu	37	19	44001379	44001379	+	Missense_Mutation	SNP	T	T	C	rs11083711	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	55	21	60	0	0.381818	0	T|0.939;C|0.061	0.061	strong	.	PHLDB3	30	.	NM_198850	exon6	c.A716G	p.Q239R	AGTTGCTGGAACT	.	PASS	Atlas-SNP
IDUA	3425	hgsc.bcm.edu	37	4	996165	996165	+	Missense_Mutation	SNP	G	G	A	rs6831280	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	151	73	150	0	0.483444	0	G|0.821;A|0.179	0.179	strong	.	IDUA	33	.	NM_000203	exon8	c.G1081A	p.A361T	CCCTTCGCGCAGC	.	PASS	Atlas-SNP
ANKK1	255239	hgsc.bcm.edu	37	11	113270828	113270828	+	Missense_Mutation	SNP	G	G	A	rs1800497	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	166	31	147	0	0.186747	0	G|0.703;A|0.297	0.297	strong	.	ANKK1	83	.	NM_178510	exon8	c.G2137A	p.E713K	CTGGTCGAGGCAG	.	PASS	Atlas-SNP
AGAP11	119385	hgsc.bcm.edu	37	10	88768423	88768423	+	Silent	SNP	A	A	G	rs2641562	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	47	121	0	0.546512	0	A|0.567;G|0.433	0.433	strong	.	.	.	.	NM_133447	exon12	c.A414G	p.T138T	GAAGACATGGAAA	.	PASS	Atlas-SNP
HTR1B	3351	hgsc.bcm.edu	37	6	78173018	78173018	+	Missense_Mutation	SNP	C	C	T	rs200659363		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	185	4	176	0	0.0216216	0	.	.	weak	HTR1B,rectum,carcinoma,0,1	HTR1B	55	1	NM_000863	exon1	c.G103A	p.A35T	CCTTGGCGCTGCA	.	scavenged	Atlas-SNP
BPIFB2	80341	hgsc.bcm.edu	37	20	31601670	31601670	+	Silent	SNP	C	C	T	rs45589833	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	43	74	0	0.467391	0	C|0.975;T|0.025	0.025	strong	.	.	.	.	NM_025227	exon5	c.C363T	p.R121R	CACCCGCGTGACC	.	PASS	Atlas-SNP
LPPR1	0	hgsc.bcm.edu	37	9	103947810	103947810	+	Missense_Mutation	SNP	T	T	G	rs41296085	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	227	111	246	0	0.488987	0	T|0.990;G|0.010	0.010	strong	.	.	.	.	NM_207299	exon2	c.T34G	p.S12A	AGTTATTCCATCA	.	PASS	Atlas-SNP
FMO2	2327	hgsc.bcm.edu	37	1	171154959	171154959	+	Missense_Mutation	SNP	A	A	G	rs2020870	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	106	45	119	0	0.424528	0	A|0.919;G|0.081	0.081	strong	.	FMO2	66	.	NM_001460	exon2	c.A107G	p.D36G	CTGAAGATATTGG	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228476414	228476414	+	Silent	SNP	G	G	A	rs3795791	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	96	54	99	0	0.5625	0	G|0.910;A|0.090	0.090	strong	.	OBSCN	2142	.	NM_001271223	exon43	c.G11451A	p.A3817A	CAAGGCGGCCCCC	.	PASS	Atlas-SNP
CEP63	80254	hgsc.bcm.edu	37	3	134278270	134278270	+	Missense_Mutation	SNP	C	C	T	rs1127826	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	64	27	73	0	0.421875	0	C|0.695;T|0.305	0.305	strong	.	CEP63	56	.	NM_025180	exon15	c.C1952T	p.S651L	TATCTTCGGTATG	.	PASS	Atlas-SNP
LY75	4065	hgsc.bcm.edu	37	2	160737621	160737621	+	Silent	SNP	C	C	T	rs11675155	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	105	39	121	0	0.371429	0	C|0.818;T|0.182	0.182	strong	LY75,NS,carcinoma,0,1	LY75	151	1	NM_002349	exon8	c.G1377A	p.T459T	GTTGGGCGTCTTA	.	PASS	Atlas-SNP
FUK	197258	hgsc.bcm.edu	37	16	70512349	70512349	+	Missense_Mutation	SNP	G	G	A	rs17886060	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	49	87	0	0.671233	0	G|0.990;A|0.010	0.010	strong	.	FUK	72	.	NM_145059	exon21	c.G2816A	p.R939Q	TGGCTCGGAACCT	.	PASS	Atlas-SNP
SPHKAP	80309	hgsc.bcm.edu	37	2	228882970	228882970	+	Missense_Mutation	SNP	T	T	C	rs3828161	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	214	107	305	0	0.5	0	T|0.776;C|0.224	0.224	strong	SPHKAP_ENST00000392056,colon,carcinoma,0,2	SPHKAP	750	2	NM_030623	exon7	c.A2600G	p.Q867R	CTGGACTGGCTGA	.	PASS	Atlas-SNP
LAMC1	3915	hgsc.bcm.edu	37	1	183072701	183072701	+	Silent	SNP	C	C	T	rs2296289	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	46	99	0	0.589744	0	C|0.900;T|0.100	0.100	strong	.	LAMC1	176	.	NM_002293	exon2	c.C657T	p.N219N	GGGCAACGTGGCC	.	PASS	Atlas-SNP
MATN4	8785	hgsc.bcm.edu	37	20	43933196	43933196	+	Silent	SNP	C	C	T	rs2233093	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	103	70	82	0	0.679612	0	C|0.801;T|0.199	0.199	strong	.	MATN4	57	.	NM_030592	exon3	c.G315A	p.V105V	CAGAGGCACCAGG	.	PASS	Atlas-SNP
DOCK1	1793	hgsc.bcm.edu	37	10	128830409	128830409	+	Silent	SNP	A	A	G	rs2229597	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	80	49	88	0	0.6125	0	A|0.857;G|0.143	0.143	strong	.	DOCK1	188	.	NM_001380	exon18	c.A1674G	p.A558A	CGAAGCAAAGAAG	.	PASS	Atlas-SNP
EPHA3	2042	hgsc.bcm.edu	37	3	89521725	89521725	+	Silent	SNP	T	T	C	rs1054750	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	68	67	133	0	0.985294	0	T|0.835;C|0.165	0.165	strong	EPHA3,NS,malignant_melanoma,+2,1	EPHA3	501	1	NM_005233	exon16	c.T2802C	p.G934G	CACGGGTGTGGAG	.	PASS	Atlas-SNP
OR2T34	127068	hgsc.bcm.edu	37	1	248737454	248737454	+	Missense_Mutation	SNP	A	A	G	rs79750523	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	201	83	529	1	0.412935	0.00189036	A|0.848;G|0.152	0.152	strong	.	OR2T34	72	.	NM_001001821	exon1	c.T605C	p.M202T	GTGAGCATCTTAT	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228526665	228526665	+	Silent	SNP	T	T	C	rs505629	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	159	158	234	1	0.993711	0.0042735	T|0.479;C|0.521	0.521	strong	.	OBSCN	2142	.	NM_001271223	exon80	c.T20067C	p.A6689A	CATAGCTGTGGCC	.	PASS	Atlas-SNP
RGS22	26166	hgsc.bcm.edu	37	8	100990177	100990177	+	Silent	SNP	A	A	G	rs7841915	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	232	173	303	2	0.74569	0.00660066	A|0.924;G|0.076	0.076	strong	.	RGS22	319	.	NM_015668	exon23	c.T3487C	p.L1163L	CTGCCAATTTTTT	.	PASS	Atlas-SNP
ISYNA1	51477	hgsc.bcm.edu	37	19	18545786	18545786	+	Silent	SNP	G	G	T	rs1045631	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	146	145	158	1	0.993151	0.00632911	G|0.788;T|0.212	0.212	strong	.	ISYNA1	31	.	NM_016368	exon11	c.C1614A	p.T538T	GCCATTGGTGGCA	.	PASS	Atlas-SNP
OR51G1	79324	hgsc.bcm.edu	37	11	4944986	4944986	+	Missense_Mutation	SNP	A	A	G	rs12796015	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	126	20	103	0	0.15873	0	A|0.914;G|0.086	0.086	strong	.	OR51G1	74	.	NM_001005237	exon1	c.T584C	p.I195T	TTGACAATGATGC	.	PASS	Atlas-SNP
GPR126	57211	hgsc.bcm.edu	37	6	142688811	142688811	+	Missense_Mutation	SNP	C	C	T	rs116955726	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	114	30	143	0	0.263158	0	C|0.977;T|0.023	0.023	strong	.	GPR126	192	.	NM_198569	exon3	c.C209T	p.T70M	TGTGGACGCTCCG	.	PASS	Atlas-SNP
ADAMTS2	9509	hgsc.bcm.edu	37	5	178700038	178700038	+	Missense_Mutation	SNP	C	C	G	rs146064587		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	59	25	50	0	0.423729	0	C|1.000;G|0.000	0.000	weak	.	ADAMTS2	190	.	NM_021599	exon3	c.G562C	p.E188Q	AGAACTCCTCCTC	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29911222	29911222	+	Missense_Mutation	SNP	C	C	T	rs1059535	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	135	52	280	0	0.385185	0	C|0.912;T|0.088	0.088	strong	.	HLA-A	89	.	NM_001242758	exon3	c.C521T	p.A174V	AGGCGGCCCATGA	.	PASS	Atlas-SNP
KIF17	57576	hgsc.bcm.edu	37	1	21024901	21024901	+	Missense_Mutation	SNP	C	C	T	rs522496	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	35	35	46	0	1	0	C|0.404;N|0.000	.	strong	KIF17,colon,carcinoma,0,1	KIF17	130	1	NM_001122819	exon6	c.G1204A	p.V402M	CCTCCACGTCATG	.	PASS	Atlas-SNP
OR13C9	286362	hgsc.bcm.edu	37	9	107380396	107380396	+	Silent	SNP	T	T	G	rs36091517	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	231	92	299	1	0.398268	0.00334448	T|0.792;G|0.208	0.208	strong	.	OR13C9	42	.	NM_001001956	exon1	c.A90C	p.L30L	GAAGATTAGCACA	.	PASS	Atlas-SNP
KLHDC7A	127707	hgsc.bcm.edu	37	1	18808711	18808711	+	Silent	SNP	G	G	C	rs2992751	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	36	12	41	0	0.333333	0	G|0.795;C|0.205	0.205	strong	.	KLHDC7A	60	.	NM_152375	exon1	c.G1236C	p.G412G	GGCCGGGACCAAT	.	PASS	Atlas-SNP
C2orf16	84226	hgsc.bcm.edu	37	2	27801759	27801759	+	Missense_Mutation	SNP	A	A	G	rs1919128	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	252	153	256	0	0.607143	0	A|0.706;G|0.294	0.294	strong	.	C2orf16	357	.	NM_032266	exon1	c.A2320G	p.I774V	ACAGATATTTTGC	.	PASS	Atlas-SNP
NLRP3	114548	hgsc.bcm.edu	37	1	247588053	247588053	+	Silent	SNP	C	C	T	rs34298354	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	68	39	87	0	0.573529	0	C|0.912;T|0.088	0.088	strong	NLRP3,NS,carcinoma,+1,1	NLRP3	286	1	NM_183395	exon3	c.C1308T	p.S436S	GACATCCAAGACC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195505247	195505247	+	Silent	SNP	G	G	T	rs76650792	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	285	136	296	0	0.477193	0	G|0.967;T|0.033	0.033	strong	.	MUC4	1505	.	NM_018406	exon3	c.C12870A	p.I4290I	GGAAATGATGGTC	.	PASS	Atlas-SNP
HJURP	55355	hgsc.bcm.edu	37	2	234749354	234749354	+	Missense_Mutation	SNP	G	G	A	rs12582	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	79	40	85	0	0.506329	0	G|0.846;A|0.154	0.154	strong	.	HJURP	72	.	NM_018410	exon8	c.C2072T	p.S691F	CGTCCGGAGCCCT	.	PASS	Atlas-SNP
MYO9B	4650	hgsc.bcm.edu	37	19	17312992	17312992	+	Silent	SNP	C	C	T	rs2305765	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	57	29	56	1	0.508772	0.0178571	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	.	scavenged	Atlas-SNP
OSBPL3	26031	hgsc.bcm.edu	37	7	24854765	24854765	+	Silent	SNP	G	G	A	rs1044956	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	99	18	122	0	0.181818	0	G|0.722;A|0.278	0.278	strong	.	OSBPL3	100	.	NM_015550	exon19	c.C2085T	p.S695S	CTGCCCGCTTAAG	.	PASS	Atlas-SNP
AGGF1	55109	hgsc.bcm.edu	37	5	76343999	76343999	+	Silent	SNP	T	T	C	rs13155212	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	103	65	86	0	0.631068	0	C|0.234;N|0.001	0.234	strong	.	AGGF1	71	.	NM_018046	exon7	c.T1215C	p.I405I	CAAAATTTGGCCC	.	PASS	Atlas-SNP
BBS1	582	hgsc.bcm.edu	37	11	66282095	66282095	+	Silent	SNP	G	G	A	rs2298806	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	20	17	34	0	0.85	0	G|0.793;A|0.207	0.207	strong	BBS1,NS,carcinoma,0,1	BBS1	58	1	NM_024649	exon4	c.G378A	p.L126L	CAGCCTGCCCCAA	.	PASS	Atlas-SNP
PAH	5053	hgsc.bcm.edu	37	12	103246700	103246700	+	Silent	SNP	C	C	T	rs1042503	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	28	65	0	0.394366	0	C|0.723;T|0.276	0.276	strong	.	PAH	77	.	NM_000277	exon7	c.G735A	p.V245V	GCCAGCCACAGGT	.	PASS	Atlas-SNP
TMC1	117531	hgsc.bcm.edu	37	9	75303653	75303653	+	Silent	SNP	C	C	T	rs2589615	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	45	22	61	0	0.488889	0	C|0.478;T|0.522	0.522	strong	.	TMC1	87	.	NM_138691	exon6	c.C45T	p.D15D	AGAAGACGAGACT	.	PASS	Atlas-SNP
MYH14	79784	hgsc.bcm.edu	37	19	50771511	50771511	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	47	109	0	0.602564	0	.	.	none	.	MYH14	261	.	NM_001145809	exon24	c.C2920T	p.R974C	GCAGCCCGCAAGC	.	PASS	Atlas-SNP
RPTN	126638	hgsc.bcm.edu	37	1	152129115	152129115	+	Missense_Mutation	SNP	T	T	C	rs113327860	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	169	37	271	0	0.218935	0	T|0.940;C|0.060	0.060	strong	RPTN,NS,carcinoma,0,2	RPTN	123	2	NM_001122965	exon3	c.A460G	p.R154G	AATCTCTGTCTTG	.	PASS	Atlas-SNP
ATHL1	80162	hgsc.bcm.edu	37	11	290050	290050	+	Silent	SNP	G	G	A	rs139686173	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	52	14	36	0	0.269231	0	G|0.986;A|0.014	0.014	strong	.	ATHL1	88	.	NM_025092	exon2	c.G234A	p.E78E	GACCGAGACCTTC	.	PASS	Atlas-SNP
OR2T12	127064	hgsc.bcm.edu	37	1	248458187	248458187	+	Missense_Mutation	SNP	G	G	A	rs200352170		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	363	97	402	0	0.267218	0	G|0.999;A|0.001	0.001	weak	.	OR2T12	113	.	NM_001004692	exon1	c.C694T	p.R232C	TCTTGCGGGCTTC	.	PASS	Atlas-SNP
POLQ	10721	hgsc.bcm.edu	37	3	121212484	121212484	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	3	118	0	0.0422535	0	.	.	none	POLQ,caecum,carcinoma,0,1	POLQ	273	1	NM_199420	exon15	c.G2363A	p.G788D	TGGATGCCAAACG	.	scavenged	Atlas-SNP
ZADH2	284273	hgsc.bcm.edu	37	18	72913537	72913537	+	Missense_Mutation	SNP	C	C	A	rs17056661	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	112	73	139	0	0.651786	0	C|0.973;A|0.027	0.027	strong	.	ZADH2	25	.	NM_175907	exon2	c.G968T	p.C323F	CTCACACACATCT	.	PASS	Atlas-SNP
LILRB1	10859	hgsc.bcm.edu	37	19	55143083	55143083	+	Missense_Mutation	SNP	T	T	C	rs1061679	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	151	149	201	0	0.986755	0	T|0.545;C|0.455	0.455	strong	.	LILRB1	140	.	NM_001081637	exon4	c.T203C	p.L68P	CAGCACTCTGGAT	.	PASS	Atlas-SNP
SALL1	6299	hgsc.bcm.edu	37	16	51174432	51174432	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	64	29	88	0	0.453125	0	.	.	none	.	SALL1	301	.	NM_002968	exon2	c.A1701G	p.I567M	GAAGGGTATGAGG	.	PASS	Atlas-SNP
DHFRL1	200895	hgsc.bcm.edu	37	3	93780109	93780109	+	Missense_Mutation	SNP	G	G	C	rs61739170	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	161	81	241	0	0.503106	0	G|0.833;C|0.167	0.167	strong	DHFRL1,NS,carcinoma,0,1	DHFRL1	25	1	NM_001195643	exon2	c.C247G	p.P83A	GTGGAGGTTCCTT	.	PASS	Atlas-SNP
NCAPD2	9918	hgsc.bcm.edu	37	12	6638197	6638197	+	Silent	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	67	23	84	0	0.343284	0	.	.	none	.	NCAPD2	99	.	NM_014865	exon27	c.C3564T	p.T1188T	CCACACCATCATG	.	PASS	Atlas-SNP
SQRDL	58472	hgsc.bcm.edu	37	15	45968435	45968435	+	Missense_Mutation	SNP	T	T	C	rs1044032	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	112	41	80	0	0.366071	0	T|0.784;C|0.216	0.216	strong	.	SQRDL	27	.	NM_021199	exon6	c.T791C	p.I264T	ACCTCATTGAAGT	.	PASS	Atlas-SNP
MVK	4598	hgsc.bcm.edu	37	12	110019338	110019338	+	Silent	SNP	C	C	T	rs2287218	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	120	61	117	0	0.508333	0	C|0.831;T|0.169	0.169	strong	.	MVK	42	.	NM_000431	exon5	c.C510T	p.D170D	GAAGGACGGGGAT	.	PASS	Atlas-SNP
RALGAPB	57148	hgsc.bcm.edu	37	20	37153554	37153554	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	370	6	404	0	0.0162162	0	.	.	none	RALGAPB,NS,carcinoma,0,1	RALGAPB	134	1	NM_020336	exon11	c.T1753C	p.F585L	CCTTACTTTATTT	.	scavenged	Atlas-SNP
CLCN1	1180	hgsc.bcm.edu	37	7	143042837	143042837	+	Silent	SNP	C	C	T	rs2272251	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	56	32	38	0	0.571429	0	C|0.502;T|0.498	0.498	strong	CLCN1,NS,carcinoma,0,1	CLCN1	141	1	NM_000083	exon17	c.C2154T	p.D718D	CGAAGACCTCTCT	.	PASS	Atlas-SNP
MCC	4163	hgsc.bcm.edu	37	5	112823998	112823998	+	Silent	SNP	C	C	T	rs348943	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	40	86	0	0.512821	0	C|0.505;T|0.495	0.495	strong	.	MCC	234	.	NM_001085377	exon1	c.G114A	p.E38E	CATCCTCTCCTCC	.	PASS	Atlas-SNP
SPHKAP	80309	hgsc.bcm.edu	37	2	228883029	228883029	+	Missense_Mutation	SNP	A	A	C	rs3811515	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	281	139	338	0	0.494662	0	A|0.784;C|0.216	0.216	strong	SPHKAP,NS,carcinoma,0,1	SPHKAP	750	1	NM_030623	exon7	c.T2541G	p.H847Q	ACTGTGATGAGGG	.	PASS	Atlas-SNP
GSG2	83903	hgsc.bcm.edu	37	17	3628212	3628212	+	Missense_Mutation	SNP	T	T	C	rs220461	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	37	13	56	0	0.351351	0	T|0.769;C|0.230	0.230	strong	.	GSG2	48	.	NM_031965	exon1	c.T983C	p.I328T	GGGGAATAGACAG	.	PASS	Atlas-SNP
CYP2W1	54905	hgsc.bcm.edu	37	7	1024855	1024855	+	Missense_Mutation	SNP	G	G	A	rs3735684	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	56	66	0	0.811594	0	G|0.936;A|0.064	0.064	strong	.	CYP2W1	28	.	NM_017781	exon4	c.G541A	p.A181T	ACCTTCGCGCTCC	.	PASS	Atlas-SNP
MLLT3	4300	hgsc.bcm.edu	37	9	20414310	20414310	+	Silent	SNP	A	A	G	rs148318848	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	105	7	103	5	0.0666667	0.0485437	.	.	weak	MLLT3,caecum,carcinoma,0,1	MLLT3	125	1	NM_004529	exon5	c.T534C	p.S178S	GCTGCTACTGCTG	.	scavenged	Atlas-SNP
EIF4G2	1982	hgsc.bcm.edu	37	11	10827592	10827592	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	205	48	203	0	0.234146	0	.	.	none	.	EIF4G2	89	.	NM_001172705	exon4	c.A110T	p.E37V	AGGAACTCGCTGA	.	PASS	Atlas-SNP
OTOP2	92736	hgsc.bcm.edu	37	17	72926660	72926660	+	Silent	SNP	C	C	T	rs61746106	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	175	70	221	0	0.4	0	C|0.972;T|0.028	0.028	strong	.	OTOP2	81	.	NM_178160	exon6	c.C930T	p.Y310Y	CATCTACGAGGTT	.	PASS	Atlas-SNP
C9orf106	414318	hgsc.bcm.edu	37	9	132084621	132084621	+	Missense_Mutation	SNP	G	G	A	rs913770	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	40	22	50	0	0.55	0	G|0.838;A|0.162	0.162	strong	.	C9orf106	7	.	NM_001012715	exon2	c.G529A	p.G177R	CCCGGGGGACACT	.	PASS	Atlas-SNP
EIF4G3	8672	hgsc.bcm.edu	37	1	21268194	21268194	+	Missense_Mutation	SNP	G	G	C	rs142103671	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	175	74	206	0	0.422857	0	G|0.991;C|0.009	0.009	strong	.	EIF4G3	300	.	NM_001198803	exon14	c.C1318G	p.P440A	TGACTGGAGTGTG	.	PASS	Atlas-SNP
GIF	2694	hgsc.bcm.edu	37	11	59612859	59612859	+	Missense_Mutation	SNP	T	T	C	rs35211634	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	49	43	91	0	0.877551	0	T|0.902;C|0.098	0.098	strong	.	GIF	43	.	NM_005142	exon1	c.A68G	p.Q23R	GAACTCTGGGTCT	.	PASS	Atlas-SNP
UHRF1BP1	54887	hgsc.bcm.edu	37	6	34826921	34826921	+	Missense_Mutation	SNP	G	G	C	rs61732793	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	36	91	0	0.493151	0	G|0.962;C|0.038	0.038	strong	.	UHRF1BP1	102	.	NM_017754	exon14	c.G2788C	p.E930Q	AGCCCTGAGAAGG	.	PASS	Atlas-SNP
FAT3	120114	hgsc.bcm.edu	37	11	92600266	92600266	+	Silent	SNP	G	G	A	rs75649640	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	49	14	73	0	0.285714	0	A|0.048;G|0.952	0.048	strong	FAT3_ENST00000409404,colon,carcinoma,0,7	FAT3	1822	7	NM_001008781	exon21	c.G12018A	p.A4006A	CTTCGCGGAGGTG	.	PASS	Atlas-SNP
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32609147	32609147	+	Missense_Mutation	SNP	A	A	T	rs12722051	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	141	82	142	0	0.58156	0	A|0.805;T|0.195	0.195	strong	.	HLA-DQA1	52	.	NM_002122	exon2	c.A143T	p.Y48F	GCCAGTACACCCA	.	PASS	Atlas-SNP
SERPINB7	8710	hgsc.bcm.edu	37	18	61471523	61471523	+	Missense_Mutation	SNP	G	G	A	rs17782413	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	28	14	37	0	0.5	0	G|0.824;A|0.176	0.176	strong	.	SERPINB7	66	.	NM_001261830	exon8	c.G797A	p.R266Q	CAAGGCGAATGAC	.	PASS	Atlas-SNP
RASSF6	166824	hgsc.bcm.edu	37	4	74459206	74459206	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	20	117	0	0.19802	0	.	.	none	.	RASSF6	68	.	NM_201431	exon4	c.T345G	p.F115L	ACTAGTAAAAGAA	.	PASS	Atlas-SNP
CYP4F11	57834	hgsc.bcm.edu	37	19	16032935	16032935	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	2	72	0	0.0235294	0	.	.	none	CYP4F11,NS,haematopoietic_neoplasm,0,3	CYP4F11	83	3	NM_001128932	exon9	c.C1027T	p.H343Y	CAAGGTGGTATAG	.	scavenged	Atlas-SNP
COL4A3	1285	hgsc.bcm.edu	37	2	228131169	228131169	+	Missense_Mutation	SNP	A	A	G	rs11677877	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	227	112	250	3	0.493392	0.012	A|0.908;G|0.092	0.092	strong	COL4A3_ENST00000328380,caecum,carcinoma,-1,2	COL4A3	293	2	NM_000091	exon22	c.A1352G	p.H451R	GAGATCACGGACT	.	scavenged	Atlas-SNP
KRT73	319101	hgsc.bcm.edu	37	12	53002197	53002197	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	9	75	0	0.130435	0	.	.	none	.	KRT73	101	.	NM_175068	exon9	c.G1406A	p.G469E	CCAGCCCCTGTGC	.	PASS	Atlas-SNP
IGSF10	285313	hgsc.bcm.edu	37	3	151155620	151155620	+	Silent	SNP	G	G	A	rs6781302	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	47	22	54	0	0.468085	0	G|0.352;A|0.648	0.648	strong	.	IGSF10	279	.	NM_178822	exon6	c.C6729T	p.N2243N	AGTTCTGTTTGTA	.	PASS	Atlas-SNP
TBC1D26	353149	hgsc.bcm.edu	37	17	15644506	15644506	+	Missense_Mutation	SNP	C	C	T	rs11650318	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	80	38	68	0	0.475	0	C|0.723;T|0.277	0.277	strong	.	TBC1D26	16	.	NM_178571	exon10	c.C617T	p.A206V	AAGATGCTTTCTG	.	PASS	Atlas-SNP
PLA2G3	50487	hgsc.bcm.edu	37	22	31536133	31536133	+	Missense_Mutation	SNP	A	A	C	rs2232176	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	37	15	49	1	0.405405	0.0204082	A|0.211;C|0.789	0.789	strong	PLA2G3_ENST00000215885,NS,carcinoma,0,4	PLA2G3	85	4	NM_015715	exon1	c.T208G	p.S70A	TACATGACTGCAG	.	scavenged	Atlas-SNP
FKBP15	23307	hgsc.bcm.edu	37	9	115936860	115936860	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	133	39	219	0	0.293233	0	.	.	none	FKBP15_ENST00000238256,NS,carcinoma,+1,2	FKBP15	128	2	NM_015258	exon22	c.C2227T	p.L743F	CTGAGAGGTTCTT	.	PASS	Atlas-SNP
LHB	3972	hgsc.bcm.edu	37	19	49519883	49519883	+	Missense_Mutation	SNP	A	A	G	rs6515	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	260	40	374	1	0.153846	0.0026738	G|1.000;|0.000	1.000	weak	LHB,NS,carcinoma,0,1	LHB	20	1	NM_000894	exon2	c.T104C	p.I35T	GCCAGGATGGCAT	.	scavenged	Atlas-SNP
FNIP2	57600	hgsc.bcm.edu	37	4	159789441	159789441	+	Missense_Mutation	SNP	C	C	A	rs62001914	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	33	77	0	0.458333	0	C|0.982;A|0.018	0.018	strong	.	FNIP2	90	.	NM_020840	exon13	c.C1653A	p.S551R	TGGGAGCAAGATC	.	PASS	Atlas-SNP
EYS	346007	hgsc.bcm.edu	37	6	65300516	65300516	+	Missense_Mutation	SNP	T	T	G	rs57312007	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	164	82	174	0	0.5	0	T|0.927;G|0.073	0.073	strong	.	EYS	527	.	NM_001142800	exon26	c.A5244C	p.L1748F	TAAGTTTAACTCA	.	PASS	Atlas-SNP
HSD17B11	51170	hgsc.bcm.edu	37	4	88293887	88293887	+	Silent	SNP	G	G	A	rs6531985	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	84	44	116	0	0.52381	0	G|0.645;A|0.355	0.355	strong	.	HSD17B11	28	.	NM_016245	exon4	c.C531T	p.V177V	GACCGAGACATGT	.	PASS	Atlas-SNP
OXNAD1	92106	hgsc.bcm.edu	37	3	16312564	16312564	+	Silent	SNP	C	C	T	rs842259	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	86	111	0	0.988506	0	C|0.609;T|0.391	0.391	strong	OXNAD1,rectum,carcinoma,0,1	OXNAD1	31	1	NM_138381	exon3	c.C105T	p.H35H	GCGCCACCTTACT	.	PASS	Atlas-SNP
MSANTD3	91283	hgsc.bcm.edu	37	9	103204577	103204577	+	Silent	SNP	C	C	G	rs35438121	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	36	9	47	0	0.25	0	C|0.884;G|0.116	0.116	strong	MSANTD3,NS,carcinoma,+2,2	MSANTD3	10	2	NM_001198805	exon2	c.C357G	p.L119L	GCAGCTCTACTTC	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228452016	228452016	+	Missense_Mutation	SNP	G	G	C	rs185523702	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	309	147	319	0	0.475728	0	G|0.990;C|0.010	0.010	strong	.	OBSCN	2142	.	NM_001271223	exon18	c.G5337C	p.E1779D	GCAGGAGGCAGGC	.	PASS	Atlas-SNP
USP39	10713	hgsc.bcm.edu	37	2	85843348	85843348	+	Silent	SNP	C	C	T	rs11544042	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	60	33	50	0	0.55	0	C|0.936;T|0.064	0.064	strong	.	USP39	33	.	NM_001256725	exon1	c.C30T	p.R10R	GTCTCGCGGTTCC	.	PASS	Atlas-SNP
ZNF792	126375	hgsc.bcm.edu	37	19	35449082	35449082	+	Silent	SNP	G	G	A	rs3746243	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	36	112	0	0.514286	0	G|0.769;A|0.231	0.231	strong	.	ZNF792	46	.	NM_175872	exon4	c.C1677T	p.D559D	AGGCCTGTCTGGT	.	PASS	Atlas-SNP
RSF1	51773	hgsc.bcm.edu	37	11	77409568	77409568	+	Silent	SNP	T	T	C	rs4945203	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	318	231	390	0	0.726415	0	T|0.813;C|0.187	0.187	strong	.	RSF1	105	.	NM_016578	exon7	c.A2679G	p.P893P	TTTGCATGGTTCA	.	PASS	Atlas-SNP
LRP1B	53353	hgsc.bcm.edu	37	2	141259376	141259376	+	Silent	SNP	G	G	A	rs35164907	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	81	36	60	0	0.444444	0	G|0.818;A|0.182	0.182	strong	.	LRP1B	1315	.	NM_018557	exon55	c.C8730T	p.C2910C	ATTGTCGCAAAGA	.	PASS	Atlas-SNP
GUCY1A2	2977	hgsc.bcm.edu	37	11	106849400	106849400	+	Silent	SNP	G	G	A	rs35760785	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	76	19	87	0	0.25	0	G|0.920;A|0.080	0.080	strong	.	GUCY1A2	180	.	NM_000855	exon3	c.C432T	p.N144N	TTCTTTGTTGGAG	.	PASS	Atlas-SNP
SIGLEC6	946	hgsc.bcm.edu	37	19	52033206	52033206	+	Missense_Mutation	SNP	G	G	A	rs2005199	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	128	70	121	0	0.546875	0	G|0.923;A|0.077	0.077	strong	SIGLEC6_ENST00000425629,rectum,carcinoma,0,2	SIGLEC6	142	2	NM_001177548	exon5	c.C817T	p.L273F	CAGGGAGGGACGA	.	PASS	Atlas-SNP
CPT1B	1375	hgsc.bcm.edu	37	22	51011376	51011376	+	Missense_Mutation	SNP	G	G	C	rs8142477	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	179	88	153	0	0.49162	0	G|0.699;C|0.301	0.301	strong	.	CPT1B	61	.	NM_001145135	exon11	c.C1280G	p.S427C	TCATAGGAGTAGG	.	PASS	Atlas-SNP
TFDP2	7029	hgsc.bcm.edu	37	3	141678667	141678667	+	Silent	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	4	93	0	0.045977	0	.	.	none	.	TFDP2	44	.	NM_001178139	exon11	c.C900T	p.F300F	AAAATTGAAAAGA	.	PASS	Atlas-SNP
FAT1	2195	hgsc.bcm.edu	37	4	187557893	187557893	+	Missense_Mutation	SNP	T	T	C	rs328418	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	273	130	250	0	0.47619	0	T|0.323;G|0.003	.	strong	.	FAT1	500	.	NM_005245	exon5	c.A3818G	p.H1273R	ATGACGTGATAGA	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	90	45	87	0	0.5	0	C|0.828;G|0.172	0.172	strong	.	MLL3	1564	.	NM_170606	exon11	c.G1577C	p.R526P	TGTAAACGATCCA	.	PASS	Atlas-SNP
MAGEA4	4103	hgsc.bcm.edu	37	X	151092968	151092968	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	95	32	158	0	0.336842	0	.	.	none	.	MAGEA4	68	.	NM_001011548	exon3	c.G832T	p.A278S	CCAAGGGCTCTGG	.	PASS	Atlas-SNP
HACL1	26061	hgsc.bcm.edu	37	3	15628040	15628040	+	Missense_Mutation	SNP	T	T	A	rs74637339	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	191	84	202	0	0.439791	0	T|0.970;A|0.030	0.030	strong	.	HACL1	33	.	NM_012260	exon6	c.A451T	p.I151F	TTTCAATAACAAA	.	PASS	Atlas-SNP
ACAN	176	hgsc.bcm.edu	37	15	89398105	89398105	+	Silent	SNP	C	C	T	rs2351491	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	254	251	195	0	0.988189	0	C|0.595;T|0.405	0.405	strong	.	ACAN	220	.	NM_001135	exon12	c.C2289T	p.P763P	GCCTCCCACTGGC	.	PASS	Atlas-SNP
TLE3	7090	hgsc.bcm.edu	37	15	70351154	70351154	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	40	15	56	0	0.375	0	.	.	none	.	TLE3	104	.	NM_001105192	exon11	c.G766A	p.D256N	CGGGGTCCTGAAA	.	PASS	Atlas-SNP
GRK7	131890	hgsc.bcm.edu	37	3	141535558	141535558	+	Missense_Mutation	SNP	A	A	G	rs36009541	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	103	56	126	0	0.543689	0	A|0.903;G|0.097	0.097	strong	.	GRK7	65	.	NM_139209	exon4	c.A1328G	p.E443G	ACAGAGAAAAGTC	.	PASS	Atlas-SNP
TRAF1	7185	hgsc.bcm.edu	37	9	123688217	123688217	+	Missense_Mutation	SNP	G	G	A	rs34119250	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	176	90	194	0	0.511364	0	G|0.955;A|0.045	0.045	strong	.	TRAF1	42	.	NM_005658	exon2	c.C137T	p.P46L	CACCTCGGGTTCT	.	PASS	Atlas-SNP
UNC13A	23025	hgsc.bcm.edu	37	19	17741047	17741047	+	Silent	SNP	A	A	G	rs10413821	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	93	93	113	0	1	0	A|0.571;G|0.429	0.429	strong	.	UNC13A	299	.	NM_001080421	exon29	c.T3576C	p.V1192V	GGAGAAAACATCC	.	PASS	Atlas-SNP
SIGLEC1	6614	hgsc.bcm.edu	37	20	3682149	3682149	+	Silent	SNP	G	G	A	rs13037869	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	131	68	182	0	0.519084	0	G|0.723;A|0.277	0.277	strong	.	SIGLEC1	210	.	NM_023068	exon6	c.C1368T	p.S456S	GTCCCCGGAGGTG	.	PASS	Atlas-SNP
OR1L8	138881	hgsc.bcm.edu	37	9	125330184	125330184	+	Silent	SNP	A	A	C	rs10985702	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	84	44	125	0	0.52381	0	A|0.580;C|0.420	0.420	strong	.	OR1L8	90	.	NM_001004454	exon1	c.T573G	p.S191S	TATGGAAGAGCAG	.	PASS	Atlas-SNP
TRIM39-RPP21	202658	hgsc.bcm.edu	37	6	30314566	30314566	+	Silent	SNP	T	T	G	rs35287137	alternate_allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	41	98	0	0.42268	0	.	.	alt	.	.	.	.	NM_001199119	exon10	c.T1491G	p.T497T	GCAGACTCAGGGT	.	PASS	Atlas-SNP
C1orf65	164127	hgsc.bcm.edu	37	1	223567267	223567267	+	Silent	SNP	C	C	T	rs6679661	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	36	39	0	0.5	0	C|0.924;T|0.076	0.076	strong	.	C1orf65	71	.	NM_152610	exon1	c.C450T	p.P150P	TTGCCCCGGAGGA	.	PASS	Atlas-SNP
CD8B	926	hgsc.bcm.edu	37	2	87073852	87073852	+	Missense_Mutation	SNP	C	C	T	rs2228022	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	328	146	380	1	0.445122	0.00263158	C|0.829;T|0.171	0.171	strong	.	CD8B	37	.	NM_004931	exon4	c.G538A	p.V180I	CCAGGACGCCAGC	.	PASS	Atlas-SNP
PRSS12	8492	hgsc.bcm.edu	37	4	119219909	119219909	+	Missense_Mutation	SNP	C	C	A	rs28661939	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	141	61	168	0	0.432624	0	C|0.873;A|0.127	0.127	strong	.	PRSS12	71	.	NM_003619	exon9	c.G1816T	p.A606S	CTGAGGCCTTCTT	.	PASS	Atlas-SNP
CHRNG	1146	hgsc.bcm.edu	37	2	233406178	233406178	+	Missense_Mutation	SNP	G	G	A	rs2289080	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	142	62	126	0	0.43662	0	G|0.968;A|0.032	0.032	strong	.	CHRNG	54	.	NM_005199	exon5	c.G445A	p.A149T	CGTTCCGCCTGCT	.	PASS	Atlas-SNP
SPAST	6683	hgsc.bcm.edu	37	2	32289034	32289034	+	Missense_Mutation	SNP	C	C	A	rs121908517	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	61	25	35	0	0.409836	0	C|1.000;A|0.000	0.000	weak	SPAST,NS,carcinoma,-1,2	SPAST	61	2	NM_199436	exon1	c.C134A	p.P45Q	AGTCGCCGCATAA	.	PASS	Atlas-SNP
ZDHHC11	79844	hgsc.bcm.edu	37	5	825286	825286	+	Missense_Mutation	SNP	G	G	T	rs2335585	bycluster;byfrequency;bysubmitter;byhapmap	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	110	14	126	1	0.127273	0.00793651	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	.	scavenged	Atlas-SNP
SLC32A1	140679	hgsc.bcm.edu	37	20	37353743	37353743	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	83	25	108	0	0.301205	0	.	.	none	.	SLC32A1	81	.	NM_080552	exon1	c.A376G	p.T126A	AACGTGACCAACG	.	PASS	Atlas-SNP
KIAA1551	55196	hgsc.bcm.edu	37	12	32135938	32135938	+	Silent	SNP	A	A	G	rs11051718	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	44	87	0	0.505747	0	A|0.920;G|0.080	0.080	strong	.	.	.	.	NM_018169	exon4	c.A2049G	p.Q683Q	AAAGCAACCTTCA	.	PASS	Atlas-SNP
SLC22A24	283238	hgsc.bcm.edu	37	11	62848568	62848568	+	Silent	SNP	C	C	G	rs11231342	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	14	105	0	0.202899	0	C|0.539;G|0.461	0.461	strong	.	SLC22A24	31	.	NM_001136506	exon9	c.G1422C	p.V474V	ACCGGACACTGCA	.	PASS	Atlas-SNP
ABCD3	5825	hgsc.bcm.edu	37	1	94930345	94930345	+	Silent	SNP	G	G	A	rs16946	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	124	123	185	1	0.991935	0.00540541	G|0.652;A|0.348	0.348	strong	.	ABCD3	62	.	NM_002858	exon3	c.G162A	p.K54K	GAAAAAGGAGCGA	.	PASS	Atlas-SNP
ITSN2	50618	hgsc.bcm.edu	37	2	24432839	24432839	+	Silent	SNP	A	A	G	rs2303296	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	105	53	117	0	0.504762	0	A|0.824;G|0.176	0.176	strong	.	ITSN2	224	.	NM_006277	exon35	c.T4321C	p.L1441L	TGTATAATTTCCC	.	PASS	Atlas-SNP
RBPJL	11317	hgsc.bcm.edu	37	20	43942698	43942698	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	53	22	71	0	0.415094	0	.	.	none	.	RBPJL	67	.	NM_014276	exon8	c.G781A	p.D261N	CAAGGAGACTTCC	.	PASS	Atlas-SNP
ZNF462	58499	hgsc.bcm.edu	37	9	109689859	109689859	+	Silent	SNP	T	T	C	rs3814540	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	129	69	156	0	0.534884	0	T|0.525;C|0.475	0.475	strong	.	ZNF462	322	.	NM_021224	exon3	c.T3666C	p.N1222N	GGCCAATGCAGAT	.	PASS	Atlas-SNP
PREP	5550	hgsc.bcm.edu	37	6	105726036	105726036	+	Missense_Mutation	SNP	C	C	T	rs1051484	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	62	34	88	0	0.548387	0	C|0.673;T|0.327	0.327	strong	.	PREP	65	.	NM_002726	exon15	c.G2116A	p.V706I	AGTCGACGTTCAG	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	91	91	142	0	1	0	0|0.015;C|0.478	0.478	strong	.	GPR112	459	.	NM_153834	exon6	c.T4618C	p.S1540P	AAATCTTCTAAAA	.	PASS	Atlas-SNP
IL31RA	133396	hgsc.bcm.edu	37	5	55206444	55206444	+	Missense_Mutation	SNP	G	G	A	rs161704	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	271	165	207	0	0.608856	0	G|0.694;N|0.000	.	strong	.	IL31RA	84	.	NM_001242637	exon12	c.G1586A	p.S529N	TGGCCAGCACCAG	.	PASS	Atlas-SNP
VPS13B	157680	hgsc.bcm.edu	37	8	100844758	100844758	+	Silent	SNP	T	T	C	rs36074608	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	18	71	0	0.230769	0	T|0.840;C|0.160	0.160	strong	VPS13B_ENST00000357162,NS,carcinoma,+1,2	VPS13B	811	2	NM_017890	exon52	c.T9567C	p.S3189S	CTTTTCTCCTGCC	.	PASS	Atlas-SNP
OR4A47	403253	hgsc.bcm.edu	37	11	48511050	48511050	+	Missense_Mutation	SNP	T	T	C	rs76991989	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	116	90	143	0	0.775862	0	T|0.981;C|0.019	0.019	strong	OR4A47,bladder,carcinoma,-1,1	OR4A47	72	1	NM_001005512	exon1	c.T706C	p.S236P	GCCCTCTCAACCT	.	PASS	Atlas-SNP
KREMEN1	83999	hgsc.bcm.edu	37	22	29533499	29533499	+	Silent	SNP	G	G	A	rs35612970	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	40	90	0	0.487805	0	G|0.861;A|0.139	0.139	strong	.	KREMEN1	46	.	NM_001039570	exon6	c.G801A	p.A267A	CTCGGCGGACATG	.	PASS	Atlas-SNP
TCTE3	6991	hgsc.bcm.edu	37	6	170144194	170144194	+	Silent	SNP	T	T	C	rs2274954	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	32	11	67	0	0.34375	0	T|0.932;C|0.068	0.068	strong	.	TCTE3	13	.	NM_174910	exon2	c.A297G	p.S99S	TTCTACTGAATGA	.	PASS	Atlas-SNP
LILRA6	79168	hgsc.bcm.edu	37	19	54744794	54744794	+	Missense_Mutation	SNP	G	G	A	rs76869766	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	247	71	315	0	0.287449	0	G|0.857;A|0.143	0.143	strong	.	LILRA6	75	.	NM_024318	exon5	c.C868T	p.H290Y	CCCCGTGGGAGGG	.	PASS	Atlas-SNP
ZNF598	90850	hgsc.bcm.edu	37	16	2048564	2048564	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	98	49	123	0	0.5	0	.	.	none	.	ZNF598	55	.	NM_178167	exon14	c.A2384G	p.Y795C	TTGTAATACTGGG	.	PASS	Atlas-SNP
AKAP13	11214	hgsc.bcm.edu	37	15	86123364	86123364	+	Missense_Mutation	SNP	G	G	A	rs7177107	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	124	45	116	0	0.362903	0	G|0.875;A|0.125	0.125	strong	.	AKAP13	394	.	NM_007200	exon7	c.G2065A	p.E689K	GTTAGCGAGTCCG	.	PASS	Atlas-SNP
RABEP1	9135	hgsc.bcm.edu	37	17	5284698	5284698	+	Silent	SNP	A	A	G	rs1143206	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	37	89	0	0.528571	0	A|0.519;G|0.481	0.481	strong	.	RABEP1	59	.	NM_004703	exon17	c.A2385G	p.Q795Q	TGAACAACTAATG	.	PASS	Atlas-SNP
ATM	472	hgsc.bcm.edu	37	11	108175462	108175462	+	Missense_Mutation	SNP	G	G	A	rs1801516	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	91	15	126	0	0.164835	0	G|0.910;A|0.090	0.090	strong	ATM_ENST00000278616,colon,carcinoma,-1,17	ATM	1657	17	NM_000051	exon37	c.G5557A	p.D1853N	CTCCAAGATACAA	.	PASS	Atlas-SNP
SLC9A5	6553	hgsc.bcm.edu	37	16	67300058	67300058	+	Silent	SNP	G	G	A	rs61744117	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	200	113	153	0	0.565	0	G|0.998;A|0.002	0.002	strong	.	SLC9A5	82	.	NM_004594	exon15	c.G2148A	p.K716K	AGAGAAGGAGGAC	.	PASS	Atlas-SNP
GIMAP4	55303	hgsc.bcm.edu	37	7	150269917	150269917	+	Silent	SNP	G	G	A	rs61741802	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	89	40	83	0	0.449438	0	G|0.972;A|0.028	0.028	strong	.	GIMAP4	61	.	NM_018326	exon3	c.G759A	p.A253A	GAAAGCGCGGATA	.	PASS	Atlas-SNP
SLC46A2	57864	hgsc.bcm.edu	37	9	115652881	115652881	+	Silent	SNP	G	G	T	rs3802491	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	18	8	39	0	0.444444	0	G|0.667;T|0.333	0.333	strong	.	SLC46A2	30	.	NM_033051	exon1	c.C81A	p.A27A	GGACGAGGCCACC	.	PASS	Atlas-SNP
NINL	22981	hgsc.bcm.edu	37	20	25456888	25456888	+	Silent	SNP	A	A	G	rs437635	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	39	77	0	0.52	0	A|0.506;G|0.494	0.494	strong	.	NINL	148	.	NM_025176	exon17	c.T3039C	p.S1013S	CTCCACACTGTGC	.	PASS	Atlas-SNP
ZNF443	10224	hgsc.bcm.edu	37	19	12542772	12542772	+	Missense_Mutation	SNP	C	C	T	rs17846016	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	184	74	169	0	0.402174	0	T|1.000;|0.000	1.000	weak	.	ZNF443	63	.	NM_005815	exon4	c.G214A	p.V72I	TTTCAACAAATCT	.	PASS	Atlas-SNP
WDR67	93594	hgsc.bcm.edu	37	8	124138855	124138855	+	Silent	SNP	G	G	A	rs16898012	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	182	40	164	0	0.21978	0	G|0.705;A|0.295	0.295	strong	.	WDR67	97	.	NM_001145088	exon13	c.G1812A	p.L604L	CCTTCTGATGACT	.	PASS	Atlas-SNP
BTN2A1	11120	hgsc.bcm.edu	37	6	26468326	26468326	+	Missense_Mutation	SNP	G	G	A	rs3734542	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	94	45	96	0	0.478723	0	G|0.937;A|0.063	0.063	strong	BTN2A1_ENST00000265424,NS,carcinoma,-1,2	BTN2A1	118	2	NM_007049	exon8	c.G1133A	p.R378Q	TAGGCCGGGAGAG	.	PASS	Atlas-SNP
UMODL1	89766	hgsc.bcm.edu	37	21	43510437	43510437	+	Missense_Mutation	SNP	A	A	C	rs17114359	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	131	55	118	1	0.419847	0.00847458	A|0.735;C|0.140;G|0.124	0.140	strong	UMODL1_ENST00000408989,colon,carcinoma,0,2	UMODL1	186	2	NM_173568	exon6	c.A820C	p.N274H	GAGCTCAATGCCT	.	scavenged	Atlas-SNP
PGM1	5236	hgsc.bcm.edu	37	1	64095111	64095111	+	Missense_Mutation	SNP	A	A	G	rs855314	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	155	75	176	0	0.483871	0	A|0.837;G|0.163	0.163	strong	.	PGM1	75	.	NM_001172818	exon2	c.A316G	p.I106V	TTGGTTATCGGAC	.	PASS	Atlas-SNP
DMD	1756	hgsc.bcm.edu	37	X	32486756	32486756	+	Silent	SNP	C	C	T	rs1800268	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	238	238	420	0	1	0	C|0.989;T|0.011	0.011	strong	.	DMD	2127	.	NM_004006	exon23	c.G3021A	p.S1007S	TTTCTTCGACATC	.	PASS	Atlas-SNP
CFHR3	10878	hgsc.bcm.edu	37	1	196757392	196757392	+	Silent	SNP	C	C	T	rs61735322	byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	49	48	83	0	0.979592	0	C|0.379;T|0.621	0.621	strong	CFHR3,NS,carcinoma,0,1	CFHR3	52	1	NM_021023	exon4	c.C477T	p.S159S	CATTTCCGAATCT	.	PASS	Atlas-SNP
ZSWIM2	151112	hgsc.bcm.edu	37	2	187698751	187698751	+	Silent	SNP	G	G	A	rs7559533	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	52	28	65	0	0.538462	0	G|0.784;A|0.216	0.216	strong	ZSWIM2,NS,carcinoma,-1,1	ZSWIM2	119	1	NM_182521	exon6	c.C750T	p.T250T	GCATTCGGTACAC	.	PASS	Atlas-SNP
CEP164	22897	hgsc.bcm.edu	37	11	117267884	117267884	+	Missense_Mutation	SNP	A	A	G	rs573455	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	67	15	63	0	0.223881	0	A|0.498;G|0.502	0.502	strong	.	CEP164	121	.	NM_001271933	exon26	c.A3365G	p.Q1122R	TTGTGCAGCAGAC	.	PASS	Atlas-SNP
CSF2RB	1439	hgsc.bcm.edu	37	22	37329999	37329999	+	Silent	SNP	C	C	T	rs1801117	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	44	28	43	0	0.636364	0	C|0.793;T|0.207	0.207	strong	.	CSF2RB	104	.	NM_000395	exon10	c.C1278T	p.S426S	CTGGAGCGAGTGG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195507332	195507332	+	Missense_Mutation	SNP	A	A	T	rs200058677		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	15	79	0	0.174419	0	.	.	weak	.	MUC4	1505	.	NM_018406	exon2	c.T11119A	p.S3707T	GACCTGAGGATGA	.	PASS	Atlas-SNP
MICAL1	64780	hgsc.bcm.edu	37	6	109770869	109770869	+	Silent	SNP	G	G	A	rs752261	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	29	13	32	0	0.448276	0	G|0.957;A|0.043	0.043	strong	.	MICAL1	79	.	NM_022765	exon10	c.C1425T	p.T475T	ATTGGGGGTCACT	.	PASS	Atlas-SNP
OSCP1	127700	hgsc.bcm.edu	37	1	36893968	36893968	+	Missense_Mutation	SNP	A	A	G	rs61308377	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	54	25	75	0	0.462963	0	A|0.891;G|0.109	0.109	strong	.	OSCP1	48	.	NM_206837	exon5	c.T625C	p.Y209H	ATACATAATGGAA	.	PASS	Atlas-SNP
CTAGE5	4253	hgsc.bcm.edu	37	14	39764176	39764176	+	Missense_Mutation	SNP	G	G	C	rs17855896	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	158	76	210	0	0.481013	0	G|0.960;C|0.040	0.040	strong	.	CTAGE5	75	.	NM_001247989	exon8	c.G630C	p.K210N	ACTGAAGATAGCA	.	PASS	Atlas-SNP
PKHD1L1	93035	hgsc.bcm.edu	37	8	110413762	110413762	+	Missense_Mutation	SNP	T	T	C	rs964307	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	178	125	224	0	0.702247	0	T|0.687;C|0.312	0.312	strong	.	PKHD1L1	522	.	NM_177531	exon14	c.T1318C	p.Y440H	AACAGTTATTTTT	.	PASS	Atlas-SNP
C1orf35	79169	hgsc.bcm.edu	37	1	228290033	228290033	+	Missense_Mutation	SNP	T	T	C	rs61825155	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	33	13	39	0	0.393939	0	T|0.990;C|0.010	0.010	strong	.	C1orf35	17	.	NM_024319	exon5	c.A425G	p.K142R	CCCAGTTTGGCGG	.	PASS	Atlas-SNP
HPS3	84343	hgsc.bcm.edu	37	3	148881673	148881673	+	Silent	SNP	C	C	T	rs3732557	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	38	95	0	0.542857	0	C|0.849;T|0.151	0.151	strong	.	HPS3	104	.	NM_032383	exon14	c.C2526T	p.H842H	GGTTCACGTCGTA	.	PASS	Atlas-SNP
DNM2	1785	hgsc.bcm.edu	37	19	10870486	10870486	+	Silent	SNP	A	A	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	102	43	122	0	0.421569	0	.	.	none	.	DNM2	175	.	NM_001005361	exon2	c.A234G	p.T78T	AAAAACAGGTAAA	.	PASS	Atlas-SNP
MYO18A	399687	hgsc.bcm.edu	37	17	27442710	27442710	+	Silent	SNP	G	G	C	rs28587908	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	68	36	104	0	0.529412	0	G|0.893;C|0.107	0.107	strong	.	MYO18A	217	.	NM_078471	exon12	c.C2199G	p.P733P	CTCCTCGGGGCCC	.	PASS	Atlas-SNP
SUN1	23353	hgsc.bcm.edu	37	7	897496	897496	+	Missense_Mutation	SNP	G	G	A	rs59910530	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	88	16	121	0	0.181818	0	G|0.839;A|0.161	0.161	strong	.	SUN1	157	.	NM_001130965	exon13	c.G1426A	p.E476K	ACAGTCGAGCACC	.	PASS	Atlas-SNP
NPSR1	387129	hgsc.bcm.edu	37	7	34917702	34917702	+	Missense_Mutation	SNP	G	G	A	rs28480169	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	200	42	216	0	0.21	0	G|0.940;A|0.060	0.060	strong	NPSR1_ENST00000359791,caecum,carcinoma,+1,1	NPSR1	134	1	NM_207173	exon9	c.G1040A	p.R347H	GTCTCCGTCAGCT	.	PASS	Atlas-SNP
KRTAP10-2	386679	hgsc.bcm.edu	37	21	45971018	45971018	+	Silent	SNP	C	C	G	rs478947	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	157	67	121	0	0.426752	0	C|0.759;G|0.241	0.241	strong	.	KRTAP10-2	21	.	NM_198693	exon1	c.G324C	p.V108V	ACAGCACACAGGC	.	PASS	Atlas-SNP
PIWIL3	440822	hgsc.bcm.edu	37	22	25144912	25144912	+	Missense_Mutation	SNP	C	C	T	rs11703684	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	66	23	120	0	0.348485	0	C|0.813;T|0.187	0.187	strong	.	PIWIL3	115	.	NM_001008496	exon12	c.G1411A	p.V471I	TCAAAACTCTTCC	.	PASS	Atlas-SNP
FNDC3A	22862	hgsc.bcm.edu	37	13	49775997	49775997	+	Missense_Mutation	SNP	A	A	G	rs45604939	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	141	60	174	0	0.425532	0	A|0.954;G|0.046	0.046	strong	.	FNDC3A	93	.	NM_001079673	exon24	c.A3049G	p.T1017A	GAGTCAACATCCT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195515340	195515340	+	Silent	SNP	G	G	A	rs79661483	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	44	47	0	0.619718	0	G|0.628;A|0.372	0.372	strong	.	MUC4	1505	.	NM_018406	exon2	c.C3111T	p.H1037H	GGTGACGTGACCT	.	PASS	Atlas-SNP
PPP1R7	5510	hgsc.bcm.edu	37	2	242122130	242122130	+	Silent	SNP	A	A	G	rs113069444	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	64	26	81	0	0.40625	0	A|0.997;G|0.002;T|0.000	0.002	strong	PPP1R7,NS,carcinoma,+2,1	PPP1R7	35	1	NM_002712	exon10	c.A975G	p.T325T	GGAGACAGTGTAC	.	PASS	Atlas-SNP
TRAK2	66008	hgsc.bcm.edu	37	2	202264156	202264156	+	Missense_Mutation	SNP	C	C	T	rs13022344	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	93	39	136	0	0.419355	0	C|0.463;T|0.537	0.537	strong	.	TRAK2	62	.	NM_015049	exon5	c.G424A	p.V142I	ATAAGACATGGTT	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228520973	228520973	+	Missense_Mutation	SNP	C	C	G	rs369909	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	36	66	0	0.461538	0	C|0.669;G|0.331	0.331	strong	.	OBSCN	2142	.	NM_001271223	exon69	c.C18676G	p.L6226V	AGAGACCTCCAGG	.	PASS	Atlas-SNP
OSBPL6	114880	hgsc.bcm.edu	37	2	179188959	179188959	+	Missense_Mutation	SNP	G	G	A	rs35032920	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	48	26	76	0	0.541667	0	G|0.960;A|0.040	0.040	strong	.	OSBPL6	178	.	NM_001201482	exon4	c.G158A	p.R53Q	TAAGTCGGCAATT	.	PASS	Atlas-SNP
OR9Q2	219957	hgsc.bcm.edu	37	11	57958497	57958497	+	Missense_Mutation	SNP	T	T	C	rs34337292	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	284	212	359	0	0.746479	0	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	.	PASS	Atlas-SNP
MEGF6	1953	hgsc.bcm.edu	37	1	3428608	3428608	+	Missense_Mutation	SNP	G	G	A	rs11585362	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	179	122	307	0	0.681564	0	G|0.738;A|0.262	0.262	strong	.	MEGF6	91	.	NM_001409	exon8	c.C938T	p.A313V	TAGCCCGCGTGAC	.	PASS	Atlas-SNP
MTERFD2	130916	hgsc.bcm.edu	37	2	242039198	242039198	+	Missense_Mutation	SNP	T	T	C	rs3796093	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	94	49	129	0	0.521277	0	T|0.899;C|0.101	0.101	strong	.	MTERFD2	33	.	NM_182501	exon2	c.A133G	p.T45A	AGGCTGTAGTCAG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195506983	195506983	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	51	9	71	0	0.176471	0	.	.	none	MUC4_ENST00000463781,NS,carcinoma,+1,2	MUC4	1505	2	NM_018406	exon2	c.C11468T	p.T3823I	AGAGGGGTGGTGT	.	scavenged	Atlas-SNP
RFX6	222546	hgsc.bcm.edu	37	6	117244374	117244374	+	Silent	SNP	T	T	C	rs7770158	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	166	79	181	0	0.475904	0	T|0.747;C|0.253	0.253	strong	.	RFX6	141	.	NM_173560	exon14	c.T1542C	p.N514N	GAACAATGCATCC	.	PASS	Atlas-SNP
ODF2L	57489	hgsc.bcm.edu	37	1	86820267	86820267	+	Silent	SNP	C	C	T	rs1182098	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	178	86	204	0	0.483146	0	C|0.282;T|0.718	0.718	strong	.	ODF2L	53	.	NM_001007022	exon16	c.G1713A	p.E571E	TGTATACTCTGCA	.	PASS	Atlas-SNP
GRAMD3	65983	hgsc.bcm.edu	37	5	125802027	125802027	+	Missense_Mutation	SNP	G	G	A	rs62394179	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	180	87	237	0	0.483333	0	G|0.787;A|0.213	0.213	strong	.	GRAMD3	30	.	NM_001146321	exon3	c.G226A	p.E76K	GACCAAGAGTAAG	.	PASS	Atlas-SNP
PINK1	65018	hgsc.bcm.edu	37	1	20960230	20960230	+	Silent	SNP	C	C	T	rs45530340	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	4	4	3	0	1	0	C|0.869;T|0.131	0.131	strong	.	PINK1	37	.	NM_032409	exon1	c.C189T	p.L63L	CGGGCTCCCTAAC	.	PASS	Atlas-SNP
CD300LG	146894	hgsc.bcm.edu	37	17	41931375	41931375	+	Missense_Mutation	SNP	A	A	G	rs12453522	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	49	83	0	0.671233	0	A|0.735;G|0.265	0.265	strong	.	CD300LG	46	.	NM_145273	exon4	c.A682G	p.T228A	GAGGACACCAGTC	.	PASS	Atlas-SNP
ITGB2	3689	hgsc.bcm.edu	37	21	46313442	46313442	+	Silent	SNP	G	G	T	rs2230529	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	303	122	237	0	0.40264	0	G|0.775;T|0.225	0.225	strong	.	ITGB2	107	.	NM_000211	exon10	c.C1101A	p.V367V	CAGGAAGACCCTG	.	PASS	Atlas-SNP
PLCL2	23228	hgsc.bcm.edu	37	3	17051450	17051450	+	Silent	SNP	C	C	A	rs28932173	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	79	46	94	0	0.582278	0	C|0.974;A|0.026	0.026	strong	PLCL2,colon,carcinoma,+1,1	PLCL2	145	1	NM_015184	exon2	c.C234A	p.R78R	ATTCCGCAGCAAT	.	PASS	Atlas-SNP
NDUFAF1	51103	hgsc.bcm.edu	37	15	41679717	41679717	+	Silent	SNP	C	C	T	rs73407109	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	142	82	144	0	0.577465	0	C|0.916;T|0.084	0.084	strong	.	NDUFAF1	39	.	NM_016013	exon5	c.G909A	p.V303V	AGTAAACACGCCA	.	PASS	Atlas-SNP
UTP20	27340	hgsc.bcm.edu	37	12	101674926	101674926	+	Silent	SNP	T	T	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	111	31	119	0	0.279279	0	.	.	none	.	UTP20	222	.	NM_014503	exon2	c.T78G	p.V26V	GAATGTTAATATT	.	PASS	Atlas-SNP
FGFR2	2263	hgsc.bcm.edu	37	10	123325034	123325034	+	Silent	SNP	C	C	T	rs1047101	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	161	87	154	0	0.540373	0	C|0.993;T|0.007	0.007	strong	.	FGFR2	758	.	NM_022970	exon3	c.G294A	p.T98T	TCTAGGCGTGGCG	.	PASS	Atlas-SNP
ALG1	56052	hgsc.bcm.edu	37	16	5132659	5132659	+	Missense_Mutation	SNP	C	C	T	rs74910062	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	17	7	17	0	0.411765	0	.	.	weak	.	ALG1	35	.	NM_019109	exon11	c.C1172T	p.A391V	TGTGTGCTGTGAA	.	PASS	Atlas-SNP
SP3	6670	hgsc.bcm.edu	37	2	174820721	174820721	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	176	3	248	0	0.0170455	0	.	.	none	SP3_ENST00000310015,NS,carcinoma,-1,1	SP3	82	1	NM_003111	exon4	c.A519G	p.I173M	CTGTGGTATCACT	.	scavenged	Atlas-SNP
TLR6	10333	hgsc.bcm.edu	37	4	38829832	38829832	+	Silent	SNP	T	T	C	rs3775073	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	113	46	137	0	0.40708	0	T|0.564;C|0.436	0.436	strong	.	TLR6	67	.	NM_006068	exon2	c.A1263G	p.K421K	GTTTTCTTTATGT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195508416	195508416	+	Silent	SNP	C	C	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	7	89	2	0.0897436	0.0224719	.	.	none	MUC4_ENST00000463781,rectum,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.G10035T	p.V3345V	GACAGGCACAGGG	.	scavenged	Atlas-SNP
NUDT10	170685	hgsc.bcm.edu	37	X	51076018	51076018	+	Silent	SNP	C	C	T	rs12846945	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	162	161	234	0	0.993827	0	C|0.864;T|0.136	0.136	strong	.	NUDT10	28	.	NM_153183	exon2	c.C201T	p.Y67Y	GGTGTACGAAGAG	.	PASS	Atlas-SNP
PASK	23178	hgsc.bcm.edu	37	2	242065944	242065944	+	Missense_Mutation	SNP	C	C	T	rs35129131	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	43	135	0	0.467391	0	C|0.981;T|0.019	0.019	strong	.	PASK	230	.	NM_015148	exon10	c.G2386A	p.E796K	ACAGCTCCCTGTC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195506917	195506917	+	Missense_Mutation	SNP	A	A	C	rs150128295	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	22	16	83	2	0.727273	0.0240964	A|0.832;C|0.168	0.168	strong	MUC4_ENST00000463781,NS,lymphoid_neoplasm,0,1	MUC4	1505	1	NM_018406	exon2	c.T11534G	p.I3845S	GAAGGGATGGTGA	.	scavenged	Atlas-SNP
SRP72	6731	hgsc.bcm.edu	37	4	57361553	57361553	+	Silent	SNP	A	A	G	rs34419325	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	204	100	282	0	0.490196	0	A|0.915;G|0.085	0.085	strong	.	SRP72	59	.	NM_006947	exon17	c.A1671G	p.K557K	AAAGAAAAAGAAG	.	PASS	Atlas-SNP
KCNA1	3736	hgsc.bcm.edu	37	12	5021984	5021984	+	Silent	SNP	T	T	A	rs4766309	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	69	75	0	1	0	T|0.233;A|0.767	0.767	strong	.	KCNA1	112	.	NM_000217	exon2	c.T1440A	p.T480T	CACCACTGCTAAC	.	PASS	Atlas-SNP
RNASE9	390443	hgsc.bcm.edu	37	14	21024786	21024786	+	Missense_Mutation	SNP	A	A	G	rs12590446	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	185	96	218	0	0.518919	0	A|0.411;G|0.589	0.589	strong	.	RNASE9	30	.	NM_001110359	exon5	c.T458C	p.F153S	ATTTCAAATGCTT	.	PASS	Atlas-SNP
LCE1C	353133	hgsc.bcm.edu	37	1	152777908	152777908	+	Missense_Mutation	SNP	C	C	T	rs2006940	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	127	62	142	0	0.488189	0	C|0.847;T|0.153	0.153	strong	.	LCE1C	40	.	NM_178351	exon2	c.G47A	p.C16Y	GGGGTGCACTTGG	.	PASS	Atlas-SNP
GPC5	2262	hgsc.bcm.edu	37	13	92345579	92345579	+	Missense_Mutation	SNP	C	C	T	rs553717	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	225	108	234	0	0.48	0	C|0.842;T|0.158	0.158	strong	GPC5,NS,carcinoma,-1,1	GPC5	140	1	NM_004466	exon3	c.C464T	p.A155V	TTGGTGCGGATGT	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	57	57	118	0	1	0	0|0.025;A|0.455	0.455	strong	.	GPR112	459	.	NM_153834	exon6	c.C1103A	p.P368H	AACCACCTACACC	.	PASS	Atlas-SNP
MGAM	8972	hgsc.bcm.edu	37	7	141705413	141705413	+	Missense_Mutation	SNP	T	T	C	rs201144916	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	163	62	242	0	0.380368	0	T|0.999;C|0.001	0.001	strong	.	MGAM	767	.	NM_004668	exon2	c.T83C	p.I28T	TCAGTATTGTTCT	.	PASS	Atlas-SNP
TEKT3	64518	hgsc.bcm.edu	37	17	15234895	15234895	+	Missense_Mutation	SNP	C	C	T	rs7226363	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	38	18	56	0	0.473684	0	C|0.794;T|0.206	0.206	strong	.	TEKT3	64	.	NM_031898	exon3	c.G8A	p.R3H	CCTACACGTTCCA	.	PASS	Atlas-SNP
ADCY10	55811	hgsc.bcm.edu	37	1	167849414	167849414	+	Silent	SNP	A	A	G	rs203849	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	152	68	196	3	0.447368	0.0153061	G|0.516;N|0.000	0.516	strong	ADCY10,NS,carcinoma,0,1	ADCY10	175	1	NM_018417	exon11	c.T1155C	p.G385G	GGCAACACCGATG	.	scavenged	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228505727	228505727	+	Missense_Mutation	SNP	C	C	T	rs3795800	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	176	83	212	0	0.471591	0	C|0.898;T|0.102	0.102	strong	.	OBSCN	2142	.	NM_001271223	exon64	c.C16855T	p.R5619C	ATGGAGCGCATCC	.	PASS	Atlas-SNP
MUC6	4588	hgsc.bcm.edu	37	11	1027995	1027995	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	110	17	106	0	0.154545	0	.	.	none	.	MUC6	408	.	NM_005961	exon15	c.C1818G	p.H606Q	TGTGGCGTGGCAC	.	PASS	Atlas-SNP
SNX7	51375	hgsc.bcm.edu	37	1	99164434	99164434	+	Silent	SNP	G	G	A	rs6577322	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	174	93	178	0	0.534483	0	G|0.762;A|0.238	0.238	strong	.	SNX7	76	.	NM_015976	exon6	c.G1011A	p.E337E	ACATGAGTACGTG	.	PASS	Atlas-SNP
PTCH1	5727	hgsc.bcm.edu	37	9	98244242	98244242	+	Silent	SNP	T	T	C	rs1805154	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	94	42	91	0	0.446809	0	T|0.976;C|0.024	0.024	strong	.	PTCH1	1850	.	NM_000264	exon5	c.A735G	p.T245T	GTATGCTGTCCCA	.	PASS	Atlas-SNP
CLCA2	9635	hgsc.bcm.edu	37	1	86891073	86891073	+	Missense_Mutation	SNP	G	G	A	rs11580625	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	170	82	193	0	0.482353	0	G|0.969;A|0.031	0.031	strong	.	CLCA2	102	.	NM_006536	exon2	c.G238A	p.V80I	AGAAGAGTATTTT	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105415497	105415497	+	Silent	SNP	T	T	C	rs201263008	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	109	50	0	0	0.458716	.	T|0.948;C|0.052	0.052	strong	AHNAK2_ENST00000333244,NS,carcinoma,0,1	AHNAK2	719	1	NM_138420	exon7	c.A6291G	p.K2097K	GTCCAGTTTGGGG	.	PASS	Atlas-SNP
TGM4	7047	hgsc.bcm.edu	37	3	44943104	44943104	+	Missense_Mutation	SNP	G	G	C	rs937838	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	177	79	195	0	0.446328	0	G|0.924;C|0.076	0.076	strong	TGM4,NS,carcinoma,0,1	TGM4	82	1	NM_003241	exon7	c.G746C	p.S249T	CAGGCAGTGCCCC	.	PASS	Atlas-SNP
MSANTD1	345222	hgsc.bcm.edu	37	4	3257593	3257593	+	Silent	SNP	C	C	T	rs362287	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	19	10	2	0	0.526316	0	C|0.700;T|0.300	0.300	strong	.	MSANTD1	14	.	NM_001042690	exon3	c.C738T	p.R246R	GCGCCGCGTGCTG	.	PASS	Atlas-SNP
MYH1	4619	hgsc.bcm.edu	37	17	10401064	10401064	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	155	40	166	0	0.258065	0	.	.	none	.	MYH1	403	.	NM_005963	exon31	c.G4352T	p.R1451M	AAGTTCCTTTGCT	.	PASS	Atlas-SNP
KLHL32	114792	hgsc.bcm.edu	37	6	97423931	97423931	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	83	23	87	0	0.277108	0	.	.	none	.	KLHL32	85	.	NM_052904	exon3	c.G82A	p.V28I	GACAGTGTCCTGG	.	PASS	Atlas-SNP
VPS53	55275	hgsc.bcm.edu	37	17	526907	526907	+	Missense_Mutation	SNP	G	G	T	rs16954056	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	33	94	0	0.402439	0	G|0.889;T|0.111	0.111	strong	.	VPS53	109	.	NM_001128159	exon11	c.C982A	p.L328I	TGGCAAGTTCTGC	.	PASS	Atlas-SNP
AMPD1	270	hgsc.bcm.edu	37	1	115231254	115231254	+	Missense_Mutation	SNP	G	G	A	rs61752479	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	204	110	222	0	0.539216	0	G|0.913;A|0.087	0.087	strong	AMPD1_ENST00000520113,NS,carcinoma,0,2	AMPD1	223	2	NM_000036	exon3	c.C242T	p.P81L	GAAATCGGACAGA	.	PASS	Atlas-SNP
MTERFD2	130916	hgsc.bcm.edu	37	2	242035544	242035544	+	Missense_Mutation	SNP	G	G	C	rs2240539	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	138	71	169	0	0.514493	0	G|0.889;C|0.111	0.111	strong	.	MTERFD2	33	.	NM_182501	exon4	c.C1015G	p.L339V	CATCCAGACTTGC	.	PASS	Atlas-SNP
CENPM	79019	hgsc.bcm.edu	37	22	42341934	42341934	+	Silent	SNP	A	A	G	rs35542507	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	35	94	0	0.406977	0	A|0.939;G|0.061	0.061	strong	CENPM,NS,carcinoma,0,1	CENPM	8	1	NM_024053	exon3	c.T213C	p.N71N	GTGAAGATTAACC	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	47	95	0	0.681159	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
BEND7	222389	hgsc.bcm.edu	37	10	13494594	13494594	+	Silent	SNP	T	T	C	rs2277222	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	255	124	318	0	0.486275	0	T|0.677;C|0.323	0.323	strong	.	BEND7	85	.	NM_001100912	exon6	c.A1011G	p.V337V	AATCTGTACCCAA	.	PASS	Atlas-SNP
TMCO4	255104	hgsc.bcm.edu	37	1	20073019	20073019	+	Silent	SNP	C	C	T	rs34281331	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	372	185	374	1	0.497312	0.0026738	C|0.973;T|0.027	0.027	strong	.	TMCO4	46	.	NM_181719	exon9	c.G687A	p.A229A	CAGAGCCGCTGCC	.	PASS	Atlas-SNP
MLH3	27030	hgsc.bcm.edu	37	14	75513828	75513828	+	Missense_Mutation	SNP	G	G	A	rs175080	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	143	69	175	0	0.482517	0	G|0.586;A|0.414	0.414	strong	.	MLH3	200	.	NM_014381	exon2	c.C2531T	p.P844L	AAACTAGGCATCT	.	PASS	Atlas-SNP
MUT	4594	hgsc.bcm.edu	37	6	49412433	49412433	+	Missense_Mutation	SNP	C	C	T	rs1141321	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	34	87	0	0.435897	0	T|0.242;G|0.135;C|0.582;A|0.041	0.242	strong	.	MUT	70	.	NM_000255	exon9	c.G1595A	p.R532H	AGACAACGTTCAG	.	PASS	Atlas-SNP
RAB11FIP1	80223	hgsc.bcm.edu	37	8	37732509	37732509	+	Silent	SNP	G	G	A	rs369997427		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	24	90	0	0.275862	0	.	.	weak	.	RAB11FIP1	105	.	NM_025151	exon3	c.C1146T	p.S382S	AGATTCGGAGAGC	.	PASS	Atlas-SNP
IRGC	56269	hgsc.bcm.edu	37	19	44223412	44223412	+	Silent	SNP	C	C	T	rs34471331	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	48	18	40	0	0.375	0	C|0.924;T|0.076	0.076	strong	.	IRGC	67	.	NM_019612	exon2	c.C702T	p.H234H	GGAGCACGACCTG	.	PASS	Atlas-SNP
CMYA5	202333	hgsc.bcm.edu	37	5	79029025	79029025	+	Silent	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	74	16	103	0	0.216216	0	.	.	none	CMYA5_ENST00000446378,NS,carcinoma,+1,2	CMYA5	643	2	NM_153610	exon2	c.T4437C	p.S1479S	ATCATCTTCTCAG	.	PASS	Atlas-SNP
ZNF608	57507	hgsc.bcm.edu	37	5	123983915	123983915	+	Missense_Mutation	SNP	G	G	T	rs6862252	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	107	54	126	0	0.504673	0	G|0.405;N|0.001	.	strong	.	ZNF608	117	.	NM_020747	exon4	c.C2162A	p.T721N	CAGTTGGTAGCTT	.	PASS	Atlas-SNP
AMOTL1	154810	hgsc.bcm.edu	37	11	94602414	94602414	+	Missense_Mutation	SNP	C	C	T	rs11020968	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	98	76	95	0	0.77551	0	C|0.899;T|0.101	0.101	strong	.	AMOTL1	95	.	NM_130847	exon12	c.C2540T	p.P847L	TGCTGCCACCCCC	.	PASS	Atlas-SNP
OGDH	4967	hgsc.bcm.edu	37	7	44747589	44747589	+	Silent	SNP	C	C	T	rs61756584	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	62	36	74	0	0.580645	0	C|0.956;G|0.000;T|0.044	0.044	strong	.	OGDH	145	.	NM_002541	exon23	c.C3063T	p.N1021N	CAAGAACTTCTCG	.	PASS	Atlas-SNP
PDE6B	5158	hgsc.bcm.edu	37	4	647931	647931	+	Silent	SNP	G	G	A	rs75695239	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	44	27	56	0	0.613636	0	G|0.949;A|0.051	0.051	strong	.	PDE6B	80	.	NM_001145291	exon5	c.G915A	p.T305T	ACGCACGCCTGAT	.	PASS	Atlas-SNP
LINGO1	84894	hgsc.bcm.edu	37	15	77907535	77907535	+	Silent	SNP	C	C	G	rs2271396	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	166	166	131	0	1	0	C|0.298;G|0.702	0.702	strong	.	LINGO1	76	.	NM_032808	exon2	c.G714C	p.L238L	TCGGTACAGCCTC	.	PASS	Atlas-SNP
PGLYRP3	114771	hgsc.bcm.edu	37	1	153277423	153277423	+	Missense_Mutation	SNP	C	C	T	rs843971	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	120	44	146	0	0.366667	0	C|0.580;T|0.420	0.420	strong	.	PGLYRP3	55	.	NM_052891	exon3	c.G376A	p.G126S	CCTTACCTATCTT	.	PASS	Atlas-SNP
ADAL	161823	hgsc.bcm.edu	37	15	43632549	43632549	+	Silent	SNP	T	T	C	rs2278857	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	132	51	109	0	0.386364	0	T|0.487;C|0.513	0.513	strong	.	ADAL	48	.	NM_001012969	exon6	c.T342C	p.T114T	TGCTACTGGTAGA	.	PASS	Atlas-SNP
SPATA31E1	286234	hgsc.bcm.edu	37	9	90501448	90501448	+	Missense_Mutation	SNP	C	C	A	rs4076795	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	36	12	47	0	0.333333	0	C|0.297;N|0.002	.	strong	C9orf79,caecum,carcinoma,0,1	.	.	1	NM_178828	exon4	c.C2046A	p.D682E	TTCTGACTTTGCA	.	PASS	Atlas-SNP
PFKP	5214	hgsc.bcm.edu	37	10	3178001	3178001	+	Silent	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	118	37	112	0	0.313559	0	.	.	none	.	PFKP	182	.	NM_002627	exon21	c.G2196A	p.V732V	ACCTGTGGCAGAG	.	PASS	Atlas-SNP
LILRA6	79168	hgsc.bcm.edu	37	19	54744722	54744722	+	Missense_Mutation	SNP	T	T	C	rs66585874	alternate_allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	159	25	225	0	0.157233	0	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
HTT	3064	hgsc.bcm.edu	37	4	3213832	3213832	+	Silent	SNP	G	G	A	rs362336	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	64	25	57	0	0.390625	0	G|0.718;A|0.282	0.282	strong	.	HTT	221	.	NM_002111	exon48	c.G6591A	p.E2197E	TGCAGAGCCGGCG	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	18	63	0	0.257143	0	T|0.303;G|0.002	0.303	strong	.	NOD1	79	.	NM_006092	exon6	c.G796A	p.E266K	CCTCCTCGGGGTC	.	PASS	Atlas-SNP
ZNF343	79175	hgsc.bcm.edu	37	20	2464112	2464112	+	Missense_Mutation	SNP	T	T	C	rs61740142	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	77	38	95	0	0.493506	0	T|0.932;C|0.068	0.068	strong	.	ZNF343	47	.	NM_024325	exon6	c.A1495G	p.R499G	CTCGCCTACACTC	.	PASS	Atlas-SNP
PGD	5226	hgsc.bcm.edu	37	1	10473196	10473196	+	Silent	SNP	C	C	T	rs2229687	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	37	86	0	0.451219	0	C|0.656;T|0.344	0.344	strong	PGD,NS,carcinoma,0,1	PGD	39	1	NM_002631	exon8	c.C732T	p.D244D	CCAAGACACCGAT	.	PASS	Atlas-SNP
ENTPD7	57089	hgsc.bcm.edu	37	10	101458487	101458487	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	153	76	247	0	0.496732	0	.	.	none	.	ENTPD7	44	.	NM_020354	exon10	c.A1207G	p.I403V	AATGGCATATATC	.	PASS	Atlas-SNP
OR10H3	26532	hgsc.bcm.edu	37	19	15853150	15853150	+	Silent	SNP	C	C	T	rs16980824	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	57	27	89	0	0.473684	0	C|0.720;T|0.280	0.280	strong	.	OR10H3	53	.	NM_013938	exon1	c.C948T	p.S316S	AAGCTCCTAATGG	.	PASS	Atlas-SNP
SIGLEC14	100049587	hgsc.bcm.edu	37	19	52149165	52149165	+	Silent	SNP	G	G	A	rs71358847	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	382	328	465	1	0.858639	0.00215054	G|0.621;A|0.379	0.379	strong	.	SIGLEC14	46	.	NM_001098612	exon3	c.C570T	p.P190P	GGTCTCGGGGTCC	.	PASS	Atlas-SNP
TRIM49B	283116	hgsc.bcm.edu	37	11	49053390	49053390	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	150	3	174	1	0.02	0.00574713	.	.	none	TRIM49B,NS,NS,-1,1	TRIM49B	27	1	NM_001206626	exon1	c.T239C	p.V80A	GAAAAGTCAGTCT	.	scavenged	Atlas-SNP
PRRG4	79056	hgsc.bcm.edu	37	11	32852167	32852167	+	Missense_Mutation	SNP	C	C	T	rs61889489	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	39	4	65	0	0.102564	0	C|0.945;T|0.055	0.055	strong	.	PRRG4	15	.	NM_024081	exon2	c.C92T	p.A31V	AGCATGCGGGAGA	.	PASS	Atlas-SNP
SCTR	6344	hgsc.bcm.edu	37	2	120199139	120199139	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	48	23	53	0	0.479167	0	.	.	none	.	SCTR	45	.	NM_002980	exon12	c.G1177A	p.G393R	CCTCCCCATTGAG	.	PASS	Atlas-SNP
ARHGAP33	115703	hgsc.bcm.edu	37	19	36273534	36273534	+	Silent	SNP	G	G	A	rs2291067	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	74	74	92	0	1	0	G|0.834;A|0.166	0.166	strong	.	ARHGAP33	102	.	NM_052948	exon14	c.G1266A	p.L422L	GCGTCTGGTGCGG	.	PASS	Atlas-SNP
GLO1	2739	hgsc.bcm.edu	37	6	38650631	38650631	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	95	5	82	0	0.0526316	0	.	.	none	.	GLO1	12	.	NM_006708	exon4	c.A329G	p.D110G	GTCTCATCATCTT	.	PASS	Atlas-SNP
C5orf64	285668	hgsc.bcm.edu	37	5	60982841	60982841	+	Missense_Mutation	SNP	G	G	A	rs16893687	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	294	96	281	0	0.326531	0	G|0.539;A|0.461	0.461	strong	.	C5orf64	9	.	NM_173667	exon3	c.G169A	p.A57T	CTGACCGCTGAAG	.	PASS	Atlas-SNP
USP54	159195	hgsc.bcm.edu	37	10	75258558	75258558	+	Silent	SNP	G	G	A	rs61749235	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	99	98	130	0	0.989899	0	G|0.989;A|0.011	0.011	strong	.	USP54	178	.	NM_152586	exon22	c.C4884T	p.T1628T	ACCAGGGGTTCGG	.	PASS	Atlas-SNP
ENGASE	64772	hgsc.bcm.edu	37	17	77073941	77073941	+	Silent	SNP	T	T	C	rs56353542	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	29	12	42	0	0.413793	0	T|0.945;C|0.055	0.055	strong	.	ENGASE	55	.	NM_001042573	exon3	c.T411C	p.D137D	CCTGGATGACAGG	.	PASS	Atlas-SNP
FARP2	9855	hgsc.bcm.edu	37	2	242407746	242407746	+	Silent	SNP	A	A	G	rs10933559	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	31	64	0	0.364706	0	A|0.804;G|0.196	0.196	strong	.	FARP2	92	.	NM_014808	exon18	c.A2085G	p.L695L	CCGCCTATGCGGA	.	PASS	Atlas-SNP
DENND3	22898	hgsc.bcm.edu	37	8	142170884	142170884	+	Silent	SNP	C	C	T	rs2289001	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	200	39	217	0	0.195	0	C|0.724;T|0.276	0.276	strong	DENND3,NS,carcinoma,0,1	DENND3	127	1	NM_014957	exon9	c.C1110T	p.F370F	CATCTTCAGGTAC	.	PASS	Atlas-SNP
FAM5B	57795	hgsc.bcm.edu	37	1	177242695	177242695	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	190	35	209	0	0.184211	0	.	.	none	.	FAM5B	191	.	NM_021165	exon5	c.G741T	p.L247F	TGTCTTGGTACAG	.	PASS	Atlas-SNP
RP1L1	94137	hgsc.bcm.edu	37	8	10467160	10467160	+	Missense_Mutation	SNP	G	G	A	rs62490855	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	39	8	40	0	0.205128	0	G|0.853;A|0.147	0.147	strong	.	RP1L1	453	.	NM_178857	exon4	c.C4448T	p.A1483V	ATGGTGGCTCCGG	.	PASS	Atlas-SNP
MGMT	4255	hgsc.bcm.edu	37	10	131565064	131565064	+	Missense_Mutation	SNP	A	A	G	rs2308321	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	36	83	0	0.461538	0	A|0.927;G|0.073	0.073	strong	.	MGMT	32	.	NM_002412	exon5	c.A520G	p.I174V	ATCCTCATCCCGT	.	PASS	Atlas-SNP
SLC6A3	6531	hgsc.bcm.edu	37	5	1411412	1411412	+	Silent	SNP	T	T	C	rs6347	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	30	66	0	0.416667	0	T|0.671;C|0.329	0.329	strong	.	SLC6A3	102	.	NM_001044	exon9	c.A1215G	p.S405S	CCAGGCTGAGGAC	.	PASS	Atlas-SNP
MTIF2	4528	hgsc.bcm.edu	37	2	55470662	55470662	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	422	328	256	0	0.777251	0	.	.	none	.	MTIF2	64	.	NM_002453	exon12	c.T1454C	p.L485P	TTCCACAGTAGAT	.	PASS	Atlas-SNP
RP1L1	94137	hgsc.bcm.edu	37	8	10465942	10465942	+	Missense_Mutation	SNP	T	T	A	rs28446662	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	56	46	77	0	0.821429	0	T|0.764;A|0.236	0.236	strong	.	RP1L1	453	.	NM_178857	exon4	c.A5666T	p.D1889V	TCTACATCTTCTG	.	PASS	Atlas-SNP
ZNF280A	129025	hgsc.bcm.edu	37	22	22868700	22868700	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	219	3	221	0	0.0136986	0	.	.	none	ZNF280A,colon,carcinoma,0,1	ZNF280A	67	1	NM_080740	exon2	c.A1255G	p.N419D	TTGTGTTTTCATG	.	scavenged	Atlas-SNP
PCDHB13	56123	hgsc.bcm.edu	37	5	140595756	140595756	+	Silent	SNP	C	C	T	rs17844617	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	32	17	44	0	0.53125	0	C|0.855;T|0.145	0.145	strong	.	PCDHB13	142	.	NM_018933	exon1	c.C2061T	p.T687T	GCTCACCGTCTAC	.	PASS	Atlas-SNP
SGK1	6446	hgsc.bcm.edu	37	6	134494426	134494426	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	103	31	175	0	0.300971	0	.	.	none	.	SGK1	387	.	NM_001143676	exon7	c.C688A	p.L230M	TTTTCAGGATTGC	.	PASS	Atlas-SNP
AGTPBP1	23287	hgsc.bcm.edu	37	9	88204462	88204462	+	Silent	SNP	A	A	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	119	48	142	0	0.403361	0	.	.	none	.	AGTPBP1	128	.	NM_015239	exon20	c.T2583C	p.Y861Y	ATGTTCATAATAA	.	PASS	Atlas-SNP
TULP1	7287	hgsc.bcm.edu	37	6	35477032	35477032	+	Missense_Mutation	SNP	A	A	G	rs2064317	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	89	42	100	0	0.47191	0	A|0.642;G|0.358	0.358	strong	TULP1,NS,carcinoma,0,1	TULP1	51	1	NM_003322	exon8	c.T776C	p.I259T	TTCTTTATCACCG	.	PASS	Atlas-SNP
GCKR	2646	hgsc.bcm.edu	37	2	27741665	27741665	+	Missense_Mutation	SNP	G	G	A	rs141361209	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	123	46	107	0	0.373984	0	G|0.999;A|0.001	0.001	strong	GCKR,NS,carcinoma,0,1	GCKR	73	1	NM_001486	exon17	c.G1433A	p.R478H	TCCAGCGTGAGCT	.	PASS	Atlas-SNP
ERLEC1	27248	hgsc.bcm.edu	37	2	54035447	54035447	+	Silent	SNP	A	A	G	rs1127362	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	88	69	68	0	0.784091	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
FHL5	9457	hgsc.bcm.edu	37	6	97063555	97063555	+	Silent	SNP	A	A	G	rs9398148	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	108	108	117	0	1	0	A|0.613;G|0.387	0.387	strong	FHL5,caecum,carcinoma,+2,1	FHL5	73	1	NM_020482	exon7	c.A762G	p.K254K	CGGGAAATGCTCT	.	PASS	Atlas-SNP
MEF2D	4209	hgsc.bcm.edu	37	1	156450719	156450719	+	Silent	SNP	G	G	A	rs1185700	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	136	57	106	0	0.419118	0	G|0.766;A|0.234	0.234	strong	.	MEF2D	43	.	NM_005920	exon4	c.C303T	p.P101P	CCCGTCGGGCTCG	.	PASS	Atlas-SNP
CALML5	51806	hgsc.bcm.edu	37	10	5541181	5541181	+	Missense_Mutation	SNP	T	T	C	rs10904516	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	57	28	67	0	0.491228	0	T|0.625;C|0.375	0.375	strong	CALML5,rectum,carcinoma,0,2	CALML5	25	2	NM_017422	exon1	c.A221G	p.K74R	GCCTTCTTCGCCG	.	PASS	Atlas-SNP
FAHD1	81889	hgsc.bcm.edu	37	16	1877558	1877558	+	Missense_Mutation	SNP	G	G	A	rs3743853	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	123	102	118	0	0.829268	0	G|0.882;A|0.118	0.118	strong	.	FAHD1	18	.	NM_031208	exon1	c.G328A	p.D110N	GTGCAGGACGAGT	.	PASS	Atlas-SNP
USHBP1	83878	hgsc.bcm.edu	37	19	17361116	17361116	+	Missense_Mutation	SNP	G	G	A	rs1043963	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	103	50	136	0	0.485437	0	G|0.948;A|0.052	0.052	strong	.	USHBP1	85	.	NM_031941	exon13	c.C2030T	p.A677V	AGCACCGCCACCT	.	PASS	Atlas-SNP
RIOK1	83732	hgsc.bcm.edu	37	6	7393452	7393452	+	Silent	SNP	C	C	T	rs2274212	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	106	51	101	0	0.481132	0	C|0.560;T|0.440	0.440	strong	RIOK1,colon,carcinoma,+1,1	RIOK1	36	1	NM_031480	exon2	c.C192T	p.D64D	TTATGACGATGAT	.	PASS	Atlas-SNP
ZNF93	81931	hgsc.bcm.edu	37	19	20026163	20026163	+	Silent	SNP	G	G	C	rs150804499	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	27	14	27	0	0.518519	0	G|0.991;C|0.009	0.009	strong	.	ZNF93	81	.	NM_031218	exon2	c.G78C	p.R26R	ACAGCGGAATCTA	.	PASS	Atlas-SNP
OR10H4	126541	hgsc.bcm.edu	37	19	16060658	16060658	+	Missense_Mutation	SNP	A	A	G	rs11880184	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	37	78	0	0.506849	0	A|0.722;G|0.278	0.278	strong	.	OR10H4	48	.	NM_001004465	exon1	c.A841G	p.T281A	ACCTATACTGTCT	.	PASS	Atlas-SNP
PREP	5550	hgsc.bcm.edu	37	6	105821449	105821449	+	Silent	SNP	A	A	G	rs9486069	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	65	65	79	0	1	0	A|0.586;G|0.414	0.414	strong	.	PREP	65	.	NM_002726	exon5	c.T390C	p.Y130Y	GAACGCATAACCT	.	PASS	Atlas-SNP
RASA3	22821	hgsc.bcm.edu	37	13	114795333	114795333	+	Missense_Mutation	SNP	C	C	T	rs200024629	by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	48	23	43	0	0.479167	0	C|1.000;T|0.000	0.000	strong	.	RASA3	83	.	NM_007368	exon5	c.G403A	p.E135K	TGACCTCGCTCAG	.	PASS	Atlas-SNP
JMJD1C	221037	hgsc.bcm.edu	37	10	64974537	64974537	+	Missense_Mutation	SNP	A	A	T	rs10761725	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	117	38	129	0	0.324786	0	A|0.395;T|0.605	0.605	strong	JMJD1C_ENST00000399262,NS,carcinoma,+2,2	JMJD1C	347	2	NM_032776	exon8	c.T1390A	p.S464T	CTGACGAATGAAT	.	PASS	Atlas-SNP
RPS6KB2	6199	hgsc.bcm.edu	37	11	67202156	67202156	+	Missense_Mutation	SNP	C	C	T	rs13859	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	11	89	0	0.129412	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
ANKRD35	148741	hgsc.bcm.edu	37	1	145562881	145562881	+	Silent	SNP	T	T	C	rs10910824	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	31	17	22	0	0.548387	0	A|0.133;C|0.355	0.355	strong	.	ANKRD35	96	.	NM_144698	exon10	c.T2569C	p.L857L	GCTCTGTTGGAAA	.	PASS	Atlas-SNP
TUBB8	347688	hgsc.bcm.edu	37	10	93816	93816	+	Silent	SNP	C	C	T	rs9329305	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	133	67	80	0	0.503759	0	C|0.751;T|0.249	0.249	strong	TUBB8,NS,carcinoma,0,1	TUBB8	62	1	NM_177987	exon4	c.G516A	p.S172S	CTTGGGCGAGGGC	.	PASS	Atlas-SNP
MSRB3	253827	hgsc.bcm.edu	37	12	65857078	65857078	+	Silent	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	27	113	0	0.36	0	.	.	none	.	MSRB3	80	.	NM_198080	exon6	c.C555T	p.A185A	CCCGGCCCAGGCA	.	PASS	Atlas-SNP
NDST3	9348	hgsc.bcm.edu	37	4	118975146	118975146	+	Silent	SNP	C	C	T	rs13152576	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	142	70	211	0	0.492958	0	C|0.816;T|0.184	0.184	strong	.	NDST3	107	.	NM_004784	exon2	c.C81T	p.I27I	CATTATCATTTCT	.	PASS	Atlas-SNP
MFF	56947	hgsc.bcm.edu	37	2	228221725	228221725	+	Silent	SNP	A	A	G	rs74713223	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	40	17	51	0	0.425	0	A|0.847;G|0.153	0.153	strong	MFF,NS,carcinoma,0,1	MFF	48	1	NM_020194	exon11	c.A921G	p.L307L	ACGTCTACAACTT	.	PASS	Atlas-SNP
EEA1	8411	hgsc.bcm.edu	37	12	93195435	93195435	+	Missense_Mutation	SNP	T	T	A	rs73362428	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	40	21	64	0	0.525	0	T|0.983;A|0.017	0.017	strong	.	EEA1	104	.	NM_003566	exon20	c.A2713T	p.M905L	TTTCCATCTGCAC	.	PASS	Atlas-SNP
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33037061	33037061	+	Silent	SNP	G	G	C	rs1126544	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	41	9	66	0	0.219512	0	G|0.903;C|0.097	0.097	strong	.	HLA-DPA1	20	.	NM_033554	exon3	c.C363G	p.T121T	AAACACGGTCACC	.	PASS	Atlas-SNP
DSCAML1	57453	hgsc.bcm.edu	37	11	117403235	117403235	+	Missense_Mutation	SNP	G	G	T	rs3741280	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	74	14	109	0	0.189189	0	G|0.640;T|0.360	0.360	strong	DSCAML1,NS,carcinoma,0,1	DSCAML1	286	1	NM_020693	exon4	c.C694A	p.H232N	ACCTGTGTTCTGG	.	PASS	Atlas-SNP
FUCA2	2519	hgsc.bcm.edu	37	6	143823157	143823157	+	Missense_Mutation	SNP	T	T	C	rs3762002	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	65	7	76	0	0.107692	0	T|0.749;C|0.251	0.251	strong	.	FUCA2	28	.	NM_032020	exon5	c.A1066G	p.M356V	ACCCCATTTGCCT	.	PASS	Atlas-SNP
VWDE	221806	hgsc.bcm.edu	37	7	12419108	12419108	+	Missense_Mutation	SNP	A	A	T	rs6967241	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	24	129	0	0.247423	0	A|0.382;T|0.618	0.618	strong	VWDE_ENST00000275358,NS,carcinoma,0,1	VWDE	123	1	NM_001135924	exon6	c.T874A	p.F292I	CCTTAAAGCCTGC	.	PASS	Atlas-SNP
TMPRSS5	80975	hgsc.bcm.edu	37	11	113561057	113561057	+	Silent	SNP	A	A	G	rs7110738	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	137	36	138	0	0.262774	0	A|0.259;G|0.741	0.741	strong	.	TMPRSS5	69	.	NM_030770	exon11	c.T1102C	p.L368L	TGAACAAGGGCAC	.	PASS	Atlas-SNP
HSPA6	3310	hgsc.bcm.edu	37	1	161495885	161495885	+	Silent	SNP	T	T	C	rs404508	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	198	197	213	1	0.99495	0.00469484	T|0.229;G|0.001;C|0.770	0.770	strong	.	HSPA6	53	.	NM_002155	exon1	c.T1437C	p.T479T	GGTGACTTTTGAC	.	PASS	Atlas-SNP
CTSS	1520	hgsc.bcm.edu	37	1	150720261	150720261	+	Silent	SNP	C	C	A	rs140408537	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	163	99	226	1	0.607362	0.00442478	C|0.995;A|0.005	0.005	strong	.	CTSS	31	.	NM_004079	exon7	c.G888T	p.V296V	GTTTTTCACAAGC	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	50	43	65	0	0.86	0	G|0.515;A|0.485	0.485	strong	.	ZNF7	62	.	NM_003416	exon5	c.G562A	p.G188R	AGTCAGGGAGAGA	.	PASS	Atlas-SNP
BMP2K	55589	hgsc.bcm.edu	37	4	79832870	79832870	+	Missense_Mutation	SNP	A	A	T	rs116710382	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	135	70	151	0	0.518519	0	A|0.993;T|0.007	0.007	strong	.	BMP2K	169	.	NM_198892	exon16	c.A3169T	p.N1057Y	AGGGGGAATGTCT	.	PASS	Atlas-SNP
C17orf59	54785	hgsc.bcm.edu	37	17	8093324	8093324	+	Missense_Mutation	SNP	C	C	G	rs150061068	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	65	31	47	0	0.476923	0	C|0.995;G|0.005	0.005	strong	.	C17orf59	19	.	NM_017622	exon1	c.G135C	p.E45D	CTCTTCCTCCCCG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195513474	195513474	+	Silent	SNP	T	T	G	rs77382269	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	224	55	163	3	0.245536	0.0184049	T|0.945;G|0.055	0.055	strong	MUC4_ENST00000463781,NS,carcinoma,0,5	MUC4	1505	5	NM_018406	exon2	c.A4977C	p.T1659T	GTGACCTGTGGAT	.	scavenged	Atlas-SNP
BEND3	57673	hgsc.bcm.edu	37	6	107391396	107391396	+	Silent	SNP	G	G	A	rs3814073	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	41	80	0	0.476744	0	G|0.783;A|0.217	0.217	strong	.	BEND3	70	.	NM_001080450	exon5	c.C999T	p.N333N	GAAGTCGTTCAGC	.	PASS	Atlas-SNP
EHD2	30846	hgsc.bcm.edu	37	19	48229169	48229169	+	Silent	SNP	A	A	G	rs8111184	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	59	29	69	0	0.491525	0	A|0.861;G|0.139	0.139	strong	.	EHD2	59	.	NM_014601	exon4	c.A603G	p.S201S	GTTCTCAGAGGCC	.	PASS	Atlas-SNP
IL24	11009	hgsc.bcm.edu	37	1	207074905	207074905	+	Missense_Mutation	SNP	T	T	C	rs1150258	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	195	87	256	0	0.446154	0	T|0.623;G|0.003	.	strong	.	IL24	20	.	NM_001185156	exon5	c.T373C	p.Y125H	AAAAACTACCACA	.	PASS	Atlas-SNP
PASK	23178	hgsc.bcm.edu	37	2	242082262	242082262	+	Silent	SNP	T	T	C	rs6709462	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	76	43	84	1	0.565789	0.0119048	T|0.480;C|0.520	0.520	strong	PASK_ENST00000234040,colon,carcinoma,-1,2	PASK	230	2	NM_001252122	exon2	c.A186G	p.T62T	GAGCGCTGTCCTG	.	scavenged	Atlas-SNP
SIMC1	375484	hgsc.bcm.edu	37	5	175772208	175772208	+	Silent	SNP	C	C	T	rs17622467	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	173	71	164	0	0.410405	0	C|0.896;N|0.000	.	strong	.	.	.	.	NM_198567	exon9	c.C1134T	p.I378I	CGTGATCGACCGA	.	PASS	Atlas-SNP
SLFNL1	200172	hgsc.bcm.edu	37	1	41486245	41486245	+	Missense_Mutation	SNP	C	C	T	rs1138293	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	77	20	78	0	0.25974	0	C|0.874;T|0.126	0.126	strong	.	SLFNL1	37	.	NM_001168247	exon3	c.G88A	p.A30T	GCTCTGCGGGTAG	.	PASS	Atlas-SNP
CDH5	1003	hgsc.bcm.edu	37	16	66432381	66432381	+	Missense_Mutation	SNP	T	T	C	rs16956504	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	90	31	106	0	0.344444	0	T|0.940;C|0.060	0.060	strong	.	CDH5	111	.	NM_001795	exon10	c.T1508C	p.I503T	CCGCAATAGACAA	.	PASS	Atlas-SNP
TCHH	7062	hgsc.bcm.edu	37	1	152084216	152084216	+	Missense_Mutation	SNP	C	C	G	rs201131683	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	100	13	111	0	0.13	0	C|0.986;G|0.013	0.013	strong	TCHH,NS,lymphoid_neoplasm,0,1	TCHH	275	1	NM_007113	exon3	c.G1477C	p.E493Q	CCTCCTCCTCGAG	.	PASS	Atlas-SNP
ARHGEF37	389337	hgsc.bcm.edu	37	5	149003626	149003626	+	Missense_Mutation	SNP	G	G	A	rs113997100	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	57	32	70	0	0.561404	0	G|0.967;A|0.033	0.033	strong	ARHGEF37,NS,carcinoma,-1,1	ARHGEF37	45	1	NM_001001669	exon10	c.G1387A	p.A463T	GAGGACGCACTGG	.	PASS	Atlas-SNP
KRT75	9119	hgsc.bcm.edu	37	12	52818377	52818377	+	Missense_Mutation	SNP	C	C	T	rs61730614	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	165	82	175	0	0.49697	0	C|0.848;T|0.152	0.152	strong	KRT75,rectum,NS,0,2	KRT75	75	2	NM_004693	exon9	c.G1580A	p.R527Q	AAGCCCCGGTTGC	.	PASS	Atlas-SNP
GRK7	131890	hgsc.bcm.edu	37	3	141535608	141535608	+	Missense_Mutation	SNP	C	C	A	rs33928105	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	128	71	160	0	0.554688	0	C|0.899;A|0.101	0.101	strong	.	GRK7	65	.	NM_139209	exon4	c.C1378A	p.P460T	AACTTTCCTCGCC	.	PASS	Atlas-SNP
CRIPAK	285464	hgsc.bcm.edu	37	4	1388631	1388631	+	Missense_Mutation	SNP	C	C	G	rs200849975	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	47	7	73	0	0.148936	0	C|0.935;G|0.065	0.065	strong	CRIPAK,rectum,carcinoma,0,2	CRIPAK	185	2	NM_175918	exon1	c.C332G	p.P111R	CGTGCCCATGTGG	.	PASS	Atlas-SNP
DST	667	hgsc.bcm.edu	37	6	56494071	56494071	+	Silent	SNP	A	A	G	rs112640831	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	128	66	168	0	0.515625	0	A|0.974;G|0.026;T|0.000	0.026	strong	.	DST	1427	.	NM_001723	exon18	c.T2841C	p.N947N	ATGAACATTTTGC	.	PASS	Atlas-SNP
APOC4	346	hgsc.bcm.edu	37	19	45448036	45448036	+	Missense_Mutation	SNP	T	T	C	rs1132899	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	64	33	89	0	0.515625	0	T|0.387;C|0.613	0.613	strong	.	APOC4	6	.	NM_001646	exon2	c.T107C	p.L36P	GAACCCTGAGCCC	.	PASS	Atlas-SNP
SIPA1	6494	hgsc.bcm.edu	37	11	65417434	65417434	+	Silent	SNP	G	G	A	rs746429	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	63	14	69	0	0.222222	0	G|0.736;A|0.264	0.264	strong	.	SIPA1	45	.	NM_006747	exon13	c.G2760A	p.A920A	GGAGGCGGGCAGT	.	PASS	Atlas-SNP
CCL14	6358	hgsc.bcm.edu	37	17	34313612	34313612	+	Missense_Mutation	SNP	G	G	A	rs75238886	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	104	54	97	0	0.519231	0	G|0.973;A|0.027	0.027	strong	.	CCL14	22	.	NM_032962	exon1	c.C74T	p.S25F	CGTGAGGAGGATT	.	PASS	Atlas-SNP
THSD4	79875	hgsc.bcm.edu	37	15	71953045	71953045	+	Silent	SNP	G	G	A	rs62024298	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	55	136	0	0.56701	0	G|0.678;A|0.322	0.322	strong	.	THSD4	75	.	NM_024817	exon7	c.G1329A	p.T443T	CATCACGGAGATG	.	PASS	Atlas-SNP
MS4A14	84689	hgsc.bcm.edu	37	11	60182970	60182970	+	Missense_Mutation	SNP	A	A	T	rs7131283	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	234	52	224	0	0.222222	0	A|0.376;T|0.624	0.624	strong	.	MS4A14	120	.	NM_001261828	exon6	c.A628T	p.N210Y	GAAGAAAATGATC	.	PASS	Atlas-SNP
OR10J5	127385	hgsc.bcm.edu	37	1	159505297	159505297	+	Silent	SNP	C	C	T	rs4656837	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	112	111	160	0	0.991071	0	C|0.414;T|0.586	0.586	strong	OR10J5,NS,carcinoma,0,1	OR10J5	68	1	NM_001004469	exon1	c.G501A	p.P167P	ACAGAACGGCAAA	.	PASS	Atlas-SNP
PTOV1	53635	hgsc.bcm.edu	37	19	50360989	50360989	+	Missense_Mutation	SNP	A	A	G	rs59595912	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	193	92	212	0	0.476684	0	A|0.928;G|0.072	0.072	strong	.	PTOV1	41	.	NM_017432	exon7	c.A754G	p.I252V	GTCCAGATCGTCA	.	PASS	Atlas-SNP
IQGAP2	10788	hgsc.bcm.edu	37	5	75923285	75923285	+	Silent	SNP	C	C	T	rs2431351	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	527	525	540	2	0.996205	0.0037037	C|0.452;T|0.548	0.548	strong	IQGAP2,NS,carcinoma,0,1	IQGAP2	186	1	NM_006633	exon14	c.C1572T	p.A524A	GCAAGCCGTCGAT	.	PASS	Atlas-SNP
TRIM65	201292	hgsc.bcm.edu	37	17	73886888	73886888	+	Missense_Mutation	SNP	A	A	G	rs3760128	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	77	44	52	0	0.571429	0	A|0.500;G|0.500	0.500	strong	TRIM65,NS,carcinoma,0,1	TRIM65	23	1	NM_173547	exon6	c.T1526C	p.L509P	GGCCCCAGAGGGA	.	PASS	Atlas-SNP
MYO5C	55930	hgsc.bcm.edu	37	15	52517714	52517714	+	Missense_Mutation	SNP	C	C	T	rs3825801	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	160	159	193	0	0.99375	0	C|0.886;T|0.114	0.114	strong	MYO5C,NS,carcinoma,0,1	MYO5C	162	1	NM_018728	exon26	c.G3223A	p.E1075K	CTTTTTCGAACTC	.	PASS	Atlas-SNP
CEP192	55125	hgsc.bcm.edu	37	18	13001512	13001512	+	Missense_Mutation	SNP	G	G	C	rs4499304	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	45	18	47	0	0.4	0	G|0.535;C|0.465	0.465	strong	CEP192_ENST00000506447,NS,carcinoma,0,1	CEP192	340	1	NM_032142	exon3	c.G221C	p.G74A	CATCCGGGTCATC	.	PASS	Atlas-SNP
MYO7A	4647	hgsc.bcm.edu	37	11	76919478	76919478	+	Missense_Mutation	SNP	C	C	A	rs948962	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	119	76	149	0	0.638655	0	C|0.478;A|0.522	0.522	strong	.	MYO7A	164	.	NM_000260	exon43	c.C5860A	p.L1954I	CAGGTCCTCAGCG	.	PASS	Atlas-SNP
NOTCH2NL	388677	hgsc.bcm.edu	37	1	145273366	145273366	+	Nonsense_Mutation	SNP	C	C	T	rs140871032	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	1284	166	1271	2	0.129283	0.00157356	C|0.964;T|0.036	0.036	strong	NOTCH2NL_ENST00000362074,NS,haematopoietic_neoplasm,0,2	NOTCH2NL	100	2	NM_203458	exon3	c.C220T	p.R74X	GTGTCTCGACCTT	.	scavenged	Atlas-SNP
TM7SF3	51768	hgsc.bcm.edu	37	12	27143508	27143508	+	Missense_Mutation	SNP	G	G	A	rs10771314	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	80	38	117	0	0.475	0	G|0.933;A|0.067	0.067	strong	.	TM7SF3	41	.	NM_016551	exon6	c.C743T	p.P248L	TGTCCCGGGAGGG	.	PASS	Atlas-SNP
SLC38A4	55089	hgsc.bcm.edu	37	12	47186770	47186770	+	Missense_Mutation	SNP	C	C	T	rs2429467	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	173	83	177	0	0.479769	0	C|0.921;T|0.079	0.079	strong	.	SLC38A4	58	.	NM_001143824	exon2	c.G85A	p.G29R	CTATCCCGATGTA	.	PASS	Atlas-SNP
PPID	5481	hgsc.bcm.edu	37	4	159631991	159631991	+	Missense_Mutation	SNP	G	G	T	rs9410	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	112	49	130	0	0.4375	0	G|0.586;T|0.237	0.237	strong	.	PPID	22	.	NM_005038	exon8	c.C904A	p.L302I	GGTCTAGTTCAAG	.	PASS	Atlas-SNP
CCDC169	728591	hgsc.bcm.edu	37	13	36828237	36828237	+	Missense_Mutation	SNP	T	T	C	rs9546897	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	31	29	39	0	0.935484	0	T|0.629;C|0.371	0.371	strong	.	CCDC169	20	.	NM_001144981	exon5	c.A359G	p.K120R	AGAGTCTTCTTTT	.	PASS	Atlas-SNP
PLIN4	729359	hgsc.bcm.edu	37	19	4511365	4511365	+	Silent	SNP	C	C	G	rs116973517	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	223	99	234	1	0.443946	0.0042735	C|0.937;G|0.063	0.063	strong	.	PLIN4	191	.	NM_001080400	exon3	c.G2565C	p.V855V	ACCGGTCACCCCA	.	PASS	Atlas-SNP
ESPNL	339768	hgsc.bcm.edu	37	2	239010719	239010719	+	Silent	SNP	T	T	C	rs36066915	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	53	53	72	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
ITGB3	3690	hgsc.bcm.edu	37	17	45360730	45360730	+	Missense_Mutation	SNP	T	T	C	rs5918	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	65	34	57	0	0.523077	0	T|0.884;C|0.116	0.116	strong	.	ITGB3	157	.	NM_000212	exon3	c.T176C	p.L59P	TGCCTCTGGGCTC	.	PASS	Atlas-SNP
HTR1B	3351	hgsc.bcm.edu	37	6	78172992	78172992	+	Silent	SNP	G	G	A	rs6298	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	235	126	224	0	0.53617	0	G|0.712;A|0.288	0.288	strong	.	HTR1B	55	.	NM_000863	exon1	c.C129T	p.S43S	GGAGATGGAGTCC	.	PASS	Atlas-SNP
VCL	7414	hgsc.bcm.edu	37	10	75865065	75865065	+	Silent	SNP	G	G	A	rs767809	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	34	66	0	0.478873	0	G|0.604;A|0.396	0.396	strong	.	VCL	77	.	NM_003373	exon16	c.G2388A	p.P796P	CTCCCCGATGGTG	.	PASS	Atlas-SNP
CTNND1	1500	hgsc.bcm.edu	37	11	57563991	57563991	+	Silent	SNP	C	C	T	rs10896644	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	121	94	169	1	0.77686	0.00591716	C|0.728;T|0.272	0.272	strong	.	CTNND1	203	.	NM_001085461	exon6	c.C483T	p.D161D	ACCAGACGGGTTG	.	PASS	Atlas-SNP
NOMO1	23420	hgsc.bcm.edu	37	16	14969016	14969016	+	Missense_Mutation	SNP	T	T	A	rs79100490	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	883	330	586	1	0.373726	0.00170648	.	.	weak	.	NOMO1	60	.	NM_014287	exon19	c.T2178A	p.N726K	CGGCAATGAGGAA	.	PASS	Atlas-SNP
DHX38	9785	hgsc.bcm.edu	37	16	72139184	72139184	+	Silent	SNP	C	C	A	rs2074626	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	127	62	107	0	0.488189	0	C|0.529;A|0.471	0.471	strong	DHX38,NS,carcinoma,0,2	DHX38	91	2	NM_014003	exon17	c.C2316A	p.A772A	GCCTGCCCTGGCT	.	PASS	Atlas-SNP
MUC20	200958	hgsc.bcm.edu	37	3	195452770	195452770	+	Silent	SNP	G	G	A	rs71271396	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	613	221	655	1	0.360522	0.00152672	G|0.500;A|0.500	0.500	strong	.	MUC20	84	.	NM_152673	exon3	c.G783A	p.T261T	AACAACGACTTCC	.	PASS	Atlas-SNP
SDC3	9672	hgsc.bcm.edu	37	1	31347399	31347399	+	Missense_Mutation	SNP	C	C	T	rs4949184	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	68	46	86	0	0.676471	0	C|0.795;T|0.205	0.205	strong	.	SDC3	45	.	NM_014654	exon4	c.G907A	p.D303N	GCTCATCCCGGAT	.	PASS	Atlas-SNP
PTPN13	5783	hgsc.bcm.edu	37	4	87696476	87696476	+	Silent	SNP	G	G	A	rs12499471	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	128	48	137	0	0.375	0	G|0.906;A|0.094	0.094	strong	.	PTPN13	203	.	NM_080685	exon34	c.G5676A	p.T1892T	ACTAACGTGCAAC	.	PASS	Atlas-SNP
NCOR2	9612	hgsc.bcm.edu	37	12	124821413	124821413	+	Missense_Mutation	SNP	G	G	A	rs2230944	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	33	26	12	0	0.787879	0	G|0.970;A|0.030	0.030	strong	.	NCOR2	475	.	NM_006312	exon40	c.C6001T	p.P2001S	GGTGAGGTGCGAG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195506914	195506914	+	Missense_Mutation	SNP	G	G	A	rs186560307	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	21	17	82	0	0.809524	0	A|0.147;C|0.034;G|0.819	0.147	strong	.	MUC4	1505	.	NM_018406	exon2	c.C11537T	p.P3846L	GAGGAAGGGATGG	.	PASS	Atlas-SNP
CAV3	859	hgsc.bcm.edu	37	3	8787220	8787220	+	Silent	SNP	T	T	C	rs13087941	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	38	71	0	0.520548	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
NFASC	23114	hgsc.bcm.edu	37	1	204943947	204943947	+	Silent	SNP	C	C	A	rs2246662	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	55	26	73	0	0.472727	0	C|0.611;A|0.389	0.389	strong	.	NFASC	396	.	NM_015090	exon14	c.C1587A	p.V529V	GGAGGTCAAAGGT	.	PASS	Atlas-SNP
CD300E	342510	hgsc.bcm.edu	37	17	72613352	72613352	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	248	5	291	1	0.0201613	0.00343643	.	.	none	CD300E_ENST00000426295,right_upper_lobe,carcinoma,-1,2	CD300E	70	2	NM_181449	exon2	c.A293G	p.D98G	CCAGCATCATCTT	.	scavenged	Atlas-SNP
ARHGAP33	115703	hgsc.bcm.edu	37	19	36275074	36275074	+	Silent	SNP	G	G	A	rs62112163	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	197	197	184	0	1	0	G|0.833;A|0.167	0.167	strong	ARHGAP33,NS,carcinoma,0,1	ARHGAP33	102	1	NM_052948	exon16	c.G1422A	p.R474R	ACCCAGGTCCATG	.	PASS	Atlas-SNP
TAF4B	6875	hgsc.bcm.edu	37	18	23872235	23872235	+	Missense_Mutation	SNP	A	A	G	rs12963653	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	49	101	0	0.485149	0	A|0.796;G|0.204	0.204	strong	.	TAF4B	71	.	NM_005640	exon8	c.A1616G	p.N539S	GAGGCAATGAAAA	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228550426	228550426	+	Missense_Mutation	SNP	C	C	T	rs35155240	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	174	88	192	0	0.505747	0	C|0.851;T|0.149	0.149	strong	.	OBSCN	2142	.	NM_001271223	exon91	c.C21682T	p.P7228S	TCCCAGCCCCCAG	.	PASS	Atlas-SNP
HBP1	26959	hgsc.bcm.edu	37	7	106826381	106826381	+	Silent	SNP	C	C	T	rs7794598	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	31	116	0	0.424658	0	C|0.818;T|0.182	0.182	strong	.	HBP1	31	.	NM_001244262	exon4	c.C564T	p.H188H	AAGACACGAAAGG	.	PASS	Atlas-SNP
NPHP1	4867	hgsc.bcm.edu	37	2	110922703	110922703	+	Silent	SNP	C	C	T	rs11675767	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	98	98	118	0	1	0	C|0.575;T|0.425	0.425	strong	.	NPHP1	68	.	NM_207181	exon7	c.G654A	p.E218E	ACTTGACTCTTGG	.	PASS	Atlas-SNP
ZNF646	9726	hgsc.bcm.edu	37	16	31090094	31090094	+	Missense_Mutation	SNP	G	G	A	rs78522165	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	138	53	140	0	0.384058	0	A|0.052;C|0.000;G|0.948	0.052	strong	.	ZNF646	133	.	NM_014699	exon2	c.G2449A	p.A817T	TGGCAGGCTGGGG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195507262	195507262	+	Missense_Mutation	SNP	T	T	G	rs367631576	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	96	19	83	2	0.197917	0.0240964	.	.	weak	MUC4_ENST00000463781,NS,haematopoietic_neoplasm,0,1	MUC4	1505	1	NM_018406	exon2	c.A11189C	p.H3730P	GTGACATGAAGAG	.	scavenged	Atlas-SNP
NEB	4703	hgsc.bcm.edu	37	2	152382759	152382759	+	Silent	SNP	T	T	C	rs61730765	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	103	47	130	0	0.456311	0	T|0.975;C|0.025	0.025	strong	.	NEB	1697	.	NM_001271208	exon150	c.A22068G	p.K7356K	GACATGTTTCTCT	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	51	31	73	0	0.607843	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
C14orf37	145407	hgsc.bcm.edu	37	14	58605156	58605156	+	Silent	SNP	G	G	A	rs61748937	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	175	98	218	0	0.56	0	G|0.989;A|0.011	0.011	strong	.	C14orf37	87	.	NM_001001872	exon2	c.C921T	p.A307A	GGCAGAGGCAGCT	.	PASS	Atlas-SNP
CAND2	23066	hgsc.bcm.edu	37	3	12861608	12861608	+	Missense_Mutation	SNP	G	G	A	rs3817121	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	74	38	87	0	0.513514	0	A|0.144;G|0.856	0.144	strong	CAND2_ENST00000456430,NS,carcinoma,-2,2	CAND2	138	2	NM_001162499	exon11	c.G2968A	p.V990I	AGCACCGTCATCA	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	46	8	62	1	0.173913	0.016129	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	.	scavenged	Atlas-SNP
MUC6	4588	hgsc.bcm.edu	37	11	1026084	1026084	+	Silent	SNP	G	G	A	rs12801568	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	142	112	101	0	0.788732	0	G|0.937;A|0.063	0.063	strong	.	MUC6	408	.	NM_005961	exon21	c.C2604T	p.C868C	GAGGGTGCAGGTG	.	PASS	Atlas-SNP
OR5L1	219437	hgsc.bcm.edu	37	11	55579068	55579068	+	Silent	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	143	8	113	0	0.0559441	0	.	.	none	OR5L1,colon,carcinoma,0,3	OR5L1	145	3	NM_001004738	exon1	c.C126T	p.N42N	AGCCAACCTGGGC	.	scavenged	Atlas-SNP
KLHL6	89857	hgsc.bcm.edu	37	3	183211906	183211906	+	Silent	SNP	A	A	G	rs1520101	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	152	152	189	0	1	0	A|0.359;G|0.641	0.641	strong	.	KLHL6	100	.	NM_130446	exon5	c.T1311C	p.N437N	CTCCACATTGTTG	.	PASS	Atlas-SNP
TPCN2	219931	hgsc.bcm.edu	37	11	68840160	68840160	+	Missense_Mutation	SNP	A	A	G	rs3750965	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	162	116	130	0	0.716049	0	A|0.718;G|0.282	0.282	strong	TPCN2,colon,carcinoma,0,1	TPCN2	63	1	NM_139075	exon12	c.A1127G	p.K376R	CCCACAAACAGGC	.	PASS	Atlas-SNP
FAM185A	222234	hgsc.bcm.edu	37	7	102389697	102389697	+	Missense_Mutation	SNP	C	C	T	rs141352868	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	158	70	180	0	0.443038	0	C|0.937;T|0.063	0.063	strong	.	FAM185A	10	.	NM_001145269	exon1	c.C43T	p.L15F	TTCCGTCTCTGTC	.	PASS	Atlas-SNP
OR5P2	120065	hgsc.bcm.edu	37	11	7817959	7817959	+	Silent	SNP	G	G	A	rs73406603	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	81	69	70	1	0.851852	0.0142857	G|0.739;A|0.261	0.261	strong	OR5P2,brain,glioma,0,1	OR5P2	68	1	NM_153444	exon1	c.C531T	p.F177F	GGGAGCGAAATCA	.	scavenged	Atlas-SNP
NCKAP5L	57701	hgsc.bcm.edu	37	12	50189807	50189807	+	Silent	SNP	C	C	A	rs2720298	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	35	20	45	0	0.571429	0	C|0.433;A|0.567	0.567	strong	.	NCKAP5L	142	.	NM_001037806	exon8	c.G1836T	p.S612S	GGGGTACGATTCT	.	PASS	Atlas-SNP
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32552060	32552060	+	Missense_Mutation	SNP	A	A	T	rs16822820	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	55	13	44	0	0.236364	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
ZNF687	57592	hgsc.bcm.edu	37	1	151259543	151259543	+	Missense_Mutation	SNP	G	G	A	rs3748545	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	77	35	84	0	0.454545	0	G|0.880;A|0.120	0.120	strong	.	ZNF687	94	.	NM_020832	exon2	c.G776A	p.G259E	TTGCTGGGGTGCC	.	PASS	Atlas-SNP
ATP10D	57205	hgsc.bcm.edu	37	4	47560015	47560015	+	Missense_Mutation	SNP	A	A	G	rs34169638	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	65	65	100	1	1	0.01	A|0.940;G|0.060	0.060	strong	.	ATP10D	168	.	NM_020453	exon12	c.A2159G	p.N720S	CCTGCAACCTGTG	.	PASS	Atlas-SNP
NDRG4	65009	hgsc.bcm.edu	37	16	58540875	58540875	+	Silent	SNP	G	G	A	rs17821543	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	61	45	67	0	0.737705	0	G|0.951;A|0.049	0.049	strong	.	NDRG4	29	.	NM_001130487	exon10	c.G732A	p.V244V	GAACGTGGTGAAC	.	PASS	Atlas-SNP
CLEC16A	23274	hgsc.bcm.edu	37	16	11272482	11272482	+	Missense_Mutation	SNP	G	G	A	rs72650691	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	13	13	12	0	1	0	.	.	weak	CLEC16A,NS,carcinoma,-1,1	CLEC16A	101	1	NM_015226	exon23	c.G3097A	p.A1033T	GCTGCCGCCTGCA	.	PASS	Atlas-SNP
OR5P2	120065	hgsc.bcm.edu	37	11	7818151	7818151	+	Silent	SNP	G	G	A	rs73406606	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	59	60	0	0.830986	0	G|0.739;A|0.261	0.261	strong	OR5P2,brain,glioma,0,1	OR5P2	68	1	NM_153444	exon1	c.C339T	p.A113A	GGCCATGGCAGCC	.	PASS	Atlas-SNP
OR8H1	219469	hgsc.bcm.edu	37	11	56058197	56058197	+	Silent	SNP	G	G	A	rs1842674	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	152	38	177	0	0.25	0	G|0.650;A|0.350	0.350	strong	OR8H1,NS,carcinoma,-1,1	OR8H1	89	1	NM_001005199	exon1	c.C342T	p.L114L	TGATGAGAGAAGA	.	PASS	Atlas-SNP
HFE	3077	hgsc.bcm.edu	37	6	26091179	26091179	+	Missense_Mutation	SNP	C	C	G	rs1799945	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	202	93	201	0	0.460396	0	C|0.898;G|0.102	0.102	strong	.	HFE	37	.	NM_139006	exon2	c.C187G	p.H63D	TATGATCATGAGA	.	PASS	Atlas-SNP
TTC16	158248	hgsc.bcm.edu	37	9	130493513	130493513	+	Silent	SNP	A	A	G	rs482095	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	178	72	184	0	0.404494	0	A|0.372;G|0.628	0.628	strong	.	TTC16	55	.	NM_144965	exon14	c.A2451G	p.K817K	CAGCAAAACTGAG	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	116	116	0	0	1	.	T|0.581;C|0.419	0.419	strong	.	AHNAK2	719	.	NM_138420	exon7	c.A6319G	p.M2107V	CTCTCATTTCCAC	.	PASS	Atlas-SNP
CLEC18A	348174	hgsc.bcm.edu	37	16	69985383	69985383	+	Silent	SNP	G	G	A	rs79631099		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	379	124	300	2	0.327177	0.00666667	G|0.500;A|0.500	0.500	weak	CLEC18A,NS,carcinoma,0,1	CLEC18A	9	1	NM_001271197	exon2	c.G114A	p.P38P	GGCTCCGATGGCC	.	scavenged	Atlas-SNP
HELZ2	85441	hgsc.bcm.edu	37	20	62194238	62194238	+	Silent	SNP	C	C	T	rs34996572	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	99	38	83	0	0.383838	0	C|0.984;T|0.016	0.016	strong	.	.	.	.	NM_001037335	exon9	c.G5937A	p.P1979P	CCCCTGCGGCGTC	.	PASS	Atlas-SNP
MAGI1	9223	hgsc.bcm.edu	37	3	65464386	65464386	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	146	38	169	0	0.260274	0	.	.	none	.	MAGI1	481	.	NM_001033057	exon4	c.G638C	p.G213A	TTAGAGCCAGACT	.	PASS	Atlas-SNP
DGKH	160851	hgsc.bcm.edu	37	13	42803315	42803315	+	Silent	SNP	G	G	A	rs376522940		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	67	10	71	0	0.149254	0	.	.	weak	.	DGKH	106	.	NM_178009	exon30	c.G3654A	p.S1218S	ACAGTCGGAGGTG	.	PASS	Atlas-SNP
OR10H2	26538	hgsc.bcm.edu	37	19	15839174	15839174	+	Silent	SNP	C	C	T	rs74730938		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	194	66	183	0	0.340206	0	T|1.000;|0.000	1.000	weak	.	OR10H2	59	.	NM_013939	exon1	c.C321T	p.F107F	CAGCTTCGGCTTC	.	PASS	Atlas-SNP
BRMS1	25855	hgsc.bcm.edu	37	11	66105194	66105194	+	Missense_Mutation	SNP	G	G	A	rs1052566	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	43	8	63	0	0.186047	0	G|0.765;A|0.235	0.235	strong	.	BRMS1	42	.	NM_001024957	exon10	c.C818T	p.A273V	GTCCAGGCCAGTG	.	PASS	Atlas-SNP
DLX3	1747	hgsc.bcm.edu	37	17	48072225	48072225	+	Silent	SNP	G	G	A	rs33937843	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	122	70	137	0	0.57377	0	G|0.912;A|0.088	0.088	strong	.	DLX3	28	.	NM_005220	exon1	c.C138T	p.P46P	GTGCTGGGGAGCG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195509651	195509651	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	117	39	59	0	0.333333	0	.	.	none	MUC4_ENST00000463781,trunk,malignant_melanoma,0,2	MUC4	1505	2	NM_018406	exon2	c.C8800T	p.L2934F	AGGAAAGGCTGGT	.	scavenged	Atlas-SNP
MYLK2	85366	hgsc.bcm.edu	37	20	30414621	30414621	+	Silent	SNP	C	C	T	rs6089088	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	159	75	175	0	0.471698	0	C|0.986;T|0.014	0.014	strong	.	MYLK2	76	.	NM_033118	exon8	c.C1104T	p.F368F	GCTCTTCGAGAGG	.	PASS	Atlas-SNP
PTGES2	80142	hgsc.bcm.edu	37	9	130884753	130884753	+	Missense_Mutation	SNP	C	C	T	rs13283456	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	41	19	51	0	0.463415	0	C|0.879;T|0.121	0.121	strong	.	PTGES2	14	.	NM_025072	exon6	c.G893A	p.R298H	TGGAGGCGGTGCC	.	PASS	Atlas-SNP
CXCL2	2920	hgsc.bcm.edu	37	4	74964830	74964830	+	Missense_Mutation	SNP	C	C	T	rs186397980	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	22	13	6	0	0.590909	0	C|0.981;T|0.019	0.019	strong	.	CXCL2	6	.	NM_002089	exon1	c.G8A	p.R3H	GTGGCGCGGGCCA	.	PASS	Atlas-SNP
MYBPH	4608	hgsc.bcm.edu	37	1	203144833	203144833	+	Silent	SNP	G	G	A	rs12145010	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	149	79	205	0	0.530201	0	G|0.915;A|0.085	0.085	strong	.	MYBPH	41	.	NM_004997	exon1	c.C51T	p.T17T	AGATGCGGTCTCC	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29912856	29912856	+	Missense_Mutation	SNP	A	A	T	rs2231119	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	127	49	238	0	0.385827	0	A|0.345;T|0.655	0.655	strong	HLA-A,NS,carcinoma,0,1	HLA-A	89	1	NM_001242758	exon6	c.A1033T	p.T345S	AGTTACACTCAGG	.	PASS	Atlas-SNP
PTGIS	5740	hgsc.bcm.edu	37	20	48156249	48156249	+	Silent	SNP	G	G	A	rs61322884	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	31	19	36	0	0.612903	0	G|0.982;A|0.018	0.018	strong	.	PTGIS	60	.	NM_000961	exon5	c.C531T	p.Y177Y	AGTCAGGTAGCCG	.	PASS	Atlas-SNP
DZIP3	9666	hgsc.bcm.edu	37	3	108373022	108373022	+	Silent	SNP	G	G	A	rs2969901	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	67	33	98	0	0.492537	0	G|0.717;A|0.283	0.283	strong	.	DZIP3	111	.	NM_014648	exon19	c.G2064A	p.L688L	GCAGTTGAGGAAA	.	PASS	Atlas-SNP
VCX	26609	hgsc.bcm.edu	37	X	7811747	7811747	+	Missense_Mutation	SNP	T	T	C	rs80291436	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	76	75	126	1	0.986842	0.00793651	T|0.449;C|0.551	0.551	strong	.	VCX	28	.	NM_013452	exon3	c.T311C	p.L104P	ACCCCCTGAGTCA	.	PASS	Atlas-SNP
OXTR	5021	hgsc.bcm.edu	37	3	8809184	8809184	+	Silent	SNP	G	G	A	rs237902	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	53	30	66	0	0.566038	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
PCSK1	5122	hgsc.bcm.edu	37	5	95751785	95751785	+	Missense_Mutation	SNP	T	T	C	rs6232	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	168	80	170	0	0.47619	0	T|0.968;C|0.032	0.032	strong	.	PCSK1	93	.	NM_000439	exon6	c.A661G	p.N221D	GATTATTTGCTTG	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1264965	1264965	+	Silent	SNP	G	G	A	rs4963051	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	485	330	370	1	0.680412	0.0027027	G|0.873;A|0.127	0.127	strong	.	MUC5B	473	.	NM_002458	exon31	c.G6855A	p.T2285T	AGCCACGGCCACA	.	PASS	Atlas-SNP
GFAP	2670	hgsc.bcm.edu	37	17	42989088	42989088	+	Silent	SNP	C	C	T	rs2289681	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	125	67	80	0	0.536	0	C|0.850;T|0.150	0.150	strong	.	GFAP	88	.	NM_001131019	exon5	c.G858A	p.R286R	CTGGCGCCGGTAG	.	PASS	Atlas-SNP
ACAN	176	hgsc.bcm.edu	37	15	89400023	89400023	+	Missense_Mutation	SNP	A	A	G	rs12899191	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	39	32	50	1	0.820513	0.02	G|1.000;|0.000	1.000	weak	AGC1,caecum,carcinoma,0,3	ACAN	220	3	NM_001135	exon12	c.A4207G	p.T1403A	GAGACTACTGCCC	.	scavenged	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	54	28	62	0	0.518519	0	T|0.691;C|0.309	0.309	strong	.	NUP133	111	.	NM_018230	exon10	c.A1217G	p.Q406R	GTCAACTGACACA	.	PASS	Atlas-SNP
ARL6IP1	23204	hgsc.bcm.edu	37	16	18809333	18809333	+	Silent	SNP	G	G	A	rs138748723	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	225	3	223	0	0.0133333	0	G|0.996;A|0.004	0.004	strong	ARL6IP1,colon,carcinoma,0,1	ARL6IP1	23	1	NM_015161	exon3	c.C204T	p.S68S	AACGCCGGACAGA	.	scavenged	Atlas-SNP
SPATA31E1	286234	hgsc.bcm.edu	37	9	90503007	90503007	+	Missense_Mutation	SNP	A	A	G	rs11789780	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	42	20	61	0	0.47619	0	A|0.555;G|0.445	0.445	strong	C9orf79,NS,carcinoma,0,3	.	.	3	NM_178828	exon4	c.A3605G	p.D1202G	GTGCGGACAAGGG	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179414318	179414318	+	Missense_Mutation	SNP	C	C	T	rs747122	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	107	46	120	0	0.429907	0	C|0.882;T|0.118	0.118	strong	.	TTN	18412	.	NM_001267550	exon338	c.G92131A	p.V30711M	CAACCACTGGATC	.	PASS	Atlas-SNP
CSPG4	1464	hgsc.bcm.edu	37	15	75969335	75969335	+	Missense_Mutation	SNP	C	C	T	rs77237106	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	54	29	54	0	0.537037	0	C|0.919;T|0.081	0.081	strong	.	CSPG4	175	.	NM_001897	exon10	c.G5525A	p.R1842Q	GTGAGCCGGAGTG	.	PASS	Atlas-SNP
OR4C6	219432	hgsc.bcm.edu	37	11	55433040	55433040	+	Missense_Mutation	SNP	T	T	C	rs11230600	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	90	13	112	0	0.144444	0	T|0.759;C|0.241	0.241	strong	.	OR4C6	114	.	NM_001004704	exon1	c.T398C	p.I133T	CGATCATCATGAG	.	PASS	Atlas-SNP
VWF	7450	hgsc.bcm.edu	37	12	6138595	6138595	+	Silent	SNP	C	C	T	rs1800380	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	88	44	100	0	0.5	0	C|0.766;T|0.234	0.234	strong	.	VWF	338	.	NM_000552	exon22	c.G2880A	p.R960R	GATGTACCGGCCA	.	PASS	Atlas-SNP
UBR4	23352	hgsc.bcm.edu	37	1	19486689	19486689	+	Silent	SNP	G	G	A	rs139582695	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	171	88	192	0	0.51462	0	G|0.999;A|0.001	0.001	strong	UBR4,caecum,carcinoma,-1,1	UBR4	415	1	NM_020765	exon39	c.C5493T	p.A1831A	CCCGACGGCTGAA	.	PASS	Atlas-SNP
CDON	50937	hgsc.bcm.edu	37	11	125891162	125891162	+	Silent	SNP	A	A	G	rs35131477	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	45	73	0	0.775862	0	A|0.963;G|0.037	0.037	strong	.	CDON	137	.	NM_016952	exon3	c.T330C	p.P110P	TGTCGCAGGGCCA	.	PASS	Atlas-SNP
SAMD4B	55095	hgsc.bcm.edu	37	19	39873858	39873858	+	Silent	SNP	T	T	G	rs140996761	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	105	52	162	0	0.495238	0	T|0.996;G|0.004	0.004	strong	.	SAMD4B	48	.	NM_018028	exon15	c.T1983G	p.V661V	CCCGGTTCCTGGG	.	PASS	Atlas-SNP
KCNH6	81033	hgsc.bcm.edu	37	17	61611423	61611423	+	Silent	SNP	T	T	C	rs7225568	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	161	85	197	0	0.52795	0	C|0.529;N|0.000	0.529	strong	KCNH6,NS,malignant_melanoma,+2,1	KCNH6	122	1	NM_030779	exon5	c.T852C	p.D284D	CAGCGATCAGGAC	.	PASS	Atlas-SNP
ADAR	103	hgsc.bcm.edu	37	1	154573967	154573967	+	Missense_Mutation	SNP	T	T	C	rs2229857	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	145	145	159	0	1	0	T|0.384;C|0.616	0.616	strong	.	ADAR	113	.	NM_015840	exon2	c.A1151G	p.K384R	TTTCTTTTGGTCT	.	PASS	Atlas-SNP
C4orf17	84103	hgsc.bcm.edu	37	4	100443720	100443720	+	Missense_Mutation	SNP	G	G	A	rs13143848	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	117	60	133	0	0.512821	0	G|0.699;A|0.301	0.301	strong	C4orf17,NS,carcinoma,0,1	C4orf17	42	1	NM_032149	exon3	c.G191A	p.G64E	TGTGGGGAGTTGG	.	PASS	Atlas-SNP
GPATCH1	55094	hgsc.bcm.edu	37	19	33579128	33579128	+	Silent	SNP	T	T	C	rs7259333	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	33	144	0	0.37931	0	T|0.549;C|0.451	0.451	strong	.	GPATCH1	79	.	NM_018025	exon2	c.T162C	p.S54S	CTTTAGTGGAGGT	.	PASS	Atlas-SNP
KRTAP10-6	386674	hgsc.bcm.edu	37	21	46011583	46011583	+	Nonsense_Mutation	SNP	G	G	T	rs233303	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	122	68	127	0	0.557377	0	G|0.788;T|0.212	0.212	strong	.	KRTAP10-6	57	.	NM_198688	exon1	c.C783A	p.C261X	GGAGGTGCAGCAA	.	PASS	Atlas-SNP
ZFPM1	161882	hgsc.bcm.edu	37	16	88594567	88594567	+	Silent	SNP	C	C	T	rs35121729	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	120	118	85	1	0.983333	0.0117647	C|0.911;T|0.089	0.089	strong	ZFPM1,NS,carcinoma,0,1	ZFPM1	32	1	NM_153813	exon6	c.C633T	p.C211C	CACGTGCCCGGCC	.	scavenged	Atlas-SNP
IZUMO1	284359	hgsc.bcm.edu	37	19	49247786	49247786	+	Silent	SNP	G	G	A	rs8108468	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	60	25	88	0	0.416667	0	G|0.551;A|0.449	0.449	strong	.	IZUMO1	30	.	NM_182575	exon4	c.C321T	p.F107F	CTTCACGAAGAGA	.	PASS	Atlas-SNP
VSIG1	340547	hgsc.bcm.edu	37	X	107315933	107315933	+	Missense_Mutation	SNP	G	G	A	rs17254305	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	105	104	167	0	0.990476	0	0|0.004;A|0.013	0.013	strong	.	VSIG1	126	.	NM_001170553	exon5	c.G547A	p.V183I	TGTAGCGTTCAAG	.	PASS	Atlas-SNP
CENPE	1062	hgsc.bcm.edu	37	4	104082349	104082349	+	Silent	SNP	C	C	T	rs2251634	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	140	57	195	0	0.407143	0	T|0.446;G|0.001	0.446	strong	.	CENPE	253	.	NM_001813	exon20	c.G2025A	p.Q675Q	CTCCAACTGGCTT	.	PASS	Atlas-SNP
FBXO25	26260	hgsc.bcm.edu	37	8	381344	381344	+	Missense_Mutation	SNP	C	C	G	rs28438773	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	80	54	110	0	0.675	0	C|0.860;G|0.140	0.140	strong	.	FBXO25	25	.	NM_183420	exon3	c.C138G	p.I46M	CAGTATCTTAAAT	.	PASS	Atlas-SNP
PQLC2	54896	hgsc.bcm.edu	37	1	19652874	19652874	+	Missense_Mutation	SNP	G	G	A	rs41264079	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	43	23	35	0	0.534884	0	G|0.938;A|0.062	0.062	strong	PQLC2,NS,carcinoma,0,2	PQLC2	34	2	NM_001040125	exon5	c.G518A	p.G173D	AGTCGGGCAGCAA	.	PASS	Atlas-SNP
TNRC6C	57690	hgsc.bcm.edu	37	17	76093866	76093866	+	Silent	SNP	T	T	C	rs2290906	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	90	46	66	0	0.511111	0	T|0.737;C|0.263	0.263	strong	.	TNRC6C	173	.	NM_001142640	exon18	c.T4338C	p.S1446S	GCCTTCTTCGAGT	.	PASS	Atlas-SNP
SPATA17	128153	hgsc.bcm.edu	37	1	217915324	217915324	+	Silent	SNP	C	C	T	rs34347452	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	29	29	37	0	1	0	C|0.870;T|0.130	0.130	strong	.	SPATA17	59	.	NM_138796	exon6	c.C403T	p.L135L	AAGGCACTGGAGG	.	PASS	Atlas-SNP
PRKAG3	53632	hgsc.bcm.edu	37	2	219691801	219691801	+	Missense_Mutation	SNP	G	G	A	rs33985460	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	134	64	176	0	0.477612	0	G|0.961;A|0.039	0.039	strong	.	PRKAG3	47	.	NM_017431	exon10	c.C1018T	p.R340W	AGGGCCGGGGCAG	.	PASS	Atlas-SNP
MBL2	4153	hgsc.bcm.edu	37	10	54528266	54528266	+	Silent	SNP	G	G	C	rs930507	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	28	8	47	0	0.285714	0	G|0.238;C|0.762	0.762	strong	MBL2,colon,carcinoma,0,1	MBL2	55	1	NM_000242	exon4	c.C378G	p.L126L	GAAGGTGAGCCCT	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105411162	105411162	+	Silent	SNP	C	C	T	rs61316883	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	127	68	123	0	0.535433	0	C|0.980;T|0.020	0.020	strong	.	AHNAK2	719	.	NM_138420	exon7	c.G10626A	p.L3542L	GCCCTCCAGGAGT	.	PASS	Atlas-SNP
FLCN	201163	hgsc.bcm.edu	37	17	17125868	17125868	+	Silent	SNP	T	T	A	rs113938514	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	88	49	84	0	0.556818	0	T|0.971;A|0.029	0.029	strong	FLCN_ENST00000389169,NS,carcinoma,-1,2	FLCN	87	2	NM_144997	exon7	c.A726T	p.T242T	CAGCGATGTCAGC	.	PASS	Atlas-SNP
IL1B	3553	hgsc.bcm.edu	37	2	113590390	113590390	+	Silent	SNP	G	G	A	rs1143634	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	158	74	180	0	0.468354	0	G|0.828;A|0.172	0.172	strong	.	IL1B	35	.	NM_000576	exon5	c.C315T	p.F105F	TGTGTCGAAGAAG	.	PASS	Atlas-SNP
ASCC3	10973	hgsc.bcm.edu	37	6	100964147	100964147	+	Missense_Mutation	SNP	G	G	C	rs240780	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	84	97	1	0.965517	0.0103093	G|0.308;C|0.692	0.692	strong	ASCC3,NS,carcinoma,0,1	ASCC3	205	1	NM_006828	exon39	c.C5984G	p.S1995C	GGAAGGGACTCGA	.	scavenged	Atlas-SNP
JAKMIP3	282973	hgsc.bcm.edu	37	10	133966522	133966522	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	106	27	96	0	0.254717	0	.	.	none	.	JAKMIP3	69	.	NM_001105521	exon16	c.G2062A	p.E688K	TTGGCCGAAAAGG	.	PASS	Atlas-SNP
ANO4	121601	hgsc.bcm.edu	37	12	101520847	101520847	+	Silent	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	84	22	94	0	0.261905	0	.	.	none	.	ANO4	183	.	NM_178826	exon26	c.G2762A	p.X921X	GGCCGTGACCATG	.	PASS	Atlas-SNP
ODF4	146852	hgsc.bcm.edu	37	17	8243469	8243469	+	Missense_Mutation	SNP	T	T	C	rs12943505	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	54	111	0	0.556701	0	T|0.790;C|0.210	0.210	strong	.	ODF4	23	.	NM_153007	exon1	c.T100C	p.W34R	GCAGGATGGGGCA	.	PASS	Atlas-SNP
EXPH5	23086	hgsc.bcm.edu	37	11	108381247	108381247	+	Missense_Mutation	SNP	C	C	T	rs2640779	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	186	52	198	1	0.27957	0.00505051	C|0.760;T|0.240	0.240	strong	EXPH5,NS,adenoma,0,2	EXPH5	193	2	NM_015065	exon6	c.G4987A	p.G1663R	GCTTTCCGTTCTC	.	scavenged	Atlas-SNP
SLC15A2	6565	hgsc.bcm.edu	37	3	121646641	121646641	+	Silent	SNP	A	A	G	rs1143670	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	76	37	100	0	0.486842	0	A|0.537;G|0.463	0.463	strong	.	SLC15A2	92	.	NM_021082	exon14	c.A1161G	p.A387A	CCTAGCATGCCTG	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105420215	105420215	+	Missense_Mutation	SNP	T	T	C	rs2278607	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	155	78	190	0	0.503226	0	T|0.812;C|0.187	0.187	strong	.	AHNAK2	719	.	NM_138420	exon7	c.A1573G	p.T525A	GGCCAGTACCCGC	.	PASS	Atlas-SNP
MSH4	4438	hgsc.bcm.edu	37	1	76269460	76269460	+	Missense_Mutation	SNP	G	G	A	rs5745325	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	128	61	122	0	0.476562	0	G|0.737;A|0.263	0.263	strong	.	MSH4	147	.	NM_002440	exon2	c.G289A	p.A97T	ACAGTTGCATCAA	.	PASS	Atlas-SNP
CEACAM4	1089	hgsc.bcm.edu	37	19	42132314	42132314	+	Missense_Mutation	SNP	G	G	C	rs1126454	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	62	32	67	0	0.516129	0	G|0.462;C|0.537	0.537	strong	.	CEACAM4	42	.	NM_001817	exon2	c.C85G	p.H29D	GCGGGTGCCAGAA	.	PASS	Atlas-SNP
CLDN18	51208	hgsc.bcm.edu	37	3	137743508	137743508	+	Missense_Mutation	SNP	A	A	T	rs17204075	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	144	64	158	0	0.444444	0	A|0.903;T|0.097	0.097	strong	.	CLDN18	33	.	NM_016369	exon3	c.A445T	p.M149L	TTCTGGATGTCCA	.	PASS	Atlas-SNP
ZNF714	148206	hgsc.bcm.edu	37	19	21300142	21300142	+	Silent	SNP	A	A	C	rs112722125	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	25	25	30	0	1	0	A|0.933;C|0.067	0.067	strong	.	ZNF714	121	.	NM_182515	exon5	c.A672C	p.G224G	TACTGGAGAGAAA	.	PASS	Atlas-SNP
OR56A1	120796	hgsc.bcm.edu	37	11	6048408	6048408	+	Missense_Mutation	SNP	C	C	A	rs151331727	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	163	36	133	0	0.220859	0	C|0.996;A|0.004	0.004	strong	.	OR56A1	73	.	NM_001001917	exon1	c.G527T	p.C176F	TCCCCACAGTAAT	.	PASS	Atlas-SNP
UBR1	197131	hgsc.bcm.edu	37	15	43237572	43237572	+	Silent	SNP	T	T	C	rs16957277	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	222	98	220	0	0.441441	0	T|0.928;C|0.072	0.072	strong	.	UBR1	124	.	NM_174916	exon47	c.A5205G	p.Q1735Q	AGTCTCTTGGCTC	.	PASS	Atlas-SNP
PRLHR	2834	hgsc.bcm.edu	37	10	120354472	120354472	+	Silent	SNP	C	C	T	rs938700	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	177	96	163	0	0.542373	0	C|0.950;T|0.050	0.050	strong	PRLHR,NS,carcinoma,0,2	PRLHR	41	2	NM_004248	exon2	c.G285A	p.T95T	GAAGTTCGTCACG	.	PASS	Atlas-SNP
ZRANB2	9406	hgsc.bcm.edu	37	1	71538191	71538191	+	Silent	SNP	A	A	G	rs11556475	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	262	128	341	0	0.48855	0	A|0.898;G|0.102	0.102	strong	.	ZRANB2	75	.	NM_203350	exon5	c.T342C	p.Y114Y	TTCTATATATTCA	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	49	99	0	0.710145	0	C|0.321;T|0.679	0.321	strong	.	OR5B3	65	.	NM_001005469	exon1	c.A592G	p.I198V	CATAAATAAGAAC	.	PASS	Atlas-SNP
ACPT	93650	hgsc.bcm.edu	37	19	51293955	51293955	+	Silent	SNP	G	G	A	rs2162784	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	50	20	58	0	0.4	0	G|0.892;A|0.108	0.108	strong	.	ACPT	43	.	NM_033068	exon2	c.G216A	p.T72T	GACCACGGTGAGA	.	PASS	Atlas-SNP
ODF3L1	161753	hgsc.bcm.edu	37	15	76017452	76017452	+	Missense_Mutation	SNP	C	C	T	rs55905564	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	43	59	0	0.589041	0	C|0.806;T|0.194	0.194	strong	.	ODF3L1	10	.	NM_175881	exon2	c.C122T	p.P41L	CAGGTCCGGGGCC	.	PASS	Atlas-SNP
CAMKK2	10645	hgsc.bcm.edu	37	12	121712301	121712301	+	Missense_Mutation	SNP	C	C	T	rs28360477	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	83	36	78	0	0.433735	0	C|0.971;T|0.029	0.029	strong	.	CAMKK2	87	.	NM_153500	exon2	c.G29A	p.S10N	TTGCTGCTGGGCT	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105418504	105418504	+	Missense_Mutation	SNP	G	G	T	rs151013711	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	153	65	107	0	0.424837	0	G|0.875;T|0.125	0.125	strong	.	AHNAK2	719	.	NM_138420	exon7	c.C3284A	p.A1095D	TTGAGGGCCACTT	.	PASS	Atlas-SNP
LGALS9	3965	hgsc.bcm.edu	37	17	25970642	25970642	+	Missense_Mutation	SNP	A	A	T	rs361498	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	278	145	316	1	0.521583	0.00316456	A|0.874;T|0.126	0.126	strong	.	LGALS9	29	.	NM_009587	exon5	c.A536T	p.Q179L	GCAGACAAAAAGT	.	PASS	Atlas-SNP
FIGN	55137	hgsc.bcm.edu	37	2	164467750	164467750	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	105	30	120	0	0.285714	0	.	.	none	.	FIGN	106	.	NM_018086	exon3	c.T592A	p.Y198N	TACTATAAGTAGA	.	PASS	Atlas-SNP
PCP2	126006	hgsc.bcm.edu	37	19	7698320	7698320	+	Silent	SNP	C	C	T	rs1862514	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	209	106	248	0	0.507177	0	C|0.738;T|0.262	0.262	strong	.	PCP2	6	.	NM_174895	exon1	c.G24A	p.T8T	TTCCTCCGTCTTC	.	PASS	Atlas-SNP
HLA-G	3135	hgsc.bcm.edu	37	6	29796451	29796451	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	197	4	200	0	0.0203046	0	.	.	none	HLA-G,NS,carcinoma,0,1	HLA-G	90	1	NM_002127	exon4	c.G475A	p.A159T	TGGACCGCAGCGG	.	scavenged	Atlas-SNP
KDM4C	23081	hgsc.bcm.edu	37	9	6981115	6981115	+	Missense_Mutation	SNP	G	G	A	rs35049841	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	23	8	47	0	0.347826	0	G|0.998;A|0.002	0.002	strong	.	KDM4C	186	.	NM_001146696	exon9	c.G1178A	p.R393Q	CATCCCGAAGGTA	.	PASS	Atlas-SNP
SSPN	8082	hgsc.bcm.edu	37	12	26383834	26383834	+	Missense_Mutation	SNP	G	G	A	rs12313670	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	41	24	85	0	0.585366	0	G|0.928;A|0.072	0.072	strong	.	SSPN	19	.	NM_005086	exon3	c.G557A	p.S186N	GTACCAGCGTCAC	.	PASS	Atlas-SNP
IGSF9B	22997	hgsc.bcm.edu	37	11	133807819	133807819	+	Silent	SNP	G	G	A	rs329635	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	165	113	162	0	0.684848	0	G|0.918;A|0.082	0.082	strong	.	IGSF9B	290	.	NM_014987	exon4	c.C447T	p.I149I	GGCCTCGATGTAC	.	PASS	Atlas-SNP
IGF1R	3480	hgsc.bcm.edu	37	15	99478225	99478225	+	Silent	SNP	G	G	A	rs2229765	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	231	142	157	0	0.614719	0	G|0.625;A|0.375	0.375	strong	.	IGF1R	147	.	NM_000875	exon16	c.G3129A	p.E1043E	GCGTGAGAGGATT	.	PASS	Atlas-SNP
CYP24A1	1591	hgsc.bcm.edu	37	20	52775528	52775528	+	Silent	SNP	C	C	T	rs2296239	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	147	69	173	0	0.469388	0	C|0.677;T|0.323	0.323	strong	.	CYP24A1	75	.	NM_000782	exon8	c.G1125A	p.P375P	TAAATACGGCATA	.	PASS	Atlas-SNP
CYP4F12	66002	hgsc.bcm.edu	37	19	15807830	15807830	+	Silent	SNP	T	T	C	rs593421	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	125	58	107	0	0.464	0	T|0.770;C|0.230	0.230	strong	.	CYP4F12	89	.	NM_023944	exon13	c.T1510C	p.L504L	CTGGAATTGATCA	.	PASS	Atlas-SNP
PDIA2	64714	hgsc.bcm.edu	37	16	335373	335373	+	Missense_Mutation	SNP	C	C	T	rs2685127	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	115	24	148	0	0.208696	0	C|0.898;T|0.102	0.102	strong	.	PDIA2	51	.	NM_006849	exon6	c.C857T	p.T286M	ACCAGACGCTGGC	.	PASS	Atlas-SNP
MFHAS1	9258	hgsc.bcm.edu	37	8	8654898	8654898	+	Silent	SNP	C	C	T	rs3827812	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	115	22	96	0	0.191304	0	C|0.876;T|0.124	0.124	strong	MFHAS1,NS,carcinoma,0,1	MFHAS1	58	1	NM_004225	exon2	c.G3102A	p.P1034P	CACAGTCGGCGTG	.	PASS	Atlas-SNP
IRS1	3667	hgsc.bcm.edu	37	2	227661043	227661043	+	Silent	SNP	T	T	C	rs1801123	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	64	25	64	0	0.390625	0	T|0.776;C|0.224	0.224	strong	IRS1,NS,carcinoma,0,1	IRS1	141	1	NM_005544	exon1	c.A2412G	p.A804A	ATCATCTGCTGTT	.	PASS	Atlas-SNP
ZZEF1	23140	hgsc.bcm.edu	37	17	4015997	4015997	+	Silent	SNP	A	A	G	rs58625333	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	129	58	98	0	0.449612	0	A|0.736;G|0.264	0.264	strong	.	ZZEF1	195	.	NM_015113	exon5	c.T972C	p.N324N	GCTGGCATTCCTC	.	PASS	Atlas-SNP
MED24	9862	hgsc.bcm.edu	37	17	38186106	38186106	+	Silent	SNP	C	C	T	rs11555255	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	148	83	156	0	0.560811	0	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
FAM65B	9750	hgsc.bcm.edu	37	6	24818785	24818785	+	Silent	SNP	A	A	G	rs9358802	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	130	129	142	0	0.992308	0	A|0.664;G|0.336	0.336	strong	FAM65B_ENST00000259698,NS,carcinoma,0,1	FAM65B	134	1	NM_014722	exon21	c.T3000C	p.A1000A	TTTCAGAGCCAGG	.	PASS	Atlas-SNP
BMPER	168667	hgsc.bcm.edu	37	7	34009946	34009946	+	Silent	SNP	C	C	T	rs10265207	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	119	118	168	1	0.991597	0.00595238	C|0.570;T|0.430	0.430	strong	.	BMPER	131	.	NM_133468	exon6	c.C408T	p.G136G	GGAGGGCGTTGTC	.	PASS	Atlas-SNP
PLCB3	5331	hgsc.bcm.edu	37	11	64023971	64023971	+	Silent	SNP	G	G	A	rs7943988	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	131	23	158	0	0.175573	0	G|0.807;A|0.193	0.193	strong	.	PLCB3	103	.	NM_000932	exon9	c.G822A	p.L274L	CCGGCTGCTCATC	.	PASS	Atlas-SNP
MEF2A	4205	hgsc.bcm.edu	37	15	100252892	100252892	+	Silent	SNP	A	A	G	rs34851361	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	168	55	140	0	0.327381	0	A|0.949;G|0.051	0.051	strong	.	MEF2A	138	.	NM_005587	exon11	c.A1416G	p.P472P	TTCTCCAATTGTG	.	PASS	Atlas-SNP
TNS1	7145	hgsc.bcm.edu	37	2	218712606	218712606	+	Silent	SNP	G	G	A	rs1364641	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	67	29	80	0	0.432836	0	G|0.592;A|0.408	0.408	strong	.	TNS1	251	.	NM_022648	exon17	c.C2259T	p.S753S	CTGACGGGAGGAT	.	PASS	Atlas-SNP
OR51D1	390038	hgsc.bcm.edu	37	11	4661285	4661285	+	Missense_Mutation	SNP	A	A	G	rs905871	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	322	59	272	0	0.18323	0	A|0.794;G|0.206	0.206	strong	.	OR51D1	49	.	NM_001004751	exon1	c.A265G	p.I89V	TCCTCTATCACCA	.	PASS	Atlas-SNP
ROBO1	6091	hgsc.bcm.edu	37	3	78700901	78700901	+	Silent	SNP	G	G	T	rs6795556	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	43	102	0	0.505882	0	G|0.764;T|0.236	0.236	strong	.	ROBO1	833	.	NM_002941	exon19	c.C2793A	p.T931T	CGCGTAGGTACTA	.	PASS	Atlas-SNP
TOM1	10043	hgsc.bcm.edu	37	22	35743124	35743124	+	Silent	SNP	G	G	C	rs2071745	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	41	18	55	0	0.439024	0	G|0.667;C|0.333	0.333	strong	.	TOM1	43	.	NM_001135732	exon15	c.G1404C	p.G468G	TGAGGGGCCCCCG	.	PASS	Atlas-SNP
SEMA6D	80031	hgsc.bcm.edu	37	15	48063374	48063374	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	159	2	115	0	0.0125786	0	.	.	none	SEMA6D_ENST00000558014,NS,carcinoma,-1,2	SEMA6D	322	2	NM_153618	exon19	c.T2614C	p.S872P	CGGCGTTCTGTTG	.	scavenged	Atlas-SNP
ITPR2	3709	hgsc.bcm.edu	37	12	26784850	26784850	+	Silent	SNP	G	G	A	rs2230372	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	112	49	131	0	0.4375	0	G|0.527;A|0.473	0.473	strong	.	ITPR2	270	.	NM_002223	exon22	c.C2883T	p.H961H	ATCCTCGTGCTCG	.	PASS	Atlas-SNP
CLCA2	9635	hgsc.bcm.edu	37	1	86920904	86920904	+	Silent	SNP	A	A	G	rs2390057	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	118	63	141	0	0.533898	0	A|0.686;G|0.314	0.314	strong	CLCA2,NS,carcinoma,0,1	CLCA2	102	1	NM_006536	exon14	c.A2526G	p.Q842Q	ACCCCAAATTTCC	.	PASS	Atlas-SNP
TERT	7015	hgsc.bcm.edu	37	5	1294086	1294086	+	Silent	SNP	C	C	T	rs2736098	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	19	11	16	0	0.578947	0	C|0.792;T|0.208	0.208	strong	.	TERT	2594	.	NM_001193376	exon2	c.G915A	p.A305A	GGGGCCCGCGTGG	.	PASS	Atlas-SNP
RTN4IP1	84816	hgsc.bcm.edu	37	6	107019974	107019974	+	Missense_Mutation	SNP	C	C	T	rs372866009		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	26	96	0	0.366197	0	.	.	weak	RTN4IP1,NS,carcinoma,0,1	RTN4IP1	31	1	NM_032730	exon9	c.G1088A	p.R363Q	ACTGGCCGGATCT	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	105	55	117	0	0.52381	0	A|0.004;C|0.245	0.245	strong	.	HIST1H3I	28	.	NM_003533	exon1	c.A348G	p.K116K	GACGCGTTTGGCG	.	PASS	Atlas-SNP
MLL3	58508	hgsc.bcm.edu	37	7	151873853	151873853	+	Silent	SNP	C	C	T	rs6464211	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	169	80	190	0	0.473373	0	C|0.643;T|0.357	0.357	strong	.	MLL3	1564	.	NM_170606	exon38	c.G8685A	p.Q2895Q	GGATGCCTGAATG	.	PASS	Atlas-SNP
DDX31	64794	hgsc.bcm.edu	37	9	135538050	135538050	+	Silent	SNP	C	C	T	rs35918594	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	50	49	74	1	0.98	0.0135135	C|0.934;T|0.066	0.066	strong	DDX31,caecum,carcinoma,-1,1	DDX31	76	1	NM_022779	exon2	c.G423A	p.A141A	ACTGGACGCTTGG	.	scavenged	Atlas-SNP
HLA-C	3107	hgsc.bcm.edu	37	6	31239449	31239449	+	Missense_Mutation	SNP	C	C	G	rs28626310	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	194	106	188	0	0.546392	0	C|0.840;G|0.160	0.160	strong	.	HLA-C	92	.	NM_002117	exon2	c.G270C	p.K90N	CTTGTACTTCTGT	.	PASS	Atlas-SNP
FAT1	2195	hgsc.bcm.edu	37	4	187538942	187538942	+	Missense_Mutation	SNP	T	T	G	rs1280098	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	67	31	85	0	0.462687	0	T|0.357;G|0.629;A|0.015	0.629	strong	.	FAT1	500	.	NM_005245	exon10	c.A8798C	p.Q2933P	CCACCTTGGGGGT	.	PASS	Atlas-SNP
TNXB	7148	hgsc.bcm.edu	37	6	32020512	32020512	+	Missense_Mutation	SNP	T	T	C	rs17207895	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	74	50	170	1	0.675676	0.00588235	T|0.981;C|0.019	0.019	strong	.	TNXB	553	.	NM_019105	exon26	c.A9044G	p.K3015R	TGCATCTTGTATT	.	PASS	Atlas-SNP
UVSSA	57654	hgsc.bcm.edu	37	4	1369885	1369885	+	Silent	SNP	G	G	A	rs11724369	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	125	56	138	0	0.448	0	G|0.793;A|0.207	0.207	strong	.	.	.	.	NM_020894	exon10	c.G1497A	p.A499A	CCGGGCGCCTGTG	.	PASS	Atlas-SNP
MYOM1	8736	hgsc.bcm.edu	37	18	3075746	3075746	+	Silent	SNP	G	G	A	rs1143657	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	62	30	79	0	0.483871	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
TRIM50	135892	hgsc.bcm.edu	37	7	72738561	72738561	+	Silent	SNP	G	G	T	rs61741334	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	214	96	241	0	0.448598	0	G|0.978;T|0.022	0.022	strong	.	TRIM50	78	.	NM_178125	exon2	c.C225A	p.I75I	GGCTTCGATCACC	.	PASS	Atlas-SNP
ARL2	402	hgsc.bcm.edu	37	11	64789194	64789194	+	Missense_Mutation	SNP	T	T	C	rs664226	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	31	9	51	0	0.290323	0	T|0.439;C|0.561	0.561	strong	ARL2,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	ARL2	11	1	NM_001667	exon5	c.T422C	p.V141A	CCCAGGTCCTGGA	.	PASS	Atlas-SNP
OR51L1	119682	hgsc.bcm.edu	37	11	5020509	5020509	+	Silent	SNP	C	C	T	rs11035066	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	359	354	372	0	0.986072	0	C|0.718;T|0.282	0.282	strong	.	OR51L1	60	.	NM_001004755	exon1	c.C297T	p.C99C	TGCTTGCTATGCT	.	PASS	Atlas-SNP
FRAS1	80144	hgsc.bcm.edu	37	4	79437155	79437155	+	Silent	SNP	C	C	T	rs3749487	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	156	70	212	0	0.448718	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
ZNF235	9310	hgsc.bcm.edu	37	19	44791537	44791537	+	Missense_Mutation	SNP	G	G	A	rs149947768	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	41	147	0	0.476744	0	G|0.998;A|0.002	0.002	strong	.	ZNF235	60	.	NM_004234	exon5	c.C2051T	p.T684M	TGACACGTATAGG	.	PASS	Atlas-SNP
ARSD	414	hgsc.bcm.edu	37	X	2836184	2836184	+	Missense_Mutation	SNP	C	C	T	rs73632976	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	132	19	140	0	0.143939	0	C|0.915;T|0.085	0.085	strong	.	ARSD	47	.	NM_001669	exon5	c.G524A	p.G175D	GGCATGCCGTAGA	.	PASS	Atlas-SNP
HTT	3064	hgsc.bcm.edu	37	4	3107140	3107140	+	Silent	SNP	C	C	T	rs184820567	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	145	70	182	0	0.482759	0	C|0.999;T|0.001	0.001	strong	.	HTT	221	.	NM_002111	exon5	c.C585T	p.H195H	GGCTCACCTGGTT	.	PASS	Atlas-SNP
XAF1	54739	hgsc.bcm.edu	37	17	6663895	6663895	+	Silent	SNP	C	C	G	rs2271231	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	222	108	202	1	0.486486	0.00495049	C|0.550;G|0.450	0.450	strong	XAF1,colon,carcinoma,+2,1	XAF1	16	1	NM_017523	exon4	c.C396G	p.R132R	CTGTCGCAGTGAA	.	scavenged	Atlas-SNP
WDR38	401551	hgsc.bcm.edu	37	9	127616537	127616537	+	Missense_Mutation	SNP	A	A	G	rs12375547	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	81	79	99	0	0.975309	0	A|0.541;G|0.459	0.459	strong	.	WDR38	21	.	NM_001276376	exon2	c.A29G	p.K10R	CTCAGAAGATGGC	.	PASS	Atlas-SNP
RPTN	126638	hgsc.bcm.edu	37	1	152127455	152127455	+	Missense_Mutation	SNP	T	T	C	rs75957773	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	269	139	318	0	0.516729	0	T|0.884;C|0.116	0.116	strong	RPTN,NS,carcinoma,0,1	RPTN	123	1	NM_001122965	exon3	c.A2120G	p.E707G	TGCTCTTCCTCTG	.	PASS	Atlas-SNP
RIN3	79890	hgsc.bcm.edu	37	14	93118668	93118668	+	Missense_Mutation	SNP	C	C	T	rs3742717	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	94	55	135	1	0.585106	0.00740741	C|0.777;T|0.223	0.223	strong	RIN3,rectum,carcinoma,-1,1	RIN3	81	1	NM_024832	exon6	c.C1274T	p.T425M	AGGACACGCCCCG	.	scavenged	Atlas-SNP
FAM114A1	92689	hgsc.bcm.edu	37	4	38880046	38880046	+	Missense_Mutation	SNP	T	T	C	rs11555334	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	102	50	118	0	0.490196	0	T|0.757;C|0.243	0.243	strong	.	FAM114A1	42	.	NM_138389	exon3	c.T347C	p.L116P	ATTATCTGGTAAG	.	PASS	Atlas-SNP
GSPT1	2935	hgsc.bcm.edu	37	16	11969724	11969724	+	Silent	SNP	G	G	C	rs33657	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	241	55	229	0	0.228216	0	G|0.405;C|0.595	0.595	strong	.	GSPT1	71	.	NM_002094	exon14	c.C1755G	p.V585V	TTGTTTGACAAAA	.	PASS	Atlas-SNP
YIPF7	285525	hgsc.bcm.edu	37	4	44652030	44652030	+	Missense_Mutation	SNP	C	C	T	rs2348353	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	126	56	137	0	0.444444	0	C|0.816;T|0.184	0.184	strong	.	YIPF7	33	.	NM_182592	exon2	c.G160A	p.A54T	CATAGGCATTAGA	.	PASS	Atlas-SNP
USHBP1	83878	hgsc.bcm.edu	37	19	17366313	17366313	+	Missense_Mutation	SNP	C	C	T	rs12459398	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	57	27	56	0	0.473684	0	C|0.765;T|0.235	0.235	strong	.	USHBP1	85	.	NM_031941	exon10	c.G1573A	p.V525M	GGAGCACGTGAGC	.	PASS	Atlas-SNP
ABCG2	9429	hgsc.bcm.edu	37	4	89052323	89052323	+	Missense_Mutation	SNP	G	G	T	rs2231142	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	121	64	193	0	0.528926	0	G|0.883;T|0.117	0.117	strong	ABCG2,NS,carcinoma,0,1	ABCG2	151	1	NM_004827	exon5	c.C421A	p.Q141K	AGAACTGTAAGTT	.	PASS	Atlas-SNP
FRMD5	84978	hgsc.bcm.edu	37	15	44198049	44198049	+	Silent	SNP	A	A	G	rs2306674	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	204	91	176	0	0.446078	0	A|0.815;G|0.185	0.185	strong	.	FRMD5	45	.	NM_032892	exon6	c.T528C	p.A176A	AATCTCAGCAATT	.	PASS	Atlas-SNP
NEBL	10529	hgsc.bcm.edu	37	10	21108377	21108377	+	Silent	SNP	C	C	T	rs1006363	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	135	71	217	0	0.525926	0	C|0.789;T|0.211	0.211	strong	.	NEBL	199	.	NM_006393	exon20	c.G2031A	p.R677R	GTTTCGCCTCACT	.	PASS	Atlas-SNP
MYO1C	4641	hgsc.bcm.edu	37	17	1386314	1386314	+	Silent	SNP	C	C	T	rs112029113	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	106	45	133	0	0.424528	0	C|0.989;T|0.011	0.011	strong	.	MYO1C	57	.	NM_001080779	exon4	c.G387A	p.T129T	ACGCTCCGTGCGC	.	PASS	Atlas-SNP
DNAI1	27019	hgsc.bcm.edu	37	9	34500821	34500821	+	Missense_Mutation	SNP	G	G	A	rs11793196	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	51	32	69	0	0.627451	0	G|0.812;A|0.188	0.188	strong	.	DNAI1	72	.	NM_012144	exon11	c.G1003A	p.V335I	CTGTCCGTCACTG	.	PASS	Atlas-SNP
DSG1	1828	hgsc.bcm.edu	37	18	28919913	28919913	+	Missense_Mutation	SNP	G	G	A	rs34302455	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	104	48	127	1	0.461538	0.00787402	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	.	scavenged	Atlas-SNP
PCDHB10	56126	hgsc.bcm.edu	37	5	140573442	140573442	+	Silent	SNP	C	C	G	rs622424	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	140	61	124	0	0.435714	0	C|0.549;G|0.451	0.451	strong	.	PCDHB10	177	.	NM_018930	exon1	c.C1317G	p.V439V	AACGGTCCTGGTC	.	PASS	Atlas-SNP
DTX4	23220	hgsc.bcm.edu	37	11	58940278	58940278	+	Silent	SNP	G	G	T	rs12796683	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	136	38	117	0	0.279412	0	G|0.762;T|0.238	0.238	strong	.	DTX4	84	.	NM_015177	exon1	c.G210T	p.T70T	AGACACGGGTGAG	.	PASS	Atlas-SNP
ADAM21	8747	hgsc.bcm.edu	37	14	70924507	70924507	+	Silent	SNP	A	A	C	rs3751524	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	119	69	153	2	0.579832	0.0130719	A|0.780;C|0.220	0.220	strong	ADAM21,NS,carcinoma,0,1	ADAM21	181	1	NM_003813	exon2	c.A291C	p.A97A	CCGTGCACTCCTG	.	scavenged	Atlas-SNP
C1orf177	163747	hgsc.bcm.edu	37	1	55307501	55307501	+	Silent	SNP	A	A	G	rs41297871	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	29	82	0	0.5	0	A|0.737;G|0.263	0.263	strong	.	C1orf177	36	.	NM_001110533	exon10	c.A1212G	p.G404G	TAAGGGAAAGTGC	.	PASS	Atlas-SNP
NACAD	23148	hgsc.bcm.edu	37	7	45123857	45123857	+	Missense_Mutation	SNP	A	A	G	rs7790844	bycluster;byfrequency;by2hit2allele;byhapmap	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	9	7	13	1	0.777778	0.0769231	A|0.007;G|0.993	0.993	strong	NACAD,NS,carcinoma,0,1	NACAD	44	1	NM_001146334	exon2	c.T1922C	p.V641A	GTCATAACGGAGT	.	scavenged	Atlas-SNP
EXT1	2131	hgsc.bcm.edu	37	8	118847782	118847782	+	Silent	SNP	G	G	A	rs11546829	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	15	74	0	0.2	0	G|0.774;A|0.226	0.226	strong	EXT1,NS,carcinoma,0,1	EXT1	98	1	NM_000127	exon3	c.C1065T	p.C355C	AGGGACGCAGGCA	.	PASS	Atlas-SNP
OR1L8	138881	hgsc.bcm.edu	37	9	125330325	125330325	+	Silent	SNP	C	C	G	rs10985703	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	91	48	128	0	0.527473	0	C|0.662;G|0.338	0.338	strong	.	OR1L8	90	.	NM_001004454	exon1	c.G432C	p.L144L	CACCAGCAGGACA	.	PASS	Atlas-SNP
OR4A15	81328	hgsc.bcm.edu	37	11	55135435	55135435	+	Missense_Mutation	SNP	C	C	T	rs1425193	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	111	23	130	0	0.207207	0	C|0.778;T|0.222	0.222	strong	.	OR4A15	161	.	NM_001005275	exon1	c.C76T	p.P26S	CCAACACCTTCAG	.	PASS	Atlas-SNP
ST3GAL3	6487	hgsc.bcm.edu	37	1	44290530	44290530	+	Missense_Mutation	SNP	A	A	G	rs37458	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	53	53	60	0	1	0	A|0.707;G|0.293	0.293	strong	.	ST3GAL3	56	.	NM_174963	exon5	c.A382G	p.T128A	GAGGACACAGCCT	.	PASS	Atlas-SNP
CDH5	1003	hgsc.bcm.edu	37	16	66432423	66432423	+	Missense_Mutation	SNP	T	T	C	rs1049970	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	107	107	109	0	1	0	T|0.282;C|0.718	0.718	strong	CDH5,NS,carcinoma,0,2	CDH5	111	2	NM_001795	exon10	c.T1550C	p.I517T	AATTCATCTTGAA	.	PASS	Atlas-SNP
CDH11	1009	hgsc.bcm.edu	37	16	65038674	65038674	+	Silent	SNP	G	G	A	rs35182	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	137	46	106	0	0.335766	0	G|0.923;A|0.077	0.077	strong	.	CDH11	260	.	NM_001797	exon3	c.C99T	p.P33P	GAAGGAGGGCCGC	.	PASS	Atlas-SNP
NLRP13	126204	hgsc.bcm.edu	37	19	56413532	56413532	+	Silent	SNP	G	G	A	rs7258847	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	37	63	0	0.513889	0	G|0.824;A|0.176	0.176	strong	.	NLRP13	220	.	NM_176810	exon9	c.C2658T	p.H886H	TGACAAGTGCTTG	.	PASS	Atlas-SNP
ATP12A	479	hgsc.bcm.edu	37	13	25255705	25255705	+	Silent	SNP	C	C	A	rs41288276	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	36	83	0	0.507042	0	C|0.942;A|0.058	0.058	strong	.	ATP12A	172	.	NM_001185085	exon2	c.C15A	p.T5T	GAAAACCCCAGAA	.	PASS	Atlas-SNP
ESYT2	57488	hgsc.bcm.edu	37	7	158534372	158534372	+	Silent	SNP	G	G	A	rs57686648	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	83	41	94	0	0.493976	0	G|0.759;A|0.241	0.241	strong	ESYT2,NS,malignant_melanoma,-1,1	ESYT2	70	1	NM_020728	exon17	c.C2091T	p.A697A	AGGGCCGGCCTCA	.	PASS	Atlas-SNP
CENPE	1062	hgsc.bcm.edu	37	4	104041448	104041448	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	196	4	196	0	0.0204082	0	.	.	none	CENPE,NS,carcinoma,+2,1	CENPE	253	1	NM_001813	exon44	c.A7186G	p.S2396G	TAGCACTTTCTTT	.	scavenged	Atlas-SNP
COL18A1	80781	hgsc.bcm.edu	37	21	46896303	46896303	+	Silent	SNP	C	C	G	rs2230687	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	96	33	84	0	0.34375	0	C|0.793;G|0.207	0.207	strong	.	COL18A1	129	.	NM_030582	exon5	c.C1377G	p.P459P	ACCCCCCGTCACC	.	PASS	Atlas-SNP
MTMR2	8898	hgsc.bcm.edu	37	11	95569326	95569326	+	Silent	SNP	G	G	T	rs61735577	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	106	16	135	0	0.150943	0	G|0.969;T|0.031	0.031	strong	.	MTMR2	79	.	NM_016156	exon14	c.C1756A	p.R586R	TCATCCGTGGATT	.	PASS	Atlas-SNP
KIF17	57576	hgsc.bcm.edu	37	1	21042094	21042094	+	Silent	SNP	G	G	A	rs12046928	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	54	22	62	0	0.407407	0	G|0.810;A|0.190	0.190	strong	.	KIF17	130	.	NM_001122819	exon2	c.C270T	p.Y90Y	CTGGCCGTAGGCA	.	PASS	Atlas-SNP
PPTC7	160760	hgsc.bcm.edu	37	12	110974890	110974890	+	Silent	SNP	T	T	C	rs10849900	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	30	75	0	0.410959	0	T|0.725;C|0.275	0.275	strong	PPTC7,NS,carcinoma,0,1	PPTC7	30	1	NM_139283	exon6	c.A867G	p.P289P	GTCATCTGGCTTT	.	PASS	Atlas-SNP
MPV17L2	84769	hgsc.bcm.edu	37	19	18304700	18304700	+	Missense_Mutation	SNP	A	A	G	rs874628	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	155	66	180	0	0.425806	0	A|0.783;G|0.217	0.217	strong	.	MPV17L2	12	.	NM_032683	exon2	c.A214G	p.M72V	TGCAGCATGGGTC	.	PASS	Atlas-SNP
LILRA6	79168	hgsc.bcm.edu	37	19	54745665	54745665	+	Missense_Mutation	SNP	C	C	T	rs1052966	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	584	93	604	0	0.159247	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
TYMP	1890	hgsc.bcm.edu	37	22	50964236	50964236	+	Missense_Mutation	SNP	G	G	A	rs11479	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	93	41	68	0	0.44086	0	G|0.877;A|0.123	0.123	strong	.	TYMP	25	.	NM_001257989	exon10	c.C1427T	p.S476L	AAGGGCGAGGGGG	.	PASS	Atlas-SNP
TYW1	55253	hgsc.bcm.edu	37	7	66648199	66648199	+	Silent	SNP	G	G	A	rs7776775	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	74	32	111	0	0.432432	0	.	.	weak	.	TYW1	71	.	NM_018264	exon14	c.G1785A	p.G595G	CCTGGGGAATCCT	.	PASS	Atlas-SNP
OR52R1	119695	hgsc.bcm.edu	37	11	4825010	4825010	+	Missense_Mutation	SNP	T	T	A	rs6578533	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	16	73	0	0.173913	0	A|0.369;N|0.000	0.369	strong	.	OR52R1	81	.	NM_001005177	exon1	c.A601T	p.N201Y	GCCCATTCCCACG	.	PASS	Atlas-SNP
STK32C	282974	hgsc.bcm.edu	37	10	134040367	134040367	+	Silent	SNP	C	C	T	rs12413251	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	104	36	103	0	0.346154	0	C|0.932;T|0.068	0.068	strong	.	STK32C	61	.	NM_173575	exon4	c.G576A	p.T192T	CCTCACCGTGTCC	.	PASS	Atlas-SNP
COL4A1	1282	hgsc.bcm.edu	37	13	110850842	110850842	+	Silent	SNP	A	A	G	rs995224	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	37	85	0	0.430233	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
MPI	4351	hgsc.bcm.edu	37	15	75189930	75189930	+	Silent	SNP	A	A	G	rs1130741	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	202	201	150	0	0.995049	0	A|0.574;G|0.426	0.426	strong	.	MPI	32	.	NM_002435	exon8	c.A1131G	p.V377V	GACAGTAATAGCC	.	PASS	Atlas-SNP
ITFG2	55846	hgsc.bcm.edu	37	12	2930731	2930731	+	Silent	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	4	125	0	0.0412371	0	.	.	none	.	ITFG2	38	.	NM_018463	exon8	c.C816T	p.G272G	TAGTGGCTCTGGC	.	PASS	Atlas-SNP
ZNF460	10794	hgsc.bcm.edu	37	19	57802116	57802116	+	Silent	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	140	33	140	0	0.235714	0	.	.	none	.	ZNF460	59	.	NM_006635	exon3	c.C207T	p.A69A	TCTGGCCTTGCCT	.	PASS	Atlas-SNP
HLA-G	3135	hgsc.bcm.edu	37	6	29797696	29797696	+	Silent	SNP	A	A	G	rs1130363	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	76	76	112	1	1	0.00892857	A|0.442;G|0.558	0.558	strong	.	HLA-G	90	.	NM_002127	exon6	c.A999G	p.R333R	GTGGAGAAAGAAG	.	PASS	Atlas-SNP
LILRB4	11006	hgsc.bcm.edu	37	19	55175009	55175009	+	Missense_Mutation	SNP	G	G	T	rs11540761	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	195	114	178	0	0.584615	0	G|0.810;T|0.190	0.190	strong	.	LILRB4	86	.	NM_006847	exon2	c.G54T	p.R18S	CCCCAGGACCCAC	.	PASS	Atlas-SNP
UNK	85451	hgsc.bcm.edu	37	17	73819525	73819525	+	Silent	SNP	C	C	T	rs8078208	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	49	88	0	0.485149	0	C|0.528;T|0.472	0.472	strong	UNK_ENST00000293218,NS,carcinoma,0,4	UNK	87	4	NM_001080419	exon15	c.C2199T	p.S733S	CTTCTCCGACCTG	.	PASS	Atlas-SNP
PCDHB12	56124	hgsc.bcm.edu	37	5	140590139	140590139	+	Missense_Mutation	SNP	G	G	A	rs61741192	byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	126	73	158	0	0.579365	0	G|0.875;A|0.125	0.125	strong	.	PCDHB12	179	.	NM_018932	exon1	c.G1660A	p.A554T	CTGGACGCCAACG	.	PASS	Atlas-SNP
CLEC18B	497190	hgsc.bcm.edu	37	16	74451960	74451960	+	Silent	SNP	C	C	T	rs3869429		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	613	58	262	0	0.0946166	0	.	.	weak	CLEC18B,NS,carcinoma,-1,4	CLEC18B	45	4	NM_001011880	exon3	c.G453A	p.T151T	CACCTGCGTGTAG	.	scavenged	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195509955	195509955	+	Silent	SNP	A	A	C	rs71635078	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	152	117	123	0	0.769737	0	C|1.000;|0.000	1.000	weak	.	MUC4	1505	.	NM_018406	exon2	c.T8496G	p.S2832S	AGGAAGAGAGGTG	.	PASS	Atlas-SNP
ZMAT4	79698	hgsc.bcm.edu	37	8	40438757	40438757	+	Missense_Mutation	SNP	T	T	C	rs17851751	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	10	91	0	0.140845	0	T|0.790;C|0.210	0.210	strong	ZMAT4,NS,adenoma,0,1	ZMAT4	47	1	NM_024645	exon6	c.A601G	p.T201A	AGATGGTACATCT	.	PASS	Atlas-SNP
LAMA5	3911	hgsc.bcm.edu	37	20	60901762	60901762	+	Missense_Mutation	SNP	C	C	T	rs11699758	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	144	79	170	0	0.548611	0	C|0.974;T|0.026	0.026	strong	.	LAMA5	268	.	NM_005560	exon40	c.G5269A	p.V1757I	GGTGAACGTGGCC	.	PASS	Atlas-SNP
PROSER1	80209	hgsc.bcm.edu	37	13	39587166	39587166	+	Silent	SNP	A	A	G	rs11147745	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	141	66	163	0	0.468085	0	A|0.781;G|0.219	0.219	strong	.	.	.	.	NM_025138	exon11	c.T2223C	p.P741P	TGAGCTAGGATGA	.	PASS	Atlas-SNP
HIST1H1D	3007	hgsc.bcm.edu	37	6	26234883	26234883	+	Silent	SNP	A	A	G	rs2050950	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	155	66	176	0	0.425806	0	A|0.854;G|0.146	0.146	strong	.	HIST1H1D	40	.	NM_005320	exon1	c.T279C	p.T93T	CACCAGAGTACCT	.	PASS	Atlas-SNP
CDHR3	222256	hgsc.bcm.edu	37	7	105636765	105636765	+	Silent	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	51	4	42	0	0.0784314	0	.	.	none	.	CDHR3	153	.	NM_152750	exon6	c.C678T	p.I226I	GAACATCGTGAAC	.	PASS	Atlas-SNP
TTC39A	22996	hgsc.bcm.edu	37	1	51753904	51753904	+	Silent	SNP	G	G	A	rs17392930	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	79	44	82	0	0.556962	0	A|0.028;C|0.000;G|0.971	0.028	strong	.	TTC39A	40	.	NM_001144832	exon18	c.C1671T	p.I557I	TGCCTGGATTCGA	.	PASS	Atlas-SNP
NUDCD3	23386	hgsc.bcm.edu	37	7	44444122	44444122	+	Missense_Mutation	SNP	G	G	A	rs11550029	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	52	67	0	0.753623	0	G|0.890;A|0.110	0.110	strong	NUDCD3,NS,carcinoma,0,1	NUDCD3	20	1	NM_015332	exon4	c.C703T	p.R235C	GGACGCGCTCCCC	.	PASS	Atlas-SNP
EFCAB14	9813	hgsc.bcm.edu	37	1	47152515	47152515	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	191	3	249	0	0.0157068	0	.	.	none	KIAA0494,colon,carcinoma,+1,1	.	.	1	NM_014774	exon8	c.A1015G	p.R339G	ACTGTCTTTTCAG	.	scavenged	Atlas-SNP
POM121L12	285877	hgsc.bcm.edu	37	7	53103382	53103382	+	Silent	SNP	G	G	T	rs72598685	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	60	27	52	0	0.45	0	G|0.718;T|0.282	0.282	strong	.	POM121L12	146	.	NM_182595	exon1	c.G18T	p.P6P	AGCTCCGGCCGAG	.	PASS	Atlas-SNP
CCDC88C	440193	hgsc.bcm.edu	37	14	91773568	91773568	+	Silent	SNP	T	T	C	rs1970912	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	31	16	39	0	0.516129	0	C|0.517;N|0.000	0.517	strong	.	CCDC88C	192	.	NM_001080414	exon18	c.A3009G	p.L1003L	CTTCTTTAGCTAC	.	PASS	Atlas-SNP
SLC13A1	6561	hgsc.bcm.edu	37	7	122809234	122809234	+	Missense_Mutation	SNP	T	T	C	rs2140516	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	187	100	230	0	0.534759	0	A|0.003;C|0.297	0.297	strong	SLC13A1,NS,meningioma,0,1	SLC13A1	110	1	NM_022444	exon4	c.A521G	p.N174S	GATCCGTTGAAGT	.	PASS	Atlas-SNP
CTNNA1	1495	hgsc.bcm.edu	37	5	138266546	138266546	+	Silent	SNP	G	G	A	rs1059110	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	171	84	207	1	0.491228	0.00483092	G|0.693;A|0.307	0.307	strong	.	CTNNA1	114	.	NM_001903	exon16	c.G2220A	p.S740S	TACATCGGATGTC	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	128	62	145	0	0.484375	0	C|0.663;T|0.337	0.337	strong	.	APOL5	45	.	NM_030642	exon3	c.C815T	p.T272M	TCTGGACGGCTAG	.	PASS	Atlas-SNP
PRPF19	27339	hgsc.bcm.edu	37	11	60666341	60666341	+	Silent	SNP	G	G	A	rs3763840	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	188	186	193	0	0.989362	0	G|0.691;A|0.309	0.309	strong	.	PRPF19	62	.	NM_014502	exon12	c.C1047T	p.S349S	GCAGCCGGAGGTC	.	PASS	Atlas-SNP
NBPF15	284565	hgsc.bcm.edu	37	1	148594455	148594455	+	Missense_Mutation	SNP	A	A	G	rs1043751	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	226	28	230	19	0.123894	0.0826087	A|0.996;G|0.004	0.004	strong	NBPF15,NS,carcinoma,-1,1	NBPF15	20	1	NM_173638	exon19	c.A1828G	p.R610G	CTGGATAGATGTT	.	scavenged	Atlas-SNP
EIF2AK1	27102	hgsc.bcm.edu	37	7	6080686	6080686	+	Missense_Mutation	SNP	A	A	T	rs34909691	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	178	137	187	0	0.769663	0	A|0.978;T|0.022	0.022	strong	.	EIF2AK1	76	.	NM_014413	exon9	c.T956A	p.L319H	GACTCAAGTTCAC	.	PASS	Atlas-SNP
RASSF6	166824	hgsc.bcm.edu	37	4	74451073	74451073	+	Missense_Mutation	SNP	A	A	G	rs12507775	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	122	43	117	0	0.352459	0	A|0.733;G|0.267	0.267	strong	.	RASSF6	68	.	NM_201431	exon6	c.T487C	p.S163P	GATAAGATAAATA	.	PASS	Atlas-SNP
TTLL1	25809	hgsc.bcm.edu	37	22	43435812	43435812	+	Silent	SNP	C	C	T	rs1052163	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	46	21	68	0	0.456522	0	C|0.665;T|0.335	0.335	strong	.	TTLL1	41	.	NM_012263	exon11	c.G1242A	p.S414S	TCTCCCCGAGTCT	.	PASS	Atlas-SNP
KRTAP12-2	353323	hgsc.bcm.edu	37	21	46086719	46086719	+	Missense_Mutation	SNP	A	A	G	rs63164960	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	106	62	89	0	0.584906	0	A|0.470;G|0.530	0.530	strong	.	KRTAP12-2	10	.	NM_181684	exon1	c.T85C	p.S29P	GGCAGGAGCTGGG	.	PASS	Atlas-SNP
TET1	80312	hgsc.bcm.edu	37	10	70405541	70405541	+	Missense_Mutation	SNP	A	A	G	rs72799515	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	151	65	176	0	0.430464	0	A|0.980;G|0.020	0.020	strong	.	TET1	255	.	NM_030625	exon4	c.A3055G	p.K1019E	ACCAATAAAAGTA	.	PASS	Atlas-SNP
KRTAP10-9	386676	hgsc.bcm.edu	37	21	46047418	46047418	+	Silent	SNP	C	C	T	rs8126553	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	165	165	144	0	1	0	C|0.234;T|0.766	0.766	strong	.	KRTAP10-9	24	.	NM_198690	exon1	c.C330T	p.C110C	GTGCTGCGTGCCC	.	PASS	Atlas-SNP
OR1N2	138882	hgsc.bcm.edu	37	9	125315542	125315542	+	Silent	SNP	C	C	T	rs1831369	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	147	76	207	0	0.517007	0	C|0.682;N|0.000	.	strong	OR1N2,NS,carcinoma,0,1	OR1N2	51	1	NM_001004457	exon1	c.C94T	p.L32L	CTCCTTCTAGGAC	.	PASS	Atlas-SNP
EFCAB4B	84766	hgsc.bcm.edu	37	12	3789452	3789452	+	Missense_Mutation	SNP	C	C	T	rs17836273	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	132	68	126	0	0.515152	0	C|0.866;T|0.134	0.134	strong	.	EFCAB4B	100	.	NM_001144958	exon5	c.G292A	p.A98T	CATCAGCATCCAG	.	PASS	Atlas-SNP
KRTAP4-11	653240	hgsc.bcm.edu	37	17	39274157	39274157	+	Silent	SNP	G	G	A	rs76095941		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	59	9	55	0	0.152542	0	G|0.500;A|0.500	0.500	weak	KRTAP4-11,NS,carcinoma,0,8	KRTAP4-11	94	8	NM_033059	exon1	c.C411T	p.P137P	GCAGCTGGGGTGG	.	PASS	Atlas-SNP
AP5Z1	9907	hgsc.bcm.edu	37	7	4823971	4823971	+	Silent	SNP	C	C	T	rs17135121	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	79	57	71	0	0.721519	0	C|0.761;T|0.239	0.239	strong	KIAA0415_ENST00000450194,NS,carcinoma,0,2	.	.	2	NM_014855	exon6	c.C759T	p.S253S	GCACAGCGGCCCC	.	PASS	Atlas-SNP
ARMC5	79798	hgsc.bcm.edu	37	16	31476458	31476458	+	Missense_Mutation	SNP	C	C	T	rs11150624	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	104	104	101	0	1	0	C|0.636;T|0.364	0.364	strong	ARMC5_ENST00000457010,brain,glioma,0,1	ARMC5	94	1	NM_024742	exon4	c.C2114T	p.A705V	GCCCCGCGCCCAG	.	PASS	Atlas-SNP
CCDC154	645811	hgsc.bcm.edu	37	16	1486462	1486462	+	Missense_Mutation	SNP	C	C	T	rs35583599	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	48	10	42	0	0.208333	0	C|0.928;T|0.072	0.072	strong	CCDC154,NS,lymphoid_neoplasm,0,1	CCDC154	27	1	NM_001143980	exon13	c.G1471A	p.A491T	CTTCGGCGGAAAT	.	PASS	Atlas-SNP
RAD51D	5892	hgsc.bcm.edu	37	17	33433487	33433487	+	Missense_Mutation	SNP	C	C	T	rs4796033	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	90	51	101	0	0.566667	0	C|0.903;T|0.097	0.097	strong	.	RAD51D	53	.	NM_001142571	exon6	c.G554A	p.R185Q	ATCCTCCGGAGAG	.	PASS	Atlas-SNP
CYP4F3	4051	hgsc.bcm.edu	37	19	15760035	15760035	+	Silent	SNP	C	C	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	125	36	105	0	0.288	0	.	.	none	.	CYP4F3	69	.	NM_001199209	exon6	c.C591G	p.L197L	CAGCCTCATGACC	.	PASS	Atlas-SNP
CTBS	1486	hgsc.bcm.edu	37	1	85029085	85029085	+	Missense_Mutation	SNP	A	A	G	rs143993403	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	42	120	0	0.43299	0	A|0.997;G|0.003	0.003	strong	.	CTBS	24	.	NM_004388	exon6	c.T812C	p.I271T	TTTGCAATGGTAC	.	PASS	Atlas-SNP
SPINT4	391253	hgsc.bcm.edu	37	20	44352620	44352620	+	Missense_Mutation	SNP	G	G	A	rs6017667	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	63	24	95	0	0.380952	0	G|0.508;A|0.492	0.492	strong	.	SPINT4	17	.	NM_178455	exon2	c.G217A	p.G73S	TTCTCCGGCTGTA	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	42	129	0	0.482759	0	A|0.518;G|0.482	0.482	strong	.	VSTM4	83	.	NM_144984	exon2	c.T203C	p.F68S	GAGTCGAAGGAGT	.	PASS	Atlas-SNP
MEP1A	4224	hgsc.bcm.edu	37	6	46787399	46787399	+	Missense_Mutation	SNP	C	C	T	rs376658556		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	232	5	231	0	0.0215517	0	.	.	weak	MEP1A,colon,carcinoma,0,1	MEP1A	93	1	NM_005588	exon7	c.C514T	p.R172W	ACGGACCGGGATG	.	scavenged	Atlas-SNP
ITGA3	3675	hgsc.bcm.edu	37	17	48155425	48155425	+	Missense_Mutation	SNP	G	G	A	rs2230392	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	38	81	0	0.44186	0	G|0.907;A|0.093	0.093	strong	ITGA3,NS,carcinoma,0,1	ITGA3	128	1	NM_005501	exon17	c.G2155A	p.A719T	CTCATCGCCTTTG	.	PASS	Atlas-SNP
TGM6	343641	hgsc.bcm.edu	37	20	2398017	2398017	+	Silent	SNP	G	G	A	rs2295077	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	48	34	45	0	0.708333	0	G|0.719;A|0.281	0.281	strong	.	TGM6	126	.	NM_198994	exon10	c.G1476A	p.K492K	CACCAAGCCCAGC	.	PASS	Atlas-SNP
AHRR	57491	hgsc.bcm.edu	37	5	422955	422955	+	Missense_Mutation	SNP	C	C	G	rs2292596	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	84	35	86	0	0.416667	0	C|0.670;G|0.330	0.330	strong	AHRR,brain,glioma,0,2	AHRR	67	2	NM_001242412	exon6	c.C565G	p.P189A	GGGCAGCCCCCGC	.	PASS	Atlas-SNP
PIGZ	80235	hgsc.bcm.edu	37	3	196674879	196674879	+	Silent	SNP	A	A	G	rs12636891	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	53	52	75	0	0.981132	0	A|0.453;G|0.547	0.547	strong	.	PIGZ	34	.	NM_025163	exon3	c.T889C	p.L297L	AGTGCAAGAAGTT	.	PASS	Atlas-SNP
CCDC102A	92922	hgsc.bcm.edu	37	16	57562804	57562804	+	Missense_Mutation	SNP	G	G	A	rs12935069	bycluster;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	4	4	0	0	1	.	G|0.001;A|0.999	0.999	strong	.	CCDC102A	22	.	NM_033212	exon2	c.C286T	p.R96W	ACCACCGGCGCAT	.	PASS	Atlas-SNP
PDE4A	5141	hgsc.bcm.edu	37	19	10531491	10531491	+	Silent	SNP	C	C	T	rs117495488	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	32	18	2	0	0.5625	0	C|0.987;T|0.013	0.013	strong	.	PDE4A	236	.	NM_001111307	exon1	c.C51T	p.P17P	ACTGCCCGGGCCC	.	PASS	Atlas-SNP
COL4A3	1285	hgsc.bcm.edu	37	2	228128568	228128568	+	Missense_Mutation	SNP	G	G	A	rs34505188	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	44	129	0	0.435644	0	G|0.907;A|0.093	0.093	strong	COL4A3_ENST00000328380,NS,carcinoma,+1,2	COL4A3	293	2	NM_000091	exon21	c.G1223A	p.R408H	GAGGCCGCCCAGG	.	PASS	Atlas-SNP
AKNA	80709	hgsc.bcm.edu	37	9	117103973	117103973	+	Missense_Mutation	SNP	A	A	G	rs2250242	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	47	47	54	0	1	0	A|0.404;G|0.596	0.596	strong	.	AKNA	119	.	NM_030767	exon21	c.T3907C	p.S1303P	TTGAAGATGCTTT	.	PASS	Atlas-SNP
AGBL1	123624	hgsc.bcm.edu	37	15	86940622	86940622	+	Silent	SNP	T	T	C	rs4362360	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	143	143	146	0	1	0	T|0.292;C|0.708	0.708	strong	.	AGBL1	151	.	NM_152336	exon17	c.T2262C	p.T754T	GATCACTGCTCGA	.	PASS	Atlas-SNP
OR56B1	387748	hgsc.bcm.edu	37	11	5758386	5758386	+	Missense_Mutation	SNP	C	C	T	rs62621167	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	115	22	128	0	0.191304	0	C|0.962;T|0.038	0.038	strong	.	OR56B1	38	.	NM_001005180	exon1	c.C640T	p.L214F	GCATGGCTTGGAA	.	PASS	Atlas-SNP
CCKBR	887	hgsc.bcm.edu	37	11	6291466	6291466	+	Silent	SNP	A	A	G	rs77873910	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	77	16	70	0	0.207792	0	A|0.986;G|0.014	0.014	strong	CCKBR_ENST00000525462,NS,carcinoma,+2,2	CCKBR	232	2	NM_176875	exon3	c.A552G	p.L184L	CGGACTACTCATG	.	PASS	Atlas-SNP
TGM4	7047	hgsc.bcm.edu	37	3	44929287	44929287	+	Missense_Mutation	SNP	G	G	C	rs2271087	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	52	28	79	0	0.538462	0	G|0.677;C|0.322	0.322	strong	.	TGM4	82	.	NM_003241	exon3	c.G300C	p.E100D	CAAAGAGGTGAGC	.	PASS	Atlas-SNP
HDLBP	3069	hgsc.bcm.edu	37	2	242192848	242192848	+	Missense_Mutation	SNP	T	T	C	rs7578199	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	142	72	178	0	0.507042	0	T|0.798;C|0.202	0.202	strong	.	HDLBP	118	.	NM_005336	exon10	c.A1253G	p.N418S	GCCACATTGACAT	.	PASS	Atlas-SNP
AATF	26574	hgsc.bcm.edu	37	17	35346641	35346641	+	Silent	SNP	T	T	C	rs1045056	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	133	61	146	0	0.458647	0	T|0.782;C|0.218	0.218	strong	.	AATF	36	.	NM_012138	exon7	c.T1245C	p.S415S	GCGCTCTGTCTAT	.	PASS	Atlas-SNP
CELSR2	1952	hgsc.bcm.edu	37	1	109806834	109806834	+	Silent	SNP	C	C	T	rs6698843	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	53	51	77	0	0.962264	0	C|0.633;T|0.367	0.367	strong	.	CELSR2	228	.	NM_001408	exon10	c.C5136T	p.P1712P	GGGGCCCGGCCAT	.	PASS	Atlas-SNP
NEK11	79858	hgsc.bcm.edu	37	3	130799314	130799314	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	18	77	0	0.257143	0	.	.	none	.	NEK11	76	.	NM_024800	exon4	c.C218G	p.T73S	ATGAAACTGTACA	.	PASS	Atlas-SNP
DBH	1621	hgsc.bcm.edu	37	9	136507473	136507473	+	Missense_Mutation	SNP	G	G	A	rs5320	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	40	107	0	0.45977	0	G|0.905;A|0.095	0.095	strong	.	DBH	86	.	NM_000787	exon3	c.G631A	p.A211T	TCAGACGCGTGCA	.	PASS	Atlas-SNP
NT5DC3	51559	hgsc.bcm.edu	37	12	104186946	104186946	+	Silent	SNP	G	G	T	rs1866295	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	140	71	142	0	0.507143	0	G|0.708;T|0.292	0.292	strong	.	NT5DC3	113	.	NM_001031701	exon9	c.C1015A	p.R339R	ACCTCCGCTTATC	.	PASS	Atlas-SNP
CD99	4267	hgsc.bcm.edu	37	X	2656258	2656258	+	Missense_Mutation	SNP	G	G	A	rs35112869	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	487	366	678	1	0.75154	0.00147493	G|0.960;A|0.040	0.040	strong	.	CD99	12	.	NM_002414	exon9	c.G493A	p.D165N	GAGGTGGACATGG	.	PASS	Atlas-SNP
AVPR1B	553	hgsc.bcm.edu	37	1	206230986	206230986	+	Silent	SNP	G	G	A	rs28676508	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	44	22	37	0	0.5	0	G|0.775;A|0.225	0.225	strong	AVPR1B,rectum,carcinoma,0,1	AVPR1B	47	1	NM_000707	exon2	c.G1119A	p.S373S	CCTCTCGAGCCGC	.	PASS	Atlas-SNP
ESF1	51575	hgsc.bcm.edu	37	20	13695680	13695680	+	Silent	SNP	C	C	T	rs6110019	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	113	113	166	0	1	0	C|0.707;T|0.293	0.293	strong	.	ESF1	77	.	NM_001276380	exon14	c.G2397A	p.R799R	TTCTTTCCGTTCT	.	PASS	Atlas-SNP
TNS1	7145	hgsc.bcm.edu	37	2	218682771	218682771	+	Silent	SNP	A	A	G	rs3796026	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	19	94	0	0.327586	0	A|0.689;G|0.311	0.311	strong	.	TNS1	251	.	NM_022648	exon24	c.T3972C	p.G1324G	ATAGCCACCATAG	.	PASS	Atlas-SNP
LRP8	7804	hgsc.bcm.edu	37	1	53792651	53792651	+	Missense_Mutation	SNP	A	A	C	rs3820198	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	31	62	0	0.424658	0	C|0.538;N|0.000	0.538	strong	.	LRP8	58	.	NM_004631	exon2	c.T138G	p.D46E	TTCGCAATCCTTG	.	PASS	Atlas-SNP
AXIN1	8312	hgsc.bcm.edu	37	16	396264	396264	+	Silent	SNP	A	A	G	rs1805105	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	58	82	0	1	0	A|0.335;G|0.665	0.665	strong	.	AXIN1	290	.	NM_181050	exon2	c.T762C	p.D254D	GTCCTCATCCATG	.	PASS	Atlas-SNP
FAT1	2195	hgsc.bcm.edu	37	4	187629137	187629137	+	Silent	SNP	A	A	G	rs4862726	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	62	23	69	0	0.370968	0	A|0.975;G|0.025	0.025	strong	.	FAT1	500	.	NM_005245	exon2	c.T1845C	p.F615F	TAAACTAAAGAAA	.	PASS	Atlas-SNP
LRRFIP1	9208	hgsc.bcm.edu	37	2	238671328	238671328	+	Silent	SNP	A	A	G	rs868119	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	294	132	374	0	0.44898	0	A|0.732;G|0.268	0.268	strong	.	LRRFIP1	171	.	NM_001137552	exon11	c.A972G	p.E324E	GAAAGAACAACAC	.	PASS	Atlas-SNP
ABCC11	85320	hgsc.bcm.edu	37	16	48226479	48226479	+	Silent	SNP	C	C	T	rs12443685	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	162	83	136	0	0.512346	0	C|0.860;T|0.140	0.140	strong	.	ABCC11	177	.	NM_033151	exon19	c.G2658A	p.K886K	CGTGACCTTGGTG	.	PASS	Atlas-SNP
ADAMDEC1	27299	hgsc.bcm.edu	37	8	24261526	24261526	+	Missense_Mutation	SNP	A	A	G	rs3765124	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	127	96	150	0	0.755906	0	A|0.687;G|0.313	0.313	strong	.	ADAMDEC1	69	.	NM_014479	exon13	c.A1331G	p.N444S	GTACCAATCTCTG	.	PASS	Atlas-SNP
VEZF1	7716	hgsc.bcm.edu	37	17	56056550	56056550	+	Silent	SNP	C	C	G	rs1135655	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	209	86	221	0	0.411483	0	C|0.907;G|0.093	0.093	strong	.	VEZF1	50	.	NM_007146	exon5	c.G1101C	p.L367L	CAGTCTCAGTGTT	.	PASS	Atlas-SNP
FCGR2A	2212	hgsc.bcm.edu	37	1	161479745	161479745	+	Missense_Mutation	SNP	A	A	G	rs1801274	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	478	476	575	0	0.995816	0	G|0.474;N|0.000	0.474	strong	.	FCGR2A	38	.	NM_001136219	exon4	c.A500G	p.H167R	TCTCCCATTTGGA	.	PASS	Atlas-SNP
EYS	346007	hgsc.bcm.edu	37	6	66042231	66042231	+	Missense_Mutation	SNP	T	T	G	rs12207746	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	39	19	56	0	0.487179	0	T|0.889;G|0.111	0.111	strong	.	EYS	527	.	NM_001142801	exon12	c.A1846C	p.I616L	TTACGATAAATCC	.	PASS	Atlas-SNP
DSPP	1834	hgsc.bcm.edu	37	4	88536919	88536919	+	Silent	SNP	T	T	C	rs369387818	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	65	7	91	1	0.107692	0.010989	.	.	weak	DSPP,NS,carcinoma,0,3	DSPP	174	3	NM_014208	exon5	c.T3105C	p.D1035D	CAGCGATAGCAGT	.	scavenged	Atlas-SNP
HSPA8	3312	hgsc.bcm.edu	37	11	122928622	122928622	+	Silent	SNP	A	A	G	rs4802	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	28	21	50	0	0.75	0	A|0.653;G|0.347	0.347	strong	.	HSPA8	168	.	NM_006597	exon9	c.T1761C	p.A587A	CTTCTCAGCAGTC	.	PASS	Atlas-SNP
CSNK2A1	1457	hgsc.bcm.edu	37	20	472938	472938	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	60	16	78	0	0.266667	0	.	.	none	.	CSNK2A1	36	.	NM_001895	exon8	c.C581T	p.S194F	TATCGGGAAGCAA	.	PASS	Atlas-SNP
ITGB2	3689	hgsc.bcm.edu	37	21	46330674	46330674	+	Silent	SNP	C	C	A	rs11088969	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	37	77	0	0.381443	0	C|0.796;A|0.204	0.204	strong	.	ITGB2	107	.	NM_000211	exon2	c.G24T	p.L8L	GGCGAGCAGTGGG	.	PASS	Atlas-SNP
TNS1	7145	hgsc.bcm.edu	37	2	218712918	218712918	+	Silent	SNP	C	C	T	rs3796031	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	32	88	0	0.463768	0	C|0.418;T|0.582	0.582	strong	TNS1_ENST00000446903,NS,carcinoma,-1,2	TNS1	251	2	NM_022648	exon17	c.G1947A	p.S649S	CTGCCACGAATTC	.	PASS	Atlas-SNP
PTPRF	5792	hgsc.bcm.edu	37	1	44083507	44083507	+	Silent	SNP	T	T	C	rs641365	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	226	107	256	1	0.473451	0.00390625	C|0.789;G|0.000;T|0.211	0.789	strong	.	PTPRF	172	.	NM_002840	exon25	c.T4296C	p.G1432G	CATGGGTGATTTC	.	PASS	Atlas-SNP
USP20	10868	hgsc.bcm.edu	37	9	132636920	132636920	+	Silent	SNP	C	C	T	rs35899714	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	130	59	142	0	0.453846	0	C|0.937;T|0.063	0.063	strong	.	USP20	186	.	NM_001008563	exon18	c.C1806T	p.H602H	CAGCCACGTCTCC	.	PASS	Atlas-SNP
ADAMTSL3	57188	hgsc.bcm.edu	37	15	84488636	84488636	+	Missense_Mutation	SNP	A	A	G	rs4483821	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	194	193	182	0	0.994845	0	A|0.386;G|0.614	0.614	strong	.	ADAMTSL3	290	.	NM_207517	exon6	c.A437G	p.H146R	AGGGGCATTACTA	.	PASS	Atlas-SNP
MAPK8IP3	23162	hgsc.bcm.edu	37	16	1814440	1814440	+	Missense_Mutation	SNP	A	A	G	rs2294619	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	87	95	0	1	0	A|0.741;G|0.259	0.259	strong	MAPK8IP3_ENST00000250894,NS,carcinoma,0,2	MAPK8IP3	164	2	NM_015133	exon19	c.A2257G	p.T753A	GCCCACACGTCTC	.	PASS	Atlas-SNP
DGCR6L	85359	hgsc.bcm.edu	37	22	20307256	20307256	+	Silent	SNP	G	G	A	rs7235	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	325	136	300	0	0.418462	0	G|0.703;A|0.297	0.297	strong	DGCR6L,NS,carcinoma,0,1	DGCR6L	9	1	NM_033257	exon2	c.C177T	p.T59T	GAACACGGTGCCG	.	PASS	Atlas-SNP
CYP1A2	1544	hgsc.bcm.edu	37	15	75047426	75047426	+	Silent	SNP	C	C	T	rs2470890	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	34	22	40	0	0.647059	0	C|0.616;T|0.384	0.384	strong	.	CYP1A2	70	.	NM_000761	exon7	c.C1548T	p.N516N	CATCAACTGAAGA	.	PASS	Atlas-SNP
ZNF624	57547	hgsc.bcm.edu	37	17	16527357	16527357	+	Silent	SNP	G	G	A	rs62072859	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	120	64	161	0	0.533333	0	G|0.948;A|0.052	0.052	strong	.	ZNF624	91	.	NM_020787	exon6	c.C843T	p.C281C	CTTTTCGCATGTA	.	PASS	Atlas-SNP
NIF3L1	60491	hgsc.bcm.edu	37	2	201768238	201768238	+	Missense_Mutation	SNP	C	C	T	rs7917	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	217	110	272	0	0.506912	0	C|0.715;T|0.285	0.285	strong	.	NIF3L1	51	.	NM_001136039	exon7	c.C971T	p.T324I	ATGATACTTTGGA	.	PASS	Atlas-SNP
TSPYL6	388951	hgsc.bcm.edu	37	2	54482989	54482989	+	Silent	SNP	C	C	T	rs6740641	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	185	146	83	0	0.789189	0	C|0.869;G|0.001;T|0.130	0.130	strong	TSPYL6,NS,carcinoma,0,1	TSPYL6	54	1	NM_001003937	exon1	c.G300A	p.A100A	AGAGGCCGCTTCT	.	PASS	Atlas-SNP
OR10AD1	121275	hgsc.bcm.edu	37	12	48596254	48596254	+	Silent	SNP	A	A	C	rs11830378	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	95	41	79	0	0.431579	0	A|0.938;C|0.062	0.062	strong	OR10AD1,colon,carcinoma,-1,1	OR10AD1	24	1	NM_001004134	exon1	c.T822G	p.P274P	GGAGAAAGGTTTG	.	PASS	Atlas-SNP
SIGLEC5	8778	hgsc.bcm.edu	37	19	52130830	52130830	+	Silent	SNP	C	C	A	rs8107754	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	80	87	1	0.97561	0.0114943	C|0.575;A|0.425	0.425	strong	SIGLEC5,NS,carcinoma,-1,1	SIGLEC5	67	1	NM_003830	exon6	c.G1167T	p.G389G	CCAGGGCCCAGCT	.	scavenged	Atlas-SNP
PDXDC1	23042	hgsc.bcm.edu	37	16	15095675	15095675	+	Silent	SNP	C	C	A	rs9921162	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	173	67	147	0	0.387283	0	C|0.773;A|0.227	0.227	strong	PDXDC1,NS,carcinoma,0,1	PDXDC1	59	1	NM_015027	exon4	c.C204A	p.L68L	GAATCTCATGCAT	.	PASS	Atlas-SNP
FAN1	22909	hgsc.bcm.edu	37	15	31229420	31229420	+	Silent	SNP	T	T	C	rs2955795	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	107	107	141	0	1	0	T|0.603;C|0.397	0.397	strong	.	FAN1	77	.	NM_014967	exon14	c.T3015C	p.H1005H	CTGCCATGTGGTT	.	PASS	Atlas-SNP
DENND5B	160518	hgsc.bcm.edu	37	12	31648826	31648826	+	Missense_Mutation	SNP	C	C	T	rs4930979	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	114	55	140	0	0.482456	0	C|0.605;T|0.395	0.395	strong	.	DENND5B	114	.	NM_144973	exon2	c.G155A	p.R52K	GTTCTTCTCAAAG	.	PASS	Atlas-SNP
MAP4K4	9448	hgsc.bcm.edu	37	2	102472459	102472459	+	Silent	SNP	A	A	G	rs1139583	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	56	24	79	0	0.428571	0	A|0.881;G|0.119	0.119	strong	.	MAP4K4	111	.	NM_004834	exon13	c.A1254G	p.E418E	GCGGGAAGCTAGA	.	PASS	Atlas-SNP
TLR10	81793	hgsc.bcm.edu	37	4	38777173	38777173	+	Silent	SNP	A	A	T	rs10856838	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	144	68	137	0	0.472222	0	A|0.721;T|0.279	0.279	strong	.	TLR10	87	.	NM_001017388	exon2	c.T39A	p.I13I	CATAACAATACTA	.	PASS	Atlas-SNP
TMEM225	338661	hgsc.bcm.edu	37	11	123753958	123753958	+	Missense_Mutation	SNP	C	C	T	rs35551906	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	79	111	0	0.782178	0	C|0.945;T|0.055	0.055	strong	.	TMEM225	56	.	NM_001013743	exon4	c.G565A	p.E189K	TATCTTCGATAGA	.	PASS	Atlas-SNP
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32609195	32609195	+	Missense_Mutation	SNP	G	G	A	rs36219699	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	54	108	0	0.627907	0	G|0.915;A|0.085	0.085	strong	.	HLA-DQA1	52	.	NM_002122	exon2	c.G191A	p.R64K	TGGAGAGGAAGGA	.	PASS	Atlas-SNP
HR	55806	hgsc.bcm.edu	37	8	21984765	21984765	+	Missense_Mutation	SNP	C	C	T	rs73549523	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	165	127	173	1	0.769697	0.00578035	C|0.933;T|0.067	0.067	strong	.	HR	71	.	NM_018411	exon3	c.G1190A	p.C397Y	TCAGGGCAGCCGC	.	PASS	Atlas-SNP
PNPLA1	285848	hgsc.bcm.edu	37	6	36275458	36275458	+	Missense_Mutation	SNP	T	T	C	rs4713956	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	173	78	182	0	0.450867	0	C|0.644;N|0.000	0.644	strong	PNPLA1_ENST00000394571,NS,carcinoma,-1,6	PNPLA1	92	6	NM_001145717	exon8	c.T1564C	p.S522P	AGACATTCGGGAT	.	PASS	Atlas-SNP
RPTOR	57521	hgsc.bcm.edu	37	17	78820351	78820351	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	88	27	76	0	0.306818	0	.	.	none	.	RPTOR	122	.	NM_001163034	exon11	c.G1291A	p.E431K	CCACCCGAACAGC	.	PASS	Atlas-SNP
THBS2	7058	hgsc.bcm.edu	37	6	169648767	169648767	+	Silent	SNP	G	G	A	rs12178180	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	60	10	97	0	0.166667	0	A|0.184;C|0.000;G|0.816	0.184	strong	.	THBS2	230	.	NM_003247	exon4	c.C354T	p.N118N	GGGGCCGTTGGAG	.	PASS	Atlas-SNP
KRT83	3889	hgsc.bcm.edu	37	12	52713088	52713088	+	Missense_Mutation	SNP	G	G	A	rs2857663	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	278	126	283	1	0.453237	0.00353357	G|0.876;A|0.124	0.124	strong	KRT83,NS,carcinoma,+2,1	KRT83	64	1	NM_002282	exon2	c.C445T	p.R149C	ACTCGCGGTTTTG	.	PASS	Atlas-SNP
FOXRED2	80020	hgsc.bcm.edu	37	22	36897427	36897427	+	Silent	SNP	T	T	C	rs5756223	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	124	53	110	0	0.427419	0	T|0.944;C|0.056	0.056	strong	.	FOXRED2	48	.	NM_001102371	exon5	c.A1077G	p.A359A	GCCGAATGCATTT	.	PASS	Atlas-SNP
DSPP	1834	hgsc.bcm.edu	37	4	88536460	88536460	+	Silent	SNP	C	C	T	rs199691318	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	65	17	101	0	0.261538	0	.	.	weak	.	DSPP	174	.	NM_014208	exon5	c.C2646T	p.S882S	TGATAGCAGTGAC	.	PASS	Atlas-SNP
SPPL2A	84888	hgsc.bcm.edu	37	15	51017488	51017488	+	Silent	SNP	G	G	T	rs140457962	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	223	127	229	0	0.569507	0	G|0.995;T|0.005	0.005	strong	.	SPPL2A	26	.	NM_032802	exon12	c.C1179A	p.I393I	GAAATAGATCAGT	.	PASS	Atlas-SNP
DSPP	1834	hgsc.bcm.edu	37	4	88537357	88537357	+	Silent	SNP	T	T	C	rs146317878	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	127	45	144	2	0.354331	0.0138889	T|0.922;C|0.078	0.078	strong	DSPP,rectum,carcinoma,0,1	DSPP	174	1	NM_014208	exon5	c.T3543C	p.S1181S	TAGCAGTGATAGC	.	scavenged	Atlas-SNP
DBC1	1620	hgsc.bcm.edu	37	9	121930344	121930344	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	115	16	106	0	0.13913	0	.	.	none	.	DBC1	194	.	NM_014618	exon8	c.G1304A	p.S435N	GCGCAGCTGTTGT	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	172	112	130	0	0.651163	0	C|0.482;G|0.518	0.518	strong	.	CDT1	30	.	NM_030928	exon10	c.C1587G	p.L529L	GGACCTCGCCCAC	.	PASS	Atlas-SNP
FUS	2521	hgsc.bcm.edu	37	16	31193942	31193942	+	Silent	SNP	C	C	A	rs741810	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	224	96	206	0	0.428571	0	C|0.783;A|0.217	0.217	strong	FUS,caecum,carcinoma,0,1	FUS	52	1	NM_001170634	exon3	c.C147A	p.G49G	TTCAGGCTATGGC	.	PASS	Atlas-SNP
DCC	1630	hgsc.bcm.edu	37	18	50278563	50278563	+	Silent	SNP	T	T	C	rs112141078	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	98	43	110	0	0.438776	0	T|0.986;C|0.014	0.014	strong	.	DCC	360	.	NM_005215	exon2	c.T231C	p.D77D	GAAAGATGGCATT	.	PASS	Atlas-SNP
VPS26A	9559	hgsc.bcm.edu	37	10	70892791	70892791	+	Silent	SNP	C	C	T	rs5030932	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	40	87	0	0.512821	0	C|0.795;T|0.205	0.205	strong	VPS26A,NS,carcinoma,0,1	VPS26A	24	1	NM_004896	exon2	c.C141T	p.S47S	AGAATCCGTTTCA	.	PASS	Atlas-SNP
ZNF878	729747	hgsc.bcm.edu	37	19	12157507	12157507	+	Silent	SNP	G	G	C	rs11668160	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	53	26	78	0	0.490566	0	G|0.981;C|0.019	0.019	strong	.	ZNF878	172	.	NM_001080404	exon2	c.C72G	p.S24S	TTTCTGGGAAGGA	.	PASS	Atlas-SNP
HIST1H2BI	8346	hgsc.bcm.edu	37	6	26273368	26273368	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	108	22	109	0	0.203704	0	.	.	none	.	HIST1H2BI	29	.	NM_003525	exon1	c.C165G	p.I55M	CGGCATCTCGTCC	.	PASS	Atlas-SNP
BPIFB4	149954	hgsc.bcm.edu	37	20	31671411	31671411	+	Silent	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	178	48	215	0	0.269663	0	.	.	none	.	.	.	.	NM_182519	exon3	c.C408T	p.L136L	GGGCCTCGGGCGA	.	PASS	Atlas-SNP
SPICE1	152185	hgsc.bcm.edu	37	3	113222054	113222054	+	Silent	SNP	G	G	A	rs75865495	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	98	47	110	0	0.479592	0	G|0.955;A|0.045	0.045	strong	.	SPICE1	130	.	NM_144718	exon3	c.C120T	p.T40T	ATGAACGGTTAGA	.	PASS	Atlas-SNP
TUBB8	347688	hgsc.bcm.edu	37	10	93714	93714	+	Silent	SNP	A	A	T	rs41288743	alternate_allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	48	5	50	0	0.104167	0	.	.	alt	TUBB8,NS,carcinoma,0,1	TUBB8	62	1	NM_177987	exon4	c.T618A	p.A206A	ATACAGAGCTTCG	.	scavenged	Atlas-SNP
GATA5	140628	hgsc.bcm.edu	37	20	61040951	61040951	+	Silent	SNP	C	C	T	rs6587239	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	60	23	67	0	0.383333	0	C|0.469;T|0.531	0.531	strong	GATA5,NS,haematopoietic_neoplasm,-2,4	GATA5	22	4	NM_080473	exon5	c.G852A	p.K284K	GCTTTCCTTCTTC	.	PASS	Atlas-SNP
IL5RA	3568	hgsc.bcm.edu	37	3	3139910	3139910	+	Silent	SNP	T	T	C	rs141948767	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	244	109	268	0	0.446721	0	T|0.998;C|0.002	0.002	strong	.	IL5RA	55	.	NM_001243099	exon6	c.A432G	p.S144S	TAAACGTGAATAA	.	PASS	Atlas-SNP
C22orf23	84645	hgsc.bcm.edu	37	22	38341134	38341134	+	Silent	SNP	T	T	C	rs139859	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	272	114	325	1	0.419118	0.00307692	T|0.238;C|0.762	0.762	strong	.	C22orf23	21	.	NM_032561	exon5	c.A396G	p.T132T	CTTCCCTGTGGCA	.	PASS	Atlas-SNP
OR5B3	441608	hgsc.bcm.edu	37	11	58170374	58170374	+	Missense_Mutation	SNP	T	T	C	rs12280114	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	74	50	95	0	0.675676	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
METTL12	751071	hgsc.bcm.edu	37	11	62434173	62434173	+	Missense_Mutation	SNP	G	G	A	rs11231181	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	76	75	80	0	0.986842	0	G|0.803;A|0.197	0.197	strong	.	METTL12	11	.	NM_001043229	exon3	c.G373A	p.G125S	GGCCCAGGCCAAA	.	PASS	Atlas-SNP
LILRB3	11025	hgsc.bcm.edu	37	19	54725913	54725913	+	Missense_Mutation	SNP	C	C	T	rs199822090	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	213	84	233	0	0.394366	0	C|0.931;T|0.069	0.069	strong	.	LILRB3	67	.	NM_006864	exon4	c.G445A	p.G149R	GATATCCCTTCTG	.	PASS	Atlas-SNP
DYSF	8291	hgsc.bcm.edu	37	2	71780248	71780248	+	Silent	SNP	C	C	T	rs35721373	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	134	65	170	0	0.485075	0	C|0.967;T|0.033	0.033	strong	.	DYSF	536	.	NM_001130982	exon21	c.C1956T	p.Y652Y	GAACTACGGGAAC	.	PASS	Atlas-SNP
ELSPBP1	64100	hgsc.bcm.edu	37	19	48517538	48517538	+	Missense_Mutation	SNP	G	G	A	rs62129078	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	122	65	134	0	0.532787	0	G|0.845;A|0.155	0.155	strong	.	ELSPBP1	29	.	NM_022142	exon3	c.G181A	p.G61S	TACAACGGCCAGT	.	PASS	Atlas-SNP
MST1L	11223	hgsc.bcm.edu	37	1	17085614	17085614	+	Silent	SNP	G	G	A	rs3891100	bycluster;byfrequency;by2hit2allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	66	8	62	0	0.121212	0	G|0.990;A|0.010	0.010	strong	.	.	.	.	NM_001271733	exon9	c.C1107T	p.T369T	CTTGCGGGTCTTG	.	PASS	Atlas-SNP
OTOP3	347741	hgsc.bcm.edu	37	17	72943126	72943126	+	Silent	SNP	G	G	A	rs8066909	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	88	40	72	0	0.454545	0	G|0.683;A|0.317	0.317	strong	OTOP3,NS,carcinoma,0,1	OTOP3	64	1	NM_178233	exon6	c.G1176A	p.A392A	CCTGGCGGGCACA	.	PASS	Atlas-SNP
GPR112	139378	hgsc.bcm.edu	37	X	135431236	135431236	+	Missense_Mutation	SNP	T	T	C	rs5930932	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	183	182	282	1	0.994536	0.0035461	0|0.015;C|0.499	0.499	strong	.	GPR112	459	.	NM_153834	exon6	c.T5371C	p.F1791L	AATTGCTTTTCTT	.	PASS	Atlas-SNP
ARSB	411	hgsc.bcm.edu	37	5	78135201	78135201	+	Silent	SNP	C	C	T	rs25413	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	194	70	150	0	0.360825	0	C|0.727;T|0.273	0.273	strong	ARSB,NS,carcinoma,-1,1	ARSB	47	1	NM_198709	exon7	c.G1191A	p.P397P	GAAGTTCGGGTCA	.	PASS	Atlas-SNP
CCR3	1232	hgsc.bcm.edu	37	3	46306700	46306700	+	Silent	SNP	T	T	C	rs4987053	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	216	98	241	0	0.453704	0	T|0.903;C|0.097	0.097	strong	.	CCR3	52	.	NM_178328	exon3	c.T114C	p.Y38Y	CTACTATGATGAC	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179438866	179438866	+	Missense_Mutation	SNP	C	C	T	rs10164753	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	189	98	194	1	0.518519	0.00515464	C|0.944;T|0.056	0.056	strong	.	TTN	18412	.	NM_001267550	exon326	c.G71993A	p.R23998H	ATCACACGGAATT	.	PASS	Atlas-SNP
ZMYND10	51364	hgsc.bcm.edu	37	3	50379257	50379257	+	Missense_Mutation	SNP	G	G	A	rs142613783	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	60	31	70	0	0.516667	0	G|0.995;A|0.005	0.005	strong	.	ZMYND10	37	.	NM_015896	exon10	c.C1105T	p.R369W	GCAGCCGCAGGTC	.	PASS	Atlas-SNP
NRXN1	9378	hgsc.bcm.edu	37	2	50464109	50464109	+	Splice_Site	SNP	C	C	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	160	35	80	0	0.21875	0	.	.	none	.	NRXN1	1118	.	NM_001135659	exon20	c.3485-1G>T	.	TCCCAGCTGGAAA	.	PASS	Atlas-SNP
TNN	63923	hgsc.bcm.edu	37	1	175087884	175087884	+	Silent	SNP	C	C	T	rs2269654	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	156	76	159	1	0.487179	0.00628931	C|0.865;T|0.135	0.135	strong	TNN,NS,carcinoma,0,2	TNN	297	2	NM_022093	exon11	c.C2574T	p.G858G	GCCGGGCATGGAG	.	scavenged	Atlas-SNP
PHIP	55023	hgsc.bcm.edu	37	6	79688366	79688366	+	Silent	SNP	T	T	C	rs12209235	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	128	59	168	0	0.460938	0	T|0.952;C|0.048	0.048	strong	.	PHIP	177	.	NM_017934	exon24	c.A2832G	p.T944T	AATCCATGTTGAT	.	PASS	Atlas-SNP
SESN1	27244	hgsc.bcm.edu	37	6	109323519	109323519	+	Missense_Mutation	SNP	G	G	T	rs2273668	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	83	45	96	0	0.542169	0	G|0.927;T|0.073	0.073	strong	.	SESN1	29	.	NM_014454	exon2	c.C307A	p.L103I	GTCCTAGTGGTCG	.	PASS	Atlas-SNP
SAMSN1	64092	hgsc.bcm.edu	37	21	15873026	15873026	+	Missense_Mutation	SNP	T	T	C	rs62227165	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	223	141	188	0	0.632287	0	T|0.985;C|0.015	0.015	strong	.	SAMSN1	112	.	NM_001256370	exon7	c.A796G	p.T266A	TTGGTGTTTTGCA	.	PASS	Atlas-SNP
EIF2AK3	9451	hgsc.bcm.edu	37	2	88879131	88879131	+	Silent	SNP	T	T	C	rs1805164	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	45	15	50	0	0.333333	0	T|0.725;C|0.275	0.275	strong	.	EIF2AK3	160	.	NM_004836	exon11	c.A1791G	p.Q597Q	CAGGCATTGAATT	.	PASS	Atlas-SNP
DSG2	1829	hgsc.bcm.edu	37	18	29125854	29125854	+	Silent	SNP	A	A	G	rs1042769	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	52	52	82	0	1	0	T|0.014;G|0.185	0.185	strong	.	DSG2	115	.	NM_001943	exon15	c.A2505G	p.T835T	CAAGACACTAGCT	.	PASS	Atlas-SNP
MLLT1	4298	hgsc.bcm.edu	37	19	6222552	6222552	+	Silent	SNP	C	C	T	rs139655596	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	27	15	30	0	0.555556	0	C|0.981;T|0.019	0.019	strong	.	MLLT1	47	.	NM_005934	exon6	c.G690A	p.S230S	CTTCCGCGAGGTG	.	PASS	Atlas-SNP
LPIN1	23175	hgsc.bcm.edu	37	2	11913845	11913845	+	Silent	SNP	G	G	C	rs145180224	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	121	34	100	0	0.280992	0	G|0.991;C|0.009	0.009	strong	.	LPIN1	99	.	NM_001261428	exon6	c.G843C	p.S281S	TAATTCGGATAGA	.	PASS	Atlas-SNP
LAT	27040	hgsc.bcm.edu	37	16	28996225	28996225	+	Silent	SNP	T	T	C	rs41301797	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	31	41	0	0.449275	0	T|0.500;C|0.500	0.500	weak	.	LAT	22	.	NM_001014989	exon1	c.T43C	p.L15L	CCCGTCTTGGGGG	.	PASS	Atlas-SNP
GPR78	27201	hgsc.bcm.edu	37	4	8588950	8588950	+	Missense_Mutation	SNP	C	C	T	rs61746144	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	193	86	247	0	0.445596	0	C|0.986;T|0.014	0.014	strong	.	GPR78	58	.	NM_080819	exon3	c.C952T	p.R318C	ACCCCGCGCCCAG	.	PASS	Atlas-SNP
XRCC6BP1	91419	hgsc.bcm.edu	37	12	58335626	58335626	+	Missense_Mutation	SNP	A	A	T	rs3751325	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	56	30	62	0	0.535714	0	A|0.640;T|0.360	0.360	strong	XRCC6BP1,NS,carcinoma,0,1	XRCC6BP1	22	1	NM_033276	exon1	c.A142T	p.S48C	TTCACCAGCAACC	.	PASS	Atlas-SNP
C5orf45	51149	hgsc.bcm.edu	37	5	179285752	179285752	+	Silent	SNP	G	G	A	rs10060182	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	39	54	0	0.52	0	G|0.579;A|0.421	0.421	strong	C5orf45,colon,carcinoma,0,1	C5orf45	23	1	NM_016175	exon1	c.C45T	p.C15C	GAGGCGGCAGCTG	.	PASS	Atlas-SNP
LRRC27	80313	hgsc.bcm.edu	37	10	134151131	134151131	+	Silent	SNP	G	G	T	rs116451295	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	118	56	146	0	0.474576	0	G|0.984;T|0.016	0.016	strong	LRRC27,rectum,carcinoma,0,2	LRRC27	64	2	NM_001143757	exon3	c.G273T	p.P91P	GCTTCCGAACCTG	.	PASS	Atlas-SNP
SNN	8303	hgsc.bcm.edu	37	16	11769963	11769963	+	Silent	SNP	C	C	T	rs1050069	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	45	45	72	0	1	0	C|0.685;T|0.315	0.315	strong	.	SNN	7	.	NM_003498	exon2	c.C48T	p.I16I	AGTCATCGTCATC	.	PASS	Atlas-SNP
LRP1	4035	hgsc.bcm.edu	37	12	57587714	57587714	+	Missense_Mutation	SNP	C	C	T	rs367968116		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	105	38	108	0	0.361905	0	.	.	weak	LRP1,NS,lymphoid_neoplasm,-1,1	LRP1	428	1	NM_002332	exon48	c.C7837T	p.R2613W	CGCTGCCGGGACG	.	PASS	Atlas-SNP
PRR21	643905	hgsc.bcm.edu	37	2	240982389	240982389	+	Missense_Mutation	SNP	C	C	G	rs143417758		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	12	7	29	0	0.583333	0	.	.	weak	.	PRR21	53	.	NM_001080835	exon1	c.G11C	p.C4S	GATGAACAGGCAT	.	PASS	Atlas-SNP
ZPLD1	131368	hgsc.bcm.edu	37	3	102157365	102157365	+	Missense_Mutation	SNP	A	A	T	rs6784362	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	154	63	171	0	0.409091	0	A|0.881;N|0.000	.	strong	ZPLD1,NS,carcinoma,-2,1	ZPLD1	82	1	NM_175056	exon2	c.A82T	p.I28F	CTAACAATTAGAG	.	PASS	Atlas-SNP
ARNTL	406	hgsc.bcm.edu	37	11	13380068	13380068	+	Silent	SNP	C	C	T	rs138340325	byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	94	3	120	0	0.0319149	0	C|1.000;T|0.000	0.000	strong	ARNTL,NS,carcinoma,0,1	ARNTL	46	1	NM_001030272	exon7	c.C309T	p.N103N	ATGCAACGCAATG	.	scavenged	Atlas-SNP
C16orf3	750	hgsc.bcm.edu	37	16	90095558	90095558	+	Missense_Mutation	SNP	C	C	T	rs76646627	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	127	20	92	3	0.15748	0.0326087	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
CDHR1	92211	hgsc.bcm.edu	37	10	85978991	85978991	+	Silent	SNP	C	C	T	rs7895270	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	93	51	78	0	0.548387	0	C|0.735;T|0.265	0.265	strong	.	CDHR1	122	.	NM_001171971	exon17	c.C2197T	p.L733L	GTGAATCTGTACT	.	PASS	Atlas-SNP
RAB40B	10966	hgsc.bcm.edu	37	17	80616397	80616397	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	119	31	126	0	0.260504	0	.	.	none	.	RAB40B	24	.	NM_006822	exon5	c.G535A	p.G179R	CCATCCCATGCCG	.	PASS	Atlas-SNP
ZNF587	84914	hgsc.bcm.edu	37	19	58371202	58371202	+	Silent	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	224	13	180	0	0.0580357	0	.	.	none	.	ZNF587	53	.	NM_032828	exon3	c.C1422T	p.G474G	ATTTGGCAATAAG	.	PASS	Atlas-SNP
ATAD5	79915	hgsc.bcm.edu	37	17	29214387	29214387	+	Missense_Mutation	SNP	T	T	C	rs11657270	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	105	48	107	0	0.457143	0	T|0.887;C|0.113	0.113	strong	.	ATAD5	150	.	NM_024857	exon19	c.T4255C	p.Y1419H	ACCCTTTATCGTA	.	PASS	Atlas-SNP
AAMDC	28971	hgsc.bcm.edu	37	11	77583266	77583266	+	Missense_Mutation	SNP	G	G	A	rs2186564	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	140	108	152	0	0.771429	0	G|0.876;N|0.000	.	strong	C11orf67,NS,carcinoma,0,1	.	.	1	NM_024684	exon4	c.G274A	p.V92M	ATTGATGTGCGGG	.	PASS	Atlas-SNP
WDR27	253769	hgsc.bcm.edu	37	6	170070723	170070723	+	Missense_Mutation	SNP	A	A	G	rs4236176	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	41	22	67	0	0.536585	0	A|0.485;G|0.515	0.515	strong	.	WDR27	129	.	NM_182552	exon4	c.T398C	p.L133P	TCATCCAGGCTCA	.	PASS	Atlas-SNP
C10orf120	399814	hgsc.bcm.edu	37	10	124457906	124457906	+	Silent	SNP	C	C	T	rs2901343	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	166	73	262	0	0.439759	0	C|0.580;T|0.420	0.420	strong	.	C10orf120	55	.	NM_001010912	exon3	c.G351A	p.P117P	GTAGTCCGGAGAC	.	PASS	Atlas-SNP
SRSF9	8683	hgsc.bcm.edu	37	12	120907332	120907332	+	Silent	SNP	C	C	T	rs11548264	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	46	18	45	0	0.391304	0	C|0.961;T|0.039	0.039	strong	.	SRSF9	14	.	NM_003769	exon1	c.G81A	p.E27E	GTCCTTCTCGCGC	.	PASS	Atlas-SNP
ELOVL1	64834	hgsc.bcm.edu	37	1	43830438	43830438	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	79	42	93	0	0.531646	0	.	.	none	.	ELOVL1	18	.	NM_001256399	exon5	c.T346C	p.F116L	TGGAGAAGAGGAA	.	PASS	Atlas-SNP
FOXK1	221937	hgsc.bcm.edu	37	7	4802035	4802035	+	Silent	SNP	A	A	G	rs1053753	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	40	40	38	0	1	0	A|0.728;G|0.272	0.272	strong	.	FOXK1	64	.	NM_001037165	exon9	c.A2142G	p.V714V	TGCTGTAACCACA	.	PASS	Atlas-SNP
RNF139	11236	hgsc.bcm.edu	37	8	125499363	125499363	+	Silent	SNP	G	G	A	rs72713066	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	77	17	110	0	0.220779	0	G|0.919;A|0.081	0.081	strong	.	RNF139	57	.	NM_007218	exon2	c.G1473A	p.S491S	TGAGTCGGGAAGT	.	PASS	Atlas-SNP
TMEM26	219623	hgsc.bcm.edu	37	10	63170292	63170292	+	Silent	SNP	A	A	G	rs7083475	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	118	67	146	0	0.567797	0	A|0.802;G|0.198	0.198	strong	.	TMEM26	47	.	NM_178505	exon6	c.T895C	p.L299L	GTTGCAACACCAC	.	PASS	Atlas-SNP
KIAA0368	23392	hgsc.bcm.edu	37	9	114182353	114182353	+	Silent	SNP	C	C	T	rs16916080	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	53	29	82	1	0.54717	0.0121951	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	.	scavenged	Atlas-SNP
CCDC168	643677	hgsc.bcm.edu	37	13	103388880	103388880	+	Missense_Mutation	SNP	T	T	C	rs17592459	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	164	81	197	0	0.493902	0	T|0.978;C|0.022	0.022	strong	.	.	.	.	NM_001146197	exon4	c.A14167G	p.M4723V	GTGGCATAAAGCT	.	PASS	Atlas-SNP
EAF1	85403	hgsc.bcm.edu	37	3	15477872	15477872	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	168	35	158	0	0.208333	0	.	.	none	.	EAF1	16	.	NM_033083	exon5	c.A550C	p.I184L	GACATTATTGAAC	.	PASS	Atlas-SNP
TAF3	83860	hgsc.bcm.edu	37	10	8006798	8006798	+	Missense_Mutation	SNP	A	A	G	rs4747647	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	68	30	75	0	0.441176	0	A|0.444;G|0.556	0.556	strong	TAF3,NS,carcinoma,0,1	TAF3	93	1	NM_031923	exon3	c.A1325G	p.N442S	CGAACAATTTCAC	.	PASS	Atlas-SNP
DMBT1	1755	hgsc.bcm.edu	37	10	124358421	124358421	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	43	14	62	0	0.325581	0	.	.	none	.	DMBT1	677	.	NM_007329	exon26	c.G3088A	p.V1030I	AATGTCGTCTGCA	.	PASS	Atlas-SNP
C1orf111	284680	hgsc.bcm.edu	37	1	162344069	162344069	+	Silent	SNP	G	G	A	rs13823	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	117	49	133	0	0.418803	0	G|0.952;A|0.048	0.048	strong	.	C1orf111	26	.	NM_182581	exon3	c.C555T	p.C185C	GGCCACGCACTTG	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105418502	105418502	+	Missense_Mutation	SNP	G	G	T	rs201268922	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	156	31	108	0	0.198718	0	.	.	weak	.	AHNAK2	719	.	NM_138420	exon7	c.C3286A	p.L1096I	CCTTGAGGGCCAC	.	PASS	Atlas-SNP
ALAS1	211	hgsc.bcm.edu	37	3	52237970	52237970	+	Silent	SNP	C	C	T	rs352168	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	72	105	0	1	0	C|0.549;T|0.451	0.451	strong	.	ALAS1	56	.	NM_000688	exon5	c.C519T	p.I173I	GGACATCATGCAA	.	PASS	Atlas-SNP
NSMCE4A	54780	hgsc.bcm.edu	37	10	123727280	123727280	+	Silent	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	113	2	147	1	0.0176991	0.00680272	.	.	none	NSMCE4A,caecum,carcinoma,-2,1	NSMCE4A	12	1	NM_001167865	exon4	c.C543T	p.L181L	ACGGATGAGTTCT	.	scavenged	Atlas-SNP
LMX1A	4009	hgsc.bcm.edu	37	1	165218792	165218792	+	Silent	SNP	G	G	A	rs10753668	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	143	73	182	0	0.51049	0	G|0.743;A|0.257	0.257	strong	.	LMX1A	87	.	NM_001174069	exon4	c.C349T	p.L117L	AGCTCAGGTGGTA	.	PASS	Atlas-SNP
MKI67	4288	hgsc.bcm.edu	37	10	129901570	129901570	+	Missense_Mutation	SNP	C	C	T	rs11016072	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	96	36	130	0	0.375	0	C|0.927;T|0.073	0.073	strong	.	MKI67	363	.	NM_002417	exon13	c.G8534A	p.R2845H	TGGGCACGTGTCC	.	PASS	Atlas-SNP
RC3H1	149041	hgsc.bcm.edu	37	1	173961985	173961985	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	148	3	162	0	0.0202703	0	.	.	none	RC3H1,NS,carcinoma,+1,1	RC3H1	110	1	NM_172071	exon1	c.C139T	p.R47C	CCTTGCGGTGGAG	.	scavenged	Atlas-SNP
SYT8	90019	hgsc.bcm.edu	37	11	1857751	1857751	+	Missense_Mutation	SNP	C	C	G	rs3741231	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	153	107	102	0	0.699346	0	C|0.667;G|0.333	0.333	strong	.	SYT8	29	.	NM_138567	exon6	c.C655G	p.P219A	CGTCTGCCACTGG	.	PASS	Atlas-SNP
FBN3	84467	hgsc.bcm.edu	37	19	8168545	8168545	+	Missense_Mutation	SNP	C	C	T	rs33967815	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	131	49	131	0	0.374046	0	C|0.769;T|0.231	0.231	strong	.	FBN3	300	.	NM_032447	exon38	c.G4840A	p.G1614S	AGATGCCGGAGTG	.	PASS	Atlas-SNP
E2F2	1870	hgsc.bcm.edu	37	1	23845566	23845566	+	Missense_Mutation	SNP	G	G	A	rs139052092	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	128	64	126	0	0.5	0	G|0.998;A|0.002	0.002	strong	.	E2F2	31	.	NM_004091	exon5	c.C794T	p.T265I	ATCACTGTCTGCT	.	PASS	Atlas-SNP
WDFY4	57705	hgsc.bcm.edu	37	10	49987998	49987998	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	79	26	79	0	0.329114	0	.	.	none	.	WDFY4	205	.	NM_020945	exon19	c.C3410T	p.P1137L	TGGAACCTGAGGA	.	PASS	Atlas-SNP
ZFP36L1	677	hgsc.bcm.edu	37	14	69259598	69259598	+	Splice_Site	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	34	6	63	0	0.176471	0	.	.	none	.	ZFP36L1	47	.	NM_004926	exon2	c.57+1G>A	.	CCTTTACCTTGCA	.	PASS	Atlas-SNP
CERS3	204219	hgsc.bcm.edu	37	15	101041921	101041921	+	Missense_Mutation	SNP	T	T	C	rs60405735	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	114	73	101	0	0.640351	0	T|0.888;C|0.112	0.112	strong	.	.	.	.	NM_178842	exon4	c.A134G	p.Y45C	AAAGCATATGGAA	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179416556	179416556	+	Silent	SNP	A	A	C	rs11897366	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	108	47	128	0	0.435185	0	A|0.880;C|0.120	0.120	strong	.	TTN	18412	.	NM_001267550	exon335	c.T91071G	p.T30357T	GAATCCAGTAACT	.	PASS	Atlas-SNP
RASGRP3	25780	hgsc.bcm.edu	37	2	33759395	33759395	+	Silent	SNP	C	C	T	rs35933402	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	49	123	0	0.563218	0	C|0.890;T|0.110	0.110	strong	.	RASGRP3	87	.	NM_170672	exon12	c.C1089T	p.S363S	GCTTTCCCTGGAC	.	PASS	Atlas-SNP
RFPL1	5988	hgsc.bcm.edu	37	22	29837537	29837537	+	Missense_Mutation	SNP	T	T	C	rs3804076	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	170	78	242	0	0.458824	0	T|0.702;C|0.298	0.298	strong	RFPL1,colon,carcinoma,0,1	RFPL1	43	1	NM_021026	exon2	c.T380C	p.M127T	TGGATATGACCTT	.	PASS	Atlas-SNP
C1orf65	164127	hgsc.bcm.edu	37	1	223568034	223568034	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	242	5	275	0	0.0206612	0	.	.	none	C1orf65,trunk,malignant_melanoma,+1,1	C1orf65	71	1	NM_152610	exon1	c.G1217A	p.R406H	CCTGTCGCAAGAG	.	scavenged	Atlas-SNP
ZFP64	55734	hgsc.bcm.edu	37	20	50803444	50803444	+	Silent	SNP	C	C	T	rs36027430	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	191	88	232	1	0.460733	0.00431034	C|0.865;T|0.135	0.135	strong	.	ZFP64	240	.	NM_018197	exon2	c.G213A	p.S71S	TTCCTCCGATACA	.	PASS	Atlas-SNP
XAB2	56949	hgsc.bcm.edu	37	19	7694393	7694393	+	Silent	SNP	G	G	A	rs4134809	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	135	60	127	0	0.444444	0	G|0.720;A|0.280	0.280	strong	.	XAB2	69	.	NM_020196	exon1	c.C21T	p.L7L	CCGCGAGAGTCGC	.	PASS	Atlas-SNP
THBS1	7057	hgsc.bcm.edu	37	15	39885301	39885301	+	Silent	SNP	T	T	C	rs2228263	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	115	57	131	0	0.495652	0	T|0.841;C|0.159	0.159	strong	.	THBS1	106	.	NM_003246	exon18	c.T2868C	p.D956D	GACCGATTTCCGC	.	PASS	Atlas-SNP
CLDN5	7122	hgsc.bcm.edu	37	22	19511925	19511925	+	Nonsense_Mutation	SNP	G	G	A	rs885985	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	27	20	18	0	0.740741	0	G|0.554;A|0.446	0.446	strong	.	CLDN5	22	.	NM_001130861	exon1	c.C109T	p.Q37X	CCTCCTGGGTCTG	.	PASS	Atlas-SNP
RPP38	10557	hgsc.bcm.edu	37	10	15145361	15145361	+	Silent	SNP	G	G	A	rs35539850	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	43	106	0	0.573333	0	T|0.000;G|0.863;C|0.000;A|0.136	0.136	strong	.	RPP38	26	.	NM_001265601	exon2	c.G48A	p.T16T	TAAGACGAGACCT	.	PASS	Atlas-SNP
PHF2	5253	hgsc.bcm.edu	37	9	96407920	96407920	+	Silent	SNP	C	C	T	rs7038310	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	44	21	47	0	0.477273	0	C|0.932;T|0.068	0.068	strong	.	PHF2	113	.	NM_005392	exon4	c.C309T	p.D103D	TGAAGACGTGGTG	.	PASS	Atlas-SNP
GPRIN1	114787	hgsc.bcm.edu	37	5	176026138	176026138	+	Missense_Mutation	SNP	T	T	A	rs201635586	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	125	35	171	0	0.28	0	T|0.795;A|0.205	0.205	strong	.	GPRIN1	77	.	NM_052899	exon2	c.A698T	p.E233V	GGATCCTCCTTCC	.	PASS	Atlas-SNP
UHRF1BP1	54887	hgsc.bcm.edu	37	6	34831856	34831856	+	Missense_Mutation	SNP	T	T	C	rs13205210	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	109	49	132	0	0.449541	0	T|0.851;C|0.149	0.149	strong	.	UHRF1BP1	102	.	NM_017754	exon15	c.T3293C	p.M1098T	TCTCCATGAAGAG	.	PASS	Atlas-SNP
NAV3	89795	hgsc.bcm.edu	37	12	78574783	78574783	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	103	18	120	0	0.174757	0	.	.	none	.	NAV3	506	.	NM_014903	exon29	c.C5584A	p.L1862I	TTAGGACTTTCTC	.	PASS	Atlas-SNP
SETX	23064	hgsc.bcm.edu	37	9	135139901	135139901	+	Missense_Mutation	SNP	T	T	C	rs1056899	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	48	22	70	0	0.458333	0	T|0.505;C|0.495	0.495	strong	.	SETX	234	.	NM_015046	exon26	c.A7759G	p.I2587V	GCTGTATATGGCT	.	PASS	Atlas-SNP
MCL1	4170	hgsc.bcm.edu	37	1	150550920	150550920	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	107	28	154	0	0.261682	0	.	.	none	.	MCL1	27	.	NM_021960	exon2	c.T736G	p.L246V	GAGACAACGATTT	.	PASS	Atlas-SNP
CEP152	22995	hgsc.bcm.edu	37	15	49048705	49048705	+	Missense_Mutation	SNP	G	G	C	rs16961560	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	50	19	49	0	0.38	0	G|0.933;C|0.067	0.067	strong	.	CEP152	145	.	NM_014985	exon20	c.C2740G	p.L914V	TTTCAAGCTCACT	.	PASS	Atlas-SNP
PTPRF	5792	hgsc.bcm.edu	37	1	44083519	44083519	+	Silent	SNP	G	G	A	rs641351	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	228	111	255	0	0.486842	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
IRX5	10265	hgsc.bcm.edu	37	16	54967096	54967096	+	Missense_Mutation	SNP	C	C	A	rs13336114	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	6	4	1	0	0.666667	0	C|0.632;A|0.368	0.368	strong	.	IRX5	41	.	NM_005853	exon3	c.C763A	p.P255T	AAGGAGCCGCCCT	.	PASS	Atlas-SNP
SYT6	148281	hgsc.bcm.edu	37	1	114680310	114680310	+	Missense_Mutation	SNP	G	G	A	rs41274114	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	167	85	192	0	0.508982	0	G|0.820;A|0.180	0.180	strong	.	SYT6	66	.	NM_205848	exon3	c.C623T	p.T208I	TCAAAGGTGGGGT	.	PASS	Atlas-SNP
MARCH10	162333	hgsc.bcm.edu	37	17	60813627	60813627	+	Silent	SNP	G	G	A	rs2041283	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	128	127	140	0	0.992188	0	G|0.692;A|0.308	0.308	strong	.	MARCH10	102	.	NM_001100875	exon6	c.C1602T	p.N534N	TGCACTGTTTACT	.	PASS	Atlas-SNP
SPTBN5	51332	hgsc.bcm.edu	37	15	42145049	42145049	+	Silent	SNP	C	C	T	rs55978013	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	204	118	134	0	0.578431	0	C|0.936;T|0.064	0.064	strong	.	SPTBN5	171	.	NM_016642	exon60	c.G10215A	p.E3405E	GAGTCCCTCCCAG	.	PASS	Atlas-SNP
SYNE1	23345	hgsc.bcm.edu	37	6	152529260	152529260	+	Silent	SNP	G	G	A	rs3798756	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	26	97	0	0.356164	0	G|0.854;A|0.146	0.146	strong	.	SYNE1	3227	.	NM_182961	exon125	c.C22671T	p.I7557I	GTCAATGATCCCC	.	PASS	Atlas-SNP
DTNB	1838	hgsc.bcm.edu	37	2	25655772	25655772	+	Silent	SNP	T	T	C	rs7583475	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	66	66	62	0	1	0	T|0.743;C|0.257	0.257	strong	.	DTNB	43	.	NM_021907	exon14	c.A1440G	p.A480A	CAGCTCTGCCAGC	.	PASS	Atlas-SNP
GALC	2581	hgsc.bcm.edu	37	14	88407888	88407888	+	Missense_Mutation	SNP	A	A	G	rs398607	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	106	46	110	0	0.433962	0	A|0.576;G|0.424	0.424	strong	.	GALC	48	.	NM_000153	exon15	c.T1685C	p.I562T	CACTTTATAGTCA	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	51	50	50	0	0.980392	0	G|0.595;T|0.005	.	strong	.	GOLGA1	60	.	NM_002077	exon14	c.C1274T	p.T425M	GCCCGCGTTCTCT	.	PASS	Atlas-SNP
SVEP1	79987	hgsc.bcm.edu	37	9	113191533	113191533	+	Silent	SNP	C	C	T	rs75212846	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	47	24	46	0	0.510638	0	C|0.963;T|0.037	0.037	strong	.	SVEP1	326	.	NM_153366	exon35	c.G5697A	p.V1899V	TTCACACACAGGA	.	PASS	Atlas-SNP
CDC42BPG	55561	hgsc.bcm.edu	37	11	64597205	64597205	+	Silent	SNP	G	G	T	rs7936466	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	10	7	7	0	0.7	0	G|0.734;T|0.266	0.266	strong	.	CDC42BPG	101	.	NM_017525	exon30	c.C3705A	p.G1235G	CCGGTCGCCCAGC	.	PASS	Atlas-SNP
CD82	3732	hgsc.bcm.edu	37	11	44640268	44640268	+	Missense_Mutation	SNP	A	A	G	rs1139971	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	63	12	65	0	0.190476	0	A|0.450;G|0.550	0.550	strong	.	CD82	27	.	NM_002231	exon9	c.A721G	p.I241V	GCCATCATCGAGG	.	PASS	Atlas-SNP
ADAMTS19	171019	hgsc.bcm.edu	37	5	129040056	129040056	+	Missense_Mutation	SNP	A	A	T	rs11749126	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	189	101	157	0	0.534392	0	A|0.890;T|0.110	0.110	strong	.	ADAMTS19	216	.	NM_133638	exon21	c.A3266T	p.Y1089F	AATGCTATGTGTG	.	PASS	Atlas-SNP
PTPN13	5783	hgsc.bcm.edu	37	4	87692393	87692393	+	Missense_Mutation	SNP	G	G	A	rs12500797	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	241	122	277	1	0.506224	0.00361011	G|0.939;A|0.061	0.061	strong	PTPN13,NS,carcinoma,-2,1	PTPN13	203	1	NM_080685	exon31	c.G4888A	p.E1630K	TGTGTGGAGCAAA	.	PASS	Atlas-SNP
C6orf136	221545	hgsc.bcm.edu	37	6	30615413	30615413	+	Silent	SNP	T	T	C	rs146616682	by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	67	44	59	0	0.656716	0	T|0.994;C|0.006	0.006	strong	.	C6orf136	31	.	NM_001161376	exon1	c.T405C	p.I135I	AGAGATTCGTAGC	.	PASS	Atlas-SNP
KRT84	3890	hgsc.bcm.edu	37	12	52777439	52777439	+	Silent	SNP	A	A	G	rs1614888	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	109	55	134	0	0.504587	0	A|0.686;G|0.314	0.314	strong	.	KRT84	61	.	NM_033045	exon2	c.T690C	p.S230S	CTGATCACTGACC	.	PASS	Atlas-SNP
HRG	3273	hgsc.bcm.edu	37	3	186390627	186390627	+	Missense_Mutation	SNP	C	C	T	rs9898	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	85	81	0	1	0	C|0.544;T|0.456	0.456	strong	HRG,NS,adenoma,0,1	HRG	81	1	NM_000412	exon5	c.C610T	p.P204S	AACTGCCCCAGAC	.	PASS	Atlas-SNP
SERPINI1	5274	hgsc.bcm.edu	37	3	167510472	167510472	+	Silent	SNP	G	G	A	rs2229697	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	132	69	158	0	0.522727	0	G|0.875;A|0.125	0.125	strong	.	SERPINI1	52	.	NM_005025	exon4	c.G576A	p.S192S	GAAGTCGCAGTTT	.	PASS	Atlas-SNP
CRYBG3	131544	hgsc.bcm.edu	37	3	97607290	97607290	+	Silent	SNP	G	G	A	rs13065340	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	106	42	136	1	0.396226	0.00735294	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	.	scavenged	Atlas-SNP
CFHR2	3080	hgsc.bcm.edu	37	1	196918741	196918741	+	Missense_Mutation	SNP	G	G	A	rs79351096	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	213	103	247	0	0.483568	0	G|0.983;A|0.017	0.017	strong	CFHR2_ENST00000367415,NS,carcinoma,-1,1	CFHR2	73	1	NM_005666	exon2	c.G215A	p.C72Y	TAACGTGCGCAGA	.	PASS	Atlas-SNP
VTN	7448	hgsc.bcm.edu	37	17	26694483	26694483	+	Silent	SNP	A	A	G	rs2227728	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	130	71	146	0	0.546154	0	A|0.881;G|0.119	0.119	strong	.	VTN	45	.	NM_000638	exon8	c.T1344C	p.N448N	GCGAAGATTGACT	.	PASS	Atlas-SNP
PSG8	440533	hgsc.bcm.edu	37	19	43269699	43269699	+	Missense_Mutation	SNP	C	C	T	rs7260508	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	13	9	24	0	0.692308	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
PTPN12	5782	hgsc.bcm.edu	37	7	77256150	77256150	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	178	37	189	0	0.207865	0	.	.	none	.	PTPN12	83	.	NM_002835	exon13	c.A1154G	p.D385G	ACAATGATAGATA	.	PASS	Atlas-SNP
CCDC79	283847	hgsc.bcm.edu	37	16	66792714	66792714	+	Missense_Mutation	SNP	T	T	C	rs363156	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	59	21	81	0	0.355932	0	T|0.651;C|0.349	0.349	strong	.	CCDC79	32	.	NM_001136505	exon18	c.A1958G	p.Q653R	AGTCGTTGTCTTC	.	PASS	Atlas-SNP
EHD2	30846	hgsc.bcm.edu	37	19	48219893	48219893	+	Silent	SNP	C	C	T	rs11550017	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	34	16	28	0	0.470588	0	C|0.939;T|0.061	0.061	strong	.	EHD2	59	.	NM_014601	exon2	c.C24T	p.G8G	GCGGGGCGGGGCA	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	103	53	178	0	0.514563	0	C|0.806;A|0.194	0.194	strong	.	DSG1	176	.	NM_001942	exon11	c.C1493A	p.T498N	CGAACACTAAAAT	.	PASS	Atlas-SNP
LRRC16B	90668	hgsc.bcm.edu	37	14	24529260	24529260	+	Silent	SNP	C	C	T	rs58283036	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	71	80	0	1	0	C|0.788;T|0.212	0.212	strong	.	LRRC16B	120	.	NM_138360	exon23	c.C1950T	p.D650D	CGAGGACGTCTGG	.	PASS	Atlas-SNP
C9orf173	441476	hgsc.bcm.edu	37	9	140147273	140147273	+	Missense_Mutation	SNP	C	C	T	rs61759822	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	32	80	0	0.426667	0	C|0.847;T|0.153	0.153	strong	.	C9orf173	19	.	NM_001004353	exon5	c.C652T	p.L218F	TCCCTGCTTCAGG	.	PASS	Atlas-SNP
DRAXIN	374946	hgsc.bcm.edu	37	1	11771988	11771988	+	Silent	SNP	A	A	G	rs17037327	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	59	23	65	0	0.38983	0	A|0.885;G|0.115	0.115	strong	.	.	.	.	NM_198545	exon4	c.A723G	p.L241L	AGACTTAAAACCT	.	PASS	Atlas-SNP
ALMS1	7840	hgsc.bcm.edu	37	2	73679990	73679990	+	Missense_Mutation	SNP	T	T	A	rs6724782	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	80	79	91	0	0.9875	0	T|0.691;A|0.309	0.309	strong	.	ALMS1	384	.	NM_015120	exon8	c.T6333A	p.S2111R	AGGTAGTCATGTA	.	PASS	Atlas-SNP
MEFV	4210	hgsc.bcm.edu	37	16	3297175	3297175	+	Silent	SNP	T	T	C	rs224207	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	192	27	175	0	0.140625	0	T|0.407;C|0.593	0.593	strong	MEFV_ENST00000541159,NS,carcinoma,-2,2	MEFV	170	2	NM_000243	exon5	c.A1428G	p.Q476Q	ATGCTCTTGCTGC	.	PASS	Atlas-SNP
GJA3	2700	hgsc.bcm.edu	37	13	20716411	20716411	+	Silent	SNP	C	C	T	rs11617415	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	64	43	57	0	0.671875	0	C|0.755;T|0.245	0.245	strong	GJA3,caecum,carcinoma,0,1	GJA3	32	1	NM_021954	exon2	c.G1017A	p.A339A	CTTGAGCGCCGGG	.	PASS	Atlas-SNP
ITIH3	3699	hgsc.bcm.edu	37	3	52833805	52833805	+	Missense_Mutation	SNP	C	C	A	rs3617	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	34	34	50	0	1	0	T|0.010;G|0.001	.	strong	ITIH3_ENST00000449956,NS,carcinoma,0,2	ITIH3	132	2	NM_002217	exon9	c.C943A	p.Q315K	GATATGCAAGAGG	.	PASS	Atlas-SNP
C1orf168	199920	hgsc.bcm.edu	37	1	57257817	57257817	+	Silent	SNP	T	T	C	rs2298130	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	114	61	107	0	0.535088	0	T|0.778;C|0.222	0.222	strong	.	C1orf168	102	.	NM_001004303	exon2	c.A669G	p.K223K	CCAGCTTTTTCTG	.	PASS	Atlas-SNP
KIAA0355	9710	hgsc.bcm.edu	37	19	34842488	34842488	+	Silent	SNP	T	T	C	rs392340	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	38	21	46	0	0.552632	0	T|0.473;C|0.527	0.527	strong	.	KIAA0355	105	.	NM_014686	exon13	c.T2895C	p.D965D	GGAGGATGTGAAC	.	PASS	Atlas-SNP
TRIOBP	11078	hgsc.bcm.edu	37	22	38119213	38119213	+	Missense_Mutation	SNP	G	G	A	rs12628603	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	49	76	0	0.532609	0	G|0.436;A|0.564	0.564	strong	.	TRIOBP	262	.	NM_001039141	exon7	c.G650A	p.S217N	GCCGGAGCGCAGG	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29911228	29911228	+	Missense_Mutation	SNP	A	A	C	rs9256983	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	136	50	274	1	0.367647	0.00364964	A|0.277;C|0.043;G|0.004;T|0.676	0.043	strong	.	HLA-A	89	.	NM_001242758	exon3	c.A527C	p.E176A	CCCATGAGGCGGA	.	PASS	Atlas-SNP
CCDC110	256309	hgsc.bcm.edu	37	4	186380295	186380295	+	Silent	SNP	A	A	G	rs36007437	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	42	130	0	0.482759	0	A|0.623;G|0.377	0.377	strong	.	CCDC110	78	.	NM_152775	exon6	c.T1446C	p.N482N	AACCAGATTCTTA	.	PASS	Atlas-SNP
SLIT2	9353	hgsc.bcm.edu	37	4	20493415	20493415	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	106	32	147	0	0.301887	0	.	.	none	.	SLIT2	290	.	NM_004787	exon9	c.T807A	p.S269R	TTGTAGTGTTTTG	.	PASS	Atlas-SNP
WDR4	10785	hgsc.bcm.edu	37	21	44270229	44270229	+	Missense_Mutation	SNP	C	C	T	rs6586250	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	77	40	58	0	0.519481	0	C|0.748;T|0.252	0.252	strong	.	WDR4	35	.	NM_018669	exon11	c.G1169A	p.R390Q	GGACTCCGGCGCC	.	PASS	Atlas-SNP
MTDH	92140	hgsc.bcm.edu	37	8	98656966	98656966	+	Missense_Mutation	SNP	G	G	T	rs17854373	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	8	8	2	0	1	0	G|0.973;T|0.027	0.027	strong	MTDH,NS,carcinoma,0,1	MTDH	54	1	NM_178812	exon1	c.G232T	p.A78S	GCCGGCGCCCGCA	.	PASS	Atlas-SNP
CCDC90B	60492	hgsc.bcm.edu	37	11	82973004	82973004	+	Silent	SNP	C	C	T	rs8789	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	110	87	112	0	0.790909	0	C|0.508;A|0.022	.	strong	.	CCDC90B	20	.	NM_021825	exon9	c.G714A	p.S238S	AAACACCGAAGCT	.	PASS	Atlas-SNP
EPHX1	2052	hgsc.bcm.edu	37	1	226026406	226026406	+	Missense_Mutation	SNP	A	A	G	rs2234922	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	74	35	86	0	0.472973	0	A|0.779;G|0.221	0.221	strong	.	EPHX1	57	.	NM_001136018	exon4	c.A416G	p.H139R	CAGGCCATACCCC	.	PASS	Atlas-SNP
SPICE1	152185	hgsc.bcm.edu	37	3	113169205	113169205	+	Silent	SNP	C	C	T	rs11920725	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	111	50	156	0	0.45045	0	C|0.931;T|0.069	0.069	strong	.	SPICE1	130	.	NM_144718	exon15	c.G2301A	p.Q767Q	AGGTAACTGAACA	.	PASS	Atlas-SNP
HLA-G	3135	hgsc.bcm.edu	37	6	29795657	29795657	+	Silent	SNP	G	G	A	rs1630185	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	112	107	114	0	0.955357	0	G|0.518;A|0.482	0.482	strong	.	HLA-G	90	.	NM_002127	exon2	c.G36A	p.L12L	CCTGCTGCTCTCG	.	PASS	Atlas-SNP
SRSF4	6429	hgsc.bcm.edu	37	1	29475341	29475341	+	Missense_Mutation	SNP	C	C	T	rs2230678	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	69	95	0	1	0	C|0.384;T|0.616	0.616	strong	.	SRSF4	44	.	NM_005626	exon6	c.G1066A	p.G356S	TCCTGCCCTTCCT	.	PASS	Atlas-SNP
TEX35	84066	hgsc.bcm.edu	37	1	178489978	178489978	+	Missense_Mutation	SNP	T	T	G	rs3813636	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	159	157	222	0	0.987421	0	C|0.001;G|0.385;T|0.614	0.385	strong	TEX35,NS,carcinoma,0,3	TEX35	15	3	NM_001170722	exon7	c.T536G	p.L179R	GCTCACTGGATCC	.	PASS	Atlas-SNP
RNF150	57484	hgsc.bcm.edu	37	4	141789457	141789457	+	Silent	SNP	T	T	A	rs61744098	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	174	91	203	0	0.522988	0	T|0.961;A|0.039	0.039	strong	.	RNF150	94	.	NM_020724	exon7	c.A1275T	p.V425V	AAGTTCTACATCA	.	PASS	Atlas-SNP
TACC2	10579	hgsc.bcm.edu	37	10	123903133	123903133	+	Missense_Mutation	SNP	G	G	A	rs12765679	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	59	26	62	0	0.440678	0	G|0.854;A|0.146	0.146	strong	.	TACC2	271	.	NM_206862	exon7	c.G5746A	p.E1916K	GCTGCAGAACACA	.	PASS	Atlas-SNP
TTC29	83894	hgsc.bcm.edu	37	4	147788728	147788728	+	Silent	SNP	G	G	A	rs35231662	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	179	77	220	0	0.430168	0	G|0.938;A|0.062	0.062	strong	.	TTC29	63	.	NM_031956	exon8	c.C807T	p.D269D	CTTTTTGTCACTT	.	PASS	Atlas-SNP
TEP1	7011	hgsc.bcm.edu	37	14	20849169	20849169	+	Silent	SNP	G	G	A	rs2228039	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	109	52	104	0	0.477064	0	G|0.935;A|0.065	0.065	strong	.	TEP1	224	.	NM_007110	exon33	c.C4683T	p.F1561F	GGTAAGGAACTTC	.	PASS	Atlas-SNP
NOTCH3	4854	hgsc.bcm.edu	37	19	15295134	15295134	+	Silent	SNP	G	G	A	rs1043996	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	128	127	122	0	0.992188	0	G|0.460;T|0.004	.	strong	NOTCH3_ENST00000263388,colon,carcinoma,-2,2	NOTCH3	340	2	NM_000435	exon16	c.C2538T	p.C846C	CTGATCGCAGGAA	.	PASS	Atlas-SNP
ZNF573	126231	hgsc.bcm.edu	37	19	38230720	38230720	+	Missense_Mutation	SNP	C	C	G	rs3752365	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	46	23	64	0	0.5	0	C|0.852;G|0.148	0.148	strong	.	ZNF573	63	.	NM_001172690	exon5	c.G671C	p.G224A	GCCTTCCCACACT	.	PASS	Atlas-SNP
TYW1	55253	hgsc.bcm.edu	37	7	66660247	66660247	+	Silent	SNP	T	T	C	rs71563186		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	130	31	204	0	0.238462	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
TMEM127	55654	hgsc.bcm.edu	37	2	96919642	96919642	+	Silent	SNP	C	C	T	rs3852673	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	165	74	157	0	0.448485	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
AGAP1	116987	hgsc.bcm.edu	37	2	236817442	236817442	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	153	20	116	0	0.130719	0	.	.	none	.	AGAP1	95	.	NM_014914	exon11	c.C1216T	p.P406S	AAAGTCCCAGGGA	.	PASS	Atlas-SNP
FAM194B	220081	hgsc.bcm.edu	37	13	46170609	46170609	+	Missense_Mutation	SNP	C	C	T	rs3014939	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	99	47	134	0	0.474747	0	C|0.695;T|0.305	0.305	strong	.	FAM194B	42	.	NM_182542	exon3	c.G532A	p.E178K	TTTCCTCTTCTAG	.	PASS	Atlas-SNP
HIPK2	28996	hgsc.bcm.edu	37	7	139316360	139316360	+	Silent	SNP	C	C	T	rs28579164	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	48	120	0	0.64	0	C|0.834;T|0.166	0.166	strong	.	HIPK2	192	.	NM_022740	exon3	c.G1215A	p.S405S	ATACTCCGAAGCT	.	PASS	Atlas-SNP
C11orf86	254439	hgsc.bcm.edu	37	11	66743098	66743098	+	Missense_Mutation	SNP	C	C	T	rs118060724	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	44	32	54	0	0.727273	0	C|0.969;T|0.031	0.031	strong	.	C11orf86	7	.	NM_001136485	exon1	c.C265T	p.R89W	CTGAGGCGGTACC	.	PASS	Atlas-SNP
SPHKAP	80309	hgsc.bcm.edu	37	2	228883721	228883721	+	Missense_Mutation	SNP	T	T	C	rs3811514	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	98	98	105	0	1	0	T|0.388;C|0.612	0.612	strong	.	SPHKAP	750	.	NM_030623	exon7	c.A1849G	p.K617E	ATCCCTTGGCAAT	.	PASS	Atlas-SNP
SACS	26278	hgsc.bcm.edu	37	13	23908034	23908034	+	Silent	SNP	A	A	G	rs2737700	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	95	47	90	0	0.494737	0	A|0.664;G|0.336	0.336	strong	.	SACS	871	.	NM_014363	exon10	c.T9981C	p.A3327A	ACAGCCAGCTTTC	.	PASS	Atlas-SNP
PRAMEF4	400735	hgsc.bcm.edu	37	1	12942119	12942119	+	Missense_Mutation	SNP	C	C	T	rs75355616	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	41	18	42	0	0.439024	0	C|0.785;T|0.215	0.215	strong	.	PRAMEF4	62	.	NM_001009611	exon3	c.G431A	p.R144K	CGTCCTCTCATCC	.	PASS	Atlas-SNP
CRISPLD2	83716	hgsc.bcm.edu	37	16	84922859	84922859	+	Silent	SNP	C	C	T	rs767050	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	74	74	62	0	1	0	T|0.620;G|0.006	0.620	strong	CRISPLD2,NS,carcinoma,0,1	CRISPLD2	36	1	NM_031476	exon14	c.C1329T	p.A443A	GACAGCCGTGCAC	.	PASS	Atlas-SNP
XRCC1	7515	hgsc.bcm.edu	37	19	44057574	44057574	+	Missense_Mutation	SNP	G	G	A	rs1799782	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	50	126	0	0.49505	0	G|0.905;A|0.095	0.095	strong	.	XRCC1	47	.	NM_006297	exon6	c.C580T	p.R194W	TGATCCGGCTGAA	.	PASS	Atlas-SNP
CLPSL1	340204	hgsc.bcm.edu	37	6	35755658	35755658	+	Silent	SNP	A	A	G	rs12211728	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	91	53	0	0.98913	0	A|0.641;G|0.359	0.359	strong	.	.	.	.	NM_001010886	exon3	c.A237G	p.Q79Q	TGGCCAATATAGA	.	PASS	Atlas-SNP
CDHR3	222256	hgsc.bcm.edu	37	7	105615426	105615426	+	Missense_Mutation	SNP	G	G	C	rs34426483	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	212	91	234	0	0.429245	0	G|0.824;C|0.176	0.176	strong	.	CDHR3	153	.	NM_152750	exon2	c.G183C	p.Q61H	TCCCCAGATAGTC	.	PASS	Atlas-SNP
ZNF442	79973	hgsc.bcm.edu	37	19	12461745	12461745	+	Silent	SNP	A	A	G	rs117398535	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	46	18	54	0	0.391304	0	A|0.995;G|0.005	0.005	strong	ZNF442,middle_lobe,carcinoma,0,1	ZNF442	102	1	NM_030824	exon6	c.T654C	p.F218F	CCAAAAAAAGGCT	.	PASS	Atlas-SNP
CDCA2	157313	hgsc.bcm.edu	37	8	25364331	25364331	+	Missense_Mutation	SNP	G	G	A	rs4872318	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	52	39	59	0	0.75	0	G|0.761;A|0.239	0.239	strong	.	CDCA2	78	.	NM_152562	exon15	c.G2149A	p.V717I	GCTTCTGTAACTG	.	PASS	Atlas-SNP
SMCR9	140776	hgsc.bcm.edu	37	17	17326605	17326605	+	Silent	SNP	A	A	G	rs7225831	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	23	10	18	0	0.434783	0	A|0.600;G|0.400	0.400	strong	.	.	.	.	NM_001243312	exon3	c.A420G	p.A140A	TGGGGCAAATGCC	.	PASS	Atlas-SNP
BRD3	8019	hgsc.bcm.edu	37	9	136915508	136915508	+	Silent	SNP	C	C	T	rs2301576	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	31	19	40	0	0.612903	0	C|0.923;T|0.077	0.077	strong	.	BRD3	82	.	NM_007371	exon5	c.G702A	p.P234P	GACAGGCGGCGTA	.	PASS	Atlas-SNP
PCSK9	255738	hgsc.bcm.edu	37	1	55505679	55505679	+	Missense_Mutation	SNP	G	G	A	rs145886902	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	106	22	87	0	0.207547	0	G|0.999;A|0.001	0.001	strong	.	PCSK9	76	.	NM_174936	exon1	c.G169A	p.E57K	GCACCCGAGCACG	.	PASS	Atlas-SNP
BMP1	649	hgsc.bcm.edu	37	8	22054197	22054197	+	Silent	SNP	T	T	C	rs2229777	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	64	15	46	0	0.234375	0	A|0.000;C|0.125;T|0.875	0.125	strong	.	BMP1	131	.	NM_001199	exon14	c.T1770C	p.A590A	AGCTGCTTGTGGC	.	PASS	Atlas-SNP
P2RX4	5025	hgsc.bcm.edu	37	12	121660787	121660787	+	Silent	SNP	T	T	C	rs25643	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	109	58	127	0	0.53211	0	C|0.421;N|0.000;T|0.579	0.421	strong	P2RX4,NS,carcinoma,0,1	P2RX4	27	1	NM_001256796	exon6	c.T513C	p.S171S	CGGGTCTGTCAAG	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	186	186	227	0	1	0	0|0.015;A|0.479	0.479	strong	.	GPR112	459	.	NM_153834	exon6	c.C3638A	p.T1213N	ATGAGACCACACC	.	PASS	Atlas-SNP
ABCA4	24	hgsc.bcm.edu	37	1	94467447	94467447	+	Silent	SNP	G	G	A	rs1801359	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	46	108	0	0.5	0	G|0.860;A|0.140	0.140	strong	.	ABCA4	275	.	NM_000350	exon45	c.C6249T	p.I2083I	GAGTGCGATGGCT	.	PASS	Atlas-SNP
SLC35G6	643664	hgsc.bcm.edu	37	17	7386234	7386234	+	Missense_Mutation	SNP	G	G	A	rs200251320	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	124	21	150	0	0.169355	0	G|0.793;A|0.207	0.207	strong	POLR2A_ENST00000412468,extremity,malignant_melanoma,0,1	.	.	1	NM_001102614	exon2	c.G931A	p.V311M	GACATCGTGGGGG	.	scavenged	Atlas-SNP
MLL2	8085	hgsc.bcm.edu	37	12	49427919	49427919	+	Silent	SNP	T	T	C	rs61942218	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	65	35	83	0	0.538462	0	T|0.964;C|0.036	0.036	strong	.	MLL2	1173	.	NM_003482	exon38	c.A10671G	p.P3557P	AGCTTCTGGGAAC	.	PASS	Atlas-SNP
GPAA1	8733	hgsc.bcm.edu	37	8	145139727	145139727	+	Silent	SNP	C	C	T	rs4977165	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	85	100	0	1	0	C|0.892;T|0.108	0.108	strong	.	GPAA1	40	.	NM_003801	exon8	c.C1113T	p.I371I	CTCCATCGGCCTC	.	PASS	Atlas-SNP
KRT6B	3854	hgsc.bcm.edu	37	12	52841179	52841179	+	Missense_Mutation	SNP	T	T	C	rs61746354	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	83	48	84	0	0.578313	0	T|0.961;C|0.039	0.039	strong	.	KRT6B	90	.	NM_005555	exon9	c.A1490G	p.Y497C	CCGCCATAGCCAC	.	PASS	Atlas-SNP
DOPEY1	23033	hgsc.bcm.edu	37	6	83810482	83810482	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	305	4	305	2	0.0131148	0.00655738	.	.	none	DOPEY1,caecum,carcinoma,+1,3	DOPEY1	190	3	NM_015018	exon4	c.G197A	p.R66H	GCAAACGCCTAGC	.	scavenged	Atlas-SNP
B4GALNT1	2583	hgsc.bcm.edu	37	12	58025813	58025813	+	Silent	SNP	G	G	C	rs774896	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	18	12	15	0	0.666667	0	G|0.665;C|0.335	0.335	strong	.	B4GALNT1	53	.	NM_001478	exon2	c.G103G	p.A35A	GAGGTAGCCGGAG	.	PASS	Atlas-SNP
ACAN	176	hgsc.bcm.edu	37	15	89402051	89402051	+	Missense_Mutation	SNP	A	A	G	rs1042630	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	76	76	63	0	1	0	A|0.343;G|0.657	0.657	strong	ACAN,NS,carcinoma,0,1	ACAN	220	1	NM_001135	exon12	c.A6235G	p.I2079V	GGGGACATTAGTG	.	PASS	Atlas-SNP
SLC5A11	115584	hgsc.bcm.edu	37	16	24888593	24888593	+	Silent	SNP	A	A	G	rs8052587	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	225	160	202	1	0.711111	0.00495049	A|0.850;G|0.150	0.150	strong	.	SLC5A11	97	.	NM_052944	exon7	c.A492G	p.A164A	GTATGCAGGTGCC	.	PASS	Atlas-SNP
RTN2	6253	hgsc.bcm.edu	37	19	45998247	45998247	+	Silent	SNP	A	A	G	rs10401270	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	57	33	59	0	0.578947	0	A|0.870;G|0.130	0.130	strong	.	RTN2	45	.	NM_206900	exon3	c.T96C	p.S32S	AAAATCAGAGTCG	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	60	30	126	0	0.5	0	G|0.732;A|0.268	0.268	strong	.	UNC93A	66	.	NM_018974	exon6	c.G874A	p.V292I	CAGTTCGTCGGCT	.	PASS	Atlas-SNP
TIMP3	7078	hgsc.bcm.edu	37	22	33253292	33253292	+	Silent	SNP	C	C	T	rs11547635	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	198	96	200	0	0.484848	0	C|0.870;N|0.000	.	strong	.	TIMP3	31	.	NM_000362	exon3	c.C261T	p.S87S	AGCTTCCGAGAGT	.	PASS	Atlas-SNP
TRIM25	7706	hgsc.bcm.edu	37	17	54978794	54978794	+	Missense_Mutation	SNP	G	G	A	rs205498	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	110	56	178	0	0.509091	0	G|0.231;A|0.769	0.769	strong	.	TRIM25	52	.	NM_005082	exon4	c.C1073T	p.P358L	GGGGTGGGCTCCT	.	PASS	Atlas-SNP
FGFBP2	83888	hgsc.bcm.edu	37	4	15964501	15964501	+	Silent	SNP	G	G	A	rs2286459	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	12	5	16	0	0.416667	0	G|0.528;A|0.472	0.472	strong	.	FGFBP2	22	.	NM_031950	exon1	c.C252T	p.F84F	AGCAGCGAAAGCC	.	PASS	Atlas-SNP
TMEM213	155006	hgsc.bcm.edu	37	7	138486096	138486096	+	Missense_Mutation	SNP	G	G	C	rs61729750	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	50	50	81	0	1	0	G|0.334;C|0.666	0.666	strong	.	TMEM213	20	.	NM_001085429	exon2	c.G107C	p.S36T	GCTCAAGCTTGAC	.	PASS	Atlas-SNP
PADI2	11240	hgsc.bcm.edu	37	1	17413152	17413152	+	Missense_Mutation	SNP	C	C	T	rs61749340	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	117	58	109	0	0.495726	0	C|0.994;T|0.006	0.006	strong	.	PADI2	72	.	NM_007365	exon7	c.G698A	p.R233Q	AGCTTCCGCCGGC	.	PASS	Atlas-SNP
HLA-DPB1	3115	hgsc.bcm.edu	37	6	33052981	33052981	+	Missense_Mutation	SNP	C	C	A	rs14362	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	158	85	190	0	0.537975	0	C|0.874;A|0.126	0.126	strong	.	HLA-DPB1	28	.	NM_002121	exon3	c.C619A	p.L207M	ACCAGCCTGGATA	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228494790	228494790	+	Missense_Mutation	SNP	G	G	A	rs435776	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	303	138	321	0	0.455446	0	G|0.711;A|0.289	0.289	strong	OBSCN_ENST00000570156,NS,carcinoma,0,2	OBSCN	2142	2	NM_001271223	exon56	c.G14986A	p.G4996R	GTACGCGGAGTGG	.	PASS	Atlas-SNP
SMC1B	27127	hgsc.bcm.edu	37	22	45767421	45767421	+	Missense_Mutation	SNP	C	C	T	rs56174639	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	170	76	209	0	0.447059	0	C|0.874;T|0.126	0.126	strong	.	SMC1B	215	.	NM_148674	exon14	c.G2243A	p.C748Y	ATAATACATTGAG	.	PASS	Atlas-SNP
TP53BP1	7158	hgsc.bcm.edu	37	15	43748304	43748304	+	Silent	SNP	A	A	G	rs690367	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	156	54	150	0	0.346154	0	A|0.491;G|0.509	0.509	strong	.	TP53BP1	157	.	NM_001141980	exon12	c.T2502C	p.D834D	TGAAGAATCTTGC	.	PASS	Atlas-SNP
ANK3	288	hgsc.bcm.edu	37	10	61868716	61868716	+	Silent	SNP	C	C	A	rs3750800	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	96	51	128	0	0.53125	0	C|0.791;A|0.209	0.209	strong	.	ANK3	703	.	NM_001204404	exon28	c.G3048T	p.T1016T	GGGGGCCGTACAC	.	PASS	Atlas-SNP
INSRR	3645	hgsc.bcm.edu	37	1	156814027	156814027	+	Missense_Mutation	SNP	G	G	A	rs56252149	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	44	25	42	0	0.568182	0	G|0.826;A|0.174	0.174	strong	INSRR_ENST00000368195,NS,carcinoma,0,2	INSRR	309	2	NM_014215	exon15	c.C2783T	p.P928L	CCCACAGGGGTGG	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	112	49	139	0	0.4375	0	T|0.409;G|0.591	0.591	strong	.	USH2A	1168	.	NM_206933	exon52	c.A10232C	p.E3411A	CAATGTTCTGTGG	.	PASS	Atlas-SNP
KIAA1524	57650	hgsc.bcm.edu	37	3	108295135	108295135	+	Missense_Mutation	SNP	G	G	T	rs116097126	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	105	58	119	0	0.552381	0	G|0.987;T|0.013	0.013	strong	.	KIAA1524	82	.	NM_020890	exon8	c.C877A	p.P293T	AATCAGGATCCTT	.	PASS	Atlas-SNP
GHR	2690	hgsc.bcm.edu	37	5	42719344	42719344	+	Missense_Mutation	SNP	C	C	A	rs6184	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	249	155	227	1	0.62249	0.00440529	C|0.974;A|0.026	0.026	strong	GHR,NS,carcinoma,-2,1	GHR	94	1	NM_001242399	exon10	c.C1756A	p.P586T	GGGAGGCCTGGGA	.	PASS	Atlas-SNP
CDHR5	53841	hgsc.bcm.edu	37	11	617378	617378	+	Silent	SNP	C	C	T	rs61877856	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	76	52	62	0	0.684211	0	C|0.680;T|0.320	0.320	strong	.	CDHR5	77	.	NM_021924	exon15	c.G2511A	p.A837A	ACCGGGCGCATCG	.	PASS	Atlas-SNP
MICA	100507436	hgsc.bcm.edu	37	6	31380153	31380153	+	Missense_Mutation	SNP	T	T	C	rs199843678	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	81	7	139	3	0.0864198	0.0215827	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	.	scavenged	Atlas-SNP
KDELC1	79070	hgsc.bcm.edu	37	13	103450973	103450973	+	Silent	SNP	T	T	C	rs7994595	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	45	22	83	0	0.488889	0	T|0.916;C|0.084	0.084	strong	.	KDELC1	66	.	NM_024089	exon1	c.A48G	p.P16P	GAGTGCTGGAACT	.	PASS	Atlas-SNP
RELN	5649	hgsc.bcm.edu	37	7	103162607	103162607	+	Silent	SNP	G	G	A	rs2075038	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	100	47	87	0	0.47	0	G|0.964;A|0.036	0.036	strong	.	RELN	593	.	NM_173054	exon48	c.C7530T	p.P2510P	GGTCTCGGGGTCA	.	PASS	Atlas-SNP
SYCP2L	221711	hgsc.bcm.edu	37	6	10906256	10906256	+	Silent	SNP	A	A	G	rs4713039	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	51	32	57	0	0.627451	0	A|0.797;G|0.202	0.202	strong	.	SYCP2L	101	.	NM_001040274	exon9	c.A645G	p.K215K	CAGGAAAGACCTT	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105417766	105417766	+	Missense_Mutation	SNP	G	G	A	rs2396457	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	63	63	0	0	1	.	G|0.824;A|0.176	0.176	strong	.	AHNAK2	719	.	NM_138420	exon7	c.C4022T	p.S1341F	GGGGCAGACACCC	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	37	73	0	0.513889	0	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	.	PASS	Atlas-SNP
SIX5	147912	hgsc.bcm.edu	37	19	46268902	46268902	+	Missense_Mutation	SNP	C	C	T	rs2341097	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	123	61	145	0	0.495935	0	C|0.678;T|0.322	0.322	strong	SIX5,NS,carcinoma,0,1	SIX5	35	1	NM_175875	exon3	c.G2077A	p.V693M	TCAGCACGGTGTG	.	PASS	Atlas-SNP
DLC1	10395	hgsc.bcm.edu	37	8	12957475	12957475	+	Missense_Mutation	SNP	C	C	T	rs532841	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	21	21	43	0	1	0	C|0.490;T|0.510	0.510	strong	DLC1,NS,carcinoma,0,1	DLC1	411	1	NM_182643	exon9	c.G2371A	p.V791M	GCTCCACCACGTT	.	PASS	Atlas-SNP
WDR65	149465	hgsc.bcm.edu	37	1	43675467	43675467	+	Silent	SNP	G	G	A	rs2453412	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	144	142	208	0	0.986111	0	G|0.250;A|0.750	0.750	strong	.	WDR65	76	.	NM_152498	exon11	c.G1809A	p.S603S	CATCTCGCATTCT	.	PASS	Atlas-SNP
TLN2	83660	hgsc.bcm.edu	37	15	63125804	63125804	+	Silent	SNP	G	G	A	rs142793310	byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	84	24	130	0	0.285714	0	G|1.000;A|0.000	0.000	strong	.	TLN2	253	.	NM_015059	exon52	c.G7104A	p.Q2368Q	AGCCCAGAGGGAG	.	PASS	Atlas-SNP
SGCG	6445	hgsc.bcm.edu	37	13	23808782	23808782	+	Silent	SNP	T	T	C	rs1800350	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	84	43	143	0	0.511905	0	T|0.859;C|0.141	0.141	strong	.	SGCG	64	.	NM_000231	exon3	c.T228C	p.D76D	AAAAGATGGACTG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195509880	195509880	+	Silent	SNP	C	C	T	rs201889850		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	132	19	122	0	0.143939	0	.	.	weak	.	MUC4	1505	.	NM_018406	exon2	c.G8571A	p.V2857V	TGTGGACACTGAG	.	PASS	Atlas-SNP
ST3GAL4	6484	hgsc.bcm.edu	37	11	126277216	126277216	+	Silent	SNP	C	C	T	rs2230278	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	118	83	150	0	0.70339	0	C|0.657;T|0.343	0.343	strong	.	ST3GAL4	25	.	NM_001254757	exon5	c.C252T	p.Y84Y	TGCTTACGAGCTG	.	PASS	Atlas-SNP
WBSCR28	135886	hgsc.bcm.edu	37	7	73279482	73279482	+	Missense_Mutation	SNP	T	T	C	rs13227841	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	76	74	91	0	0.973684	0	T|0.403;C|0.597	0.597	strong	.	WBSCR28	24	.	NM_182504	exon2	c.T232C	p.W78R	GCTCTCTGGGCTG	.	PASS	Atlas-SNP
MAP3K1	4214	hgsc.bcm.edu	37	5	56155672	56155672	+	Missense_Mutation	SNP	A	A	G	rs56069227	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	206	128	225	0	0.621359	0	A|0.976;G|0.024	0.024	strong	.	MAP3K1	355	.	NM_005921	exon3	c.A764G	p.N255S	CTGGCAACTCCCC	.	PASS	Atlas-SNP
LRIT1	26103	hgsc.bcm.edu	37	10	85992511	85992511	+	Silent	SNP	T	T	C	rs3814209	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	73	135	0	1	0	T|0.496;C|0.503	0.503	strong	LRIT1,right_upper_lobe,carcinoma,-1,1	LRIT1	73	1	NM_015613	exon4	c.A1044G	p.P348P	AGTCGGTGGCTCA	.	PASS	Atlas-SNP
PGLYRP2	114770	hgsc.bcm.edu	37	19	15582863	15582863	+	Missense_Mutation	SNP	C	C	T	rs34440547	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	42	29	64	0	0.690476	0	C|0.808;T|0.192	0.192	strong	.	PGLYRP2	116	.	NM_052890	exon3	c.G1181A	p.R394Q	CGGCCCCGATAAG	.	PASS	Atlas-SNP
EFHB	151651	hgsc.bcm.edu	37	3	19961331	19961331	+	Silent	SNP	T	T	C	rs2929362	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	191	97	218	0	0.507853	0	T|0.652;G|0.040;C|0.133;A|0.175	0.133	strong	.	EFHB	186	.	NM_144715	exon3	c.A990G	p.S330S	CAGTACTGAAATT	.	PASS	Atlas-SNP
SGIP1	84251	hgsc.bcm.edu	37	1	67109335	67109335	+	Missense_Mutation	SNP	A	A	G	rs7526812	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	112	55	143	0	0.491071	0	A|0.749;G|0.251	0.251	strong	SGIP1,NS,carcinoma,0,1	SGIP1	272	1	NM_032291	exon7	c.A392G	p.K131R	TTCTTAAGAATGC	.	PASS	Atlas-SNP
NSD1	64324	hgsc.bcm.edu	37	5	176721151	176721151	+	Missense_Mutation	SNP	T	T	C	rs34165241	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	29	81	0	0.337209	0	T|0.952;C|0.048	0.048	strong	.	NSD1	416	.	NM_022455	exon23	c.T6782C	p.M2261T	ACCAGATGCTGTC	.	PASS	Atlas-SNP
KCNK12	56660	hgsc.bcm.edu	37	2	47748558	47748558	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	170	43	74	0	0.252941	0	.	.	none	.	KCNK12	11	.	NM_022055	exon2	c.G781A	p.D261N	CCAGGTCCCCGAA	.	PASS	Atlas-SNP
IL7R	3575	hgsc.bcm.edu	37	5	35871273	35871273	+	Silent	SNP	C	C	T	rs2228141	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	118	47	118	0	0.398305	0	C|0.867;G|0.000;T|0.133	0.133	strong	.	IL7R	200	.	NM_002185	exon4	c.C495T	p.H165H	AATGCACGATGTA	.	PASS	Atlas-SNP
TTC9C	283237	hgsc.bcm.edu	37	11	62496519	62496519	+	Silent	SNP	T	T	C	rs584845	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	144	27	175	0	0.1875	0	T|0.690;C|0.310	0.310	strong	.	TTC9C	12	.	NM_173810	exon1	c.T199C	p.L67L	AACATATTGCATA	.	PASS	Atlas-SNP
RALGDS	5900	hgsc.bcm.edu	37	9	135982088	135982088	+	Silent	SNP	A	A	C	rs2073822	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	130	74	136	0	0.569231	0	A|0.759;C|0.241	0.241	strong	.	RALGDS	75	.	NM_006266	exon8	c.T1461G	p.S487S	CAGGGCAGAGAGG	.	PASS	Atlas-SNP
ADAMTS7	11173	hgsc.bcm.edu	37	15	79069121	79069121	+	Silent	SNP	A	A	G	rs11854507	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	45	68	0	0.529412	0	A|0.706;G|0.294	0.294	strong	.	ADAMTS7	142	.	NM_014272	exon10	c.T1530C	p.A510A	GTCCACAGCTGCA	.	PASS	Atlas-SNP
TMEM140	55281	hgsc.bcm.edu	37	7	134849213	134849213	+	Missense_Mutation	SNP	G	G	A	rs3800592	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	150	148	179	0	0.986667	0	G|0.536;A|0.464	0.464	strong	.	TMEM140	18	.	NM_018295	exon2	c.G20A	p.R7Q	GGCCTCGGTGGCG	.	PASS	Atlas-SNP
STRC	161497	hgsc.bcm.edu	37	15	43897499	43897499	+	Missense_Mutation	SNP	T	T	C	rs56042996		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	408	137	373	1	0.335784	0.00268097	.	.	weak	.	STRC	58	.	NM_153700	exon19	c.A3893G	p.H1298R	GCCTGGTGGAGGG	.	PASS	Atlas-SNP
NELFCD	51497	hgsc.bcm.edu	37	20	57564695	57564695	+	Silent	SNP	C	C	T	rs17851253	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	99	54	122	0	0.545455	0	C|0.929;T|0.071	0.071	strong	TH1L,colon,carcinoma,+1,2	.	.	2	NM_198976	exon6	c.C711T	p.A237A	GTTTGCCGTAAGT	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29911063	29911063	+	Missense_Mutation	SNP	T	T	G	rs199474485	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	108	40	191	0	0.37037	0	G|0.303;T|0.697	0.303	strong	.	HLA-A	89	.	NM_001242758	exon3	c.T362G	p.I121R	TCCAGATAATGTA	.	PASS	Atlas-SNP
PTPRZ1	5803	hgsc.bcm.edu	37	7	121616250	121616250	+	Silent	SNP	G	G	A	rs4629793	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	38	72	0	0.527778	0	G|0.681;A|0.319	0.319	strong	.	PTPRZ1	605	.	NM_001206838	exon5	c.G480A	p.A160A	TGATGCGGACCGA	.	PASS	Atlas-SNP
SREBF2	6721	hgsc.bcm.edu	37	22	42293140	42293140	+	Missense_Mutation	SNP	G	G	C	rs2228313	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	39	23	50	0	0.589744	0	G|0.936;C|0.064	0.064	strong	.	SREBF2	99	.	NM_004599	exon14	c.G2580C	p.R860S	CTCCAGGAGCTCC	.	PASS	Atlas-SNP
GOLGB1	2804	hgsc.bcm.edu	37	3	121386377	121386377	+	Missense_Mutation	SNP	T	T	A	rs144495540	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	248	115	264	1	0.46371	0.00378788	T|0.999;A|0.001	0.001	strong	.	GOLGB1	319	.	NM_001256486	exon20	c.A9515T	p.D3172V	CTTTGGTCTCGTT	.	PASS	Atlas-SNP
CCDC13	152206	hgsc.bcm.edu	37	3	42772038	42772038	+	Missense_Mutation	SNP	A	A	T	rs12495805	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	120	57	105	0	0.475	0	A|0.792;T|0.208	0.208	strong	.	CCDC13	71	.	NM_144719	exon13	c.T1639A	p.S547T	TCTCTGACACTTG	.	PASS	Atlas-SNP
TCOF1	6949	hgsc.bcm.edu	37	5	149755744	149755744	+	Missense_Mutation	SNP	G	G	C	rs2071240	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	111	56	118	0	0.504505	0	G|0.948;C|0.052	0.052	strong	.	TCOF1	154	.	NM_001135243	exon13	c.G1993C	p.A665P	ACCCAAGCCCCCC	.	PASS	Atlas-SNP
DNAH8	1769	hgsc.bcm.edu	37	6	38854646	38854646	+	Missense_Mutation	SNP	T	T	C	rs142328376	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	122	50	146	0	0.409836	0	T|0.996;C|0.004	0.004	strong	.	DNAH8	1239	.	NM_001206927	exon57	c.T8339C	p.I2780T	CTACTATTGTTGA	.	PASS	Atlas-SNP
LGR5	8549	hgsc.bcm.edu	37	12	71977787	71977787	+	Missense_Mutation	SNP	T	T	C	rs17109924	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	157	75	178	1	0.477707	0.00561798	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	.	scavenged	Atlas-SNP
SLFN13	146857	hgsc.bcm.edu	37	17	33768383	33768383	+	Missense_Mutation	SNP	T	T	A	rs11657183	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	34	16	46	0	0.470588	0	T|0.891;A|0.109	0.109	strong	.	SLFN13	79	.	NM_144682	exon6	c.A1925T	p.D642V	TTTCTATCACTGT	.	PASS	Atlas-SNP
PRKCQ	5588	hgsc.bcm.edu	37	10	6472891	6472891	+	Silent	SNP	G	G	T	rs11258747	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	29	11	39	0	0.37931	0	G|0.847;T|0.153	0.153	strong	.	PRKCQ	113	.	NM_006257	exon17	c.C1846A	p.R616R	GTTCTCGCACGAA	.	PASS	Atlas-SNP
LAMP3	27074	hgsc.bcm.edu	37	3	182853670	182853670	+	Missense_Mutation	SNP	T	T	C	rs482912	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	86	120	0	0.988506	0	T|0.458;C|0.542	0.542	strong	.	LAMP3	48	.	NM_014398	exon5	c.A952G	p.I318V	GGTAAATTGTCTC	.	PASS	Atlas-SNP
ZNF594	84622	hgsc.bcm.edu	37	17	5087040	5087040	+	Missense_Mutation	SNP	A	A	G	rs9908414	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	50	19	67	0	0.38	0	A|0.710;G|0.290	0.290	strong	ZNF594,caecum,carcinoma,0,1	ZNF594	89	1	NM_032530	exon2	c.T512C	p.I171T	TGTATAATAAGAT	.	PASS	Atlas-SNP
OR5L2	26338	hgsc.bcm.edu	37	11	55595115	55595115	+	Missense_Mutation	SNP	C	C	T	rs71490506	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	205	143	254	0	0.697561	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
CEP57L1	285753	hgsc.bcm.edu	37	6	109480562	109480562	+	Missense_Mutation	SNP	T	T	C	rs61743581	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	330	173	374	0	0.524242	0	T|0.887;C|0.113	0.113	strong	.	CEP57L1	24	.	NM_001271853	exon9	c.T913C	p.W305R	ACTTCCTGGTGTA	.	PASS	Atlas-SNP
EXD1	161829	hgsc.bcm.edu	37	15	41483682	41483682	+	Silent	SNP	A	A	G	rs1971131	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	91	39	78	0	0.428571	0	A|0.702;G|0.298	0.298	strong	EXD1,NS,carcinoma,0,2	EXD1	52	2	NM_152596	exon8	c.T648C	p.P216P	ATATTTAGGGGCT	.	PASS	Atlas-SNP
TTC3	7267	hgsc.bcm.edu	37	21	38572565	38572565	+	Silent	SNP	C	C	T	rs150750778	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	287	56	240	0	0.195122	0	C|0.998;T|0.002	0.002	strong	.	TTC3	182	.	NM_001001894	exon45	c.C5883T	p.H1961H	ATGCCACGAGGTG	.	PASS	Atlas-SNP
TMPRSS11A	339967	hgsc.bcm.edu	37	4	68810246	68810246	+	Silent	SNP	G	G	A	rs1370840	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	99	51	146	0	0.515152	0	G|0.710;A|0.290	0.290	strong	TMPRSS11A,NS,carcinoma,0,1	TMPRSS11A	74	1	NM_001114387	exon3	c.C243T	p.T81T	ATTTTCGGTCGTC	.	PASS	Atlas-SNP
FRG1	2483	hgsc.bcm.edu	37	4	190878658	190878658	+	Splice_Site	SNP	G	G	A	rs76810924		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	196	3	240	4	0.0153061	0.0166667	G|0.875;A|0.125	0.125	weak	FRG1,right_upper_lobe,carcinoma,0,1	FRG1	76	1	NM_004477	exon6	c.537+1G>A	.	ATCAAGGTAATGA	.	scavenged	Atlas-SNP
KRTAP4-11	653240	hgsc.bcm.edu	37	17	39274415	39274415	+	Silent	SNP	C	C	T	rs425487		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	6	78	1	0.084507	0.0128205	.	.	weak	KRTAP4-11,NS,carcinoma,-1,11	KRTAP4-11	94	11	NM_033059	exon1	c.G153A	p.R51R	CTGGGGCCTGCAG	.	scavenged	Atlas-SNP
CRIPAK	285464	hgsc.bcm.edu	37	4	1388324	1388324	+	Missense_Mutation	SNP	A	A	C	rs74377230	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	111	17	139	0	0.153153	0	A|0.833;C|0.167	0.167	weak	CRIPAK,caecum,carcinoma,0,1	CRIPAK	185	1	NM_175918	exon1	c.A25C	p.N9H	TGTGCCAATGTGG	.	PASS	Atlas-SNP
FLG2	388698	hgsc.bcm.edu	37	1	152329369	152329369	+	Missense_Mutation	SNP	C	C	G	rs2282302	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	103	74	100	0	0.718447	0	C|0.848;G|0.152	0.152	strong	.	FLG2	431	.	NM_001014342	exon3	c.G893C	p.C298S	GACTGACAAGAAC	.	PASS	Atlas-SNP
OR5P2	120065	hgsc.bcm.edu	37	11	7818313	7818313	+	Silent	SNP	C	C	T	rs73406609	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	83	72	73	0	0.86747	0	C|0.741;T|0.259	0.259	strong	.	OR5P2	68	.	NM_153444	exon1	c.G177A	p.L59L	GTGGCTCAGAAAG	.	PASS	Atlas-SNP
LAMC2	3918	hgsc.bcm.edu	37	1	183187603	183187603	+	Silent	SNP	C	C	T	rs1129723	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	95	49	126	0	0.515789	0	C|0.734;T|0.266	0.266	strong	.	LAMC2	113	.	NM_005562	exon4	c.C483T	p.V161V	AGCTGTCACTGGA	.	PASS	Atlas-SNP
FAM170B	170370	hgsc.bcm.edu	37	10	50339754	50339754	+	Missense_Mutation	SNP	G	G	T	rs73302786	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	130	66	135	0	0.507692	0	G|0.844;T|0.156	0.156	strong	.	FAM170B	20	.	NM_001164484	exon2	c.C756A	p.D252E	CTGTTGGTCATGT	.	PASS	Atlas-SNP
ECT2L	345930	hgsc.bcm.edu	37	6	139223635	139223635	+	Splice_Site	SNP	A	A	T	rs200545869	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	31	12	76	0	0.387097	0	A|0.999;T|0.001	0.001	weak	.	ECT2L	75	.	NM_001195037	exon21	c.2588-2A>T	.	TTTTACAGATGTC	.	PASS	Atlas-SNP
PRG4	10216	hgsc.bcm.edu	37	1	186277989	186277989	+	Silent	SNP	A	A	G	rs3737940	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	81	79	113	0	0.975309	0	A|0.735;G|0.265	0.265	strong	.	PRG4	259	.	NM_005807	exon7	c.A3138G	p.P1046P	AAAACCAAAGACG	.	PASS	Atlas-SNP
PSTK	118672	hgsc.bcm.edu	37	10	124742858	124742858	+	Silent	SNP	G	G	A	rs45498396	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	91	50	118	0	0.549451	0	G|0.842;A|0.158	0.158	strong	.	PSTK	34	.	NM_153336	exon3	c.G579A	p.R193R	CCAGAGGCCACAG	.	PASS	Atlas-SNP
PSPH	5723	hgsc.bcm.edu	37	7	56088786	56088786	+	Silent	SNP	A	A	T	rs202027697	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	162	26	138	0	0.160494	0	A|0.749;T|0.251	0.251	strong	.	PSPH	23	.	NM_004577	exon4	c.T120A	p.V40V	GTCCTCAACGCCA	.	PASS	Atlas-SNP
CCDC168	643677	hgsc.bcm.edu	37	13	103397387	103397387	+	Missense_Mutation	SNP	T	T	G	rs7339187	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	118	54	114	0	0.457627	0	T|0.916;G|0.084	0.084	strong	.	.	.	.	NM_001146197	exon4	c.A5660C	p.Q1887P	CCATTTTGGGTCT	.	PASS	Atlas-SNP
PSG8	440533	hgsc.bcm.edu	37	19	43269704	43269704	+	Silent	SNP	T	T	C	rs62112127	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	14	9	24	0	0.642857	0	T|0.624;C|0.376	0.376	strong	.	PSG8	101	.	NM_001130168	exon1	c.A30G	p.T10T	GCGCTGTGTGCAG	.	PASS	Atlas-SNP
BCKDHB	594	hgsc.bcm.edu	37	6	80816415	80816415	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	60	21	37	0	0.35	0	.	.	none	.	BCKDHB	36	.	NM_000056	exon1	c.C5T	p.A2V	GGATGGCGGTTGT	.	PASS	Atlas-SNP
SLITRK3	22865	hgsc.bcm.edu	37	3	164908529	164908529	+	Silent	SNP	C	C	T	rs76663597	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	178	85	200	0	0.477528	0	C|0.994;T|0.006	0.006	strong	SLITRK3,caecum,carcinoma,0,1	SLITRK3	263	1	NM_014926	exon2	c.G90A	p.P30P	GGGAATCGGGGTA	.	PASS	Atlas-SNP
ARAP3	64411	hgsc.bcm.edu	37	5	141059649	141059649	+	Silent	SNP	A	A	G	rs417503	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	63	62	68	0	0.984127	0	A|0.229;G|0.771	0.771	strong	.	ARAP3	139	.	NM_022481	exon2	c.T405C	p.P135P	AGGAGGAGGCCTT	.	PASS	Atlas-SNP
C2CD2	25966	hgsc.bcm.edu	37	21	43327793	43327793	+	Silent	SNP	C	C	T	rs3746904	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	46	30	0	0.534884	0	C|0.655;T|0.345	0.345	strong	C2CD2,NS,carcinoma,0,1	C2CD2	47	1	NM_015500	exon9	c.G1119A	p.S373S	CAGCACCGAGCTG	.	PASS	Atlas-SNP
ATP6V1H	51606	hgsc.bcm.edu	37	8	54682289	54682289	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	189	4	244	0	0.021164	0	.	.	none	ATP6V1H_ENST00000359530,NS,carcinoma,+1,2	ATP6V1H	66	2	NM_015941	exon11	c.A1064G	p.Y355C	GAACTGTATTCAT	.	scavenged	Atlas-SNP
CRISP3	10321	hgsc.bcm.edu	37	6	49701439	49701439	+	Missense_Mutation	SNP	C	C	A	rs1864312	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	99	122	0	0.980198	0	C|0.618;A|0.382	0.382	strong	.	CRISP3	67	.	NM_001190986	exon5	c.G469T	p.A157S	CCACTGCGTTGGG	.	PASS	Atlas-SNP
STK36	27148	hgsc.bcm.edu	37	2	219562675	219562675	+	Missense_Mutation	SNP	G	G	A	rs1863704	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	146	61	166	1	0.417808	0.0060241	G|0.767;A|0.233	0.233	strong	STK36,rectum,carcinoma,0,1	STK36	111	1	NM_015690	exon25	c.G3008A	p.G1003D	TTATAGGTGTCTT	.	scavenged	Atlas-SNP
GPR87	53836	hgsc.bcm.edu	37	3	151011969	151011969	+	Silent	SNP	G	G	A	rs1048408	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	162	67	201	0	0.41358	0	G|0.533;A|0.467	0.467	strong	.	GPR87	52	.	NM_023915	exon3	c.C1065T	p.Y355Y	ATCAGTGTAATCA	.	PASS	Atlas-SNP
PPP1R11	6992	hgsc.bcm.edu	37	6	30036471	30036471	+	Silent	SNP	C	C	A	rs2074482	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	46	24	67	0	0.521739	0	C|0.809;A|0.191	0.191	strong	.	PPP1R11	10	.	NM_021959	exon2	c.C174A	p.S58S	CTCATCCAAATGT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195505872	195505872	+	Silent	SNP	A	A	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	5	66	0	0.0588235	0	.	.	none	MUC4_ENST00000463781,NS,carcinoma,-2,2	MUC4	1505	2	NM_018406	exon2	c.T12579G	p.L4193L	GACAGGAAGAGGG	.	scavenged	Atlas-SNP
DIP2C	22982	hgsc.bcm.edu	37	10	429977	429977	+	Silent	SNP	G	G	A	rs10904083	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	110	40	97	0	0.363636	0	G|0.663;A|0.337	0.337	strong	DIP2C,NS,carcinoma,0,3	DIP2C	195	3	NM_014974	exon16	c.C1866T	p.G622G	GTTCGCGCCGTCC	.	PASS	Atlas-SNP
SDAD1	55153	hgsc.bcm.edu	37	4	76881233	76881233	+	Missense_Mutation	SNP	G	G	T	rs34627298	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	158	81	152	0	0.512658	0	G|0.922;T|0.078	0.078	strong	.	SDAD1	47	.	NM_018115	exon17	c.C1469A	p.A490D	TTTTCAGCATTCT	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	54	28	68	0	0.518519	0	C|0.903;T|0.097	0.097	strong	.	WDR73	15	.	NM_032856	exon7	c.G746A	p.R249H	CAAAGACGCCCAT	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1266561	1266561	+	Silent	SNP	G	G	A	rs200970694	byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	384	14	333	1	0.0364583	0.003003	G|0.989;A|0.011	0.011	strong	MUC5B,NS,carcinoma,0,2	MUC5B	473	2	NM_002458	exon31	c.G8451A	p.R2817R	CAGCAGGACCACC	.	scavenged	Atlas-SNP
PLEKHA5	54477	hgsc.bcm.edu	37	12	19427764	19427764	+	Missense_Mutation	SNP	T	T	C	rs76626801	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	56	29	94	0	0.517857	0	T|0.989;C|0.011	0.011	strong	.	PLEKHA5	198	.	NM_001256470	exon11	c.T1160C	p.V387A	TCAATGTTAGCCT	.	PASS	Atlas-SNP
NPC1	4864	hgsc.bcm.edu	37	18	21140367	21140367	+	Missense_Mutation	SNP	G	G	A	rs80358251	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	70	113	0	0.985915	0	G|0.991;A|0.009	0.009	strong	.	NPC1	114	.	NM_000271	exon6	c.C709T	p.P237S	TACATGGTGCTGT	.	PASS	Atlas-SNP
CCL2	6347	hgsc.bcm.edu	37	17	32583269	32583269	+	Silent	SNP	T	T	C	rs4586	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	128	55	143	0	0.429688	0	T|0.496;C|0.504	0.504	strong	.	CCL2	10	.	NM_002982	exon2	c.T105C	p.C35C	CTGCTGTTATAAC	.	PASS	Atlas-SNP
PANK1	53354	hgsc.bcm.edu	37	10	91359116	91359116	+	Silent	SNP	C	C	T	rs11592870	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	149	74	177	1	0.496644	0.00564972	C|0.981;T|0.019	0.019	strong	PANK1,colon,carcinoma,0,1	PANK1	35	1	NM_148977	exon3	c.G1203A	p.P401P	GCAGTACGGCTTT	.	scavenged	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195509769	195509769	+	Silent	SNP	A	A	G	rs77947599	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	103	69	65	1	0.669903	0.0153846	A|0.250;G|0.750	0.750	weak	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.T8682C	p.A2894A	AGGGGTAGCGTGA	.	scavenged	Atlas-SNP
ZNF135	7694	hgsc.bcm.edu	37	19	58578578	58578578	+	Silent	SNP	C	C	T	rs2229375	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	55	19	55	0	0.345455	0	C|0.659;T|0.341	0.341	strong	.	ZNF135	159	.	NM_007134	exon4	c.C798T	p.Y266Y	ACCTTACGAATGT	.	PASS	Atlas-SNP
SPRY3	10251	hgsc.bcm.edu	37	X	155004280	155004280	+	Silent	SNP	A	A	G	rs306888	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	119	25	166	0	0.210084	0	A|0.771;G|0.229	0.229	strong	.	SPRY3	52	.	NM_005840	exon2	c.A747G	p.Q249Q	GTGCCAACAGGGC	.	PASS	Atlas-SNP
EFHC2	80258	hgsc.bcm.edu	37	X	44171953	44171953	+	Missense_Mutation	SNP	T	T	C	rs17146914	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	164	163	267	0	0.993902	0	0|0.048;C|0.032	0.032	strong	.	EFHC2	81	.	NM_025184	exon2	c.A92G	p.N31S	ATAACATTGTTGC	.	PASS	Atlas-SNP
LIMD1	8994	hgsc.bcm.edu	37	3	45637439	45637439	+	Silent	SNP	T	T	C	rs267236	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	117	57	156	0	0.487179	0	T|0.317;C|0.683	0.683	strong	.	LIMD1	34	.	NM_014240	exon1	c.T1068C	p.G356G	AGCTGGTCTGGAC	.	PASS	Atlas-SNP
PCDHB8	56128	hgsc.bcm.edu	37	5	140559679	140559679	+	Silent	SNP	C	C	G	rs17844507	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	51	27	65	0	0.529412	0	C|0.863;G|0.137	0.137	strong	.	PCDHB8	199	.	NM_019120	exon1	c.C2064G	p.T688T	TCTCACCGTCTAC	.	PASS	Atlas-SNP
TRAPPC11	60684	hgsc.bcm.edu	37	4	184614874	184614874	+	Silent	SNP	C	C	T	rs4862234	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	38	103	0	0.487179	0	C|0.756;T|0.244	0.244	strong	.	.	.	.	NM_021942	exon21	c.C2370T	p.T790T	GCTCACCGCTGGC	.	PASS	Atlas-SNP
ZHX2	22882	hgsc.bcm.edu	37	8	123964953	123964953	+	Silent	SNP	C	C	T	rs3808600	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	102	29	103	0	0.284314	0	C|0.762;T|0.238	0.238	strong	.	ZHX2	106	.	NM_014943	exon3	c.C1203T	p.T401T	AGTCACCAACCAT	.	PASS	Atlas-SNP
CLSTN3	9746	hgsc.bcm.edu	37	12	7288432	7288432	+	Missense_Mutation	SNP	A	A	G	rs7302230	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	104	44	136	0	0.423077	0	A|0.964;G|0.036	0.036	strong	.	CLSTN3	84	.	NM_014718	exon5	c.A625G	p.S209G	CAGTACAGTGGTG	.	PASS	Atlas-SNP
FAM186A	121006	hgsc.bcm.edu	37	12	50744283	50744283	+	Missense_Mutation	SNP	G	G	A	rs372753266		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	149	43	176	0	0.288591	0	.	.	weak	.	FAM186A	181	.	NM_001145475	exon4	c.C6332T	p.A2111V	TTCTGAGCCTCCA	.	PASS	Atlas-SNP
OR12D3	81797	hgsc.bcm.edu	37	6	29342287	29342287	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	142	2	151	0	0.0140845	0	.	.	none	OR12D3,NS,carcinoma,+1,2	OR12D3	55	2	NM_030959	exon1	c.C778T	p.R260C	CAGGACGAATATA	.	scavenged	Atlas-SNP
LOXL2	4017	hgsc.bcm.edu	37	8	23190941	23190941	+	Silent	SNP	T	T	C	rs1010156	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	73	89	0	1	0	T|0.521;C|0.479	0.479	strong	.	LOXL2	97	.	NM_002318	exon5	c.A939G	p.S313S	GAATCTTGAGGGT	.	PASS	Atlas-SNP
SLC25A23	79085	hgsc.bcm.edu	37	19	6458240	6458240	+	Silent	SNP	G	G	C	rs2289784	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	26	15	24	0	0.576923	0	G|0.946;C|0.054	0.054	strong	SLC25A23,NS,carcinoma,0,1	SLC25A23	43	1	NM_024103	exon2	c.C252G	p.L84L	AAACATGAGCAGC	.	PASS	Atlas-SNP
GAREM	64762	hgsc.bcm.edu	37	18	30050356	30050356	+	Silent	SNP	C	C	T	rs11664566	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	81	35	72	0	0.432099	0	C|0.784;T|0.216	0.216	strong	.	.	.	.	NM_022751	exon1	c.G36A	p.K12K	CACATCCTTGAGG	.	PASS	Atlas-SNP
OR5M11	219487	hgsc.bcm.edu	37	11	56310497	56310497	+	Silent	SNP	C	C	T	rs72913727	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	64	47	71	1	0.734375	0.0140845	C|0.949;T|0.051	0.051	strong	OR5M11,right_upper_lobe,carcinoma,-1,1	OR5M11	60	1	NM_001005245	exon1	c.G237A	p.P79P	CATCTGCGGGGTT	.	scavenged	Atlas-SNP
TBX21	30009	hgsc.bcm.edu	37	17	45822579	45822579	+	Silent	SNP	G	G	A	rs12721470	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	76	29	90	0	0.381579	0	G|0.951;A|0.049	0.049	strong	.	TBX21	50	.	NM_013351	exon6	c.G1455A	p.P485P	CCGGCCGGAATCC	.	PASS	Atlas-SNP
PNKP	11284	hgsc.bcm.edu	37	19	50370404	50370404	+	Missense_Mutation	SNP	G	G	A	rs3739168	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	64	34	60	0	0.53125	0	G|0.991;A|0.009	0.009	strong	.	PNKP	71	.	NM_007254	exon2	c.C58T	p.P20S	TGGGGGGCGCTCC	.	PASS	Atlas-SNP
STK32C	282974	hgsc.bcm.edu	37	10	134038809	134038809	+	Silent	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	95	49	118	0	0.515789	0	.	.	none	.	STK32C	61	.	NM_173575	exon7	c.C804T	p.G268G	GGTCCCGCCGTTG	.	PASS	Atlas-SNP
KATNAL2	83473	hgsc.bcm.edu	37	18	44585955	44585955	+	Missense_Mutation	SNP	G	G	A	rs7233515	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	39	21	47	0	0.538462	0	G|0.601;A|0.399	0.399	strong	.	KATNAL2	64	.	NM_031303	exon5	c.G263A	p.S88N	TGGAAAGTGCCAA	.	PASS	Atlas-SNP
NLRC5	84166	hgsc.bcm.edu	37	16	57111232	57111232	+	Silent	SNP	C	C	T	rs11864231	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	181	69	140	0	0.381215	0	C|0.819;T|0.181	0.181	strong	.	NLRC5	186	.	NM_032206	exon40	c.C4860T	p.D1620D	TGGAGACGCTGGT	.	PASS	Atlas-SNP
RYR3	6263	hgsc.bcm.edu	37	15	34130697	34130697	+	Silent	SNP	G	G	C	rs75286462	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	185	111	196	0	0.6	0	G|0.975;C|0.025	0.025	strong	.	RYR3	760	.	NM_001036	exon89	c.G12516C	p.V4172V	GAACGTGAAAAAG	.	PASS	Atlas-SNP
UNC5C	8633	hgsc.bcm.edu	37	4	96127869	96127869	+	Silent	SNP	T	T	G	rs2276322	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	96	43	134	0	0.447917	0	T|0.394;G|0.606	0.606	strong	.	UNC5C	141	.	NM_003728	exon11	c.A1812C	p.P604P	GACGACTGGGCGG	.	PASS	Atlas-SNP
EN1	2019	hgsc.bcm.edu	37	2	119600674	119600674	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	96	33	89	0	0.34375	0	.	.	none	.	EN1	33	.	NM_001426	exon2	c.T1019G	p.L340R	AGGCTGAGTTCCT	.	PASS	Atlas-SNP
DMBT1	1755	hgsc.bcm.edu	37	10	124399814	124399814	+	Missense_Mutation	SNP	C	C	T	rs200589297	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	273	3	336	0	0.010989	0	C|0.999;T|0.001	0.001	strong	DMBT1_ENST00000368915,NS,carcinoma,0,3	DMBT1	677	3	NM_007329	exon52	c.C6814T	p.R2272C	ACCAGCCGCCCTT	.	scavenged	Atlas-SNP
C19orf45	374877	hgsc.bcm.edu	37	19	7573287	7573287	+	Missense_Mutation	SNP	C	C	T	rs1133378	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	111	43	112	0	0.387387	0	C|0.736;T|0.264	0.264	strong	.	C19orf45	36	.	NM_198534	exon9	c.C1489T	p.P497S	CAGCCCCCTATGT	.	PASS	Atlas-SNP
LRIT1	26103	hgsc.bcm.edu	37	10	85992478	85992478	+	Silent	SNP	T	T	C	rs3814210	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	77	76	128	1	0.987013	0.0078125	T|0.493;C|0.507	0.507	strong	LRIT1,NS,carcinoma,-1,1	LRIT1	73	1	NM_015613	exon4	c.A1077G	p.G359G	TAGTGCTCCTGGG	.	PASS	Atlas-SNP
ZHX2	22882	hgsc.bcm.edu	37	8	123964431	123964431	+	Silent	SNP	G	G	A	rs3204141	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	113	30	118	0	0.265487	0	G|0.767;A|0.233	0.233	strong	ZHX2,NS,carcinoma,0,1	ZHX2	106	1	NM_014943	exon3	c.G681A	p.S227S	CCTCTCGAGACTC	.	PASS	Atlas-SNP
CYP4F12	66002	hgsc.bcm.edu	37	19	15784386	15784386	+	Missense_Mutation	SNP	C	C	T	rs16995378	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	96	96	84	0	1	0	C|0.067;T|0.933	0.933	strong	.	CYP4F12	89	.	NM_023944	exon2	c.C47T	p.T16M	TGGCAACGTCCCC	.	PASS	Atlas-SNP
XCR1	2829	hgsc.bcm.edu	37	3	46063329	46063329	+	Silent	SNP	T	T	C	rs2230322	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	148	61	151	0	0.412162	0	T|0.794;C|0.206	0.206	strong	.	XCR1	51	.	NM_001024644	exon2	c.A111G	p.L37L	GCAGTATAGGACA	.	PASS	Atlas-SNP
PKD1L2	114780	hgsc.bcm.edu	37	16	81242198	81242198	+	Nonsense_Mutation	SNP	G	G	A	rs7499011	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	41	41	27	0	1	0	G|0.742;A|0.258	0.258	strong	.	PKD1L2	361	.	NM_001076780	exon4	c.C658T	p.Q220X	GCTCCTGGCACTG	.	PASS	Atlas-SNP
PGBD1	84547	hgsc.bcm.edu	37	6	28251890	28251890	+	Silent	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	88	4	81	0	0.0454545	0	.	.	none	.	PGBD1	106	.	NM_001184743	exon2	c.C300T	p.L100L	GGAGCTCCAGCCC	.	PASS	Atlas-SNP
PPP1R3C	5507	hgsc.bcm.edu	37	10	93390158	93390158	+	Silent	SNP	C	C	T	rs35530640	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	52	30	70	0	0.576923	0	C|0.974;T|0.026	0.026	strong	.	PPP1R3C	30	.	NM_005398	exon2	c.G480A	p.E160E	GCAGTTCTCCAGA	.	PASS	Atlas-SNP
ZCCHC16	340595	hgsc.bcm.edu	37	X	111698613	111698613	+	Silent	SNP	T	T	C	rs7053563	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	95	95	121	1	1	0.00826446	T|0.694;C|0.306	0.306	strong	.	ZCCHC16	66	.	NM_001004308	exon3	c.T657C	p.H219H	GAAACATAGTGAC	.	PASS	Atlas-SNP
ABCA12	26154	hgsc.bcm.edu	37	2	215910724	215910724	+	Missense_Mutation	SNP	T	T	G	rs11890512	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	114	53	95	0	0.464912	0	T|0.845;G|0.155	0.155	strong	ABCA12,NS,carcinoma,+1,1	ABCA12	368	1	NM_173076	exon7	c.A709C	p.N237H	GATTGTTGGGGTC	.	PASS	Atlas-SNP
EIF4A1	1973	hgsc.bcm.edu	37	17	7478498	7478498	+	Silent	SNP	G	G	A	rs78553499	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	77	43	71	0	0.558442	0	G|0.856;A|0.144	0.144	strong	.	EIF4A1	38	.	NM_001416	exon4	c.G267A	p.S89S	CATATCGATTCTG	.	PASS	Atlas-SNP
SLC1A1	6505	hgsc.bcm.edu	37	9	4576680	4576680	+	Silent	SNP	T	T	C	rs301430	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	234	81	224	0	0.346154	0	T|0.604;C|0.396	0.396	strong	.	SLC1A1	43	.	NM_004170	exon10	c.T1110C	p.T370T	TGGGACTGCGCTC	.	PASS	Atlas-SNP
TEP1	7011	hgsc.bcm.edu	37	14	20847202	20847202	+	Silent	SNP	A	A	G	rs938887	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	120	65	143	0	0.541667	0	A|0.719;C|0.001	.	strong	.	TEP1	224	.	NM_007110	exon36	c.T5190C	p.D1730D	GAGTGTATCATCG	.	PASS	Atlas-SNP
CELSR2	1952	hgsc.bcm.edu	37	1	109807099	109807099	+	Silent	SNP	G	G	A	rs6689614	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	59	59	69	0	1	0	G|0.632;A|0.368	0.368	strong	CELSR2,NS,adenoma,0,1	CELSR2	228	1	NM_001408	exon11	c.G5313A	p.P1771P	TACGCCGGAGGGG	.	PASS	Atlas-SNP
SPICE1	152185	hgsc.bcm.edu	37	3	113176122	113176122	+	Silent	SNP	G	G	A	rs7637618	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	45	111	0	0.6	0	G|0.662;A|0.338	0.338	strong	.	SPICE1	130	.	NM_144718	exon13	c.C1518T	p.P506P	TTTAACGGGCAAC	.	PASS	Atlas-SNP
ZC2HC1A	51101	hgsc.bcm.edu	37	8	79609647	79609647	+	Silent	SNP	G	G	A	rs35904168	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	54	14	56	0	0.259259	0	G|0.946;A|0.054	0.054	strong	.	.	.	.	NM_016010	exon6	c.G510A	p.K170K	GTATAAGCCACCC	.	PASS	Atlas-SNP
MCPH1	79648	hgsc.bcm.edu	37	8	6302154	6302154	+	Missense_Mutation	SNP	G	G	T	rs2083914	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	26	151	0	0.257426	0	G|0.900;T|0.100	0.100	strong	.	MCPH1	65	.	NM_001172574	exon8	c.G911T	p.R304I	TGCAAAGAAATAT	.	PASS	Atlas-SNP
LRRIQ1	84125	hgsc.bcm.edu	37	12	85466723	85466723	+	Missense_Mutation	SNP	G	G	A	rs17012533	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	145	73	153	0	0.503448	0	G|0.793;A|0.207	0.207	strong	LRRIQ1_ENST00000393217,NS,carcinoma,-1,3	LRRIQ1	512	3	NM_001079910	exon11	c.G2734A	p.A912T	GACAATGCAGGGT	.	PASS	Atlas-SNP
NEU2	4759	hgsc.bcm.edu	37	2	233899126	233899126	+	Missense_Mutation	SNP	C	C	A	rs2233391	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	77	77	95	0	1	0	C|0.668;A|0.332	0.332	strong	.	NEU2	42	.	NM_005383	exon2	c.C502A	p.H168N	CAGCTTCACGACA	.	PASS	Atlas-SNP
ANO2	57101	hgsc.bcm.edu	37	12	5674754	5674754	+	Silent	SNP	G	G	A	rs2277398	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	62	62	80	0	1	0	G|0.645;A|0.355	0.355	strong	.	ANO2	309	.	NM_020373	exon25	c.C2697T	p.S899S	ACGGGCGGACAGA	.	PASS	Atlas-SNP
TTC27	55622	hgsc.bcm.edu	37	2	32983526	32983526	+	Silent	SNP	C	C	T	rs2273665	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	109	45	125	0	0.412844	0	C|0.676;N|0.000	.	strong	TTC27,NS,carcinoma,0,1	TTC27	71	1	NM_017735	exon13	c.C1620T	p.N540N	TCGGAACAAGGAG	.	PASS	Atlas-SNP
FAM120B	84498	hgsc.bcm.edu	37	6	170627266	170627266	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	39	15	55	0	0.384615	0	.	.	none	.	FAM120B	108	.	NM_032448	exon2	c.T788C	p.I263T	GTAACATCATATT	.	PASS	Atlas-SNP
MGMT	4255	hgsc.bcm.edu	37	10	131565170	131565170	+	Missense_Mutation	SNP	A	A	G	rs2308327	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	100	46	115	0	0.46	0	A|0.923;G|0.077	0.077	strong	.	MGMT	32	.	NM_002412	exon5	c.A626G	p.K209R	TGGGGAAGCCAGG	.	PASS	Atlas-SNP
OR4F15	390649	hgsc.bcm.edu	37	15	102359203	102359203	+	Missense_Mutation	SNP	G	G	A	rs79724132	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	137	54	151	0	0.394161	0	G|0.944;A|0.056	0.056	strong	.	OR4F15	42	.	NM_001001674	exon1	c.G814A	p.A272T	TATCTTGCTATTT	.	PASS	Atlas-SNP
TNC	3371	hgsc.bcm.edu	37	9	117846570	117846570	+	Silent	SNP	C	C	T	rs2274836	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	39	91	0	0.47561	0	C|0.552;T|0.448	0.448	strong	TNC,NS,malignant_melanoma,-2,1	TNC	282	1	NM_002160	exon4	c.G2049A	p.E683E	ACCAGGCTCCAGC	.	PASS	Atlas-SNP
RBBP6	5930	hgsc.bcm.edu	37	16	24570844	24570844	+	Silent	SNP	G	G	A	rs45591839	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	37	67	0	0.637931	0	G|0.962;A|0.038	0.038	strong	.	RBBP6	158	.	NM_018703	exon8	c.G693A	p.G231G	AATTGGGAAGAAA	.	PASS	Atlas-SNP
WDR52	55779	hgsc.bcm.edu	37	3	113127991	113127991	+	Missense_Mutation	SNP	C	C	A	rs16845107	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	106	50	110	0	0.471698	0	C|0.916;A|0.084	0.084	strong	.	WDR52	151	.	NM_001164496	exon7	c.G852T	p.K284N	CTCTTCCTTATCA	.	PASS	Atlas-SNP
SLC12A7	10723	hgsc.bcm.edu	37	5	1074696	1074696	+	Silent	SNP	G	G	A	rs12515358	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	102	48	107	0	0.470588	0	G|0.976;A|0.024	0.024	strong	.	SLC12A7	97	.	NM_006598	exon16	c.C2058T	p.H686H	CTTGGTGTGGGGG	.	PASS	Atlas-SNP
CHRD	8646	hgsc.bcm.edu	37	3	184102814	184102814	+	Missense_Mutation	SNP	G	G	A	rs138882380	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	40	84	0	0.56338	0	G|1.000;A|0.000	0.000	strong	.	CHRD	149	.	NM_003741	exon14	c.G1606A	p.V536M	CTGCCCGTGCCCC	.	PASS	Atlas-SNP
SLFN12	55106	hgsc.bcm.edu	37	17	33749919	33749919	+	Missense_Mutation	SNP	A	A	C	rs1849733	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	195	88	240	1	0.451282	0.00416667	A|0.586;C|0.414	0.414	strong	SLFN12,NS,adenoma,0,1	SLFN12	56	1	NM_018042	exon2	c.T129G	p.S43R	TGAGACACTTTCA	.	PASS	Atlas-SNP
FAM166B	730112	hgsc.bcm.edu	37	9	35563361	35563361	+	Missense_Mutation	SNP	G	G	A	rs75679360	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	26	9	43	0	0.346154	0	G|0.963;A|0.037	0.037	strong	.	FAM166B	19	.	NM_001099951	exon2	c.C88T	p.R30W	TGAACCGAAGTAG	.	PASS	Atlas-SNP
VPREB1	7441	hgsc.bcm.edu	37	22	22599537	22599537	+	Missense_Mutation	SNP	G	G	A	rs1320	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	68	34	105	0	0.5	0	G|0.965;A|0.035	0.035	strong	.	VPREB1	20	.	NM_007128	exon2	c.G226A	p.D76N	CAATCAGACAAGA	.	PASS	Atlas-SNP
HLA-DPB1	3115	hgsc.bcm.edu	37	6	33048602	33048602	+	Missense_Mutation	SNP	C	C	A	rs1042131	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	51	24	55	0	0.470588	0	C|0.544;A|0.456	0.456	strong	HLA-DPB1,colon,carcinoma,-1,2	HLA-DPB1	28	2	NM_002121	exon2	c.C254A	p.A85E	CTGCTGCGGAGTA	.	PASS	Atlas-SNP
PCDH1	5097	hgsc.bcm.edu	37	5	141243646	141243646	+	Silent	SNP	A	A	G	rs3797054	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	45	82	0	0.548781	0	A|0.640;G|0.360	0.360	strong	.	PCDH1	119	.	NM_032420	exon3	c.T2250C	p.A750A	CAGCTCAGCATTG	.	PASS	Atlas-SNP
PRG2	5553	hgsc.bcm.edu	37	11	57157405	57157405	+	Silent	SNP	A	A	G	rs490358	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	73	113	1	1	0.00884956	A|0.292;G|0.708	0.708	strong	.	PRG2	65	.	NM_001243245	exon2	c.T13C	p.L5L	GAAGTAAGGGGAG	.	PASS	Atlas-SNP
ANK3	288	hgsc.bcm.edu	37	10	61941147	61941147	+	Silent	SNP	A	A	G	rs34552044	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	158	85	176	0	0.537975	0	A|0.971;G|0.029	0.029	strong	.	ANK3	703	.	NM_020987	exon18	c.T2124C	p.D708D	CACTCGATCTTCT	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105415352	105415352	+	Missense_Mutation	SNP	G	G	C	rs12890949	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	98	98	0	0	1	.	C|0.756;G|0.244	0.756	strong	.	AHNAK2	719	.	NM_138420	exon7	c.C6436G	p.L2146V	TAGTCAGGTCCTT	.	PASS	Atlas-SNP
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32632831	32632831	+	Missense_Mutation	SNP	G	G	C	rs111588946	alternate_allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	65	24	29	0	0.369231	0	T|1.000;|0.000	.	alt	.	HLA-DQB1	15	.	NM_002123	exon2	c.C123G	p.F41L	AAACTGGAACACG	.	PASS	Atlas-SNP
PTPRF	5792	hgsc.bcm.edu	37	1	44086831	44086831	+	Silent	SNP	C	C	T	rs1143702	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	245	122	294	0	0.497959	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
GLRA3	8001	hgsc.bcm.edu	37	4	175598280	175598280	+	Silent	SNP	A	A	G	rs12648678	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	157	94	139	0	0.598726	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
CALCR	799	hgsc.bcm.edu	37	7	93116299	93116299	+	Missense_Mutation	SNP	A	A	G	rs2301680	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	36	36	59	0	1	0	A|0.450;G|0.550	0.550	strong	CALCR_ENST00000359558,NS,malignant_melanoma,+1,3	CALCR	200	3	NM_001164737	exon4	c.T49C	p.S17P	TTTTTGATTTTTG	.	PASS	Atlas-SNP
NLRP7	199713	hgsc.bcm.edu	37	19	55451050	55451050	+	Silent	SNP	C	C	T	rs78028796		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	116	49	154	0	0.422414	0	.	.	weak	.	NLRP7	411	.	NM_001127255	exon4	c.G1137A	p.K379K	CTCCCCCTTCTCC	.	PASS	Atlas-SNP
LY6K	54742	hgsc.bcm.edu	37	8	143783109	143783109	+	Silent	SNP	A	A	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	179	32	193	0	0.178771	0	.	.	none	.	LY6K	23	.	NM_001160354	exon2	c.A195G	p.P65P	AGAGCCATACTGC	.	PASS	Atlas-SNP
VPS53	55275	hgsc.bcm.edu	37	17	617869	617869	+	Silent	SNP	G	G	A	rs11558129	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	45	93	0	0.48913	0	G|0.785;T|0.003	.	strong	.	VPS53	109	.	NM_001128159	exon1	c.C81T	p.I27I	CTGCTCGATGGCC	.	PASS	Atlas-SNP
MROH7	374977	hgsc.bcm.edu	37	1	55119144	55119144	+	Missense_Mutation	SNP	A	A	G	rs11206407	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	128	53	147	0	0.414062	0	A|0.655;G|0.344	0.344	strong	HEATR8_ENST00000421030,colon,carcinoma,0,2	.	.	2	NM_001039464	exon3	c.A545G	p.H182R	GGCACCATTCCAG	.	PASS	Atlas-SNP
TMPRSS2	7113	hgsc.bcm.edu	37	21	42845374	42845374	+	Silent	SNP	G	G	A	rs2298659	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	173	73	143	0	0.421965	0	G|0.780;A|0.220	0.220	strong	TMPRSS2_ENST00000454499,NS,carcinoma,0,3	TMPRSS2	148	3	NM_001135099	exon9	c.C888T	p.G296G	GCTCTCGCCGCCC	.	PASS	Atlas-SNP
FBXO39	162517	hgsc.bcm.edu	37	17	6690161	6690161	+	Silent	SNP	C	C	T	rs17853331	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	151	81	150	0	0.536424	0	C|0.771;T|0.229	0.229	strong	.	FBXO39	50	.	NM_153230	exon3	c.C1086T	p.I362I	CCTCATCATATCC	.	PASS	Atlas-SNP
NPBWR2	2832	hgsc.bcm.edu	37	20	62737888	62737888	+	Silent	SNP	G	G	A	rs41278242	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	48	24	67	0	0.5	0	G|0.975;A|0.025	0.025	strong	NPBWR2,colon,carcinoma,0,1	NPBWR2	36	1	NM_005286	exon1	c.C297T	p.P99P	GTTGACGGGCAGT	.	PASS	Atlas-SNP
UBXN2B	137886	hgsc.bcm.edu	37	8	59329496	59329496	+	Missense_Mutation	SNP	C	C	T	rs373559127		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	41	14	33	0	0.341463	0	.	.	weak	UBXN2B,NS,carcinoma,-1,1	UBXN2B	36	1	NM_001077619	exon2	c.C172T	p.R58W	AGCCCACGGACAC	.	PASS	Atlas-SNP
DOCK8	81704	hgsc.bcm.edu	37	9	286593	286593	+	Missense_Mutation	SNP	C	C	A	rs529208	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	269	266	228	1	0.988848	0.00438596	C|0.497;A|0.503	0.503	strong	.	DOCK8	401	.	NM_203447	exon3	c.C289A	p.P97T	TTCACGCCAAAGG	.	PASS	Atlas-SNP
PLG	5340	hgsc.bcm.edu	37	6	161139480	161139480	+	Silent	SNP	C	C	T	rs1130656	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	36	25	96	0	0.694444	0	C|0.636;T|0.364	0.364	strong	PLG,NS,carcinoma,0,1	PLG	150	1	NM_000301	exon8	c.C942T	p.F314F	AAACTTCCCCTGC	.	PASS	Atlas-SNP
GUCY2D	3000	hgsc.bcm.edu	37	17	7906519	7906519	+	Missense_Mutation	SNP	G	G	T	rs61749665	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	15	7	10	0	0.466667	0	G|0.623;T|0.377	0.377	strong	.	GUCY2D	82	.	NM_000180	exon2	c.G154T	p.A52S	CTCTCCGCCGTGT	.	PASS	Atlas-SNP
TRAF4	9618	hgsc.bcm.edu	37	17	27075423	27075423	+	Silent	SNP	C	C	T	rs2070265	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	89	88	96	0	0.988764	0	C|0.813;T|0.187	0.187	strong	.	TRAF4	20	.	NM_004295	exon5	c.C606T	p.F202F	GGAGTTCGTCTTT	.	PASS	Atlas-SNP
ALPP	250	hgsc.bcm.edu	37	2	233243586	233243586	+	Missense_Mutation	SNP	C	C	T	rs41415150		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	143	53	148	0	0.370629	0	C|1.000;|0.000	.	weak	.	ALPP	53	.	NM_001632	exon1	c.C74T	p.P25L	TCATCCCAGGTAA	.	PASS	Atlas-SNP
ARSD	414	hgsc.bcm.edu	37	X	2833638	2833638	+	Missense_Mutation	SNP	C	C	T	rs370769167		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	108	13	141	0	0.12037	0	.	.	weak	.	ARSD	47	.	NM_001669	exon6	c.G959A	p.G320D	TATAAGCCATGCT	.	PASS	Atlas-SNP
SNN	8303	hgsc.bcm.edu	37	16	11769948	11769948	+	Silent	SNP	C	C	T	rs1050068	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	37	36	64	0	0.972973	0	C|0.695;T|0.305	0.305	strong	.	SNN	7	.	NM_003498	exon2	c.C33T	p.G11G	CACGGGCGTGGTC	.	PASS	Atlas-SNP
C9orf129	445577	hgsc.bcm.edu	37	9	96097669	96097669	+	Missense_Mutation	SNP	C	C	T	rs76495316	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	272	125	288	0	0.459559	0	C|0.500;T|0.500	0.500	weak	.	C9orf129	18	.	NM_001098808	exon3	c.G352A	p.G118R	CCCCTCCGCTGCC	.	PASS	Atlas-SNP
RUNDC3A	10900	hgsc.bcm.edu	37	17	42392622	42392622	+	Silent	SNP	T	T	C	rs708386	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	76	34	58	0	0.447368	0	T|0.367;C|0.633	0.633	strong	.	RUNDC3A	30	.	NM_001144825	exon7	c.T729C	p.D243D	CACCGATGAGGAC	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	23	10	20	0	0.434783	0	C|0.662;T|0.338	0.338	strong	.	.	.	.	NM_001243312	exon3	c.C419T	p.A140V	ATGGGGCAAATGC	.	PASS	Atlas-SNP
TBC1D29	26083	hgsc.bcm.edu	37	17	28890301	28890301	+	Missense_Mutation	SNP	G	G	A	rs80145926	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	116	10	79	0	0.0862069	0	G|0.928;A|0.072	0.072	strong	TBC1D29,NS,carcinoma,0,1	TBC1D29	19	1	NM_015594	exon5	c.G311A	p.S104N	AGAGCAGCAGAGG	.	scavenged	Atlas-SNP
LRRC56	115399	hgsc.bcm.edu	37	11	554047	554047	+	Missense_Mutation	SNP	G	G	A	rs12793222	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	145	113	128	0	0.77931	0	G|0.781;A|0.219	0.219	strong	.	LRRC56	23	.	NM_198075	exon14	c.G1400A	p.R467Q	CCCCGCGGTGGTC	.	PASS	Atlas-SNP
PIK3AP1	118788	hgsc.bcm.edu	37	10	98469693	98469693	+	Missense_Mutation	SNP	C	C	T	rs17112076	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	137	72	146	0	0.525547	0	C|0.852;T|0.148	0.148	strong	PIK3AP1,NS,carcinoma,0,1	PIK3AP1	111	1	NM_152309	exon2	c.G61A	p.E21K	ATTCCTCGGCATC	.	PASS	Atlas-SNP
DOCK10	55619	hgsc.bcm.edu	37	2	225670845	225670845	+	Missense_Mutation	SNP	G	G	T	rs375740801		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	99	46	76	0	0.464646	0	.	.	weak	.	DOCK10	308	.	NM_014689	exon34	c.C3812A	p.A1271E	GTACCTGCTATGG	.	PASS	Atlas-SNP
LRP3	4037	hgsc.bcm.edu	37	19	33696647	33696647	+	Missense_Mutation	SNP	C	C	T	rs368108554		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	36	15	29	0	0.416667	0	.	.	weak	.	LRP3	46	.	NM_002333	exon5	c.C971T	p.T324M	TGCAGACGCTGTC	.	PASS	Atlas-SNP
CACNA1C	775	hgsc.bcm.edu	37	12	2224511	2224511	+	Silent	SNP	C	C	T	rs34419050	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	19	9	20	0	0.473684	0	C|0.990;T|0.010	0.010	strong	.	CACNA1C	1023	.	NM_001129831	exon2	c.C171T	p.D57D	CATCGACGCAGCC	.	PASS	Atlas-SNP
CUL9	23113	hgsc.bcm.edu	37	6	43188940	43188940	+	Silent	SNP	C	C	T	rs6917902	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	151	70	130	0	0.463576	0	C|0.767;T|0.233	0.233	strong	.	CUL9	248	.	NM_015089	exon34	c.C6633T	p.D2211D	GGTCGACGACGGT	.	PASS	Atlas-SNP
CNOT1	23019	hgsc.bcm.edu	37	16	58575489	58575489	+	Silent	SNP	G	G	A	rs11540994	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	168	168	161	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
CNTN6	27255	hgsc.bcm.edu	37	3	1424745	1424745	+	Silent	SNP	C	C	T	rs4684146	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	195	69	245	0	0.353846	0	C|0.816;T|0.184	0.184	strong	.	CNTN6	245	.	NM_014461	exon18	c.C2286T	p.V762V	GTTTGTCTACAGA	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	59	59	120	0	1	0	G|0.686;0|0.012	.	strong	.	DDX53	76	.	NM_182699	exon1	c.G1172T	p.R391M	AGATAAGGAAGAT	.	PASS	Atlas-SNP
ARHGEF28	64283	hgsc.bcm.edu	37	5	73181913	73181913	+	Silent	SNP	T	T	C	rs61734875	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	121	78	116	0	0.644628	0	T|0.967;C|0.033	0.033	strong	.	.	.	.	NM_001080479	exon25	c.T3294C	p.A1098A	AACTGCTACAGGT	.	PASS	Atlas-SNP
KDM4D	55693	hgsc.bcm.edu	37	11	94731905	94731905	+	Missense_Mutation	SNP	C	C	G	rs144086807	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	59	48	80	0	0.813559	0	C|0.997;G|0.003	0.003	strong	.	KDM4D	58	.	NM_018039	exon3	c.C1369G	p.P457A	CGCCCTCCTCAGA	.	PASS	Atlas-SNP
OR2W5	441932	hgsc.bcm.edu	37	1	247654498	247654498	+	Silent	SNP	G	G	A	rs61070846	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	208	81	214	0	0.389423	0	G|0.820;A|0.180	0.180	strong	.	OR2W5	97	.	NM_001004698	exon1	c.G69A	p.L23L	TGGACTGGAGAAA	.	PASS	Atlas-SNP
BPIFB4	149954	hgsc.bcm.edu	37	20	31680334	31680334	+	Missense_Mutation	SNP	C	C	T	rs17122711	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	27	19	39	0	0.703704	0	C|0.960;T|0.040	0.040	strong	.	.	.	.	NM_182519	exon9	c.C1214T	p.P405L	CCAAGCCGATGCC	.	PASS	Atlas-SNP
CALD1	800	hgsc.bcm.edu	37	7	134618496	134618496	+	Missense_Mutation	SNP	G	G	A	rs61757650	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	49	21	55	0	0.428571	0	G|0.979;A|0.021	0.021	strong	.	CALD1	150	.	NM_033138	exon5	c.G976A	p.E326K	GCAGCAGAGGAGA	.	PASS	Atlas-SNP
ITGA3	3675	hgsc.bcm.edu	37	17	48151353	48151353	+	Silent	SNP	T	T	C	rs2285524	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	45	89	0	0.625	0	T|0.775;C|0.225	0.225	strong	.	ITGA3	128	.	NM_005501	exon8	c.T1230C	p.L410L	GCTCCTTAGACAG	.	PASS	Atlas-SNP
SLC25A26	115286	hgsc.bcm.edu	37	3	66419956	66419956	+	Missense_Mutation	SNP	C	C	T	rs13874	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	74	43	106	0	0.581081	0	C|0.342;T|0.658	0.658	strong	.	SLC25A26	12	.	NM_173471	exon9	c.C623T	p.T208M	GAATTACGCTGGC	.	PASS	Atlas-SNP
TANC1	85461	hgsc.bcm.edu	37	2	160086654	160086654	+	Missense_Mutation	SNP	A	A	G	rs67270488	bycluster;byfrequency;byhapmap;alternate_allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	102	41	106	0	0.401961	0	A|0.509;CA|0.001	.	alt	.	TANC1	157	.	NM_033394	exon27	c.A4717G	p.T1573A	GCTGCCACTCCTG	.	PASS	Atlas-SNP
DMGDH	29958	hgsc.bcm.edu	37	5	78326767	78326767	+	Silent	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	133	85	104	0	0.639098	0	.	.	none	.	DMGDH	88	.	NM_013391	exon10	c.G1572A	p.Q524Q	CATAACCTGTTTA	.	PASS	Atlas-SNP
PSMD3	5709	hgsc.bcm.edu	37	17	38146154	38146154	+	Silent	SNP	T	T	C	rs9916279	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	37	16	37	0	0.432432	0	T|0.798;C|0.202	0.202	strong	.	PSMD3	56	.	NM_002809	exon5	c.T849C	p.N283N	CAACAATGAGTGG	.	PASS	Atlas-SNP
CRIPAK	285464	hgsc.bcm.edu	37	4	1388693	1388693	+	Missense_Mutation	SNP	C	C	G	rs78906219	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	25	8	43	2	0.32	0.0465116	G|1.000;|0.000	1.000	weak	CRIPAK,caecum,carcinoma,0,2	CRIPAK	185	2	NM_175918	exon1	c.C394G	p.H132D	CGTGCCCATGCGG	.	scavenged	Atlas-SNP
OTUD7B	56957	hgsc.bcm.edu	37	1	149916820	149916820	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	146	2	163	0	0.0136986	0	.	.	none	OTUD7B,caecum,carcinoma,+2,1	OTUD7B	76	1	NM_020205	exon12	c.C1468T	p.R490X	GATCTCGCTTTGA	.	scavenged	Atlas-SNP
ENPP1	5167	hgsc.bcm.edu	37	6	132172368	132172368	+	Missense_Mutation	SNP	A	A	C	rs1044498	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	64	41	81	0	0.640625	0	A|0.655;C|0.345	0.345	strong	.	ENPP1	108	.	NM_006208	exon4	c.A517C	p.K173Q	AAGGACAAGGGCG	.	PASS	Atlas-SNP
GIMAP2	26157	hgsc.bcm.edu	37	7	150389677	150389677	+	Silent	SNP	G	G	C	rs6952002	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	85	130	0	0.988372	0	G|0.525;C|0.475	0.475	strong	GIMAP2,colon,carcinoma,0,1	GIMAP2	39	1	NM_015660	exon3	c.G303C	p.L101L	CTTGCTGTCTGCA	.	PASS	Atlas-SNP
CDON	50937	hgsc.bcm.edu	37	11	125871735	125871735	+	Silent	SNP	C	C	T	rs516664	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	93	23	116	0	0.247312	0	C|0.667;T|0.333	0.333	strong	CDON,NS,carcinoma,0,2	CDON	137	2	NM_016952	exon11	c.G2037A	p.A679A	TGATGACGCTGTT	.	PASS	Atlas-SNP
PCSK1	5122	hgsc.bcm.edu	37	5	95728974	95728974	+	Missense_Mutation	SNP	G	G	C	rs6234	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	239	121	281	1	0.506276	0.00355872	G|0.744;C|0.254	0.254	strong	.	PCSK1	93	.	NM_000439	exon14	c.C1993G	p.Q665E	TGGCCTGGGAAGG	.	PASS	Atlas-SNP
FOLH1B	219595	hgsc.bcm.edu	37	11	89413824	89413824	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	313	4	204	0	0.0127796	0	.	.	none	FOLH1B,right_lower_lobe,carcinoma,-2,1	FOLH1B	93	1	NM_153696	exon8	c.G496A	p.V166I	AGCTTGGTATACA	.	scavenged	Atlas-SNP
RAVER1	125950	hgsc.bcm.edu	37	19	10439540	10439540	+	Silent	SNP	A	A	G	rs3745262	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	131	50	181	0	0.381679	0	A|0.972;G|0.028	0.028	strong	RAVER1_ENST00000293677,caecum,carcinoma,0,2	RAVER1	67	2	NM_133452	exon3	c.T585C	p.A195A	GTACTCAGCAAAG	.	PASS	Atlas-SNP
CAPRIN2	65981	hgsc.bcm.edu	37	12	30888001	30888001	+	Missense_Mutation	SNP	T	T	C	rs12146709	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	150	149	185	0	0.993333	0	T|0.805;C|0.195	0.195	strong	.	CAPRIN2	109	.	NM_023925	exon4	c.A710G	p.K237R	CCCCCTTTGAAGT	.	PASS	Atlas-SNP
INCENP	3619	hgsc.bcm.edu	37	11	61897359	61897359	+	Silent	SNP	C	C	T	rs1675133	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	58	83	0	0.816901	0	C|0.500;T|0.500	0.500	strong	INCENP_ENST00000394818,NS,carcinoma,0,3	INCENP	122	3	NM_001040694	exon4	c.C360T	p.V120V	CTCCGTCCTGCGG	.	PASS	Atlas-SNP
MYO5B	4645	hgsc.bcm.edu	37	18	47455923	47455923	+	Silent	SNP	C	C	T	rs2298628	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	44	43	48	0	0.977273	0	C|0.563;T|0.437	0.437	strong	.	MYO5B	178	.	NM_001080467	exon17	c.G2049A	p.V683V	CTCCAACACCCCG	.	PASS	Atlas-SNP
RPGRIP1	57096	hgsc.bcm.edu	37	14	21796784	21796784	+	Missense_Mutation	SNP	G	G	C	rs3748361	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	45	21	48	0	0.466667	0	G|0.722;C|0.277	0.277	strong	RPGRIP1,NS,carcinoma,0,1	RPGRIP1	213	1	NM_020366	exon18	c.G3097C	p.E1033Q	ACACCAGAGGTAA	.	PASS	Atlas-SNP
VIPR2	7434	hgsc.bcm.edu	37	7	158896517	158896517	+	Silent	SNP	G	G	A	rs2270313	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	115	56	134	0	0.486957	0	G|0.750;A|0.250	0.250	strong	.	VIPR2	53	.	NM_003382	exon4	c.C288T	p.D96D	CCATCCGTCACTC	.	PASS	Atlas-SNP
PTPRF	5792	hgsc.bcm.edu	37	1	44084739	44084739	+	Silent	SNP	C	C	T	rs1143701	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	60	26	81	0	0.433333	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
TMCO3	55002	hgsc.bcm.edu	37	13	114175032	114175032	+	Missense_Mutation	SNP	G	G	A	rs2260335	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	99	39	158	0	0.393939	0	G|0.805;A|0.195	0.195	strong	.	TMCO3	77	.	NM_017905	exon8	c.G1327A	p.A443T	GCGGGCGCCAGTG	.	PASS	Atlas-SNP
USP22	23326	hgsc.bcm.edu	37	17	20911204	20911204	+	Silent	SNP	G	G	T	rs11541311	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	89	41	112	0	0.460674	0	G|0.838;T|0.162	0.162	strong	.	USP22	45	.	NM_015276	exon9	c.C1209A	p.I403I	GGCTACGATGGGC	.	PASS	Atlas-SNP
GUCA2B	2981	hgsc.bcm.edu	37	1	42619152	42619152	+	Missense_Mutation	SNP	C	C	A	rs2297567	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	41	19	51	0	0.463415	0	C|0.831;A|0.169	0.169	strong	.	GUCA2B	9	.	NM_007102	exon1	c.C31A	p.P11T	CTCCTGCCAGGAG	.	PASS	Atlas-SNP
NBPF3	84224	hgsc.bcm.edu	37	1	21797221	21797221	+	Missense_Mutation	SNP	A	A	G	rs145790279	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	115	63	106	0	0.547826	0	A|0.992;G|0.008	0.008	strong	.	NBPF3	55	.	NM_001256416	exon4	c.C440G	p.T147R	CTGAGGAGCTCAG	.	PASS	Atlas-SNP
SCN10A	6336	hgsc.bcm.edu	37	3	38766701	38766701	+	Silent	SNP	C	C	T	rs6791171	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	137	55	153	0	0.40146	0	C|0.861;T|0.139	0.139	strong	.	SCN10A	359	.	NM_006514	exon17	c.G3192A	p.T1064T	TTTCCACGTCTCA	.	PASS	Atlas-SNP
PPP1R3D	5509	hgsc.bcm.edu	37	20	58514312	58514312	+	Silent	SNP	C	C	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	17	12	4	0	0.705882	0	.	.	none	.	PPP1R3D	23	.	NM_006242	exon1	c.G675T	p.G225G	TGCGGGCCCGCGC	.	PASS	Atlas-SNP
PEAR1	375033	hgsc.bcm.edu	37	1	156883493	156883493	+	Missense_Mutation	SNP	G	G	A	rs11264581	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	45	97	0	0.633803	0	G|0.832;A|0.168	0.168	strong	.	PEAR1	118	.	NM_001080471	exon21	c.G2654A	p.R885H	GCAGCCGCCTGGA	.	PASS	Atlas-SNP
FBXO6	26270	hgsc.bcm.edu	37	1	11728952	11728952	+	Silent	SNP	C	C	T	rs7514198	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	118	49	150	0	0.415254	0	C|0.913;T|0.087	0.087	strong	FBXO6,NS,carcinoma,+1,1	FBXO6	17	1	NM_018438	exon2	c.C237T	p.Y79Y	CTTCTACTTCCTA	.	PASS	Atlas-SNP
RBBP8NL	140893	hgsc.bcm.edu	37	20	60987737	60987737	+	Missense_Mutation	SNP	C	C	T	rs6089366	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	27	13	47	0	0.481481	0	C|0.890;T|0.110	0.110	strong	.	.	.	.	NM_080833	exon13	c.G1819A	p.E607K	CGTGCTCCTGGGT	.	PASS	Atlas-SNP
OR5W2	390148	hgsc.bcm.edu	37	11	55681566	55681566	+	Missense_Mutation	SNP	G	G	A	rs61749302	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	67	46	62	0	0.686567	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
UBASH3A	53347	hgsc.bcm.edu	37	21	43852232	43852232	+	Silent	SNP	C	C	T	rs13052676	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	99	35	79	0	0.353535	0	C|0.722;T|0.278	0.278	strong	.	UBASH3A	72	.	NM_018961	exon9	c.C1191T	p.S397S	GAAGAGCGTGCTG	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	47	46	44	0	0.978723	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
AKR1C3	8644	hgsc.bcm.edu	37	10	5138607	5138607	+	Silent	SNP	G	G	A	rs7741	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	170	67	177	0	0.394118	0	G|0.710;A|0.290	0.290	strong	.	AKR1C3	21	.	NM_001253908	exon2	c.G90A	p.P30P	GGTTCCGAGAAGT	.	PASS	Atlas-SNP
NUP133	55746	hgsc.bcm.edu	37	1	229635521	229635521	+	Silent	SNP	A	A	G	rs10916495	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	111	42	134	0	0.378378	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
AP5Z1	9907	hgsc.bcm.edu	37	7	4827330	4827330	+	Silent	SNP	C	C	T	rs17135128	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	95	77	107	0	0.810526	0	C|0.943;T|0.057	0.057	strong	KIAA0415_ENST00000450194,rectum,carcinoma,0,2	.	.	2	NM_014855	exon11	c.C1377T	p.D459D	GGTGGACGCTGGC	.	PASS	Atlas-SNP
CHMP4C	92421	hgsc.bcm.edu	37	8	82670412	82670412	+	Silent	SNP	G	G	A	rs62514262	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	107	23	104	0	0.214953	0	G|0.966;A|0.034	0.034	strong	CHMP4C,NS,carcinoma,0,1	CHMP4C	28	1	NM_152284	exon4	c.G519A	p.Q173Q	GGAACAGGAGGAA	.	PASS	Atlas-SNP
DHRS7C	201140	hgsc.bcm.edu	37	17	9676134	9676134	+	Missense_Mutation	SNP	G	G	A	rs2280490	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	40	15	30	0	0.375	0	G|0.907;A|0.093	0.093	strong	.	DHRS7C	34	.	NM_001220493	exon5	c.C680T	p.S227L	TGGTACGACCGGA	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	119	88	172	0	0.739496	0	A|0.676;G|0.324	0.324	strong	.	EXPH5	193	.	NM_015065	exon6	c.T2558C	p.L853P	TCAGTCAGTGCAG	.	PASS	Atlas-SNP
TCEB3B	51224	hgsc.bcm.edu	37	18	44560429	44560429	+	Missense_Mutation	SNP	C	C	A	rs892586	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	210	89	237	0	0.42381	0	C|0.431;A|0.569	0.569	strong	.	TCEB3B	141	.	NM_016427	exon1	c.G1207T	p.A403S	TGGTGGCAGATTT	.	PASS	Atlas-SNP
GGT1	2678	hgsc.bcm.edu	37	22	25016442	25016442	+	Missense_Mutation	SNP	C	C	T	rs3895576	bycluster;by2hit2allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	469	7	451	16	0.0149254	0.0354767	.	.	weak	GGT1,NS,carcinoma,0,1	GGT1	68	1	NM_013430	exon8	c.C530T	p.A177V	CGGCAGCCCTGGA	.	scavenged	Atlas-SNP
CHMP6	79643	hgsc.bcm.edu	37	17	78972192	78972192	+	Silent	SNP	C	C	T	rs61752553	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	125	5	137	0	0.04	0	C|0.999;T|0.001	0.001	strong	.	CHMP6	16	.	NM_024591	exon7	c.C522T	p.P174P	GGTTCCCTCCGAG	.	PASS	Atlas-SNP
DSE	29940	hgsc.bcm.edu	37	6	116756773	116756773	+	Missense_Mutation	SNP	T	T	C	rs41313440	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	80	79	87	0	0.9875	0	T|0.955;C|0.045	0.045	strong	.	DSE	98	.	NM_001080976	exon6	c.T1142C	p.V381A	AATCGGTTCCTCC	.	PASS	Atlas-SNP
SUGP1	57794	hgsc.bcm.edu	37	19	19427402	19427402	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	91	4	141	0	0.043956	0	.	.	none	.	SUGP1	63	.	NM_172231	exon2	c.G35A	p.G12E	GCCTTTCCTGGGG	.	PASS	Atlas-SNP
CDK5RAP2	55755	hgsc.bcm.edu	37	9	123301346	123301346	+	Silent	SNP	T	T	G	rs3750494	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	38	112	0	0.447059	0	T|0.918;G|0.082	0.082	strong	.	CDK5RAP2	157	.	NM_018249	exon6	c.A480C	p.L160L	TTTAGTTAGGAGA	.	PASS	Atlas-SNP
SVOPL	136306	hgsc.bcm.edu	37	7	138305806	138305806	+	Silent	SNP	T	T	C	rs3734944	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	45	80	0	0.6	0	T|0.741;C|0.259	0.259	strong	.	SVOPL	111	.	NM_001139456	exon13	c.A1338G	p.A446A	AAATGGTGCCACC	.	PASS	Atlas-SNP
ZNF568	374900	hgsc.bcm.edu	37	19	37441365	37441365	+	Missense_Mutation	SNP	T	T	C	rs547483	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	18	9	23	0	0.5	0	T|0.698;C|0.302	0.302	strong	.	ZNF568	106	.	NM_198539	exon7	c.T1310C	p.M437T	TACATATGCGAAA	.	PASS	Atlas-SNP
CTSC	1075	hgsc.bcm.edu	37	11	88027393	88027393	+	Silent	SNP	A	A	C	rs17594	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	173	30	159	0	0.17341	0	A|0.942;C|0.058	0.058	strong	.	CTSC	46	.	NM_001814	exon7	c.T1173G	p.T391T	TAGACCAGTGTGG	.	PASS	Atlas-SNP
PCDHB10	56126	hgsc.bcm.edu	37	5	140573508	140573508	+	Silent	SNP	C	C	G	rs61742867	byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	83	22	88	0	0.26506	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
SVEP1	79987	hgsc.bcm.edu	37	9	113244732	113244732	+	Missense_Mutation	SNP	G	G	T	rs41296069	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	160	56	150	0	0.35	0	G|0.934;T|0.066	0.066	strong	.	SVEP1	326	.	NM_153366	exon11	c.C2079A	p.D693E	GAAAAGGTCTCCT	.	PASS	Atlas-SNP
HRG	3273	hgsc.bcm.edu	37	3	186395113	186395113	+	Missense_Mutation	SNP	A	A	G	rs2228243	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	124	124	156	0	1	0	A|0.768;G|0.232	0.232	strong	HRG,NS,adenoma,0,2	HRG	81	2	NM_000412	exon7	c.A1019G	p.H340R	AAAGACATTCTCA	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	88	52	72	0	0.590909	0	A|0.924;T|0.076	0.076	strong	.	ICAM1	32	.	NM_000201	exon2	c.A167T	p.K56M	AGCCCAAGTTGTT	.	PASS	Atlas-SNP
MAVS	57506	hgsc.bcm.edu	37	20	3838441	3838441	+	Missense_Mutation	SNP	C	C	G	rs17857295	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	93	57	98	0	0.612903	0	C|0.764;G|0.236	0.236	strong	.	MAVS	34	.	NM_020746	exon3	c.C277G	p.Q93E	GTCTACCAGAGCT	.	PASS	Atlas-SNP
LRRC32	2615	hgsc.bcm.edu	37	11	76372052	76372052	+	Silent	SNP	A	A	G	rs3740779	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	64	93	0	0.853333	0	G|0.616;N|0.000	0.616	strong	.	LRRC32	74	.	NM_005512	exon3	c.T585C	p.G195G	GGGCAGACCCTCG	.	PASS	Atlas-SNP
LMF2	91289	hgsc.bcm.edu	37	22	50944163	50944163	+	Silent	SNP	G	G	A	rs128941	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	210	102	218	0	0.485714	0	G|0.462;A|0.538	0.538	strong	.	LMF2	40	.	NM_033200	exon6	c.C856T	p.L286L	CGTCCAGCAGCGC	.	PASS	Atlas-SNP
GUCA2B	2981	hgsc.bcm.edu	37	1	42619139	42619139	+	Silent	SNP	A	A	G	rs1047047	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	38	19	50	0	0.5	0	A|0.756;G|0.244	0.244	strong	.	GUCA2B	9	.	NM_007102	exon1	c.A18G	p.A6A	GGCTGCATCAGGG	.	PASS	Atlas-SNP
OR6N1	128372	hgsc.bcm.edu	37	1	158736445	158736445	+	Missense_Mutation	SNP	C	C	T	rs1864346	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	33	33	23	0	1	0	C|0.753;N|0.000	.	strong	.	OR6N1	96	.	NM_001005185	exon1	c.G28A	p.A10T	ATTCTGCTACCTG	.	PASS	Atlas-SNP
HID1	283987	hgsc.bcm.edu	37	17	72956124	72956124	+	Silent	SNP	G	G	A	rs3744198	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	68	44	88	0	0.647059	0	G|0.667;A|0.333	0.333	strong	.	.	.	.	NM_030630	exon7	c.C948T	p.A316A	TACATCGGCATCA	.	PASS	Atlas-SNP
GPR142	350383	hgsc.bcm.edu	37	17	72367973	72367973	+	Missense_Mutation	SNP	T	T	C	rs148514779	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	65	39	75	0	0.6	0	T|0.997;C|0.003	0.003	strong	.	GPR142	74	.	NM_181790	exon4	c.T623C	p.V208A	TCCAGGTGGTCAT	.	PASS	Atlas-SNP
AHNAK	79026	hgsc.bcm.edu	37	11	62293948	62293948	+	Silent	SNP	G	G	A	rs486903	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	116	96	98	0	0.827586	0	G|0.462;A|0.538	0.538	strong	AHNAK,NS,carcinoma,0,1	AHNAK	532	1	NM_001620	exon5	c.C7941T	p.S2647S	AGGCATGCTGAAC	.	PASS	Atlas-SNP
BARD1	580	hgsc.bcm.edu	37	2	215657089	215657089	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	109	5	153	0	0.0458716	0	.	.	none	.	BARD1	138	.	NM_000465	exon3	c.G296A	p.R99K	AGTTGTCTATTTA	.	PASS	Atlas-SNP
ZNF749	388567	hgsc.bcm.edu	37	19	57956706	57956706	+	Silent	SNP	G	G	A	rs61745342	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	103	36	96	0	0.349515	0	G|0.982;A|0.018	0.018	strong	.	ZNF749	75	.	NM_001023561	exon3	c.G2190A	p.G730G	ATGTGGGAAAGAC	.	PASS	Atlas-SNP
WIPF3	644150	hgsc.bcm.edu	37	7	29923572	29923572	+	Silent	SNP	T	T	C	rs28439342	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	48	10	45	0	0.208333	0	T|0.850;C|0.150	0.150	strong	.	WIPF3	46	.	NM_001080529	exon5	c.T462C	p.N154N	AGGCAATACCTCC	.	PASS	Atlas-SNP
IDUA	3425	hgsc.bcm.edu	37	4	995919	995919	+	Silent	SNP	G	G	C	rs6830825	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	25	10	21	0	0.4	0	G|0.815;C|0.185	0.185	strong	IDUA,NS,carcinoma,0,1	IDUA	33	1	NM_000203	exon7	c.G942C	p.A314A	GAGGGCGGACGTG	.	PASS	Atlas-SNP
HELZ2	85441	hgsc.bcm.edu	37	20	62194128	62194128	+	Missense_Mutation	SNP	G	G	A	rs3810485	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	27	20	17	0	0.740741	0	G|0.740;A|0.260	0.260	strong	.	.	.	.	NM_001037335	exon9	c.C6047T	p.P2016L	GGAGCCGGCAGCC	.	PASS	Atlas-SNP
ATXN1	6310	hgsc.bcm.edu	37	6	16327903	16327903	+	Missense_Mutation	SNP	C	C	A	rs3817753	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	44	15	47	0	0.340909	0	C|0.899;A|0.101	0.101	strong	ATXN1,rectum,carcinoma,0,1	ATXN1	117	1	NM_001128164	exon7	c.G639T	p.Q213H	CTGCTGCTGCTGA	.	PASS	Atlas-SNP
NOC3L	64318	hgsc.bcm.edu	37	10	96106240	96106240	+	Missense_Mutation	SNP	G	G	C	rs11187895	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	102	43	135	0	0.421569	0	G|0.928;C|0.072	0.072	strong	NOC3L,NS,carcinoma,0,1	NOC3L	67	1	NM_022451	exon11	c.C1331G	p.P444R	TTTTTTGGTTTAT	.	PASS	Atlas-SNP
CATSPER2	117155	hgsc.bcm.edu	37	15	43939642	43939642	+	Missense_Mutation	SNP	C	C	T	rs8042868	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	224	78	179	0	0.348214	0	C|0.822;T|0.178	0.178	strong	.	CATSPER2	49	.	NM_172097	exon3	c.G169A	p.V57I	CCAATACAAGTTT	.	PASS	Atlas-SNP
ARSD	414	hgsc.bcm.edu	37	X	2836138	2836138	+	Silent	SNP	G	G	A	rs73632974	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	111	16	118	0	0.144144	0	G|0.925;A|0.075	0.075	strong	.	ARSD	47	.	NM_001669	exon5	c.C570T	p.P190P	CACTTCGGGGGGC	.	PASS	Atlas-SNP
DNAL4	10126	hgsc.bcm.edu	37	22	39178701	39178701	+	Silent	SNP	A	A	G	rs760482	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	159	83	185	0	0.522013	0	A|0.627;G|0.373	0.373	strong	.	DNAL4	5	.	NM_005740	exon2	c.T36C	p.D12D	CTTATAATCAGCC	.	PASS	Atlas-SNP
BAD	572	hgsc.bcm.edu	37	11	64051823	64051823	+	Silent	SNP	C	C	T	rs34882006	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	50	77	0	0.714286	0	C|0.978;T|0.022	0.022	strong	.	BAD	8	.	NM_032989	exon2	c.G18A	p.E6E	CTCAAACTCTGGG	.	PASS	Atlas-SNP
SYNE1	23345	hgsc.bcm.edu	37	6	152777095	152777095	+	Missense_Mutation	SNP	A	A	C	rs17082709	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	56	129	0	0.746667	0	A|0.938;C|0.062	0.062	strong	.	SYNE1	3227	.	NM_033071	exon23	c.T2674G	p.L892V	TGCTCAAGGTCAC	.	PASS	Atlas-SNP
DSCAML1	57453	hgsc.bcm.edu	37	11	117310022	117310022	+	Silent	SNP	A	A	G	rs11216387	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	100	21	98	0	0.21	0	A|0.769;G|0.231	0.231	strong	DSCAML1,NS,carcinoma,0,1	DSCAML1	286	1	NM_020693	exon23	c.T4284C	p.T1428T	GCCACCAGTGTTG	.	PASS	Atlas-SNP
OR5F1	338674	hgsc.bcm.edu	37	11	55761528	55761528	+	Missense_Mutation	SNP	T	T	C	rs35607186	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	93	68	139	0	0.731183	0	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	.	PASS	Atlas-SNP
MIPEP	4285	hgsc.bcm.edu	37	13	24436475	24436475	+	Missense_Mutation	SNP	C	C	T	rs11551114	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	165	80	248	0	0.484848	0	C|0.909;T|0.091	0.091	strong	MIPEP,colon,carcinoma,-1,1	MIPEP	53	1	NM_005932	exon9	c.G1019A	p.R340Q	ATCCCTCGTATCA	.	PASS	Atlas-SNP
HERC4	26091	hgsc.bcm.edu	37	10	69695973	69695973	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	65	17	69	0	0.261538	0	.	.	none	.	HERC4	78	.	NM_022079	exon23	c.G2615A	p.G872D	GTTGCACCAAAGT	.	PASS	Atlas-SNP
PRDM9	56979	hgsc.bcm.edu	37	5	23527387	23527387	+	Missense_Mutation	SNP	C	C	A	rs56256550		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	116	10	88	2	0.0862069	0.0227273	.	.	weak	PRDM9,rectum,carcinoma,0,1	PRDM9	344	1	NM_020227	exon11	c.C2190A	p.S730R	CTTTAGCAATAAG	.	scavenged	Atlas-SNP
ARID4B	51742	hgsc.bcm.edu	37	1	235383188	235383188	+	Silent	SNP	A	A	G	rs4659654	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	198	195	284	1	0.984848	0.00352113	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
DHX33	56919	hgsc.bcm.edu	37	17	5354204	5354204	+	Missense_Mutation	SNP	G	G	C	rs11653658	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	111	54	136	0	0.486486	0	G|0.935;C|0.065	0.065	strong	.	DHX33	41	.	NM_020162	exon9	c.C1447G	p.H483D	CCTTATGTTCAAG	.	PASS	Atlas-SNP
SYNE1	23345	hgsc.bcm.edu	37	6	152469188	152469188	+	Missense_Mutation	SNP	C	C	G	rs2252755	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	25	15	27	0	0.6	0	C|0.627;G|0.373	0.373	strong	.	SYNE1	3227	.	NM_182961	exon137	c.G24968C	p.G8323A	GATAAGCCAACAG	.	PASS	Atlas-SNP
EXD1	161829	hgsc.bcm.edu	37	15	41476465	41476465	+	Silent	SNP	G	G	A	rs690733	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	157	83	176	0	0.528662	0	G|0.476;A|0.524	0.524	strong	.	EXD1	52	.	NM_152596	exon10	c.C1209T	p.T403T	CTCACTGGTTTCC	.	PASS	Atlas-SNP
WDR38	401551	hgsc.bcm.edu	37	9	127618775	127618775	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	61	11	56	0	0.180328	0	.	.	none	.	WDR38	21	.	NM_001045476	exon6	c.C514T	p.H172Y	ACCGTACACATCT	.	PASS	Atlas-SNP
MLL4	8085	hgsc.bcm.edu	37	19	36224705	36224705	+	Missense_Mutation	SNP	A	A	G	rs231591	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	116	116	134	1	1	0.00746269	A|0.441;G|0.559	0.559	strong	.	MLL4	229	.	NM_014727	exon30	c.A7091G	p.D2364G	CGGAAGATGGTCC	.	PASS	Atlas-SNP
TTBK2	146057	hgsc.bcm.edu	37	15	43170793	43170793	+	Missense_Mutation	SNP	A	A	G	rs6493068	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	126	48	135	0	0.380952	0	A|0.525;G|0.475	0.475	strong	.	TTBK2	82	.	NM_173500	exon2	c.T23C	p.L8P	ATATCCAGCTGCT	.	PASS	Atlas-SNP
PCDHB13	56123	hgsc.bcm.edu	37	5	140595802	140595802	+	Missense_Mutation	SNP	T	T	C	rs17844618	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	53	23	60	0	0.433962	0	T|0.856;C|0.144	0.144	strong	.	PCDHB13	142	.	NM_018933	exon1	c.T2107C	p.F703L	TTCCTCTTTTCGG	.	PASS	Atlas-SNP
DIP2C	22982	hgsc.bcm.edu	37	10	459940	459940	+	Silent	SNP	G	G	A	rs4881274	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	67	37	67	0	0.552239	0	G|0.440;A|0.560	0.560	strong	.	DIP2C	195	.	NM_014974	exon8	c.C970T	p.L324L	TCTGCAGTGCGGC	.	PASS	Atlas-SNP
BTG1	694	hgsc.bcm.edu	37	12	92538171	92538171	+	Nonsense_Mutation	SNP	G	G	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	109	20	125	0	0.183486	0	.	.	none	BTG1,NS,lymphoid_neoplasm,0,1	BTG1	30	1	NM_001731	exon2	c.C201G	p.Y67X	ACAACGGTAACCC	.	PASS	Atlas-SNP
TG	7038	hgsc.bcm.edu	37	8	134144113	134144113	+	Silent	SNP	C	C	T	rs2294024	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	129	38	153	0	0.294574	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
MTDH	92140	hgsc.bcm.edu	37	8	98703317	98703317	+	Missense_Mutation	SNP	A	A	G	rs17854374	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	45	79	0	0.775862	0	A|0.958;G|0.042	0.042	strong	.	MTDH	54	.	NM_178812	exon6	c.A949G	p.T317A	AGGAAAACTGAGC	.	PASS	Atlas-SNP
ZNF529	57711	hgsc.bcm.edu	37	19	37038092	37038092	+	Silent	SNP	T	T	C	rs2278168	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	41	79	0	0.561644	0	T|0.774;C|0.226	0.226	strong	.	ZNF529	82	.	NM_001145649	exon6	c.A1368G	p.G456G	GAACTTTCCACAC	.	PASS	Atlas-SNP
GOLGB1	2804	hgsc.bcm.edu	37	3	121413637	121413637	+	Silent	SNP	G	G	A	rs34833153	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	238	126	272	1	0.529412	0.00367647	G|0.948;A|0.052	0.052	strong	.	GOLGB1	319	.	NM_001256486	exon13	c.C5733T	p.S1911S	AACTCTGGAGAGT	.	PASS	Atlas-SNP
MIA3	375056	hgsc.bcm.edu	37	1	222833538	222833538	+	Silent	SNP	C	C	G	rs2291835	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	124	57	131	1	0.459677	0.00763359	C|0.832;G|0.168	0.168	strong	MIA3,NS,carcinoma,0,1	MIA3	167	1	NM_198551	exon24	c.C4995G	p.G1665G	GAATGGCTCTTTT	.	scavenged	Atlas-SNP
ENPP7	339221	hgsc.bcm.edu	37	17	77705045	77705045	+	Silent	SNP	T	T	C	rs8074728	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	47	20	71	0	0.425532	0	T|0.527;C|0.473	0.473	strong	.	ENPP7	63	.	NM_178543	exon1	c.T144C	p.D48D	CCAGGATGTGGAC	.	PASS	Atlas-SNP
EFCAB5	374786	hgsc.bcm.edu	37	17	28381141	28381141	+	Silent	SNP	C	C	G	rs4074170	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	245	120	280	1	0.489796	0.00357143	C|0.514;G|0.486	0.486	strong	.	EFCAB5	122	.	NM_198529	exon10	c.C2169G	p.T723T	TCCAACCTTAAGC	.	PASS	Atlas-SNP
LRRK2	120892	hgsc.bcm.edu	37	12	40671989	40671989	+	Missense_Mutation	SNP	A	A	G	rs10878307	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	168	168	201	0	1	0	A|0.947;G|0.053	0.053	strong	LRRK2_ENST00000298910,NS,NS,-2,2	LRRK2	763	2	NM_198578	exon18	c.A2167G	p.I723V	AACAGCATCATGG	.	PASS	Atlas-SNP
IL5RA	3568	hgsc.bcm.edu	37	3	3146610	3146610	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	178	44	186	0	0.247191	0	.	.	none	IL5RA,caecum,carcinoma,0,1	IL5RA	55	1	NM_001243099	exon3	c.C59T	p.A20V	AAGTCAGCTTGCA	.	PASS	Atlas-SNP
TYROBP	7305	hgsc.bcm.edu	37	19	36398454	36398454	+	Silent	SNP	G	G	C	rs111477177	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	68	39	76	0	0.573529	0	A|0.000;C|0.024;G|0.976	0.024	strong	TYROBP,NS,carcinoma,-2,1	TYROBP	15	1	NM_198125	exon3	c.C123G	p.G41G	CAGCACGCCCGGG	.	PASS	Atlas-SNP
ZNF585B	92285	hgsc.bcm.edu	37	19	37676528	37676528	+	Silent	SNP	G	G	A	rs8111369	bycluster;by2hit2allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	191	109	250	1	0.570681	0.004	G|0.500;A|0.500	0.500	weak	.	ZNF585B	91	.	NM_152279	exon5	c.C1911T	p.A637A	ACACTCGGCACAC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195509078	195509078	+	Missense_Mutation	SNP	C	C	T	rs371017154		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	34	5	46	0	0.147059	0	.	.	weak	.	MUC4	1505	.	NM_018406	exon2	c.G9373A	p.D3125N	AAGTGTCGGTGAC	.	PASS	Atlas-SNP
CNTN2	6900	hgsc.bcm.edu	37	1	205027737	205027737	+	Missense_Mutation	SNP	G	G	A	rs2275697	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	37	12	51	0	0.324324	0	G|0.790;N|0.000	.	strong	.	CNTN2	116	.	NM_005076	exon5	c.G433A	p.A145T	GTGAAAGCTCATG	.	PASS	Atlas-SNP
RAD21	5885	hgsc.bcm.edu	37	8	117864217	117864217	+	Silent	SNP	A	A	G	rs1050838	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	153	118	166	1	0.771242	0.0060241	A|0.871;G|0.129	0.129	strong	RAD21,NS,carcinoma,0,1	RAD21	95	1	NM_006265	exon11	c.T1440C	p.A480A	TTGTCCAGCTTTT	.	PASS	Atlas-SNP
NMT1	4836	hgsc.bcm.edu	37	17	43171154	43171154	+	Silent	SNP	C	C	T	rs1132898	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	81	37	110	0	0.45679	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
LPIN1	23175	hgsc.bcm.edu	37	2	11943082	11943082	+	Missense_Mutation	SNP	C	C	T	rs4669781	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	44	17	63	0	0.386364	0	C|0.968;T|0.032	0.032	strong	LPIN1_ENST00000404113,NS,carcinoma,-2,3	LPIN1	99	3	NM_001261428	exon16	c.C2083T	p.P695S	GCCAAGCCATCAA	.	PASS	Atlas-SNP
SLIT3	6586	hgsc.bcm.edu	37	5	168233474	168233474	+	Silent	SNP	G	G	A	rs3797715	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	136	76	101	0	0.558824	0	G|0.859;A|0.141	0.141	strong	.	SLIT3	224	.	NM_001271946	exon9	c.C912T	p.N304N	CGGCAAGTTGGCA	.	PASS	Atlas-SNP
MYBPC2	4606	hgsc.bcm.edu	37	19	50957600	50957600	+	Missense_Mutation	SNP	T	T	C	rs150466277	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	88	53	125	0	0.602273	0	T|0.994;C|0.006	0.006	strong	.	MYBPC2	103	.	NM_004533	exon18	c.T1988C	p.M663T	CACCAATGTACGA	.	PASS	Atlas-SNP
CDC6	990	hgsc.bcm.edu	37	17	38450248	38450248	+	Missense_Mutation	SNP	G	G	A	rs4135012	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	211	101	222	0	0.478673	0	G|0.986;A|0.014	0.014	strong	.	CDC6	53	.	NM_001254	exon6	c.G883A	p.D295N	GGCCAGGATGTAT	.	PASS	Atlas-SNP
ARHGEF10	9639	hgsc.bcm.edu	37	8	1873540	1873540	+	Silent	SNP	C	C	T	rs2272613	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	83	64	62	0	0.771084	0	C|0.925;T|0.075	0.075	strong	ARHGEF10_ENST00000398564,NS,carcinoma,0,2	ARHGEF10	255	2	NM_014629	exon22	c.C2580T	p.P860P	CATGCCCGTGATG	.	PASS	Atlas-SNP
MIA3	375056	hgsc.bcm.edu	37	1	222823669	222823669	+	Missense_Mutation	SNP	A	A	G	rs201134844	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	102	48	152	0	0.470588	0	A|0.999;G|0.001	0.001	weak	.	MIA3	167	.	NM_198551	exon9	c.A3667G	p.I1223V	AAGACTATCATGA	.	PASS	Atlas-SNP
COL6A3	1293	hgsc.bcm.edu	37	2	238258814	238258814	+	Silent	SNP	C	C	G	rs3790993	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	61	29	61	1	0.47541	0.0163934	C|0.434;G|0.566	0.566	strong	COL6A3,colon,carcinoma,-2,1	COL6A3	608	1	NM_004369	exon28	c.G6855C	p.G2285G	CCGGTTCCCGATT	.	scavenged	Atlas-SNP
PHLPP1	23239	hgsc.bcm.edu	37	18	60645509	60645509	+	Silent	SNP	C	C	T	rs34061095	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	68	34	59	0	0.5	0	C|0.951;T|0.049	0.049	strong	.	PHLPP1	164	.	NM_194449	exon17	c.C3999T	p.N1333N	GGTGAACGGAGTG	.	PASS	Atlas-SNP
HMGXB3	22993	hgsc.bcm.edu	37	5	149421502	149421502	+	Silent	SNP	A	A	G	rs2276982	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	129	70	121	0	0.542636	0	A|0.728;G|0.272	0.272	strong	.	HMGXB3	31	.	NM_014983	exon15	c.A2700G	p.E900E	GAGTGAAGAGAAT	.	PASS	Atlas-SNP
TPO	7173	hgsc.bcm.edu	37	2	1491723	1491723	+	Silent	SNP	G	G	A	rs78406347	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	110	64	80	0	0.581818	0	G|0.987;A|0.013	0.013	strong	TPO,NS,carcinoma,+1,2	TPO	224	2	NM_001206744	exon10	c.G1728A	p.A576A	TCTGGCGTCCATC	.	PASS	Atlas-SNP
PKHD1	5314	hgsc.bcm.edu	37	6	51890823	51890823	+	Missense_Mutation	SNP	G	G	A	rs9296669	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	68	93	0	0.971429	0	G|0.638;A|0.362	0.362	strong	.	PKHD1	927	.	NM_170724	exon32	c.C3785T	p.A1262V	GTGGGAGCGCCCG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195510786	195510786	+	Silent	SNP	T	T	G	rs2948677	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	213	67	167	1	0.314554	0.00598802	T|0.500;G|0.500	0.500	strong	MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	NM_018406	exon2	c.A7665C	p.T2555T	GTGACCTGTGGAT	.	scavenged	Atlas-SNP
SH2D7	646892	hgsc.bcm.edu	37	15	78390909	78390909	+	Missense_Mutation	SNP	C	C	T	rs12593575	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	35	60	0	0.402299	0	C|0.785;T|0.215	0.215	strong	.	SH2D7	26	.	NM_001101404	exon4	c.C616T	p.R206W	AGTCCCCGGAACC	.	PASS	Atlas-SNP
HDC	3067	hgsc.bcm.edu	37	15	50555544	50555544	+	Missense_Mutation	SNP	G	G	A	rs17740607	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	111	54	90	0	0.486486	0	G|0.928;A|0.072	0.072	strong	.	HDC	86	.	NM_002112	exon2	c.C92T	p.T31M	TCTGGCGTCACAC	.	PASS	Atlas-SNP
APCDD1	147495	hgsc.bcm.edu	37	18	10471773	10471773	+	Silent	SNP	C	C	G	rs3748413	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	51	27	54	0	0.529412	0	C|0.897;G|0.103	0.103	strong	.	APCDD1	57	.	NM_153000	exon3	c.C489G	p.L163L	GAAGCTCGGCCAG	.	PASS	Atlas-SNP
ABCB9	23457	hgsc.bcm.edu	37	12	123444265	123444265	+	Missense_Mutation	SNP	G	G	A	rs114398803	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	26	10	35	0	0.384615	0	G|0.999;A|0.001	0.001	strong	.	ABCB9	50	.	NM_019625	exon2	c.C518T	p.T173M	TGCAGCGTGGCCC	.	PASS	Atlas-SNP
ATXN1	6310	hgsc.bcm.edu	37	6	16327915	16327915	+	Missense_Mutation	SNP	A	A	C	rs11969612	bycluster;byfrequency;by2hit2allele;byhapmap	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	44	17	49	0	0.386364	0	A|0.571;C|0.429	0.429	strong	ATXN1,colon,carcinoma,0,1	ATXN1	117	1	NM_001128164	exon7	c.T627G	p.H209Q	ATGCTGATGCTGC	.	PASS	Atlas-SNP
TSSK2	23617	hgsc.bcm.edu	37	22	19119686	19119686	+	Silent	SNP	C	C	T	rs1052756	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	59	28	84	0	0.474576	0	C|0.851;A|0.001	.	strong	.	TSSK2	29	.	NM_053006	exon1	c.C774T	p.S258S	CGTCAGCCAGCGG	.	PASS	Atlas-SNP
OR51B5	282763	hgsc.bcm.edu	37	11	5364640	5364640	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	67	52	63	0	0.776119	0	.	.	none	.	OR51B5	60	.	NM_001005567	exon5	c.G115A	p.G39S	CATTGCCAAAAAG	.	PASS	Atlas-SNP
RRP1	8568	hgsc.bcm.edu	37	21	45217929	45217929	+	Silent	SNP	T	T	C	rs2838379	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	179	77	126	0	0.430168	0	T|0.670;C|0.330	0.330	strong	.	RRP1	23	.	NM_003683	exon8	c.T759C	p.G253G	TGAGGGTGGTGAG	.	PASS	Atlas-SNP
KNG1	3827	hgsc.bcm.edu	37	3	186437944	186437944	+	Silent	SNP	T	T	C	rs5029980	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	145	78	157	0	0.537931	0	T|0.907;C|0.093	0.093	strong	KNG1_ENST00000265023,NS,carcinoma,0,2	KNG1	129	2	NM_000893	exon2	c.T246C	p.D82D	GGGGGATTGTCCT	.	PASS	Atlas-SNP
PLEKHG4B	153478	hgsc.bcm.edu	37	5	163266	163266	+	Missense_Mutation	SNP	C	C	G	rs3810867	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	122	53	125	0	0.434426	0	C|0.689;G|0.311	0.311	strong	.	PLEKHG4B	167	.	NM_052909	exon11	c.C2011G	p.R671G	ACCCTGCGCCCAG	.	PASS	Atlas-SNP
RAB5B	5869	hgsc.bcm.edu	37	12	56383858	56383858	+	Silent	SNP	C	C	T	rs141101772	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	150	67	181	0	0.446667	0	C|0.999;T|0.001	0.001	strong	RAB5B,NS,lymphoid_neoplasm,+2,1	RAB5B	22	1	NM_002868	exon3	c.C291T	p.I97I	TGCAATCGTGGTT	.	PASS	Atlas-SNP
OR5K2	402135	hgsc.bcm.edu	37	3	98216586	98216586	+	Missense_Mutation	SNP	C	C	G	rs143260385	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	361	170	349	0	0.470914	0	C|0.994;G|0.006	0.006	strong	OR5K2,bladder,carcinoma,0,1	OR5K2	56	1	NM_001004737	exon1	c.C62G	p.P21R	ATCACCCTGAGCT	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105417581	105417581	+	Missense_Mutation	SNP	C	C	T	rs141283979	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	96	0	0	0.989691	.	C|0.984;T|0.016	0.016	strong	.	AHNAK2	719	.	NM_138420	exon7	c.G4207A	p.E1403K	CTCCCTCGGGCAC	.	PASS	Atlas-SNP
SAMD7	344658	hgsc.bcm.edu	37	3	169644710	169644710	+	Missense_Mutation	SNP	G	G	C	rs10513680	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	76	40	111	0	0.526316	0	G|0.864;C|0.136	0.136	strong	.	SAMD7	69	.	NM_182610	exon6	c.G660C	p.E220D	TGAAGAGGATCAT	.	PASS	Atlas-SNP
TAS2R31	259290	hgsc.bcm.edu	37	12	11183512	11183512	+	Silent	SNP	A	A	G	rs12370363	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	127	59	177	0	0.464567	0	A|0.785;G|0.215	0.215	strong	.	TAS2R31	24	.	NM_176885	exon1	c.T423C	p.A141A	TTGACAAGCCAAA	.	PASS	Atlas-SNP
PKD1L1	168507	hgsc.bcm.edu	37	7	47917087	47917087	+	Silent	SNP	C	C	T	rs72601626	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	57	39	101	0	0.684211	0	C|0.942;T|0.058	0.058	strong	.	PKD1L1	328	.	NM_138295	exon22	c.G3663A	p.P1221P	ACGTACCGGTTTT	.	PASS	Atlas-SNP
TRPC4	7223	hgsc.bcm.edu	37	13	38357384	38357384	+	Silent	SNP	G	G	A	rs12875527	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	172	76	218	0	0.44186	0	G|0.938;A|0.062	0.062	strong	.	TRPC4	389	.	NM_001135958	exon2	c.C87T	p.L29L	TGGCGAGAGTTCT	.	PASS	Atlas-SNP
STAB1	23166	hgsc.bcm.edu	37	3	52556890	52556890	+	Missense_Mutation	SNP	A	A	G	rs4434138	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	243	241	236	1	0.99177	0.00423729	A|0.608;G|0.392	0.392	strong	.	STAB1	178	.	NM_015136	exon62	c.A6844G	p.I2282V	GTGGGCATAGTCA	.	PASS	Atlas-SNP
PITRM1	10531	hgsc.bcm.edu	37	10	3181126	3181126	+	Missense_Mutation	SNP	C	C	T	rs17849904	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	160	85	177	0	0.53125	0	C|0.954;T|0.046	0.046	strong	.	PITRM1	109	.	NM_001242307	exon25	c.G2890A	p.V964I	CATCTACGGTTGA	.	PASS	Atlas-SNP
ASAP3	55616	hgsc.bcm.edu	37	1	23761028	23761028	+	Silent	SNP	G	G	A	rs74415268	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	104	45	92	0	0.432692	0	G|0.969;A|0.031	0.031	strong	.	ASAP3	65	.	NM_017707	exon18	c.C1833T	p.N611N	TCACCCGTTCTGG	.	PASS	Atlas-SNP
WDR52	55779	hgsc.bcm.edu	37	3	113098217	113098217	+	Missense_Mutation	SNP	G	G	A	rs58988763	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	37	19	54	0	0.513514	0	G|0.969;A|0.031	0.031	strong	.	WDR52	151	.	NM_001164496	exon17	c.C2234T	p.P745L	GTTGACGGAATAA	.	PASS	Atlas-SNP
DNA2	1763	hgsc.bcm.edu	37	10	70218913	70218913	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	3	133	1	0.029703	0.0075188	.	.	none	DNA2L,colon,carcinoma,0,2	DNA2	76	2	NM_001080449	exon5	c.G667A	p.D223N	TGAAATCTCCTGC	.	scavenged	Atlas-SNP
ZNF587	84914	hgsc.bcm.edu	37	19	58371274	58371274	+	Silent	SNP	G	G	T	rs10405892	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	357	61	245	0	0.170868	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
MTX2	10651	hgsc.bcm.edu	37	2	177194090	177194090	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	222	111	219	0	0.5	0	.	.	none	.	MTX2	25	.	NM_006554	exon8	c.A479G	p.Q160R	CCTATCAAAAACA	.	PASS	Atlas-SNP
LGR4	55366	hgsc.bcm.edu	37	11	27390144	27390144	+	Missense_Mutation	SNP	G	G	A	rs34717439	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	91	73	128	0	0.802198	0	G|0.965;A|0.035	0.035	strong	LGR4,NS,carcinoma,+1,1	LGR4	87	1	NM_018490	exon18	c.C2126T	p.T709M	ACTAACGTTACAG	.	PASS	Atlas-SNP
MFAP3	4238	hgsc.bcm.edu	37	5	153432733	153432733	+	Silent	SNP	T	T	C	rs2578386	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	134	70	169	0	0.522388	0	T|0.347;C|0.653	0.653	strong	.	MFAP3	20	.	NM_005927	exon3	c.T549C	p.A183A	GAAGGCTATCAAT	.	PASS	Atlas-SNP
SULT2B1	6820	hgsc.bcm.edu	37	19	49102599	49102599	+	Missense_Mutation	SNP	C	C	T	rs17842463	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	204	83	207	0	0.406863	0	C|0.989;T|0.011	0.011	strong	.	SULT2B1	72	.	NM_177973	exon7	c.C1034T	p.P345L	CCAGACCCAACTC	.	PASS	Atlas-SNP
SERPINA6	866	hgsc.bcm.edu	37	14	94780608	94780608	+	Silent	SNP	G	G	A	rs3748320	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	122	44	96	0	0.360656	0	G|0.833;A|0.167	0.167	strong	.	SERPINA6	102	.	NM_001756	exon2	c.C378T	p.T126T	GCCCATGGTCATT	.	PASS	Atlas-SNP
RBBP8NL	140893	hgsc.bcm.edu	37	20	60987921	60987921	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	81	31	110	0	0.382716	0	.	.	none	.	.	.	.	NM_080833	exon12	c.G1711A	p.D571N	GTTCGTCGGACTC	.	PASS	Atlas-SNP
STAC	6769	hgsc.bcm.edu	37	3	36422216	36422216	+	Silent	SNP	T	T	C	rs73052248	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	81	51	64	1	0.62963	0.015625	T|0.823;C|0.177	0.177	strong	STAC,caecum,carcinoma,0,1	STAC	78	1	NM_003149	exon1	c.T81C	p.S27S	GCCCTCTCCTGCA	.	scavenged	Atlas-SNP
C16orf3	750	hgsc.bcm.edu	37	16	90095573	90095573	+	Missense_Mutation	SNP	C	C	T	rs77382359	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	115	27	88	4	0.234783	0.0454545	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	.	scavenged	Atlas-SNP
PRSS33	260429	hgsc.bcm.edu	37	16	2834711	2834711	+	Silent	SNP	G	G	A	rs45570838	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	109	73	110	0	0.669725	0	G|0.934;A|0.066	0.066	strong	PRSS33,NS,carcinoma,0,1	PRSS33	7	1	NM_152891	exon6	c.C777T	p.N259N	TGGACGGTTGGGC	.	PASS	Atlas-SNP
SLC45A4	57210	hgsc.bcm.edu	37	8	142225990	142225990	+	Silent	SNP	G	G	A	rs2288998	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	83	10	93	0	0.120482	0	G|0.706;A|0.294	0.294	strong	.	SLC45A4	71	.	NM_001080431	exon6	c.C1656T	p.V552V	TGTGCCGACAGAG	.	PASS	Atlas-SNP
ATP13A5	344905	hgsc.bcm.edu	37	3	193081122	193081122	+	Missense_Mutation	SNP	G	G	T	rs12637558	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	70	98	0	1	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
TEK	7010	hgsc.bcm.edu	37	9	27197486	27197486	+	Missense_Mutation	SNP	G	G	T	rs35030851	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	152	70	138	0	0.460526	0	G|0.961;T|0.039	0.039	strong	.	TEK	250	.	NM_000459	exon12	c.G1798T	p.V600L	ACTTCGGTGCTAC	.	PASS	Atlas-SNP
CCDC168	643677	hgsc.bcm.edu	37	13	103399837	103399837	+	Missense_Mutation	SNP	C	C	A	rs58265842	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	37	80	0	0.451219	0	C|0.875;A|0.125	0.125	strong	.	.	.	.	NM_001146197	exon4	c.G3210T	p.R1070S	TTCCTGCCTTTTA	.	PASS	Atlas-SNP
MKI67	4288	hgsc.bcm.edu	37	10	129906980	129906980	+	Missense_Mutation	SNP	C	C	T	rs2152143	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	247	120	297	0	0.48583	0	T|0.208;G|0.007	0.208	strong	MKI67,NS,carcinoma,0,1	MKI67	363	1	NM_002417	exon13	c.G3124A	p.G1042S	ACTTGCCGACTGC	.	PASS	Atlas-SNP
MDN1	23195	hgsc.bcm.edu	37	6	90368380	90368380	+	Silent	SNP	G	G	A	rs34732313	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	132	74	191	0	0.560606	0	G|0.886;A|0.114	0.114	strong	.	MDN1	478	.	NM_014611	exon89	c.C14970T	p.A4990A	TTCATCGGCTTCC	.	PASS	Atlas-SNP
TENC1	23371	hgsc.bcm.edu	37	12	53457618	53457618	+	Silent	SNP	C	C	T	rs12816417	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	35	60	0	0.5	0	C|0.938;T|0.062	0.062	strong	TENC1,NS,carcinoma,0,1	TENC1	148	1	NM_015319	exon29	c.C4212T	p.G1404G	TGCTGGCGCCATT	.	PASS	Atlas-SNP
PCDHB10	56126	hgsc.bcm.edu	37	5	140573439	140573439	+	Silent	SNP	G	G	C	rs610836	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	149	69	130	0	0.463087	0	G|0.551;C|0.449	0.449	strong	.	PCDHB10	177	.	NM_018930	exon1	c.G1314C	p.T438T	CATAACGGTCCTG	.	PASS	Atlas-SNP
C5orf60	285679	hgsc.bcm.edu	37	5	179071892	179071892	+	Missense_Mutation	SNP	C	C	T	rs4990389	bycluster;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	232	10	329	1	0.0431034	0.00303951	C|0.994;T|0.006	0.006	strong	C5orf60,NS,carcinoma,0,2	C5orf60	24	2	NM_001142306	exon1	c.G130A	p.V44I	ACACAACAAAGAG	.	scavenged	Atlas-SNP
SPATA31E1	286234	hgsc.bcm.edu	37	9	90500405	90500405	+	Missense_Mutation	SNP	A	A	C	rs7850542	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	40	95	0	0.56338	0	A|0.303;C|0.697	0.697	strong	.	.	.	.	NM_178828	exon4	c.A1003C	p.T335P	GACCACACCTCAG	.	PASS	Atlas-SNP
CRAMP1L	57585	hgsc.bcm.edu	37	16	1664931	1664931	+	Silent	SNP	T	T	C	rs7201813	bycluster;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	7	7	8	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
HIST1H2AC	8334	hgsc.bcm.edu	37	6	26124805	26124805	+	Silent	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	128	40	134	0	0.3125	0	.	.	none	.	HIST1H2AC	29	.	NM_003512	exon1	c.G345A	p.V115V	GGCCGTGCTTCTG	.	PASS	Atlas-SNP
ESYT2	57488	hgsc.bcm.edu	37	7	158534381	158534381	+	Silent	SNP	G	G	C	rs59980573	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	39	104	0	0.5	0	G|0.740;C|0.260	0.260	strong	.	ESYT2	70	.	NM_020728	exon17	c.C2082G	p.P694P	CTCAGGGGGCTGG	.	PASS	Atlas-SNP
PFN4	375189	hgsc.bcm.edu	37	2	24342505	24342505	+	Silent	SNP	T	T	C	rs1056122	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	42	19	42	0	0.452381	0	T|0.709;C|0.291	0.291	strong	.	PFN4	16	.	NM_199346	exon4	c.A303G	p.V101V	AGTTGCTACCAGA	.	PASS	Atlas-SNP
ASGR1	432	hgsc.bcm.edu	37	17	7080316	7080316	+	Silent	SNP	C	C	T	rs55714927	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	54	89	0	0.556701	0	C|0.844;T|0.156	0.156	strong	.	ASGR1	20	.	NM_001671	exon4	c.G267A	p.K89K	CAAGCCCTTGACC	.	PASS	Atlas-SNP
SCN3B	55800	hgsc.bcm.edu	37	11	123513161	123513161	+	Silent	SNP	G	G	A	rs1275085	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	66	55	93	0	0.833333	0	G|0.914;A|0.086	0.086	strong	.	SCN3B	53	.	NM_018400	exon3	c.C438T	p.T146T	CTCCTCGGTGACT	.	PASS	Atlas-SNP
SLC41A3	54946	hgsc.bcm.edu	37	3	125726062	125726062	+	Missense_Mutation	SNP	T	T	C	rs79696429	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	27	85	0	0.385714	0	T|0.980;C|0.020	0.020	strong	.	SLC41A3	80	.	NM_017836	exon11	c.A1261G	p.I421V	GCAGGATTGTCAC	.	PASS	Atlas-SNP
PWP1	11137	hgsc.bcm.edu	37	12	108096769	108096769	+	Missense_Mutation	SNP	G	G	C	rs11547907	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	79	36	78	0	0.455696	0	G|0.964;C|0.036	0.036	strong	.	PWP1	43	.	NM_007062	exon9	c.G864C	p.L288F	GTCCTTGGGGAAA	.	PASS	Atlas-SNP
ITGA9	3680	hgsc.bcm.edu	37	3	37695260	37695260	+	Missense_Mutation	SNP	A	A	G	rs57547208	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	160	77	165	0	0.48125	0	A|0.953;G|0.047	0.047	strong	.	ITGA9	98	.	NM_002207	exon17	c.A1895G	p.Q632R	AGCTTCAGGGTAA	.	PASS	Atlas-SNP
CTNNA2	1496	hgsc.bcm.edu	37	2	80101372	80101372	+	Silent	SNP	C	C	T	rs76801084	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	39	75	0	0.541667	0	C|0.964;T|0.036	0.036	strong	CTNNA2_ENST00000466387,colon,carcinoma,+2,2	CTNNA2	462	2	NM_001164883	exon6	c.C756T	p.A252A	CATCGCCGGCATC	.	PASS	Atlas-SNP
EXO5	64789	hgsc.bcm.edu	37	1	40981230	40981230	+	Silent	SNP	G	G	A	rs3795344	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	93	45	105	0	0.483871	0	G|0.958;A|0.042	0.042	strong	.	.	.	.	NM_022774	exon3	c.G1014A	p.E338E	CGTGGAGGAGGCT	.	PASS	Atlas-SNP
SOX6	55553	hgsc.bcm.edu	37	11	16133413	16133413	+	Silent	SNP	A	A	G	rs4617548	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	114	114	137	0	1	0	A|0.493;G|0.507	0.507	strong	.	SOX6	149	.	NM_001145819	exon7	c.T873C	p.T291T	TGCCAGAGTCCGC	.	PASS	Atlas-SNP
KIAA1239	57495	hgsc.bcm.edu	37	4	37445315	37445315	+	Missense_Mutation	SNP	C	C	A	rs4634233	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	65	38	77	0	0.584615	0	C|0.819;A|0.181	0.181	strong	.	KIAA1239	79	.	NM_001144990	exon7	c.C1705A	p.L569M	ATCGAGCTGATTC	.	PASS	Atlas-SNP
ZFP42	132625	hgsc.bcm.edu	37	4	188924230	188924230	+	Missense_Mutation	SNP	C	C	T	rs149675060	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	89	44	64	0	0.494382	0	C|0.999;T|0.001	0.001	strong	.	ZFP42	87	.	NM_174900	exon4	c.C269T	p.S90L	AGGACTCACTTTT	.	PASS	Atlas-SNP
ZNF474	133923	hgsc.bcm.edu	37	5	121487969	121487969	+	Missense_Mutation	SNP	G	G	A	rs72786994	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	91	43	104	0	0.472527	0	G|0.988;A|0.012	0.012	strong	.	ZNF474	43	.	NM_207317	exon2	c.G284A	p.R95Q	GATTCCGGGTATG	.	PASS	Atlas-SNP
ESPL1	9700	hgsc.bcm.edu	37	12	53671005	53671005	+	Missense_Mutation	SNP	G	G	A	rs17125266	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	89	35	100	0	0.393258	0	G|0.939;A|0.061	0.061	strong	.	ESPL1	158	.	NM_012291	exon9	c.G2079A	p.M693I	CAAAATGCAGGAA	.	PASS	Atlas-SNP
NUDT12	83594	hgsc.bcm.edu	37	5	102895169	102895169	+	Silent	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	74	18	122	0	0.243243	0	.	.	none	.	NUDT12	27	.	NM_031438	exon3	c.G207A	p.G69G	GTCACACCTATAG	.	PASS	Atlas-SNP
TAS2R42	353164	hgsc.bcm.edu	37	12	11338669	11338669	+	Missense_Mutation	SNP	C	C	T	rs1669412	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	79	35	84	0	0.443038	0	C|0.762;T|0.238	0.238	strong	.	TAS2R42	30	.	NM_181429	exon1	c.G875A	p.R292Q	GTCTGTCGCAGCT	.	PASS	Atlas-SNP
ZBP1	81030	hgsc.bcm.edu	37	20	56189956	56189956	+	Silent	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	135	28	187	0	0.207407	0	.	.	none	ZBP1,NS,carcinoma,0,1	ZBP1	65	1	NM_001160419	exon4	c.G489A	p.T163T	GTAAATCGTCCAT	.	PASS	Atlas-SNP
TRIOBP	11078	hgsc.bcm.edu	37	22	38119902	38119902	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	170	5	167	4	0.0294118	0.0239521	.	.	none	TRIOBP_ENST00000344404,NS,carcinoma,0,4	TRIOBP	262	4	NM_001039141	exon7	c.A1339G	p.T447A	AGAGCTACACGAG	.	scavenged	Atlas-SNP
ZNF358	140467	hgsc.bcm.edu	37	19	7584223	7584223	+	Missense_Mutation	SNP	A	A	G	rs11555037	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	52	28	58	0	0.538462	0	A|0.768;G|0.231;T|0.000	0.231	strong	.	ZNF358	41	.	NM_018083	exon2	c.A95G	p.N32S	ACCCCAATCCTGA	.	PASS	Atlas-SNP
KRTAP10-2	386679	hgsc.bcm.edu	37	21	45971081	45971081	+	Silent	SNP	C	C	T	rs79593866		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	124	19	68	0	0.153226	0	.	.	weak	KRTAP10-2,trunk,malignant_melanoma,-1,1	KRTAP10-2	21	1	NM_198693	exon1	c.G261A	p.P87P	GCAAGCCGGCTGG	.	scavenged	Atlas-SNP
SYT3	84258	hgsc.bcm.edu	37	19	51140654	51140654	+	Silent	SNP	G	G	A	rs3815749	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	33	19	49	0	0.575758	0	G|0.881;A|0.119	0.119	strong	.	SYT3	85	.	NM_032298	exon1	c.C15T	p.Y5Y	ATCCTCGTAGTCT	.	PASS	Atlas-SNP
ZNF774	342132	hgsc.bcm.edu	37	15	90903502	90903502	+	Missense_Mutation	SNP	G	G	A	rs11854320	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	88	36	83	2	0.409091	0.0240964	G|0.879;A|0.121	0.121	strong	ZNF774,NS,carcinoma,0,1	ZNF774	35	1	NM_001004309	exon4	c.G439A	p.V147I	GGATATGTAGGAG	.	scavenged	Atlas-SNP
AP5Z1	9907	hgsc.bcm.edu	37	7	4821352	4821352	+	Missense_Mutation	SNP	G	G	C	rs11549840	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	124	27	116	0	0.217742	0	G|0.986;C|0.014	0.014	strong	.	.	.	.	NM_014855	exon3	c.G333C	p.Q111H	CCGGCAGCTGAGC	.	PASS	Atlas-SNP
MRGPRX3	117195	hgsc.bcm.edu	37	11	18158958	18158958	+	Missense_Mutation	SNP	C	C	T	rs61733595	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	74	57	116	0	0.77027	0	C|0.987;T|0.013	0.013	strong	MRGPRX3,colon,carcinoma,-1,1	MRGPRX3	59	1	NM_054031	exon3	c.C209T	p.A70V	TGGTCGCGGCCGA	.	PASS	Atlas-SNP
RAP1GAP	5909	hgsc.bcm.edu	37	1	21940555	21940555	+	Missense_Mutation	SNP	C	C	T	rs2275363	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	24	106	0	0.275862	0	C|0.587;T|0.413	0.413	strong	.	RAP1GAP	119	.	NM_001145658	exon8	c.G511A	p.A171T	GGGCAGCGTCCAG	.	PASS	Atlas-SNP
TNFRSF10C	8794	hgsc.bcm.edu	37	8	22974315	22974315	+	Missense_Mutation	SNP	A	A	C	rs61736405	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	118	11	120	9	0.0932203	0.075	A|0.013;C|0.987	0.987	weak	TNFRSF10C,trunk,malignant_melanoma,0,1	TNFRSF10C	30	1	NM_003841	exon5	c.A551C	p.N184T	CAATGAACACCAG	.	scavenged	Atlas-SNP
APOBEC3F	200316	hgsc.bcm.edu	37	22	39440149	39440149	+	Missense_Mutation	SNP	C	C	T	rs5750728	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	222	117	232	0	0.527027	0	C|0.534;T|0.466	0.466	strong	.	APOBEC3F	37	.	NM_001006666	exon3	c.C233T	p.A78V	AGTGCGCCCCACC	.	PASS	Atlas-SNP
C19orf53	28974	hgsc.bcm.edu	37	19	13885484	13885484	+	Missense_Mutation	SNP	A	A	G	rs10104	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	224	108	265	0	0.482143	0	A|0.669;G|0.331	0.331	strong	.	C19orf53	14	.	NM_014047	exon2	c.A116G	p.K39R	CTCCCAAGAAGGC	.	PASS	Atlas-SNP
GRK4	2868	hgsc.bcm.edu	37	4	3015553	3015553	+	Missense_Mutation	SNP	G	G	A	rs1140085	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	61	28	75	0	0.459016	0	G|0.914;A|0.086	0.086	strong	GRK4_ENST00000398052,NS,carcinoma,0,1	GRK4	72	1	NM_182982	exon8	c.G739A	p.V247I	AGATTCGTAGTAA	.	PASS	Atlas-SNP
GTF2IRD2	84163	hgsc.bcm.edu	37	7	74212036	74212036	+	Missense_Mutation	SNP	C	C	G	rs707394	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	566	233	650	1	0.411661	0.00153846	C|0.885;G|0.115	0.115	strong	GTF2IRD2,colon,carcinoma,0,1	GTF2IRD2	38	1	NM_173537	exon16	c.G1815C	p.K605N	ACAGAACTTTTTC	.	PASS	Atlas-SNP
KPRP	448834	hgsc.bcm.edu	37	1	152733301	152733301	+	Missense_Mutation	SNP	T	T	A	rs4329520	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	195	101	209	0	0.517949	0	T|0.489;A|0.511	0.511	strong	.	KPRP	152	.	NM_001025231	exon2	c.T1237A	p.C413S	GAACCATGCATAA	.	PASS	Atlas-SNP
OR6B3	150681	hgsc.bcm.edu	37	2	240984833	240984833	+	Silent	SNP	C	C	G	rs13389099	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	229	100	251	1	0.436681	0.00398406	C|0.751;G|0.249	0.249	strong	.	OR6B3	37	.	NM_173351	exon1	c.G657C	p.A219A	GATGTGCGCATAT	.	PASS	Atlas-SNP
OR7A5	26659	hgsc.bcm.edu	37	19	14938616	14938616	+	Silent	SNP	T	T	C	rs2190686	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	79	37	106	0	0.468354	0	T|0.505;C|0.495	0.495	strong	.	OR7A5	43	.	NM_017506	exon1	c.A438G	p.L146L	GGATGCTAGAACC	.	PASS	Atlas-SNP
ATP10D	57205	hgsc.bcm.edu	37	4	47560163	47560163	+	Silent	SNP	C	C	A	rs11729411	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	171	165	180	0	0.964912	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
MUC20	200958	hgsc.bcm.edu	37	3	195452799	195452799	+	Missense_Mutation	SNP	C	C	T	rs71271395	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	488	215	483	0	0.440574	0	C|0.500;T|0.500	0.500	weak	MUC20,NS,carcinoma,0,1	MUC20	84	1	NM_152673	exon3	c.C812T	p.T271I	CAGACACAGATCT	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1092920	1092920	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	4	46	0	0.0555556	0	.	.	none	.	MUC2	614	.	NM_002457	exon30	c.C4739A	p.T1580N	CACAGACCCCAAC	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1262907	1262907	+	Silent	SNP	T	T	C	rs2037089	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	126	21	133	0	0.166667	0	T|0.797;C|0.203	0.203	strong	.	MUC5B	473	.	NM_002458	exon31	c.T4797C	p.S1599S	CTGCAGTGACGAC	.	PASS	Atlas-SNP
TICRR	90381	hgsc.bcm.edu	37	15	90170237	90170237	+	Missense_Mutation	SNP	C	C	T	rs3743372	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	27	75	0	0.36	0	C|0.746;T|0.254	0.254	strong	.	.	.	.	NM_152259	exon22	c.C5653T	p.R1885C	TTCAGTCGCGCTT	.	PASS	Atlas-SNP
WIPF2	147179	hgsc.bcm.edu	37	17	38416827	38416827	+	Missense_Mutation	SNP	G	G	A	rs142659099	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	37	84	0	0.474359	0	G|0.997;A|0.003	0.003	strong	.	WIPF2	55	.	NM_133264	exon3	c.G104A	p.R35Q	AGCAGCGGGGTCG	.	PASS	Atlas-SNP
PEX14	5195	hgsc.bcm.edu	37	1	10689942	10689942	+	Silent	SNP	G	G	T	rs11539794	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	39	80	0	0.549296	0	G|0.875;T|0.125	0.125	strong	PEX14,NS,carcinoma,0,1	PEX14	40	1	NM_004565	exon9	c.G1032T	p.G344G	CCTGGGGGTGCAG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195509817	195509817	+	Silent	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	114	29	85	0	0.254386	0	.	.	none	.	MUC4	1505	.	NM_018406	exon2	c.C8634T	p.A2878A	AGGGGTGGCATGA	.	PASS	Atlas-SNP
PRAMEF10	343071	hgsc.bcm.edu	37	1	12954921	12954921	+	Missense_Mutation	SNP	A	A	G	rs199792484	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	37	18	148	2	0.486486	0.0135135	A|0.930;G|0.070	0.070	strong	PRAMEF10,NS,carcinoma,0,1	PRAMEF10	35	1	NM_001039361	exon3	c.T362C	p.V121A	GAGAGGACCCTGG	.	scavenged	Atlas-SNP
ARSD	414	hgsc.bcm.edu	37	X	2835863	2835863	+	Missense_Mutation	SNP	G	G	T	rs78034736	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	89	18	124	0	0.202247	0	G|0.920;T|0.080	0.080	strong	.	ARSD	47	.	NM_001669	exon5	c.C845A	p.A282D	GAAACAGCTTCCT	.	PASS	Atlas-SNP
COL6A5	256076	hgsc.bcm.edu	37	3	130104206	130104206	+	Silent	SNP	A	A	G	rs10212372	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	74	33	88	0	0.445946	0	A|0.613;G|0.387	0.387	strong	.	COL6A5	205	.	NM_153264	exon5	c.A1860G	p.K620K	TGAAAAAGGTAAG	.	PASS	Atlas-SNP
LRP1	4035	hgsc.bcm.edu	37	12	57587437	57587437	+	Silent	SNP	T	T	C	rs34456957	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	64	29	71	0	0.453125	0	T|0.996;C|0.004	0.004	strong	.	LRP1	428	.	NM_002332	exon47	c.T7773C	p.C2591C	CGACTGTGGGGAT	.	PASS	Atlas-SNP
TWF2	11344	hgsc.bcm.edu	37	3	52264907	52264907	+	Silent	SNP	T	T	C	rs352143	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	108	49	133	0	0.453704	0	T|0.768;G|0.002	.	strong	.	TWF2	33	.	NM_007284	exon6	c.A588G	p.K196K	GACCATTTTCTGC	.	PASS	Atlas-SNP
NAPB	63908	hgsc.bcm.edu	37	20	23377815	23377815	+	Silent	SNP	G	G	A	rs17750862	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	62	24	84	0	0.387097	0	G|0.966;A|0.034	0.034	strong	.	NAPB	22	.	NM_022080	exon3	c.C189T	p.N63N	AAATGCGTTTCCT	.	PASS	Atlas-SNP
SALL4	57167	hgsc.bcm.edu	37	20	50407966	50407966	+	Silent	SNP	C	C	T	rs13038893	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	31	30	24	0	0.967742	0	C|0.725;T|0.275	0.275	strong	SALL4,NS,carcinoma,-1,2	SALL4	168	2	NM_020436	exon2	c.G1056A	p.A352A	GTCTAGCGCCACA	.	PASS	Atlas-SNP
ALPK3	57538	hgsc.bcm.edu	37	15	85383145	85383145	+	Missense_Mutation	SNP	C	C	G	rs3803403	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	117	69	84	0	0.589744	0	C|0.808;G|0.192	0.192	strong	.	ALPK3	289	.	NM_020778	exon5	c.C1241G	p.T414S	TCGACACTCTGCG	.	PASS	Atlas-SNP
CABLES1	91768	hgsc.bcm.edu	37	18	20815908	20815908	+	Missense_Mutation	SNP	G	G	A	rs373572190		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	182	3	191	1	0.0164835	0.0052356	.	.	weak	CABLES1,NS,carcinoma,+1,1	CABLES1	32	1	NM_001100619	exon6	c.G1235A	p.R412Q	GAGCCCGGAGAAA	.	scavenged	Atlas-SNP
DMTF1	9988	hgsc.bcm.edu	37	7	86800364	86800364	+	Missense_Mutation	SNP	G	G	C	rs117360089	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	44	116	0	0.478261	0	G|0.989;C|0.011	0.011	strong	DMTF1,NS,carcinoma,0,1	DMTF1	48	1	NM_001142327	exon5	c.G286C	p.A96P	GAAGTAGCAGATG	.	PASS	Atlas-SNP
OR8H2	390151	hgsc.bcm.edu	37	11	55872657	55872657	+	Missense_Mutation	SNP	A	A	C	rs61729740	byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	171	122	277	2	0.71345	0.00722022	A|0.582;C|0.418	0.418	strong	OR8H2,NS,carcinoma,0,1	OR8H2	117	1	NM_001005200	exon1	c.A139C	p.I47L	GGGATGATATTGA	.	scavenged	Atlas-SNP
CEL	1056	hgsc.bcm.edu	37	9	135946599	135946599	+	Silent	SNP	C	C	T	rs488087	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	33	37	0	0.402439	0	C|0.760;T|0.240	0.240	strong	.	CEL	71	.	NM_001807	exon11	c.C1719T	p.P573P	CACTCCCGTGCCC	.	PASS	Atlas-SNP
FGD6	55785	hgsc.bcm.edu	37	12	95602780	95602780	+	Silent	SNP	G	G	A	rs766404	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	213	88	282	0	0.413146	0	G|0.986;A|0.014	0.014	strong	.	FGD6	127	.	NM_018351	exon2	c.C2280T	p.Y760Y	GTTCTCGTACTCT	.	PASS	Atlas-SNP
EAF2	55840	hgsc.bcm.edu	37	3	121563355	121563355	+	Silent	SNP	T	T	C	rs9884018	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	168	81	222	0	0.482143	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
PHLDB3	653583	hgsc.bcm.edu	37	19	43979589	43979589	+	Silent	SNP	G	G	T	rs1055099	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	89	88	71	0	0.988764	0	G|0.453;T|0.547	0.547	strong	.	PHLDB3	30	.	NM_198850	exon16	c.C1896A	p.T632T	AGCGGCGGTCACG	.	PASS	Atlas-SNP
SAAL1	113174	hgsc.bcm.edu	37	11	18108492	18108492	+	Silent	SNP	T	T	C	rs12363226	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	134	25	186	0	0.186567	0	T|0.823;C|0.177	0.177	strong	.	SAAL1	34	.	NM_138421	exon9	c.A963G	p.T321T	TAGCACTGTTTTC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195509964	195509964	+	Silent	SNP	A	A	G	rs71635079	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	143	142	112	1	0.993007	0.00892857	G|1.000;|0.000	1.000	weak	.	MUC4	1505	.	NM_018406	exon2	c.T8487C	p.H2829H	GGTGGCATGACCT	.	PASS	Atlas-SNP
LILRA1	11024	hgsc.bcm.edu	37	19	55106288	55106288	+	Missense_Mutation	SNP	A	A	C	rs147848714	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	210	41	255	0	0.195238	0	A|0.996;C|0.004	0.004	strong	LILRA1,colon,carcinoma,0,1	LILRA1	105	1	NM_006863	exon4	c.A229C	p.I77L	CAGGAGATTGTGA	.	PASS	Atlas-SNP
HIST1H2BF	8343	hgsc.bcm.edu	37	6	26199903	26199903	+	Silent	SNP	C	C	T	rs34961555	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	108	38	111	0	0.351852	0	C|0.953;T|0.047	0.047	strong	.	HIST1H2BF	25	.	NM_003522	exon1	c.C117T	p.S39S	CTATTCCGTGTAC	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	123	67	145	0	0.544715	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
CATSPERB	79820	hgsc.bcm.edu	37	14	92102819	92102819	+	Silent	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	180	39	212	0	0.216667	0	.	.	none	.	CATSPERB	114	.	NM_024764	exon17	c.C1692T	p.I564I	GCTGTAGATCGTT	.	PASS	Atlas-SNP
LACTB	114294	hgsc.bcm.edu	37	15	63419223	63419223	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	155	28	138	0	0.180645	0	.	.	none	.	LACTB	29	.	NM_171846	exon3	c.C590T	p.P197L	AATTCCCAGAAAA	.	PASS	Atlas-SNP
NLRP8	126205	hgsc.bcm.edu	37	19	56473460	56473460	+	Silent	SNP	T	T	C	rs6509975	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	125	50	150	0	0.4	0	C|0.330;N|0.000	0.330	strong	NLRP8_ENST00000291971,rectum,carcinoma,+1,2	NLRP8	225	2	NM_176811	exon4	c.T2070C	p.R690R	GCATCGTTGGTGG	.	PASS	Atlas-SNP
PDGFRB	5159	hgsc.bcm.edu	37	5	149509446	149509446	+	Missense_Mutation	SNP	C	C	T	rs41287110	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	123	62	175	0	0.504065	0	C|0.980;T|0.020	0.020	strong	.	PDGFRB	142	.	NM_002609	exon10	c.G1453A	p.E485K	GCTCCTCCTCCCA	.	PASS	Atlas-SNP
MUC20	200958	hgsc.bcm.edu	37	3	195453417	195453417	+	Missense_Mutation	SNP	C	C	T	rs73203948	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	30	78	0	0.422535	0	C|0.965;T|0.035	0.035	strong	.	MUC20	84	.	NM_152673	exon3	c.C1430T	p.T477M	CCCGGACGAGGCC	.	PASS	Atlas-SNP
SLC22A24	283238	hgsc.bcm.edu	37	11	62886800	62886800	+	Missense_Mutation	SNP	G	G	C	rs4963245	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	19	81	0	0.263889	0	G|0.827;C|0.173	0.173	strong	.	SLC22A24	31	.	NM_001136506	exon3	c.C514G	p.R172G	TCTTCCGTCCAAC	.	PASS	Atlas-SNP
AGL	178	hgsc.bcm.edu	37	1	100340286	100340286	+	Silent	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	4	78	0	0.0533333	0	.	.	none	.	AGL	137	.	NM_000644	exon8	c.G1002A	p.T334T	CCTTACGATTATT	.	PASS	Atlas-SNP
OVCH1	341350	hgsc.bcm.edu	37	12	29639186	29639186	+	Missense_Mutation	SNP	T	T	C	rs3847680	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	115	64	158	0	0.556522	0	T|0.367;C|0.633	0.633	strong	.	OVCH1	195	.	NM_183378	exon8	c.A988G	p.K330E	TACCCTTTCCTCT	.	PASS	Atlas-SNP
SENP7	57337	hgsc.bcm.edu	37	3	101080694	101080694	+	Silent	SNP	T	T	C	rs7616677	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	185	183	239	0	0.989189	0	T|0.604;C|0.396	0.396	strong	.	SENP7	170	.	NM_020654	exon11	c.A1488G	p.E496E	GCATAATTCAGAT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195512480	195512480	+	Missense_Mutation	SNP	A	A	G	rs200533337	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	129	31	73	0	0.24031	0	A|0.973;G|0.027	0.027	strong	MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	NM_018406	exon2	c.T5971C	p.S1991P	CTGAGGAAGCGTC	.	PASS	Atlas-SNP
SPATA13	221178	hgsc.bcm.edu	37	13	24797786	24797786	+	Missense_Mutation	SNP	G	G	A	rs9511156	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	29	15	52	0	0.517241	0	G|0.962;A|0.038	0.038	strong	.	SPATA13	92	.	NM_001166271	exon2	c.G719A	p.R240K	TCGTGAGGGACCC	.	PASS	Atlas-SNP
GALNT8	26290	hgsc.bcm.edu	37	12	4873163	4873163	+	Missense_Mutation	SNP	G	G	T	rs1468556	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	223	115	242	0	0.515695	0	G|0.627;T|0.373	0.373	strong	GALNT8,NS,adenoma,0,1	GALNT8	89	1	NM_017417	exon9	c.G1543T	p.V515F	GGACCCGTTCCAG	.	PASS	Atlas-SNP
CHD5	26038	hgsc.bcm.edu	37	1	6209363	6209363	+	Silent	SNP	T	T	C	rs12565328	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	68	20	105	0	0.294118	0	T|0.543;C|0.457	0.457	strong	.	CHD5	267	.	NM_015557	exon8	c.A1104G	p.V368V	CAGGCATACGAGA	.	PASS	Atlas-SNP
CES1	1066	hgsc.bcm.edu	37	16	55862691	55862691	+	Missense_Mutation	SNP	G	G	A	rs62028647	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	109	32	143	0	0.293578	0	G|0.622;A|0.378	0.378	strong	.	CES1	78	.	NM_001025195	exon2	c.C248T	p.S83L	GGGTACGAGGTGG	.	PASS	Atlas-SNP
SBSN	374897	hgsc.bcm.edu	37	19	36015652	36015652	+	Silent	SNP	C	C	T	rs17705633	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	63	25	97	0	0.396825	0	C|0.874;T|0.126	0.126	strong	.	SBSN	58	.	NM_001166034	exon3	c.G1710A	p.S570S	GTTGACCGAGGCC	.	PASS	Atlas-SNP
PRX	57716	hgsc.bcm.edu	37	19	40901496	40901496	+	Missense_Mutation	SNP	T	T	C	rs268673	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	83	44	121	0	0.53012	0	T|0.669;C|0.331	0.331	strong	.	PRX	151	.	NM_181882	exon7	c.A2763G	p.I921M	TGTCTCTATCATC	.	PASS	Atlas-SNP
TEX26	122046	hgsc.bcm.edu	37	13	31543095	31543095	+	Silent	SNP	C	C	T	rs2274869	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	142	70	158	0	0.492958	0	C|0.784;T|0.216	0.216	strong	.	.	.	.	NM_152325	exon6	c.C720T	p.Y240Y	TGACTACGACAAA	.	PASS	Atlas-SNP
NEUROD4	58158	hgsc.bcm.edu	37	12	55420891	55420891	+	Missense_Mutation	SNP	A	A	G	rs118105704	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	46	89	0	0.474227	0	A|0.987;G|0.013	0.013	strong	.	NEUROD4	87	.	NM_021191	exon2	c.A668G	p.H223R	TCCTTCATCTCAA	.	PASS	Atlas-SNP
LIMK2	3985	hgsc.bcm.edu	37	22	31663842	31663842	+	Silent	SNP	C	C	G	rs2228619	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	60	21	48	0	0.35	0	C|0.189;G|0.811	0.811	strong	.	LIMK2	101	.	NM_005569	exon10	c.C1209G	p.L403L	GAACCTCCTGACA	.	PASS	Atlas-SNP
SLC22A3	6581	hgsc.bcm.edu	37	6	160858188	160858188	+	Silent	SNP	G	G	A	rs2292334	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	91	35	127	0	0.384615	0	G|0.697;A|0.303	0.303	strong	.	SLC22A3	58	.	NM_021977	exon7	c.G1233A	p.A411A	CTTTGCGGCAAGC	.	PASS	Atlas-SNP
ALPPL2	251	hgsc.bcm.edu	37	2	233274475	233274475	+	Missense_Mutation	SNP	C	C	A	rs56080708	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	4	4	0	0	1	.	C|0.900;A|0.100	0.100	strong	.	ALPPL2	36	.	NM_031313	exon11	c.C1492A	p.R498S	GCGCCCCGCGCCG	.	PASS	Atlas-SNP
AOC2	314	hgsc.bcm.edu	37	17	40997461	40997461	+	Missense_Mutation	SNP	G	G	A	rs35508987	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	116	60	141	0	0.517241	0	G|0.993;A|0.007	0.007	strong	.	AOC2	61	.	NM_009590	exon1	c.G818A	p.R273Q	TGGAACGGGAGTT	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228476367	228476367	+	Missense_Mutation	SNP	A	A	T	rs3795790	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	57	30	66	0	0.526316	0	A|0.887;T|0.113	0.113	strong	.	OBSCN	2142	.	NM_001271223	exon43	c.A11404T	p.S3802C	CAAGAGAGCATAG	.	PASS	Atlas-SNP
OAS3	4940	hgsc.bcm.edu	37	12	113398919	113398919	+	Silent	SNP	G	G	A	rs2072136	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	81	35	86	0	0.432099	0	G|0.696;N|0.000	.	strong	.	OAS3	63	.	NM_006187	exon8	c.G1701A	p.S567S	CTACTCGAGGCTC	.	PASS	Atlas-SNP
GJA8	2703	hgsc.bcm.edu	37	1	147380886	147380886	+	Silent	SNP	C	C	T	rs3766503	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	55	25	66	0	0.454545	0	C|0.948;T|0.052	0.052	strong	GJA8,NS,carcinoma,0,1	GJA8	108	1	NM_005267	exon2	c.C804T	p.L268L	TCAGCTCCTAGAA	.	PASS	Atlas-SNP
CCDC180	0	hgsc.bcm.edu	37	9	100122384	100122384	+	Splice_Site	SNP	G	G	A	rs376419121		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	67	17	92	0	0.253731	0	.	.	weak	KIAA1529,mouth,carcinoma,0,1	.	.	1	NM_020893	exon26	c.3615+1G>A	.	TTTACCGTAAGGA	.	PASS	Atlas-SNP
TPTE	7179	hgsc.bcm.edu	37	21	10942923	10942923	+	Missense_Mutation	SNP	G	G	A	rs76723236	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	293	63	414	0	0.215017	0	G|0.949;A|0.051	0.051	strong	.	TPTE	513	.	NM_199261	exon12	c.C664T	p.R222W	TTACCCGCCTTCT	.	PASS	Atlas-SNP
OXGR1	27199	hgsc.bcm.edu	37	13	97639021	97639021	+	Silent	SNP	A	A	G	rs9584456	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	34	13	53	0	0.382353	0	A|0.933;G|0.067	0.067	strong	.	OXGR1	46	.	NM_080818	exon4	c.T993C	p.I331I	GTAACTAATTTTC	.	PASS	Atlas-SNP
RIMKLA	284716	hgsc.bcm.edu	37	1	42880516	42880516	+	Silent	SNP	T	T	C	rs1055055	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	94	47	96	0	0.5	0	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	.	PASS	Atlas-SNP
CHD6	84181	hgsc.bcm.edu	37	20	40049579	40049579	+	Missense_Mutation	SNP	T	T	A	rs55864139	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	252	125	281	0	0.496032	0	T|0.991;A|0.009	0.009	strong	.	CHD6	312	.	NM_032221	exon31	c.A5696T	p.N1899I	GAGATGTTAGTAG	.	PASS	Atlas-SNP
KCNN1	3780	hgsc.bcm.edu	37	19	18096220	18096220	+	Silent	SNP	C	C	T	rs76273600	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	187	104	143	0	0.55615	0	C|0.998;T|0.002	0.002	weak	.	KCNN1	74	.	NM_002248	exon6	c.C1017T	p.H339H	GCCCCACACCTAC	.	PASS	Atlas-SNP
TNS1	7145	hgsc.bcm.edu	37	2	218712936	218712936	+	Silent	SNP	C	C	T	rs3796032	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	65	31	82	0	0.476923	0	C|0.600;T|0.400	0.400	strong	.	TNS1	251	.	NM_022648	exon17	c.G1929A	p.V643V	CCTTTGCACAGCC	.	PASS	Atlas-SNP
ODF2L	57489	hgsc.bcm.edu	37	1	86822231	86822231	+	Silent	SNP	A	A	G	rs385437	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	57	30	56	0	0.526316	0	A|0.872;G|0.128	0.128	strong	.	ODF2L	53	.	NM_001007022	exon14	c.T1414C	p.L472L	CCGTCAAGGAATC	.	PASS	Atlas-SNP
ZFAT	57623	hgsc.bcm.edu	37	8	135602581	135602581	+	Silent	SNP	A	A	G	rs3739425	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	48	40	71	0	0.833333	0	A|0.709;G|0.291	0.291	strong	.	ZFAT	265	.	NM_020863	exon8	c.T2493C	p.S831S	AGGACAAGAATAA	.	PASS	Atlas-SNP
ESD	2098	hgsc.bcm.edu	37	13	47354101	47354101	+	Missense_Mutation	SNP	C	C	T	rs9778	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	44	25	75	0	0.568182	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
KLHL31	401265	hgsc.bcm.edu	37	6	53519857	53519857	+	Silent	SNP	G	G	A	rs12210809	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	162	159	184	0	0.981481	0	G|0.516;A|0.484	0.484	strong	.	KLHL31	48	.	NM_001003760	exon2	c.C214T	p.L72L	CACATAGGAAGTT	.	PASS	Atlas-SNP
CACNA1C	775	hgsc.bcm.edu	37	12	2791130	2791130	+	Missense_Mutation	SNP	C	C	T	rs71441836	alternate_allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	40	40	44	0	1	0	TGG|0.500;CGA|0.500	.	alt	CACNA1C_ENST00000399617,NS,meningioma,0,2	CACNA1C	1023	2	NM_199460	exon45	c.C5603T	p.P1868L	ACGTTCCGATGTG	.	PASS	Atlas-SNP
FAM46C	54855	hgsc.bcm.edu	37	1	118165577	118165577	+	Silent	SNP	C	C	G	rs865443	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	133	70	164	0	0.526316	0	C|0.882;G|0.118	0.118	strong	.	FAM46C	25	.	NM_017709	exon2	c.C87G	p.L29L	GGTCCTCACTGAA	.	PASS	Atlas-SNP
PCDHB11	56125	hgsc.bcm.edu	37	5	140580931	140580931	+	Missense_Mutation	SNP	C	C	G	rs799834	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	248	142	235	0	0.572581	0	C|0.497;G|0.503	0.503	strong	PCDHB11,NS,carcinoma,+2,1	PCDHB11	162	1	NM_018931	exon1	c.C1584G	p.D528E	TTTCGACTTCCGC	.	PASS	Atlas-SNP
FAM185A	222234	hgsc.bcm.edu	37	7	102427889	102427889	+	Missense_Mutation	SNP	C	C	T	rs17842496	byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	536	261	629	1	0.48694	0.00158983	C|0.859;T|0.141	0.141	strong	.	FAM185A	10	.	NM_001145268	exon7	c.C1039T	p.R347C	GAAGTTCGTAAAG	.	PASS	Atlas-SNP
DENND5B	160518	hgsc.bcm.edu	37	12	31604928	31604928	+	Silent	SNP	G	G	C	rs3205175	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	175	81	202	0	0.462857	0	G|0.814;C|0.186	0.186	strong	.	DENND5B	114	.	NM_144973	exon5	c.C1575G	p.A525A	GTCCTGGGCAGTC	.	PASS	Atlas-SNP
USP43	124739	hgsc.bcm.edu	37	17	9604775	9604775	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	44	7	76	0	0.159091	0	.	.	none	.	USP43	65	.	NM_001267576	exon12	c.A1769G	p.K590R	ACCTCAAAAGGTT	.	PASS	Atlas-SNP
NUP133	55746	hgsc.bcm.edu	37	1	229631734	229631734	+	Missense_Mutation	SNP	T	T	C	rs11805194	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	115	51	156	0	0.443478	0	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
SRRM5	100170229	hgsc.bcm.edu	37	19	44118188	44118188	+	Missense_Mutation	SNP	A	A	C	rs3815422	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	31	13	34	0	0.419355	0	A|0.799;C|0.201	0.201	strong	SRRM5,NS,carcinoma,0,1	SRRM5	38	1	NM_001145641	exon1	c.A1915C	p.S639R	AAGGAGAGCGACC	.	PASS	Atlas-SNP
FSCB	84075	hgsc.bcm.edu	37	14	44975052	44975052	+	Missense_Mutation	SNP	A	A	G	rs3825630	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	95	37	101	0	0.389474	0	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	.	PASS	Atlas-SNP
HIF3A	64344	hgsc.bcm.edu	37	19	46823803	46823803	+	Missense_Mutation	SNP	C	C	T	rs61755707	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	32	16	38	0	0.5	0	C|0.981;T|0.019	0.019	strong	.	HIF3A	154	.	NM_152795	exon9	c.C1129T	p.P377S	CCTAACCCTGGGG	.	PASS	Atlas-SNP
LILRA6	79168	hgsc.bcm.edu	37	19	54742900	54742900	+	Missense_Mutation	SNP	C	C	G	rs117376661	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	136	76	113	0	0.558824	0	C|0.953;G|0.047	0.047	strong	LILRA6,NS,carcinoma,0,1	LILRA6	75	1	NM_024318	exon8	c.G1375C	p.V459L	GGAACACCAGGAC	.	PASS	Atlas-SNP
HCAR3	8843	hgsc.bcm.edu	37	12	123200768	123200768	+	Missense_Mutation	SNP	T	T	G	rs1798192	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	120	120	132	1	1	0.00757576	T|0.481;G|0.519	0.519	strong	HCAR3_ENST00000528880,NS,carcinoma,0,1	HCAR3	49	1	NM_006018	exon1	c.A517C	p.T173P	TTGCAGTGCCATT	.	PASS	Atlas-SNP
TMF1	7110	hgsc.bcm.edu	37	3	69082708	69082708	+	Missense_Mutation	SNP	C	C	G	rs1532918	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	88	42	100	0	0.477273	0	C|0.912;G|0.088	0.088	strong	.	TMF1	77	.	NM_007114	exon10	c.G2392C	p.D798H	GCCTATCAGAAAG	.	PASS	Atlas-SNP
DSG1	1828	hgsc.bcm.edu	37	18	28919884	28919884	+	Missense_Mutation	SNP	A	A	C	rs16961689	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	88	42	138	0	0.477273	0	A|0.885;C|0.115	0.115	strong	.	DSG1	176	.	NM_001942	exon11	c.A1583C	p.Y528S	AAGTATATTCTTC	.	PASS	Atlas-SNP
CPA4	51200	hgsc.bcm.edu	37	7	129950740	129950740	+	Missense_Mutation	SNP	G	G	T	rs2171492	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	51	51	101	1	1	0.00990099	G|0.677;T|0.323	0.323	strong	.	CPA4	47	.	NM_016352	exon9	c.G907T	p.G303C	TTCAAGGGCTTCA	.	PASS	Atlas-SNP
TRPV5	56302	hgsc.bcm.edu	37	7	142609714	142609714	+	Silent	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	108	2	139	0	0.0185185	0	.	.	none	TRPV5,NS,malignant_melanoma,-2,1	TRPV5	164	1	NM_019841	exon13	c.C1722T	p.F574F	GGCGATGAACAAG	.	scavenged	Atlas-SNP
FNIP2	57600	hgsc.bcm.edu	37	4	159780274	159780274	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	339	77	345	0	0.227139	0	.	.	none	.	FNIP2	90	.	NM_020840	exon9	c.G923A	p.R308K	TTAGGAGGAAGAA	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105418481	105418481	+	Missense_Mutation	SNP	C	C	T	rs200172350	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	152	24	112	0	0.157895	0	.	.	weak	.	AHNAK2	719	.	NM_138420	exon7	c.G3307A	p.V1103I	CCTTGACGTCCAC	.	PASS	Atlas-SNP
HIST1H2AL	8332	hgsc.bcm.edu	37	6	27833174	27833174	+	Silent	SNP	A	A	G	rs41448545		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	167	94	175	0	0.562874	0	.	.	weak	.	HIST1H2AL	14	.	NM_003511	exon1	c.A42G	p.K14K	CGCCAAAGCCAAG	.	PASS	Atlas-SNP
KLB	152831	hgsc.bcm.edu	37	4	39436192	39436192	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	43	12	81	0	0.27907	0	.	.	none	.	KLB	95	.	NM_175737	exon2	c.A1188C	p.L396F	TAATTTAAGAGAA	.	PASS	Atlas-SNP
HLA-DOB	3112	hgsc.bcm.edu	37	6	32782149	32782149	+	Silent	SNP	G	G	A	rs201306170		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	143	47	225	0	0.328671	0	.	.	weak	.	HLA-DOB	17	.	NM_002120	exon3	c.C591T	p.Y197Y	GCAGGTGTAGACA	.	PASS	Atlas-SNP
ZNF749	388567	hgsc.bcm.edu	37	19	57955729	57955729	+	Missense_Mutation	SNP	G	G	A	rs2240038	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	123	49	119	0	0.398374	0	G|0.957;A|0.043	0.043	strong	.	ZNF749	75	.	NM_001023561	exon3	c.G1213A	p.A405T	GTTCATGCTGGCA	.	PASS	Atlas-SNP
MRPL10	124995	hgsc.bcm.edu	37	17	45904420	45904420	+	Missense_Mutation	SNP	C	C	T	rs11538868	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	125	62	151	0	0.496	0	C|0.761;T|0.239	0.239	strong	.	MRPL10	24	.	NM_148887	exon4	c.G403A	p.V135I	GGAAGACCTTCAT	.	PASS	Atlas-SNP
ZNF879	345462	hgsc.bcm.edu	37	5	178459426	178459426	+	Missense_Mutation	SNP	A	A	C	rs17078991	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	166	100	162	0	0.60241	0	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	.	PASS	Atlas-SNP
TBATA	219793	hgsc.bcm.edu	37	10	72534090	72534090	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	77	16	84	0	0.207792	0	.	.	none	.	.	.	.	NM_152710	exon9	c.C796A	p.L266M	TCTGCAGGAGTCC	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	38	21	38	0	0.552632	0	T|0.817;C|0.183	0.183	strong	.	ICAM3	29	.	NM_002162	exon3	c.A428G	p.D143G	GACCCATCCTCCA	.	PASS	Atlas-SNP
USP17L7	392197	hgsc.bcm.edu	37	8	11991210	11991210	+	Silent	SNP	C	C	T	rs117041743	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	20	17	22	0	0.85	0	C|0.961;T|0.039	0.039	strong	.	.	.	.	NM_001256869	exon1	c.G309A	p.P103P	GGAAAGCGGCAGT	.	PASS	Atlas-SNP
KRT37	8688	hgsc.bcm.edu	37	17	39580739	39580739	+	Missense_Mutation	SNP	C	C	A	rs9910204	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	175	86	154	0	0.491429	0	C|0.764;A|0.236	0.236	strong	KRT37,NS,carcinoma,0,1	KRT37	61	1	NM_003770	exon1	c.G37T	p.G13C	TGCAACCCAGAGG	.	PASS	Atlas-SNP
SLC12A6	9990	hgsc.bcm.edu	37	15	34544468	34544468	+	Silent	SNP	C	C	T	rs2290940	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	188	99	196	0	0.526596	0	C|0.821;T|0.179	0.179	strong	.	SLC12A6	205	.	NM_133647	exon9	c.G1236A	p.S412S	TTGACTCGAGTTA	.	PASS	Atlas-SNP
ATG4C	84938	hgsc.bcm.edu	37	1	63284834	63284834	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	114	26	162	0	0.22807	0	.	.	none	.	ATG4C	96	.	NM_178221	exon5	c.T553A	p.Y185N	GGGAAATATTCTG	.	PASS	Atlas-SNP
PLB1	151056	hgsc.bcm.edu	37	2	28761981	28761981	+	Missense_Mutation	SNP	G	G	C	rs6753929	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	160	46	171	0	0.2875	0	A|0.000;C|0.213;G|0.787	0.213	strong	.	PLB1	255	.	NM_001170585	exon11	c.G667C	p.V223L	GCATTTGTAAACC	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	322	321	251	0	0.996894	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
KRTAP10-2	386679	hgsc.bcm.edu	37	21	45971109	45971109	+	Missense_Mutation	SNP	G	G	A	rs77233671		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	123	33	54	0	0.268293	0	.	.	weak	KRTAP10-2,caecum,carcinoma,0,1	KRTAP10-2	21	1	NM_198693	exon1	c.C233T	p.S78L	CAGCACGAGGGCG	.	scavenged	Atlas-SNP
GOLGA4	2803	hgsc.bcm.edu	37	3	37368710	37368710	+	Missense_Mutation	SNP	T	T	A	rs144205536	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	106	52	150	0	0.490566	0	T|0.999;A|0.001	0.001	strong	.	GOLGA4	173	.	NM_001172713	exon15	c.T5399A	p.I1800K	GCTTAATAAAGCT	.	PASS	Atlas-SNP
NUP133	55746	hgsc.bcm.edu	37	1	229622162	229622162	+	Silent	SNP	A	A	G	rs1065675	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	113	43	150	0	0.380531	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
PPP1R12A	4659	hgsc.bcm.edu	37	12	80199958	80199958	+	Missense_Mutation	SNP	C	C	G	rs61756418	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	118	51	91	0	0.432203	0	C|0.996;G|0.004	0.004	strong	.	PPP1R12A	76	.	NM_002480	exon13	c.G1811C	p.G604A	TGTGTGCCTGCTG	.	PASS	Atlas-SNP
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32632777	32632777	+	Silent	SNP	C	C	T	rs1049068	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	102	66	41	0	0.647059	0	C|0.901;T|0.099	0.099	strong	.	HLA-DQB1	15	.	NM_002123	exon2	c.G177A	p.V59V	TCTGGTCACAAGA	.	PASS	Atlas-SNP
CCDC168	643677	hgsc.bcm.edu	37	13	103392709	103392709	+	Missense_Mutation	SNP	A	A	T	rs79592880	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	95	50	104	0	0.526316	0	A|0.922;T|0.078	0.078	strong	.	.	.	.	NM_001146197	exon4	c.T10338A	p.D3446E	TAGCTGATCTGCA	.	PASS	Atlas-SNP
SCRIB	23513	hgsc.bcm.edu	37	8	144875168	144875168	+	Missense_Mutation	SNP	G	G	A	rs202137464	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	110	83	100	0	0.754545	0	G|0.998;A|0.002	0.002	strong	.	SCRIB	192	.	NM_015356	exon29	c.C3995T	p.P1332L	TCAGGCGGGTGAG	.	PASS	Atlas-SNP
CPEB4	80315	hgsc.bcm.edu	37	5	173372015	173372015	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	362	6	297	1	0.0165746	0.003367	.	.	none	CPEB4,NS,carcinoma,-1,1	CPEB4	54	1	NM_030627	exon5	c.G1328A	p.G443D	ATGATGGCCGTGG	.	scavenged	Atlas-SNP
RBBP8NL	140893	hgsc.bcm.edu	37	20	60989185	60989185	+	Missense_Mutation	SNP	C	C	T	rs10888228	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	47	33	46	0	0.702128	0	C|0.851;T|0.149	0.149	strong	.	.	.	.	NM_080833	exon10	c.G1222A	p.A408T	CTGCTGCGGCCAG	.	PASS	Atlas-SNP
TUBG2	27175	hgsc.bcm.edu	37	17	40818451	40818451	+	Silent	SNP	G	G	A	rs76575695		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	295	127	302	0	0.430508	0	.	.	weak	TUBG2,bladder,carcinoma,+1,1	TUBG2	43	1	NM_016437	exon10	c.G1107A	p.S369S	GCCCTCGGCCCAC	.	PASS	Atlas-SNP
ARHGAP25	9938	hgsc.bcm.edu	37	2	69040500	69040500	+	Silent	SNP	G	G	A	rs2280310	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	76	76	75	0	1	0	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	.	PASS	Atlas-SNP
TDG	6996	hgsc.bcm.edu	37	12	104373829	104373829	+	Silent	SNP	C	C	A	rs75200561	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	251	14	247	1	0.0557769	0.00404858	.	.	weak	TDG,pharynx,carcinoma,0,1	TDG	43	1	NM_003211	exon3	c.C387A	p.T129T	TTTGACCTTCAAT	.	scavenged	Atlas-SNP
XIRP1	165904	hgsc.bcm.edu	37	3	39227664	39227664	+	Silent	SNP	G	G	A	rs61736155	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	62	30	81	0	0.483871	0	G|0.862;A|0.138	0.138	strong	.	XIRP1	173	.	NM_001198621	exon2	c.C3273T	p.D1091D	AAGACCGTCCTGG	.	PASS	Atlas-SNP
OR4N2	390429	hgsc.bcm.edu	37	14	20295627	20295627	+	Missense_Mutation	SNP	C	C	G	rs72663752	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	342	106	299	0	0.309942	0	C|0.916;G|0.084	0.084	strong	.	OR4N2	125	.	NM_001004723	exon1	c.C20G	p.T7R	ACAGAACAGTGAT	.	PASS	Atlas-SNP
GAA	2548	hgsc.bcm.edu	37	17	78081661	78081661	+	Silent	SNP	A	A	T	rs1800303	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	79	38	71	0	0.481013	0	A|0.890;T|0.110	0.110	strong	GAA,NS,NS,+1,1	GAA	66	1	NM_001079803	exon6	c.A921T	p.A307A	GTCGGCACACGGG	.	PASS	Atlas-SNP
PRICKLE1	144165	hgsc.bcm.edu	37	12	42854205	42854205	+	Silent	SNP	A	A	G	rs3747562	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	139	62	160	0	0.446043	0	A|0.550;G|0.450	0.450	strong	.	PRICKLE1	105	.	NM_001144882	exon8	c.T1902C	p.S634S	ATCATCAGAAAAC	.	PASS	Atlas-SNP
TET1	80312	hgsc.bcm.edu	37	10	70332862	70332862	+	Missense_Mutation	SNP	C	C	T	rs12221107	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	52	23	62	0	0.442308	0	C|0.925;T|0.075	0.075	strong	.	TET1	255	.	NM_030625	exon2	c.C767T	p.A256V	AAAGAGCAACCCC	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100681453	100681453	+	Silent	SNP	C	C	T	rs77440980	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	39	49	0	0.541667	0	C|0.963;T|0.037	0.037	strong	MUC17,NS,carcinoma,+2,1	MUC17	804	1	NM_001040105	exon3	c.C6756T	p.T2252T	TGTGACCACTTCT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195510827	195510827	+	Missense_Mutation	SNP	C	C	T	rs413807	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	339	221	245	0	0.651917	0	C|0.500;T|0.500	0.500	weak	.	MUC4	1505	.	NM_018406	exon2	c.G7624A	p.A2542T	AGGTGGCGTGACG	.	PASS	Atlas-SNP
CNGA3	1261	hgsc.bcm.edu	37	2	99013274	99013274	+	Silent	SNP	C	C	T	rs104893617	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	2	87	0	0.0229885	0	A|0.000;C|0.999;T|0.000	0.000	strong	CNGA3,NS,carcinoma,0,1	CNGA3	118	1	NM_001298	exon8	c.C1641T	p.F547F	CTACTTCGGGGAG	.	scavenged	Atlas-SNP
CDSN	1041	hgsc.bcm.edu	37	6	31084170	31084170	+	Missense_Mutation	SNP	A	A	C	rs1042127	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	34	13	44	0	0.382353	0	A|0.846;C|0.154	0.154	strong	.	CDSN	48	.	NM_001264	exon2	c.T1222G	p.S408A	AACCGGAGCTGCT	.	PASS	Atlas-SNP
CHORDC1	26973	hgsc.bcm.edu	37	11	89935586	89935586	+	Missense_Mutation	SNP	G	G	T	rs1045861	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	154	152	210	1	0.987013	0.0047619	G|0.384;T|0.616	0.616	strong	.	CHORDC1	34	.	NM_012124	exon11	c.C986A	p.A329D	GTTGTGGCATCTT	.	PASS	Atlas-SNP
TTLL11	158135	hgsc.bcm.edu	37	9	124855211	124855211	+	Missense_Mutation	SNP	C	C	T	rs61742319	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	13	12	7	0	0.923077	0	C|0.742;T|0.258	0.258	strong	.	TTLL11	67	.	NM_001139442	exon1	c.G487A	p.A163T	CCTCAGCCGCACT	.	PASS	Atlas-SNP
FUK	197258	hgsc.bcm.edu	37	16	70506907	70506907	+	Silent	SNP	T	T	C	rs7192865	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	122	78	103	0	0.639344	0	T|0.402;C|0.598	0.598	strong	FUK,NS,carcinoma,0,1	FUK	72	1	NM_145059	exon15	c.T1428C	p.P476P	GGACCCTGAGACG	.	PASS	Atlas-SNP
MYH4	4622	hgsc.bcm.edu	37	17	10363410	10363410	+	Silent	SNP	A	A	G	rs3744561	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	159	79	205	1	0.496855	0.00487805	A|0.575;G|0.425	0.425	strong	.	MYH4	349	.	NM_017533	exon14	c.T1275C	p.N425N	CACTGCATTGTAC	.	PASS	Atlas-SNP
MAG	4099	hgsc.bcm.edu	37	19	35786868	35786868	+	Silent	SNP	C	C	T	rs2301600	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	39	24	43	0	0.615385	0	C|0.780;T|0.220	0.220	strong	.	MAG	172	.	NM_080600	exon4	c.C399T	p.S133S	GCACAGCGTCCTG	.	PASS	Atlas-SNP
ZFP36L1	677	hgsc.bcm.edu	37	14	69256848	69256848	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	155	27	158	0	0.174194	0	.	.	none	.	ZFP36L1	47	.	NM_001244701	exon3	c.G626T	p.G209V	TGGATGCCGTGTG	.	PASS	Atlas-SNP
PKHD1L1	93035	hgsc.bcm.edu	37	8	110420429	110420429	+	Silent	SNP	A	A	G	rs13252234	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	88	70	155	0	0.795455	0	A|0.689;G|0.311	0.311	strong	.	PKHD1L1	522	.	NM_177531	exon18	c.A1965G	p.E655E	ATCAGAAGCTGAA	.	PASS	Atlas-SNP
PPYR1	5540	hgsc.bcm.edu	37	10	47087371	47087371	+	Silent	SNP	G	G	A	rs1048156	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	133	34	160	0	0.255639	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
UPK3A	7380	hgsc.bcm.edu	37	22	45691594	45691594	+	Silent	SNP	A	A	G	rs1057356	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	44	16	52	0	0.363636	0	A|0.474;G|0.526	0.526	strong	.	UPK3A	14	.	NM_006953	exon6	c.A858G	p.Q286Q	GCTCCAAGACTGA	.	PASS	Atlas-SNP
MUC13	56667	hgsc.bcm.edu	37	3	124646594	124646594	+	Missense_Mutation	SNP	A	A	G	rs4679392	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	187	92	243	2	0.491979	0.00823045	A|0.600;G|0.400	0.400	strong	MUC13,NS,carcinoma,0,1	MUC13	57	1	NM_033049	exon2	c.T296C	p.I99T	GTAGGTATAGGAA	.	scavenged	Atlas-SNP
ME3	10873	hgsc.bcm.edu	37	11	86267633	86267633	+	Silent	SNP	C	C	T	rs17211115	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	20	95	0	0.25641	0	C|0.784;T|0.216	0.216	strong	.	ME3	70	.	NM_006680	exon4	c.G429A	p.L143L	ACAGGCCAGCCCC	.	PASS	Atlas-SNP
AOAH	313	hgsc.bcm.edu	37	7	36763688	36763688	+	Silent	SNP	C	C	T	rs2228411	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	33	31	47	0	0.939394	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
IGSF9	57549	hgsc.bcm.edu	37	1	159904270	159904270	+	Silent	SNP	C	C	T	rs34790966	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	135	63	157	0	0.466667	0	C|0.990;T|0.010	0.010	strong	.	IGSF9	123	.	NM_001135050	exon8	c.G906A	p.V302V	GCTGGGCACACAG	.	PASS	Atlas-SNP
FAM205A	259308	hgsc.bcm.edu	37	9	34726155	34726155	+	Missense_Mutation	SNP	C	C	T	rs76045500	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	478	198	111	0	0.414226	0	C|0.937;T|0.063	0.063	strong	.	FAM205A	45	.	NM_001141917	exon4	c.G1082A	p.C361Y	CATGAACACCAGG	.	PASS	Atlas-SNP
BTBD16	118663	hgsc.bcm.edu	37	10	124096035	124096035	+	Silent	SNP	T	T	C	rs3817281	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	31	118	0	0.397436	0	T|0.613;C|0.387	0.387	strong	.	BTBD16	44	.	NM_144587	exon15	c.T1290C	p.S430S	GGAATCTCCCTCT	.	PASS	Atlas-SNP
HEATR1	55127	hgsc.bcm.edu	37	1	236729956	236729956	+	Missense_Mutation	SNP	T	T	C	rs653737	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	40	87	0	0.487805	0	T|0.891;C|0.109	0.109	strong	.	HEATR1	197	.	NM_018072	exon30	c.A4298G	p.Y1433C	TCGCCATAGGCAG	.	PASS	Atlas-SNP
ELL3	80237	hgsc.bcm.edu	37	15	44069069	44069069	+	Missense_Mutation	SNP	G	G	C	rs2277531	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	59	18	58	0	0.305085	0	G|0.819;C|0.181	0.181	strong	.	ELL3	38	.	NM_025165	exon1	c.C31G	p.Q11E	GGAGCTGTCCTCT	.	PASS	Atlas-SNP
TRPM8	79054	hgsc.bcm.edu	37	2	234854540	234854540	+	Missense_Mutation	SNP	G	G	C	rs13004520	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	63	35	66	0	0.555556	0	G|0.955;C|0.045	0.045	strong	.	TRPM8	146	.	NM_024080	exon7	c.G740C	p.R247T	TCACAAGAGATCC	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100681221	100681221	+	Missense_Mutation	SNP	G	G	C	rs147785825	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	65	34	59	0	0.523077	0	G|0.973;C|0.027	0.027	strong	.	MUC17	804	.	NM_001040105	exon3	c.G6524C	p.S2175T	TGGCCAGTTCTGC	.	PASS	Atlas-SNP
SRRM5	100170229	hgsc.bcm.edu	37	19	44117582	44117582	+	Missense_Mutation	SNP	T	T	C	rs10410000	bycluster;by2hit2allele;byhapmap	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	65	33	50	2	0.507692	0.04	C|1.000;|0.000	1.000	weak	SRRM5,colon,carcinoma,0,3	SRRM5	38	3	NM_001145641	exon1	c.T1309C	p.C437R	AGAGATTGCAGCC	.	scavenged	Atlas-SNP
DNAH17	8632	hgsc.bcm.edu	37	17	76490894	76490894	+	Silent	SNP	G	G	A	rs372912923		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	42	73	0	0.494118	0	.	.	weak	.	DNAH17	347	.	NM_173628	exon40	c.C6051T	p.Y2017Y	CCAGTCGTAATGA	.	PASS	Atlas-SNP
RRP7A	27341	hgsc.bcm.edu	37	22	42910769	42910769	+	Silent	SNP	G	G	A	rs4822146	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	236	88	252	2	0.372881	0.00793651	G|0.898;A|0.102	0.102	strong	RRP7A,NS,carcinoma,0,1	RRP7A	25	1	NM_015703	exon5	c.C477T	p.Y159Y	GTCTGCGTAGTCA	.	scavenged	Atlas-SNP
GALNTL6	442117	hgsc.bcm.edu	37	4	173232805	173232805	+	Silent	SNP	G	G	A	rs9312524	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	187	187	236	0	1	0	G|0.852;A|0.148	0.148	strong	.	GALNTL6	102	.	NM_001034845	exon4	c.G288A	p.E96E	TGAAGAGGACCAT	.	PASS	Atlas-SNP
ITSN1	6453	hgsc.bcm.edu	37	21	35147359	35147359	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	198	106	214	0	0.535354	0	.	.	none	.	ITSN1	166	.	NM_001001132	exon14	c.A1543C	p.K515Q	ACAAACAAATCTA	.	PASS	Atlas-SNP
KRTAP4-8	728224	hgsc.bcm.edu	37	17	39253835	39253835	+	Missense_Mutation	SNP	C	C	T	rs72625995	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	96	45	125	0	0.46875	0	C|0.980;T|0.020	0.020	strong	KRTAP4-8,NS,carcinoma,0,1	KRTAP4-8	57	1	NM_031960	exon1	c.G502A	p.A168T	CACAGGCTGGGCG	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1269707	1269707	+	Missense_Mutation	SNP	C	C	T	rs187569173	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	242	36	228	1	0.14876	0.00438596	C|0.967;T|0.033	0.033	strong	MUC5B,NS,carcinoma,0,2	MUC5B	473	2	NM_002458	exon31	c.C11597T	p.P3866L	AAGTGCCGACTAC	.	scavenged	Atlas-SNP
TMEM123	114908	hgsc.bcm.edu	37	11	102272884	102272884	+	Missense_Mutation	SNP	C	C	T	rs2155587	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	317	246	332	0	0.776025	0	C|0.929;T|0.071	0.071	strong	.	TMEM123	16	.	NM_052932	exon3	c.G211A	p.V71M	GTTTCACAGTACT	.	PASS	Atlas-SNP
EBP	10682	hgsc.bcm.edu	37	X	48382174	48382174	+	Silent	SNP	G	G	T	rs3048	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	55	54	77	0	0.981818	0	G|0.693;T|0.307	0.307	strong	.	EBP	30	.	NM_006579	exon2	c.G15T	p.A5A	CAACGCGGGCCCC	.	PASS	Atlas-SNP
C7orf31	136895	hgsc.bcm.edu	37	7	25194665	25194665	+	Missense_Mutation	SNP	G	G	C	rs2523072	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	131	130	156	1	0.992366	0.00641026	G|0.428;C|0.572	0.572	strong	.	C7orf31	53	.	NM_138811	exon6	c.C560G	p.T187S	GCCTTGGTTGGCA	.	PASS	Atlas-SNP
ACAN	176	hgsc.bcm.edu	37	15	89401109	89401109	+	Missense_Mutation	SNP	A	A	G	rs4932439	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	183	182	123	0	0.994536	0	A|0.243;G|0.757	0.757	strong	.	ACAN	220	.	NM_001135	exon12	c.A5293G	p.I1765V	CCAGGTATTAGTG	.	PASS	Atlas-SNP
FAM160A2	84067	hgsc.bcm.edu	37	11	6245256	6245256	+	Missense_Mutation	SNP	C	C	T	rs200289464	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	17	77	0	0.175258	0	C|0.999;T|0.001	0.001	weak	.	FAM160A2	100	.	NM_032127	exon3	c.G361A	p.D121N	CCCCATCCCCAAG	.	PASS	Atlas-SNP
RABEP1	9135	hgsc.bcm.edu	37	17	5280440	5280440	+	Silent	SNP	T	T	C	rs3026101	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	61	28	78	0	0.459016	0	T|0.635;C|0.365	0.365	strong	RABEP1,NS,haematopoietic_neoplasm,+1,1	RABEP1	59	1	NM_004703	exon14	c.T2055C	p.R685R	ATACCGTGAGGAC	.	PASS	Atlas-SNP
DNAH1	25981	hgsc.bcm.edu	37	3	52409421	52409421	+	Missense_Mutation	SNP	A	A	G	rs56002041	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	26	18	33	0	0.692308	0	A|0.943;G|0.057	0.057	strong	.	DNAH1	534	.	NM_015512	exon45	c.A7151G	p.N2384S	TGGGCAACTGGTT	.	PASS	Atlas-SNP
ORAI1	84876	hgsc.bcm.edu	37	12	122079429	122079429	+	Silent	SNP	T	T	C	rs3825174	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	149	58	163	0	0.389262	0	T|0.962;C|0.038	0.038	strong	.	ORAI1	66	.	NM_032790	exon2	c.T792C	p.V264V	ACTGGTTAGCCAT	.	PASS	Atlas-SNP
PRDM9	56979	hgsc.bcm.edu	37	5	23527385	23527385	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	128	31	89	1	0.242188	0.011236	.	.	none	PRDM9,rectum,carcinoma,-2,1	PRDM9	344	1	NM_020227	exon11	c.A2188C	p.S730R	GGCTTTAGCAATA	.	scavenged	Atlas-SNP
SVEP1	79987	hgsc.bcm.edu	37	9	113191597	113191597	+	Missense_Mutation	SNP	G	G	A	rs76469101	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	29	14	37	0	0.482759	0	G|0.980;A|0.020	0.020	strong	SVEP1,NS,carcinoma,0,1	SVEP1	326	1	NM_153366	exon35	c.C5633T	p.T1878I	GCCAGAGTATATC	.	PASS	Atlas-SNP
HYDIN	54768	hgsc.bcm.edu	37	16	70972595	70972595	+	Missense_Mutation	SNP	T	T	C	rs79004160	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	132	128	103	0	0.969697	0	T|0.489;C|0.511	0.511	strong	.	HYDIN	788	.	NM_001270974	exon44	c.A6917G	p.E2306G	TCATATTCTTCCT	.	PASS	Atlas-SNP
MYO7B	4648	hgsc.bcm.edu	37	2	128321770	128321770	+	Missense_Mutation	SNP	G	G	A	rs2404991	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	109	53	113	0	0.486239	0	G|0.541;A|0.458	0.458	strong	.	MYO7B	359	.	NM_001080527	exon3	c.G61A	p.G21S	AAGACCGGCGTGG	.	PASS	Atlas-SNP
NAGK	55577	hgsc.bcm.edu	37	2	71297695	71297695	+	Silent	SNP	T	T	C	rs2287328	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	81	37	100	0	0.45679	0	T|0.851;C|0.149	0.149	strong	.	NAGK	34	.	NM_017567	exon2	c.T231C	p.D77D	AGCAGATGGACTG	.	PASS	Atlas-SNP
RNF213	57674	hgsc.bcm.edu	37	17	78237572	78237572	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	90	4	98	0	0.0444444	0	.	.	none	.	RNF213	766	.	NM_001256071	exon2	c.T92C	p.I31T	CCCCCATAGCAGG	.	PASS	Atlas-SNP
CAND2	23066	hgsc.bcm.edu	37	3	12857493	12857493	+	Missense_Mutation	SNP	C	C	T	rs2305397	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	151	77	159	0	0.509934	0	C|0.612;T|0.386	0.386	strong	CAND2_ENST00000456430,caecum,carcinoma,0,2	CAND2	138	2	NM_001162499	exon9	c.C1427T	p.P476L	ATATGCCTGTGCT	.	PASS	Atlas-SNP
KRTAP10-9	386676	hgsc.bcm.edu	37	21	46047925	46047925	+	Silent	SNP	G	G	T	rs9979457	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	151	150	116	1	0.993378	0.00862069	G|0.347;T|0.653	0.653	strong	.	KRTAP10-9	24	.	NM_198690	exon1	c.G837T	p.P279P	CCGCCCGGCCTGC	.	PASS	Atlas-SNP
GIMAP6	474344	hgsc.bcm.edu	37	7	150324825	150324825	+	Silent	SNP	C	C	T	rs3735084	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	86	94	0	1	0	C|0.705;T|0.295	0.295	strong	GIMAP6,NS,carcinoma,0,1	GIMAP6	60	1	NM_001244072	exon3	c.G1071A	p.L357L	CTTCCCCAGCAGG	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	193	91	258	0	0.471503	0	G|0.311;N|0.000	0.311	strong	.	NSUN4	26	.	NM_199044	exon2	c.A151G	p.T51A	GACATGACTTACA	.	PASS	Atlas-SNP
MRGPRX4	117196	hgsc.bcm.edu	37	11	18194944	18194944	+	Silent	SNP	T	T	A	rs11024531	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	123	96	138	0	0.780488	0	T|0.760;A|0.240	0.240	strong	.	MRGPRX4	68	.	NM_054032	exon1	c.T141A	p.V47V	CGCGGTTGTGCTC	.	PASS	Atlas-SNP
ZNF732	654254	hgsc.bcm.edu	37	4	289272	289272	+	Missense_Mutation	SNP	C	C	T	rs112132883	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	95	46	124	0	0.484211	0	C|0.975;T|0.025	0.025	strong	.	ZNF732	117	.	NM_001137608	exon2	c.G178A	p.E60K	AGGGCTCCTTTCT	.	PASS	Atlas-SNP
ANKRD18B	441459	hgsc.bcm.edu	37	9	33572347	33572347	+	Missense_Mutation	SNP	T	T	C	rs7853994	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	167	85	151	0	0.508982	0	T|0.791;C|0.209	0.209	strong	ANKRD18B,NS,carcinoma,0,1	ANKRD18B	46	1	NM_001244752	exon16	c.T3022C	p.F1008L	ATCTACTTTCTTC	.	PASS	Atlas-SNP
TNFRSF14	8764	hgsc.bcm.edu	37	1	2488153	2488153	+	Missense_Mutation	SNP	A	A	G	rs4870	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	45	17	77	0	0.377778	0	A|0.440;G|0.560	0.560	strong	.	TNFRSF14	89	.	NM_003820	exon1	c.A50G	p.K17R	CCCCCAAAACCGA	.	PASS	Atlas-SNP
ESPL1	9700	hgsc.bcm.edu	37	12	53682457	53682457	+	Missense_Mutation	SNP	G	G	A	rs56358776	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	164	85	131	0	0.518293	0	G|0.698;A|0.302	0.302	strong	.	ESPL1	158	.	NM_012291	exon20	c.G4682A	p.R1561Q	GGCTCCGGCTCCC	.	PASS	Atlas-SNP
MCPH1	79648	hgsc.bcm.edu	37	8	6500544	6500544	+	Missense_Mutation	SNP	C	C	T	rs1057091	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	64	131	0	0.780488	0	C|0.750;T|0.250	0.250	strong	.	MCPH1	65	.	NM_024596	exon14	c.C2482T	p.P828S	TGTGCCCCTGAAA	.	PASS	Atlas-SNP
ZC3HAV1	56829	hgsc.bcm.edu	37	7	138732457	138732457	+	Silent	SNP	G	G	A	rs3735008	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	106	106	128	1	1	0.0078125	G|0.530;A|0.470	0.470	strong	ZC3HAV1,colon,carcinoma,0,1	ZC3HAV1	75	1	NM_020119	exon13	c.C2592T	p.F864F	GCTGTCGAACTGT	.	PASS	Atlas-SNP
PRPH	5630	hgsc.bcm.edu	37	12	49691250	49691250	+	Silent	SNP	A	A	G	rs73112143	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	30	17	42	0	0.566667	0	A|0.778;G|0.222	0.222	strong	.	PRPH	26	.	NM_006262	exon6	c.A1107G	p.K369K	GCTAAAAGAGGAG	.	PASS	Atlas-SNP
MYBL2	4605	hgsc.bcm.edu	37	20	42338621	42338621	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	63	25	85	0	0.396825	0	.	.	none	.	MYBL2	82	.	NM_002466	exon10	c.G1524C	p.Q508H	AGATCAGAAGTAC	.	PASS	Atlas-SNP
KRIT1	889	hgsc.bcm.edu	37	7	91842554	91842554	+	Silent	SNP	T	T	C	rs11542682	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	43	99	0	0.52439	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
OR2M2	391194	hgsc.bcm.edu	37	1	248343721	248343721	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	235	4	258	0	0.0170213	0	.	.	none	OR2M2,NS,carcinoma,0,2	OR2M2	149	2	NM_001004688	exon1	c.C434T	p.A145V	TTATGGCTACCTT	.	scavenged	Atlas-SNP
UFC1	51506	hgsc.bcm.edu	37	1	161123901	161123901	+	Silent	SNP	C	C	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	96	11	123	0	0.114583	0	.	.	none	.	UFC1	16	.	NM_016406	exon1	c.C114G	p.S38S	TCAGTCCCTTATC	.	PASS	Atlas-SNP
ARSF	416	hgsc.bcm.edu	37	X	3021870	3021870	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	152	152	248	0	1	0	.	.	none	.	ARSF	97	.	NM_004042	exon9	c.G1170T	p.K390N	TGGAAAGGTACCA	.	PASS	Atlas-SNP
BOC	91653	hgsc.bcm.edu	37	3	113004240	113004240	+	Silent	SNP	C	C	T	rs34600669	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	104	48	123	0	0.461538	0	C|0.967;T|0.033	0.033	strong	.	BOC	139	.	NM_033254	exon19	c.C2985T	p.D995D	CCCGGACGAGGGC	.	PASS	Atlas-SNP
KLHL30	377007	hgsc.bcm.edu	37	2	239049540	239049540	+	Missense_Mutation	SNP	G	G	A	rs2241985	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	100	57	92	0	0.57	0	G|0.618;A|0.382	0.382	strong	.	KLHL30	79	.	NM_198582	exon2	c.G145A	p.G49S	CACCGCGGCCTCC	.	PASS	Atlas-SNP
KIAA1211	57482	hgsc.bcm.edu	37	4	57176832	57176832	+	Missense_Mutation	SNP	T	T	C	rs79868722	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	141	70	178	0	0.496454	0	T|0.952;C|0.048	0.048	strong	.	KIAA1211	178	.	NM_020722	exon6	c.T286C	p.S96P	TTCCAGTCCAGTG	.	PASS	Atlas-SNP
DNAH6	1768	hgsc.bcm.edu	37	2	85024731	85024731	+	Silent	SNP	C	C	T	rs1192395	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	81	43	110	0	0.530864	0	C|0.902;T|0.098	0.098	strong	.	DNAH6	194	.	NM_001370	exon70	c.C11430T	p.I3810I	TTTGATCGATGAC	.	PASS	Atlas-SNP
GDF15	9518	hgsc.bcm.edu	37	19	18497137	18497137	+	Silent	SNP	G	G	A	rs6413435	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	43	106	0	0.505882	0	G|0.857;A|0.143	0.143	strong	.	GDF15	31	.	NM_004864	exon1	c.G138A	p.L46L	AGAGTTGCACTCC	.	PASS	Atlas-SNP
CPAMD8	27151	hgsc.bcm.edu	37	19	17088319	17088319	+	Missense_Mutation	SNP	G	G	T	rs55790575		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	23	23	34	0	1	0	.	.	weak	.	CPAMD8	192	.	NM_015692	exon15	c.C1758A	p.D586E	ACACACGTCGACC	.	PASS	Atlas-SNP
CBLC	23624	hgsc.bcm.edu	37	19	45296767	45296767	+	Missense_Mutation	SNP	G	G	A	rs35457630	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	52	32	70	0	0.615385	0	G|0.995;A|0.005	0.005	strong	CBLC,bladder,carcinoma,-2,1	CBLC	41	1	NM_012116	exon8	c.G1174A	p.E392K	CGCTGCGAGATCA	.	PASS	Atlas-SNP
SVEP1	79987	hgsc.bcm.edu	37	9	113189954	113189954	+	Silent	SNP	T	T	G	rs41279045	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	135	55	160	0	0.407407	0	T|0.963;G|0.037	0.037	strong	.	SVEP1	326	.	NM_153366	exon36	c.A5892C	p.G1964G	TGGTTCTCCACAG	.	PASS	Atlas-SNP
KIAA1984	84960	hgsc.bcm.edu	37	9	139701108	139701108	+	Missense_Mutation	SNP	A	A	C	rs2254143	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	59	39	72	0	0.661017	0	A|0.176;C|0.824	0.824	strong	.	KIAA1984	39	.	NM_001039374	exon11	c.A1262C	p.N421T	GCATTAACTTGCC	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105416255	105416255	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	182	9	196	1	0.0494506	0.00510204	.	.	none	AHNAK2_ENST00000333244,colon,carcinoma,+2,1	AHNAK2	719	1	NM_138420	exon7	c.T5533A	p.S1845T	CCACCGAGGCCTC	.	scavenged	Atlas-SNP
PRDM15	63977	hgsc.bcm.edu	37	21	43221555	43221555	+	Silent	SNP	G	G	A	rs2236694	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	117	80	111	0	0.683761	0	G|0.915;A|0.085	0.085	strong	PRDM15,NS,carcinoma,0,1	PRDM15	110	1	NM_022115	exon31	c.C4369T	p.L1457L	TCCCCAGGGGCGT	.	PASS	Atlas-SNP
CEP128	145508	hgsc.bcm.edu	37	14	80971261	80971261	+	Missense_Mutation	SNP	C	C	T	rs61744330	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	41	16	59	0	0.390244	0	C|0.923;T|0.077	0.077	strong	.	CEP128	146	.	NM_152446	exon23	c.G3175A	p.V1059M	AGTTCACGTATGA	.	PASS	Atlas-SNP
SMCHD1	23347	hgsc.bcm.edu	37	18	2763697	2763697	+	Silent	SNP	C	C	T	rs483547	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	129	71	156	1	0.550388	0.00641026	C|0.685;T|0.315	0.315	strong	SMCHD1,colon,carcinoma,0,3	SMCHD1	88	3	NM_015295	exon37	c.C4629T	p.G1543G	TAAAGGCTCTAAT	.	scavenged	Atlas-SNP
KCNIP4	80333	hgsc.bcm.edu	37	4	20852166	20852166	+	Silent	SNP	A	A	G	rs3765121	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	45	17	61	0	0.377778	0	A|0.672;G|0.328	0.328	strong	KCNIP4_ENST00000447367,colon,carcinoma,0,4	KCNIP4	85	4	NM_025221	exon2	c.T228C	p.N76N	TCTTACATTCTTA	.	PASS	Atlas-SNP
C2orf16	84226	hgsc.bcm.edu	37	2	27804547	27804547	+	Missense_Mutation	SNP	G	G	A	rs201164610		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	24	65	0	0.333333	0	G|0.999;A|0.001	0.001	weak	.	C2orf16	357	.	NM_032266	exon1	c.G5108A	p.R1703H	GCCATCGTGGTCC	.	PASS	Atlas-SNP
ZNF189	7743	hgsc.bcm.edu	37	9	104170796	104170796	+	Missense_Mutation	SNP	A	A	T	rs370077009		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	46	27	65	0	0.586957	0	.	.	weak	.	ZNF189	79	.	NM_003452	exon3	c.A746T	p.K249I	TTGTTAAACATCA	.	PASS	Atlas-SNP
HIP1	3092	hgsc.bcm.edu	37	7	75211414	75211414	+	Silent	SNP	A	A	G	rs237238	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	36	75	0	0.521739	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
AHNAK2	113146	hgsc.bcm.edu	37	14	105407327	105407327	+	Missense_Mutation	SNP	G	G	A	rs77215854	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	62	32	61	0	0.516129	0	G|0.980;A|0.020	0.020	strong	.	AHNAK2	719	.	NM_138420	exon7	c.C14461T	p.P4821S	GAAGAGGAATATC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195509795	195509795	+	Missense_Mutation	SNP	C	C	T	rs201497773	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	47	76	0	0.465347	0	.	.	weak	.	MUC4	1505	.	NM_018406	exon2	c.G8656A	p.A2886T	AGGAAGCGTCGGT	.	PASS	Atlas-SNP
ZMIZ1	57178	hgsc.bcm.edu	37	10	81053248	81053248	+	Silent	SNP	G	G	A	rs146995829	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	32	13	29	0	0.40625	0	G|0.995;A|0.005	0.005	strong	ZMIZ1,NS,carcinoma,+1,1	ZMIZ1	101	1	NM_020338	exon12	c.G1068A	p.T356T	CATGACGCCCTCG	.	PASS	Atlas-SNP
CACNA1G	8913	hgsc.bcm.edu	37	17	48703752	48703752	+	Silent	SNP	T	T	C	rs739925	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	136	73	129	0	0.536765	0	T|0.603;G|0.006	.	strong	.	CACNA1G	659	.	NM_018896	exon38	c.T6774C	p.P2258P	CCGGCCTACGTCC	.	PASS	Atlas-SNP
EP300	2033	hgsc.bcm.edu	37	22	41548008	41548008	+	Missense_Mutation	SNP	A	A	G	rs20551	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	225	101	216	0	0.448889	0	A|0.802;G|0.198	0.198	strong	.	EP300	367	.	NM_001429	exon15	c.A2989G	p.I997V	GAGGATATTTCAG	.	PASS	Atlas-SNP
C6orf15	29113	hgsc.bcm.edu	37	6	31079440	31079440	+	Missense_Mutation	SNP	C	C	T	rs2233982	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	109	50	96	0	0.458716	0	C|0.950;T|0.050	0.050	strong	.	C6orf15	29	.	NM_014070	exon2	c.G696A	p.M232I	GTGTGGCATGGGC	.	PASS	Atlas-SNP
TTF1	7270	hgsc.bcm.edu	37	9	135277341	135277341	+	Missense_Mutation	SNP	C	C	A	rs8999	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	66	29	93	0	0.439394	0	C|0.878;A|0.122	0.122	strong	.	TTF1	82	.	NM_007344	exon2	c.G868T	p.A290S	CCAATGCCTCAAA	.	PASS	Atlas-SNP
DNAH14	127602	hgsc.bcm.edu	37	1	225565073	225565073	+	Silent	SNP	C	C	T	rs3856155	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	316	307	353	0	0.971519	0	C|0.457;T|0.543	0.543	strong	.	DNAH14	300	.	NM_001373	exon77	c.C12345T	p.G4115G	CCAGGGCGAAAAG	.	PASS	Atlas-SNP
REV3L	5980	hgsc.bcm.edu	37	6	111631254	111631254	+	Silent	SNP	T	T	C	rs150392515		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	31	15	40	0	0.483871	0	T|1.000;C|0.000	0.000	weak	REV3L,NS,carcinoma,-2,1	REV3L	386	1	NM_002912	exon30	c.A8844G	p.R2948R	TGGCACTCGCTCC	.	PASS	Atlas-SNP
HHIPL2	79802	hgsc.bcm.edu	37	1	222713503	222713503	+	Silent	SNP	C	C	G	rs3748664	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	30	99	1	0.4	0.010101	C|0.679;G|0.321	0.321	strong	HHIPL2,colon,carcinoma,0,1	HHIPL2	122	1	NM_024746	exon4	c.G1299C	p.T433T	CTGGCGCGTGATG	.	scavenged	Atlas-SNP
RYR3	6263	hgsc.bcm.edu	37	15	34015013	34015013	+	Silent	SNP	G	G	A	rs2293027	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	83	82	90	0	0.987952	0	G|0.841;A|0.159	0.159	strong	RYR3,NS,carcinoma,+2,1	RYR3	760	1	NM_001243996	exon44	c.G6717A	p.G2239G	AAACGGGCTCTTG	.	PASS	Atlas-SNP
CFHR4	10877	hgsc.bcm.edu	37	1	196884258	196884258	+	Silent	SNP	A	A	T	rs379049		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	543	174	454	0	0.320442	0	.	.	weak	CFHR4_ENST00000367416,right_lower_lobe,carcinoma,+1,2	CFHR4	141	2	NM_001201550	exon9	c.A1530T	p.P510P	ACCACCAAGATGC	.	scavenged	Atlas-SNP
TAAR2	9287	hgsc.bcm.edu	37	6	132938817	132938817	+	Silent	SNP	G	G	A	rs61745666	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	51	12	93	1	0.235294	0.0107527	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	.	scavenged	Atlas-SNP
KRT84	3890	hgsc.bcm.edu	37	12	52774305	52774305	+	Silent	SNP	A	A	G	rs1732293	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	27	98	0	0.385714	0	A|0.682;G|0.318	0.318	strong	.	KRT84	61	.	NM_033045	exon7	c.T1266C	p.D422D	TTTGGCATCACTG	.	PASS	Atlas-SNP
UNC45A	55898	hgsc.bcm.edu	37	15	91496233	91496233	+	Missense_Mutation	SNP	G	G	A	rs149872991	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	74	48	73	0	0.648649	0	G|1.000;A|0.000	0.000	strong	.	UNC45A	57	.	NM_018671	exon18	c.G2378A	p.R793Q	TCCGCCGGGCAGC	.	PASS	Atlas-SNP
NOSTRIN	115677	hgsc.bcm.edu	37	2	169721377	169721377	+	Missense_Mutation	SNP	G	G	A	rs479661	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	68	68	82	0	1	0	G|0.133;A|0.867	0.867	strong	.	NOSTRIN	68	.	NM_001171631	exon21	c.G1589A	p.G530E	AAGAAGGAGGATG	.	PASS	Atlas-SNP
SYMPK	8189	hgsc.bcm.edu	37	19	46319415	46319415	+	Silent	SNP	G	G	C	rs1132645	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	45	19	43	0	0.422222	0	G|0.613;C|0.387	0.387	strong	.	SYMPK	104	.	NM_004819	exon26	c.C3381G	p.A1127A	GGCCGGGGCCAAG	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29910551	29910551	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	33	15	25	0	0.454545	0	.	.	none	.	HLA-A	89	.	NM_001242758	exon2	c.T91G	p.Y31D	ATGAGGTATTTCT	.	PASS	Atlas-SNP
WDR4	10785	hgsc.bcm.edu	37	21	44273858	44273858	+	Missense_Mutation	SNP	G	G	A	rs15736	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	27	6	27	0	0.222222	0	G|0.581;A|0.419	0.419	strong	.	WDR4	35	.	NM_018669	exon9	c.C796T	p.P266S	CCACAGGAGTGCT	.	PASS	Atlas-SNP
SLC41A2	84102	hgsc.bcm.edu	37	12	105199038	105199038	+	Silent	SNP	G	G	A	rs11112201	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	94	38	125	0	0.404255	0	G|0.919;A|0.081	0.081	strong	SLC41A2,NS,carcinoma,0,1	SLC41A2	66	1	NM_032148	exon10	c.C1614T	p.S538S	GGGGATGGAGAAA	.	PASS	Atlas-SNP
SFTA2	389376	hgsc.bcm.edu	37	6	30899524	30899524	+	Missense_Mutation	SNP	T	T	C	rs3131787	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	25	97	0	0.320513	0	T|0.854;C|0.146	0.146	strong	.	SFTA2	6	.	NM_205854	exon2	c.A110G	p.N37S	GAGGAATTTGTCA	.	PASS	Atlas-SNP
LRPAP1	4043	hgsc.bcm.edu	37	4	3526645	3526645	+	Missense_Mutation	SNP	C	C	T	rs11549516	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	161	74	174	0	0.459627	0	C|0.964;T|0.036	0.036	strong	LRPAP1,NS,carcinoma,-1,1	LRPAP1	29	1	NM_002337	exon2	c.G338A	p.R113H	AGGTTGCGTATGA	.	PASS	Atlas-SNP
CDON	50937	hgsc.bcm.edu	37	11	125851181	125851181	+	Silent	SNP	G	G	A	rs684805	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	19	66	0	0.253333	0	G|0.695;A|0.305	0.305	strong	.	CDON	137	.	NM_016952	exon17	c.C3039T	p.N1013N	CTGCCCGTTCATA	.	PASS	Atlas-SNP
OR2C1	4993	hgsc.bcm.edu	37	16	3406516	3406516	+	Silent	SNP	A	A	G	rs11643487	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	79	62	76	0	0.78481	0	A|0.659;G|0.341	0.341	strong	.	OR2C1	38	.	NM_012368	exon1	c.A576G	p.T192T	CGACACAAGTCTC	.	PASS	Atlas-SNP
RP1L1	94137	hgsc.bcm.edu	37	8	10464755	10464755	+	Missense_Mutation	SNP	C	C	T	rs55642448	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	85	94	0	0.988372	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
LY75	4065	hgsc.bcm.edu	37	2	160738677	160738677	+	Silent	SNP	G	G	A	rs16822581	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	136	69	144	0	0.507353	0	G|0.816;A|0.184	0.184	strong	.	LY75	151	.	NM_002349	exon7	c.C1204T	p.L402L	CTGCTAGAGAATG	.	PASS	Atlas-SNP
OTOP1	133060	hgsc.bcm.edu	37	4	4228424	4228424	+	Silent	SNP	T	T	C	rs75209324		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	37	9	34	6	0.243243	0.176471	.	.	weak	OTOP1,caecum,carcinoma,-1,2	OTOP1	118	2	NM_177998	exon1	c.A168G	p.K56K	GGCCAGTTTCTGT	.	scavenged	Atlas-SNP
SLC25A13	10165	hgsc.bcm.edu	37	7	95761057	95761057	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	104	49	123	0	0.471154	0	.	.	none	.	SLC25A13	131	.	NM_001160210	exon15	c.C1592T	p.A531V	TCACCAGCTATGG	.	PASS	Atlas-SNP
WWC1	23286	hgsc.bcm.edu	37	5	167835539	167835539	+	Missense_Mutation	SNP	C	C	T	rs17551608	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	112	80	68	0	0.714286	0	C|0.895;T|0.105	0.105	strong	.	WWC1	98	.	NM_015238	exon7	c.C748T	p.R250C	GGCTTCCGCACTG	.	PASS	Atlas-SNP
SLC29A4	222962	hgsc.bcm.edu	37	7	5339049	5339049	+	Silent	SNP	C	C	T	rs142638970	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	124	99	138	0	0.798387	0	C|0.997;T|0.003	0.003	strong	.	SLC29A4	52	.	NM_153247	exon9	c.C1200T	p.F400F	AGACTTCGTGGGC	.	PASS	Atlas-SNP
EPHX2	2053	hgsc.bcm.edu	37	8	27396208	27396208	+	Silent	SNP	G	G	A	rs4149253	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	80	14	81	0	0.175	0	G|0.907;A|0.093	0.093	strong	.	EPHX2	57	.	NM_001979	exon14	c.G1275A	p.A425A	TGAAGCGGGTAAG	.	PASS	Atlas-SNP
CEP78	84131	hgsc.bcm.edu	37	9	80879149	80879149	+	Silent	SNP	C	C	T	rs1057650	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	146	76	154	1	0.520548	0.00649351	C|0.921;T|0.079	0.079	strong	CEP78,NS,carcinoma,0,1	CEP78	79	1	NM_001098802	exon13	c.C1545T	p.I515I	TATGATCCTGGAT	.	scavenged	Atlas-SNP
FCGBP	8857	hgsc.bcm.edu	37	19	40420087	40420087	+	Silent	SNP	G	G	A	rs12460562	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	56	33	73	0	0.589286	0	G|0.862;A|0.138	0.138	strong	FCGBP,rectum,carcinoma,0,1	FCGBP	416	1	NM_003890	exon6	c.C2907T	p.A969A	CACGACGGCATCC	.	PASS	Atlas-SNP
DOCK7	85440	hgsc.bcm.edu	37	1	62960101	62960101	+	Silent	SNP	A	A	G	rs10889335	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	94	47	168	0	0.5	0	A|0.670;G|0.330	0.330	strong	.	DOCK7	184	.	NM_001271999	exon40	c.T5035C	p.L1679L	AGGTCAATCGCAG	.	PASS	Atlas-SNP
FAT2	2196	hgsc.bcm.edu	37	5	150901597	150901597	+	Silent	SNP	G	G	C	rs3734047	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	44	14	45	0	0.318182	0	G|0.858;C|0.142	0.142	strong	.	FAT2	465	.	NM_001447	exon18	c.C10557G	p.V3519V	GACATGGACACGG	.	PASS	Atlas-SNP
THNSL1	79896	hgsc.bcm.edu	37	10	25313818	25313818	+	Silent	SNP	C	C	T	rs7086282	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	33	33	46	0	1	0	C|0.530;T|0.470	0.470	strong	THNSL1,NS,carcinoma,0,1	THNSL1	70	1	NM_024838	exon3	c.C1666T	p.L556L	AGAAAACTAGCAC	.	PASS	Atlas-SNP
TPTE2	93492	hgsc.bcm.edu	37	13	20066994	20066994	+	Missense_Mutation	SNP	T	T	C	rs78472618	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	170	13	177	0	0.0764706	0	T|0.820;C|0.180	0.180	strong	TPTE2_ENST00000400230,NS,carcinoma,0,3	TPTE2	225	3	NM_199254	exon4	c.A115G	p.K39E	ACCTTTTACTGAT	.	scavenged	Atlas-SNP
PLA2G7	7941	hgsc.bcm.edu	37	6	46684222	46684222	+	Missense_Mutation	SNP	C	C	T	rs1805017	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	33	109	1	0.44	0.00917431	C|0.737;T|0.263	0.263	strong	PLA2G7,NS,carcinoma,0,1	PLA2G7	49	1	NM_005084	exon4	c.G275A	p.R92H	TCAAGGCGATCAT	.	scavenged	Atlas-SNP
GPR137C	283554	hgsc.bcm.edu	37	14	53098902	53098902	+	Missense_Mutation	SNP	G	G	A	rs762063	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	224	109	287	0	0.486607	0	G|0.569;A|0.431	0.431	strong	.	GPR137C	24	.	NM_001099652	exon4	c.G742A	p.V248I	ACTGTCGTCGTGG	.	PASS	Atlas-SNP
IGSF22	283284	hgsc.bcm.edu	37	11	18729819	18729819	+	Missense_Mutation	SNP	C	C	T	rs78892734	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	68	42	77	0	0.617647	0	C|0.972;T|0.028	0.028	strong	.	IGSF22	211	.	NM_173588	exon19	c.G3022A	p.A1008T	GCCGGGCACTGAG	.	PASS	Atlas-SNP
NEK3	4752	hgsc.bcm.edu	37	13	52710320	52710320	+	Missense_Mutation	SNP	T	T	C	rs371075629		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	230	97	232	0	0.421739	0	.	.	weak	.	NEK3	41	.	NM_002498	exon13	c.A1106G	p.N369S	GCTGTATTGGGTA	.	PASS	Atlas-SNP
HEG1	57493	hgsc.bcm.edu	37	3	124746182	124746182	+	Silent	SNP	C	C	A	rs2333041	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	195	89	206	1	0.45641	0.00485437	A|0.503;C|0.497;T|0.000	0.503	strong	HEG1,NS,carcinoma,-1,1	HEG1	109	1	NM_020733	exon3	c.G780T	p.P260P	AAAGGACGGGCTC	.	scavenged	Atlas-SNP
SEMA4B	10509	hgsc.bcm.edu	37	15	90768959	90768959	+	Silent	SNP	A	A	C	rs908044	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	90	89	53	0	0.988889	0	A|0.634;C|0.366	0.366	strong	.	SEMA4B	51	.	NM_020210	exon13	c.A1588C	p.R530R	CTGTACAGGAGCT	.	PASS	Atlas-SNP
LAMB1	3912	hgsc.bcm.edu	37	7	107626770	107626770	+	Silent	SNP	G	G	A	rs25659	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	104	42	134	0	0.403846	0	G|0.898;A|0.102	0.102	strong	.	LAMB1	185	.	NM_002291	exon6	c.C462T	p.S154S	AAAGTCGGACGAT	.	PASS	Atlas-SNP
TOR1AIP1	26092	hgsc.bcm.edu	37	1	179876988	179876988	+	Missense_Mutation	SNP	C	C	G	rs609521	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	132	66	172	0	0.5	0	C|0.442;G|0.557	0.557	strong	.	TOR1AIP1	58	.	NM_001267578	exon7	c.C830G	p.P277R	AGCAACCTTCAGT	.	PASS	Atlas-SNP
PYGB	5834	hgsc.bcm.edu	37	20	25262769	25262769	+	Missense_Mutation	SNP	G	G	A	rs2227891	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	56	32	55	0	0.571429	0	G|0.839;A|0.161	0.161	strong	.	PYGB	84	.	NM_002862	exon12	c.G1504A	p.D502N	CTGGCCGATACCA	.	PASS	Atlas-SNP
CENPE	1062	hgsc.bcm.edu	37	4	104062223	104062223	+	Silent	SNP	C	C	T	rs1381658	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	30	96	0	0.348837	0	C|0.861;T|0.139	0.139	strong	.	CENPE	253	.	NM_001813	exon36	c.G5502A	p.T1834T	TTTTAACGTAATA	.	PASS	Atlas-SNP
HR	55806	hgsc.bcm.edu	37	8	21982991	21982991	+	Missense_Mutation	SNP	T	T	C	rs74596676	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	51	42	66	0	0.823529	0	T|0.930;C|0.070	0.070	strong	.	HR	71	.	NM_018411	exon5	c.A1583G	p.Q528R	TCCTCCTGCTGCA	.	PASS	Atlas-SNP
UBR4	23352	hgsc.bcm.edu	37	1	19447882	19447882	+	Silent	SNP	G	G	A	rs34710232	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	329	175	360	1	0.531915	0.00277778	G|0.996;A|0.004	0.004	strong	UBR4,right_upper_lobe,carcinoma,-1,1	UBR4	415	1	NM_020765	exon68	c.C9942T	p.G3314G	GGACACGCCCTCA	.	PASS	Atlas-SNP
ENG	2022	hgsc.bcm.edu	37	9	130586661	130586661	+	Silent	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	116	56	154	1	0.482759	0.00649351	.	.	none	ENG,NS,carcinoma,0,1	ENG	44	1	NM_001114753	exon8	c.G1056A	p.P352P	CAGCTCCGGGCTA	.	scavenged	Atlas-SNP
AKAP3	10566	hgsc.bcm.edu	37	12	4735970	4735970	+	Missense_Mutation	SNP	A	A	G	rs2041290	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	79	22	104	0	0.278481	0	A|0.881;G|0.119	0.119	strong	.	AKAP3	212	.	NM_006422	exon4	c.T2098C	p.S700P	CTCCAGACTTGTC	.	PASS	Atlas-SNP
TRIOBP	11078	hgsc.bcm.edu	37	22	38122448	38122448	+	Silent	SNP	C	C	T	rs739137	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	8	5	4	0	0.625	0	C|0.621;T|0.379	0.379	strong	.	TRIOBP	262	.	NM_001039141	exon7	c.C3885T	p.S1295S	CAGCAGCGGGGGC	.	PASS	Atlas-SNP
OR8B8	26493	hgsc.bcm.edu	37	11	124310622	124310622	+	Silent	SNP	A	A	G	rs4296049	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	39	12	72	0	0.307692	0	A|0.756;G|0.244	0.244	strong	.	OR8B8	76	.	NM_012378	exon1	c.T360C	p.Y120Y	GCGGTCATACGCC	.	PASS	Atlas-SNP
DHX9	1660	hgsc.bcm.edu	37	1	182844020	182844020	+	Silent	SNP	C	C	T	rs11332	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	52	32	80	0	0.615385	0	C|0.865;T|0.135	0.135	strong	.	DHX9	114	.	NM_001357	exon16	c.C1746T	p.T582T	GATGACCCACTTT	.	PASS	Atlas-SNP
BFSP2	8419	hgsc.bcm.edu	37	3	133167363	133167363	+	Silent	SNP	G	G	A	rs2276737	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	102	44	117	0	0.431373	0	G|0.551;A|0.449	0.449	strong	.	BFSP2	48	.	NM_003571	exon3	c.G603A	p.A201A	AAAGGCGGCAGAA	.	PASS	Atlas-SNP
PCDHA10	56139	hgsc.bcm.edu	37	5	140238124	140238124	+	Missense_Mutation	SNP	T	T	A	rs62384480	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	51	51	122	0	1	0	T|0.967;A|0.033	0.033	strong	.	PCDHA10	358	.	NM_031859	exon1	c.T2491A	p.F831I	TCTACATTCCATT	.	PASS	Atlas-SNP
METTL3	56339	hgsc.bcm.edu	37	14	21967685	21967685	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	366	6	351	1	0.0163934	0.002849	.	.	none	METTL3,NS,adenocarcinoma,0,1	METTL3	48	1	NM_019852	exon8	c.G1403A	p.R468Q	CCTGTCCGAATGA	.	scavenged	Atlas-SNP
TOR1AIP1	26092	hgsc.bcm.edu	37	1	179852074	179852074	+	Missense_Mutation	SNP	T	T	C	rs1281378	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	98	43	128	0	0.438776	0	T|0.410;C|0.590	0.590	strong	.	TOR1AIP1	58	.	NM_001267578	exon1	c.T437C	p.M146T	CTGTTATGACCAG	.	PASS	Atlas-SNP
RNF32	140545	hgsc.bcm.edu	37	7	156469190	156469190	+	Silent	SNP	A	A	G	rs2302145	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	40	128	0	0.57971	0	A|0.477;G|0.523	0.523	strong	.	RNF32	77	.	NM_001184996	exon9	c.A930G	p.A310A	GGGTGCAGGCAGG	.	PASS	Atlas-SNP
ZIM3	114026	hgsc.bcm.edu	37	19	57649962	57649962	+	Missense_Mutation	SNP	C	C	T	rs10407445	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	62	20	96	0	0.322581	0	C|0.866;T|0.134	0.134	strong	.	ZIM3	107	.	NM_052882	exon3	c.G20A	p.R7K	GTCACTCTTCCCT	.	PASS	Atlas-SNP
IKZF3	22806	hgsc.bcm.edu	37	17	37922259	37922259	+	Silent	SNP	G	G	A	rs907092	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	119	50	108	0	0.420168	0	G|0.660;A|0.340	0.340	strong	IKZF3,NS,carcinoma,0,1	IKZF3	79	1	NM_012481	exon8	c.C1314T	p.S438S	TTTGACGGAGTCT	.	PASS	Atlas-SNP
ZNF699	374879	hgsc.bcm.edu	37	19	9408658	9408658	+	Silent	SNP	G	G	A	rs73920733	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	77	35	92	0	0.454545	0	G|0.892;A|0.108	0.108	strong	.	ZNF699	67	.	NM_198535	exon3	c.C184T	p.L62L	TGTGTAGCGGATA	.	PASS	Atlas-SNP
HERC2	8924	hgsc.bcm.edu	37	15	28386626	28386626	+	Silent	SNP	C	C	T	rs11636232	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	121	58	143	0	0.479339	0	C|0.783;T|0.217	0.217	strong	.	HERC2	501	.	NM_004667	exon78	c.G11967A	p.Q3989Q	GATTAACTGCACG	.	PASS	Atlas-SNP
TBC1D26	353149	hgsc.bcm.edu	37	17	15645289	15645289	+	Missense_Mutation	SNP	G	G	A	rs17855672	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	57	25	35	0	0.438596	0	G|0.722;A|0.278	0.278	strong	.	TBC1D26	16	.	NM_178571	exon11	c.G700A	p.G234S	TCGAGAGGCTCCT	.	PASS	Atlas-SNP
BMPR2	659	hgsc.bcm.edu	37	2	203421199	203421199	+	Silent	SNP	G	G	A	rs1061157	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	38	18	55	0	0.473684	0	G|0.907;A|0.093	0.093	strong	.	BMPR2	142	.	NM_001204	exon12	c.G2811A	p.R937R	ACAGAGGCCTAAT	.	PASS	Atlas-SNP
ALMS1	7840	hgsc.bcm.edu	37	2	73717567	73717567	+	Missense_Mutation	SNP	G	G	T	rs2056486	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	70	86	0	0.985915	0	G|0.663;T|0.337	0.337	strong	.	ALMS1	384	.	NM_015120	exon10	c.G8478T	p.R2826S	TACCAGGGCAAAT	.	PASS	Atlas-SNP
CYP19A1	1588	hgsc.bcm.edu	37	15	51529112	51529112	+	Silent	SNP	T	T	C	rs700518	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	134	134	176	2	1	0.0113636	T|0.612;C|0.388	0.388	strong	CYP19A1,NS,adenoma,0,2	CYP19A1	75	2	NM_031226	exon4	c.A240G	p.V80V	TCCATATACCCGG	.	scavenged	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228492044	228492044	+	Silent	SNP	G	G	A	rs1150910	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	48	15	60	0	0.3125	0	G|0.636;A|0.364	0.364	strong	.	OBSCN	2142	.	NM_001271223	exon53	c.G14043A	p.E4681E	CCAGGAGGCCAGA	.	PASS	Atlas-SNP
COL7A1	1294	hgsc.bcm.edu	37	3	48623124	48623124	+	Missense_Mutation	SNP	G	G	A	rs35761247	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	52	117	0	0.597701	0	G|0.962;A|0.038	0.038	strong	.	COL7A1	320	.	NM_000094	exon30	c.C3830T	p.P1277L	CTCACCGGGAGGC	.	PASS	Atlas-SNP
PUM1	9698	hgsc.bcm.edu	37	1	31426815	31426815	+	Silent	SNP	A	A	G	rs2275741	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	94	50	116	0	0.531915	0	A|0.647;G|0.353	0.353	strong	.	PUM1	107	.	NM_014676	exon15	c.T2337C	p.N779N	ACTGCCATTCGTG	.	PASS	Atlas-SNP
C15orf55	256646	hgsc.bcm.edu	37	15	34649336	34649336	+	Missense_Mutation	SNP	G	G	A	rs149177074	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	52	27	55	0	0.519231	0	G|0.998;A|0.002	0.002	strong	C15orf55_ENST00000333756,NS,lymphoid_neoplasm,0,1	C15orf55	110	1	NM_175741	exon7	c.G3043A	p.E1015K	GAGGATGAGGAAC	.	PASS	Atlas-SNP
FAM83A	84985	hgsc.bcm.edu	37	8	124206324	124206324	+	Missense_Mutation	SNP	G	G	A	rs7813708	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	16	95	0	0.186047	0	G|0.835;A|0.165	0.165	strong	.	FAM83A	64	.	NM_032899	exon3	c.G709A	p.A237T	AAATTCGCTGGCC	.	PASS	Atlas-SNP
FREM1	158326	hgsc.bcm.edu	37	9	14846036	14846036	+	Missense_Mutation	SNP	C	C	G	rs2779500	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	197	86	177	0	0.436548	0	C|0.496;G|0.504	0.504	strong	FREM1,NS,carcinoma,0,1	FREM1	261	1	NM_144966	exon9	c.G1315C	p.V439L	CGACAACCTGAAA	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	210	102	243	0	0.485714	0	G|0.831;A|0.169	0.169	strong	.	FAM13A	181	.	NM_014883	exon22	c.C2739T	p.D913D	GAATTGGTCCAGA	.	PASS	Atlas-SNP
COL22A1	169044	hgsc.bcm.edu	37	8	139749799	139749799	+	Missense_Mutation	SNP	G	G	T	rs10111520	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	95	26	98	0	0.273684	0	G|0.948;T|0.052	0.052	strong	.	COL22A1	390	.	NM_152888	exon23	c.C2107A	p.P703T	CAGGTGGTCCCAT	.	PASS	Atlas-SNP
GABRG3	2567	hgsc.bcm.edu	37	15	27765249	27765249	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	99	4	102	0	0.040404	0	.	.	none	.	GABRG3	115	.	NM_033223	exon7	c.A844G	p.T282A	GATGCTACGCCAG	.	PASS	Atlas-SNP
BSN	8927	hgsc.bcm.edu	37	3	49693972	49693972	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	45	18	62	0	0.4	0	.	.	none	.	BSN	272	.	NM_003458	exon5	c.C6983T	p.P2328L	CAGCTCCTGCCCC	.	PASS	Atlas-SNP
FAN1	22909	hgsc.bcm.edu	37	15	31197564	31197564	+	Missense_Mutation	SNP	G	G	A	rs4779794	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	61	61	92	0	1	0	G|0.626;A|0.374	0.374	strong	FAN1,NS,carcinoma,+1,1	FAN1	77	1	NM_001146095	exon2	c.G698A	p.G233E	TAAGAGGAAGTAA	.	PASS	Atlas-SNP
TRIM16	10626	hgsc.bcm.edu	37	17	15554504	15554504	+	Silent	SNP	G	G	A	rs4792642	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	77	118	1	0.987179	0.00847458	G|0.746;A|0.254	0.254	strong	.	TRIM16	45	.	NM_006470	exon4	c.C420T	p.A140A	GCAGAAGGCAGAC	.	PASS	Atlas-SNP
PRR21	643905	hgsc.bcm.edu	37	2	240982379	240982379	+	Silent	SNP	T	T	C	rs138056768	by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	18	9	33	0	0.5	0	T|0.989;C|0.011	0.011	strong	.	PRR21	53	.	NM_001080835	exon1	c.A21G	p.T7T	AAGAGCTGTGGAT	.	PASS	Atlas-SNP
SYNE1	23345	hgsc.bcm.edu	37	6	152469331	152469331	+	Silent	SNP	C	C	T	rs2252748	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	40	31	80	0	0.775	0	C|0.691;T|0.309	0.309	strong	.	SYNE1	3227	.	NM_182961	exon137	c.G24825A	p.P8275P	ACTAGCCGGGGTG	.	PASS	Atlas-SNP
CEP170	9859	hgsc.bcm.edu	37	1	243333027	243333027	+	Silent	SNP	A	A	G	rs34466343	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	432	6	511	5	0.0138889	0.00978474	.	.	weak	CEP170_ENST00000366543,NS,carcinoma,0,6	CEP170	153	6	NM_014812	exon12	c.T1746C	p.R582R	AACCCAACGTTTG	.	scavenged	Atlas-SNP
PLEKHM2	23207	hgsc.bcm.edu	37	1	16056364	16056364	+	Silent	SNP	G	G	A	rs3817269	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	63	36	52	0	0.571429	0	G|0.678;A|0.322	0.322	strong	.	PLEKHM2	94	.	NM_015164	exon14	c.G2148A	p.T716T	CCTGACGGATGCC	.	PASS	Atlas-SNP
C9orf43	257169	hgsc.bcm.edu	37	9	116191205	116191205	+	Missense_Mutation	SNP	A	A	C	rs111841972	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	108	62	137	0	0.574074	0	A|0.957;C|0.043	0.043	strong	.	C9orf43	49	.	NM_152786	exon13	c.A1133C	p.N378T	AGATGAACTACTA	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29911261	29911261	+	Missense_Mutation	SNP	C	C	G	rs3129018	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	136	100	218	0	0.735294	0	G|0.132;C|0.681;A|0.188	0.132	strong	.	HLA-A	89	.	NM_001242758	exon3	c.C560G	p.T187R	ATGGCACGTGCGT	.	PASS	Atlas-SNP
CEP170B	283638	hgsc.bcm.edu	37	14	105346632	105346632	+	Silent	SNP	G	G	A	rs72700176	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	31	88	0	0.424658	0	G|0.971;A|0.029	0.029	strong	.	.	.	.	NM_001112726	exon6	c.G342A	p.K114K	TGAAAAGTACACC	.	PASS	Atlas-SNP
SULT1A1	6817	hgsc.bcm.edu	37	16	28617472	28617472	+	Missense_Mutation	SNP	G	G	A	rs150459557	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	456	114	277	2	0.25	0.00722022	G|0.998;A|0.002	0.002	strong	SULT1A1,NS,carcinoma,0,1	SULT1A1	53	1	NM_177534	exon6	c.C680T	p.T227M	AACGACGTGTGCT	.	scavenged	Atlas-SNP
STK25	10494	hgsc.bcm.edu	37	2	242441080	242441080	+	Missense_Mutation	SNP	C	C	T	rs200593123		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	2	105	0	0.0243902	0	C|0.999;T|0.001	0.001	weak	STK25,caecum,carcinoma,0,1	STK25	32	1	NM_006374	exon3	c.G74A	p.R25H	CCAATGCGGTCGA	.	scavenged	Atlas-SNP
MAP3K5	4217	hgsc.bcm.edu	37	6	137026266	137026266	+	Silent	SNP	T	T	G	rs9321567	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	88	11	147	0	0.125	0	T|0.413;G|0.587	0.587	strong	.	MAP3K5	136	.	NM_005923	exon3	c.A594C	p.I198I	GCAAATTATTTCC	.	PASS	Atlas-SNP
BGN	633	hgsc.bcm.edu	37	X	152770230	152770230	+	Silent	SNP	G	G	A	rs4833	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	43	42	88	0	0.976744	0	G|0.631;A|0.369	0.369	strong	.	BGN	44	.	NM_001711	exon2	c.G141A	p.S47S	CACCTCGGGCGTC	.	PASS	Atlas-SNP
NID2	22795	hgsc.bcm.edu	37	14	52520746	52520746	+	Missense_Mutation	SNP	G	G	T	rs35657569	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	96	96	119	0	1	0	G|0.939;T|0.061	0.061	strong	.	NID2	201	.	NM_007361	exon4	c.C1061A	p.P354H	TCTAAAGGCTTTG	.	PASS	Atlas-SNP
MBOAT1	154141	hgsc.bcm.edu	37	6	20109956	20109956	+	Missense_Mutation	SNP	A	A	G	rs45596536	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	98	62	94	0	0.632653	0	A|0.986;G|0.014	0.014	strong	.	MBOAT1	48	.	NM_001080480	exon12	c.T1234C	p.F412L	AAAGGAAGTAATG	.	PASS	Atlas-SNP
NME8	51314	hgsc.bcm.edu	37	7	37934147	37934147	+	Silent	SNP	A	A	T	rs41276027	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	242	189	269	0	0.780992	0	A|0.761;T|0.239	0.239	strong	.	.	.	.	NM_016616	exon16	c.A1479T	p.I493I	GCAAATAGAGAAA	.	PASS	Atlas-SNP
TMPRSS5	80975	hgsc.bcm.edu	37	11	113570405	113570405	+	Silent	SNP	T	T	C	rs4936280	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	209	47	238	1	0.22488	0.00420168	T|0.231;C|0.769	0.769	strong	TMPRSS5_ENST00000299882,NS,carcinoma,-1,2	TMPRSS5	69	2	NM_030770	exon3	c.A117G	p.A39A	GCACACTGCCTGA	.	scavenged	Atlas-SNP
TPTE2	93492	hgsc.bcm.edu	37	13	20006680	20006680	+	Silent	SNP	G	G	C	rs201767816	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	170	20	149	0	0.117647	0	G|0.999;C|0.001	0.001	weak	TPTE2,mouth,carcinoma,0,1	TPTE2	225	1	NM_199254	exon17	c.C1155G	p.L385L	GTTGTAGAGATGT	.	scavenged	Atlas-SNP
DLG1	1739	hgsc.bcm.edu	37	3	196771554	196771554	+	Silent	SNP	T	T	C	rs35370245	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	119	54	182	0	0.453782	0	T|0.966;C|0.034	0.034	strong	.	DLG1	120	.	NM_004087	exon26	c.A2721G	p.K907K	GATCTGTTTCACT	.	PASS	Atlas-SNP
PYCRL	65263	hgsc.bcm.edu	37	8	144689146	144689146	+	Missense_Mutation	SNP	C	C	T	rs2242089	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	157	124	155	0	0.789809	0	C|0.785;T|0.215	0.215	strong	PYCRL,NS,carcinoma,0,1	PYCRL	14	1	NM_023078	exon3	c.G349A	p.V117M	GAGACACCCCAGC	.	PASS	Atlas-SNP
C11orf1	64776	hgsc.bcm.edu	37	11	111754574	111754574	+	Silent	SNP	A	A	C	rs1045282	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	53	13	63	0	0.245283	0	A|0.734;C|0.266	0.266	strong	.	C11orf1	15	.	NM_022761	exon4	c.A423C	p.S141S	AAAGTCAACTTAC	.	PASS	Atlas-SNP
CST4	1472	hgsc.bcm.edu	37	20	23667738	23667738	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	194	37	242	0	0.190722	0	.	.	none	.	CST4	37	.	NM_001899	exon2	c.C329G	p.P110R	AGTTCTGGCTGTT	.	PASS	Atlas-SNP
NLRP7	199713	hgsc.bcm.edu	37	19	55451232	55451232	+	Missense_Mutation	SNP	C	C	T	rs775882	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	93	38	134	0	0.408602	0	C|0.705;A|0.001	.	strong	.	NLRP7	411	.	NM_001127255	exon4	c.G955A	p.V319I	CCCTTACGTAGAT	.	PASS	Atlas-SNP
OTOP1	133060	hgsc.bcm.edu	37	4	4228425	4228425	+	Missense_Mutation	SNP	T	T	C	rs78657691	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	37	10	34	6	0.27027	0.176471	.	.	weak	OTOP1,caecum,carcinoma,0,2	OTOP1	118	2	NM_177998	exon1	c.A167G	p.K56R	GCCAGTTTCTGTG	.	scavenged	Atlas-SNP
ZYG11B	79699	hgsc.bcm.edu	37	1	53250650	53250650	+	Silent	SNP	G	G	A	rs6588443	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	93	44	121	0	0.473118	0	G|0.397;A|0.603	0.603	strong	.	ZYG11B	61	.	NM_024646	exon5	c.G1194A	p.G398G	TGCAGGGATGCCT	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	45	127	0	0.517241	0	A|0.601;G|0.399	0.399	strong	.	CR1	354	.	NM_000651	exon37	c.A6193G	p.I2065V	GAGATCATCAGAT	.	PASS	Atlas-SNP
SLC5A9	200010	hgsc.bcm.edu	37	1	48705066	48705066	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	194	87	230	1	0.448454	0.00434783	.	.	none	.	SLC5A9	82	.	NM_001135181	exon13	c.G1609A	p.A537T	TACCCAGCGCCAG	.	PASS	Atlas-SNP
ANKRD30A	91074	hgsc.bcm.edu	37	10	37486216	37486216	+	Silent	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	296	8	343	0	0.027027	0	.	.	none	ANKRD30A,colon,carcinoma,0,16	ANKRD30A	448	16	NM_052997	exon28	c.C2454T	p.P818P	GCCTCCCGAGAAG	.	scavenged	Atlas-SNP
FAM86B1	85002	hgsc.bcm.edu	37	8	12044262	12044262	+	Silent	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	324	134	260	0	0.41358	0	.	.	none	FAM86B1_ENST00000321602,NS,carcinoma,0,2	FAM86B1	7	2	NM_001083537	exon4	c.C321T	p.A107A	GAGGGCGGCATCC	.	scavenged	Atlas-SNP
CAND2	23066	hgsc.bcm.edu	37	3	12861586	12861586	+	Silent	SNP	T	T	C	rs4684883	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	63	35	71	0	0.555556	0	T|0.852;C|0.148	0.148	strong	.	CAND2	138	.	NM_001162499	exon11	c.T2946C	p.G982G	TGCAGGTCGGCCA	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	83	24	98	0	0.289157	0	C|0.652;N|0.000	.	strong	.	ITSN2	224	.	NM_147152	exon10	c.G871A	p.V291I	CATCAACGTCAGC	.	PASS	Atlas-SNP
ZBP1	81030	hgsc.bcm.edu	37	20	56189985	56189985	+	Missense_Mutation	SNP	C	C	G	rs16981187	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	183	99	247	0	0.540984	0	C|0.946;G|0.054	0.054	strong	.	ZBP1	65	.	NM_001160419	exon4	c.G460C	p.D154H	CCATGTCCAGAAG	.	PASS	Atlas-SNP
CD200R1	131450	hgsc.bcm.edu	37	3	112648107	112648107	+	Silent	SNP	G	G	A	rs373257099	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	244	108	302	0	0.442623	0	.	.	weak	CD200R1_ENST00000440122,NS,carcinoma,0,2	CD200R1	91	2	NM_138806	exon4	c.C450T	p.D150D	ATACCCGTCATGA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195507385	195507385	+	Missense_Mutation	SNP	G	G	A	rs199842409	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	37	20	56	0	0.540541	0	.	.	weak	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.C11066T	p.A3689V	GTGGATGCTGAGG	.	scavenged	Atlas-SNP
POM121L12	285877	hgsc.bcm.edu	37	7	53103554	53103554	+	Missense_Mutation	SNP	C	C	G	rs11238247	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	53	28	53	0	0.528302	0	C|0.588;G|0.412	0.412	strong	.	POM121L12	146	.	NM_182595	exon1	c.C190G	p.Q64E	CATATTCAGTACT	.	PASS	Atlas-SNP
TRIP6	7205	hgsc.bcm.edu	37	7	100465824	100465824	+	Missense_Mutation	SNP	G	G	A	rs2437100	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	50	22	55	0	0.44	0	G|0.985;A|0.015	0.015	strong	.	TRIP6	45	.	NM_003302	exon3	c.G332A	p.R111Q	GGGGTCGGGGTCA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195505827	195505827	+	Silent	SNP	A	A	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	117	4	72	4	0.034188	0.0555556	.	.	none	MUC4_ENST00000463781,NS,carcinoma,-2,3	MUC4	1505	3	NM_018406	exon2	c.T12624C	p.P4208P	AGGAAGAGGGGTG	.	scavenged	Atlas-SNP
LHB	3972	hgsc.bcm.edu	37	19	49519905	49519905	+	Missense_Mutation	SNP	A	A	G	rs35296413	alternate_allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	253	50	360	0	0.197628	0	A|0.005;T|0.995	.	alt	LHB,NS,carcinoma,0,1	LHB	20	1	NM_000894	exon2	c.T82C	p.W28R	GGCACCATGGCCG	.	PASS	Atlas-SNP
C11orf82	220042	hgsc.bcm.edu	37	11	82644904	82644904	+	Missense_Mutation	SNP	G	G	A	rs7130899	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	14	94	0	0.170732	0	G|0.454;A|0.546	0.546	strong	.	C11orf82	71	.	NM_145018	exon6	c.G2524A	p.V842I	TCTGGTGTTTCAC	.	PASS	Atlas-SNP
LEPR	3953	hgsc.bcm.edu	37	1	66075952	66075952	+	Missense_Mutation	SNP	G	G	C	rs1805094	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	138	53	175	0	0.384058	0	G|0.841;C|0.159	0.159	strong	.	LEPR	284	.	NM_001003680	exon14	c.G1968C	p.K656N	GAAAAAGGAGAAA	.	PASS	Atlas-SNP
FAM71F1	84691	hgsc.bcm.edu	37	7	128358891	128358891	+	Silent	SNP	C	C	A	rs745229	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	31	75	0	0.534483	0	C|0.797;A|0.203	0.203	strong	.	FAM71F1	42	.	NM_032599	exon3	c.C441A	p.L147L	GATTCTCCCATTG	.	PASS	Atlas-SNP
CCDC81	60494	hgsc.bcm.edu	37	11	86123556	86123556	+	Missense_Mutation	SNP	A	A	G	rs3741005	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	160	28	165	0	0.175	0	A|0.936;G|0.064	0.064	strong	.	CCDC81	89	.	NM_001156474	exon11	c.A1346G	p.Y449C	GACAATACAGAGA	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	104	47	124	0	0.451923	0	G|0.576;T|0.424	0.424	strong	.	SNED1	76	.	NM_001080437	exon29	c.G4084T	p.A1362S	ACAAAGGCCTTTC	.	PASS	Atlas-SNP
APBA3	9546	hgsc.bcm.edu	37	19	3753874	3753874	+	Silent	SNP	G	G	A	rs34868972	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	41	18	26	0	0.439024	0	G|0.908;A|0.092	0.092	strong	.	APBA3	28	.	NM_004886	exon6	c.C900T	p.I300I	GCAGCCGATGTCG	.	PASS	Atlas-SNP
DKK2	27123	hgsc.bcm.edu	37	4	107845794	107845794	+	Missense_Mutation	SNP	C	C	T	rs17037102	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	254	251	273	0	0.988189	0	C|0.879;T|0.121	0.121	strong	DKK2,NS,carcinoma,0,3	DKK2	96	3	NM_014421	exon3	c.G437A	p.R146Q	CTGTGCCGAGTAC	.	PASS	Atlas-SNP
CACNA1I	8911	hgsc.bcm.edu	37	22	40054948	40054948	+	Silent	SNP	T	T	C	rs5757761	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	48	95	0	0.521739	0	T|0.245;C|0.755	0.755	strong	CACNA1I,NS,carcinoma,0,1	CACNA1I	264	1	NM_021096	exon12	c.T2157C	p.I719I	GGAGATTGTGGGG	.	PASS	Atlas-SNP
WDR78	79819	hgsc.bcm.edu	37	1	67390416	67390416	+	Missense_Mutation	SNP	G	G	C	rs3008858	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	102	101	121	0	0.990196	0	G|0.211;C|0.789	0.789	strong	.	WDR78	102	.	NM_207014	exon1	c.C99G	p.C33W	AGTGGTGCACCAC	.	PASS	Atlas-SNP
ZNF710	374655	hgsc.bcm.edu	37	15	90611521	90611521	+	Silent	SNP	C	C	T	rs147080007	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	40	76	0	0.470588	0	C|0.989;T|0.011	0.011	strong	.	ZNF710	50	.	NM_198526	exon2	c.C1152T	p.C384C	CTTCTGCGGCCGC	.	PASS	Atlas-SNP
GPR161	23432	hgsc.bcm.edu	37	1	168059866	168059866	+	Silent	SNP	A	A	G	rs275149	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	52	35	95	0	0.673077	0	A|0.580;G|0.420	0.420	strong	GPR161,colon,carcinoma,0,2	GPR161	56	2	NM_001267609	exon5	c.T1200C	p.G400G	CTGTCCACCTGCC	.	PASS	Atlas-SNP
HNRNPA1L2	144983	hgsc.bcm.edu	37	13	53216666	53216666	+	Silent	SNP	G	G	A	rs113869751	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	54	26	63	0	0.481481	0	G|0.980;A|0.020	0.020	strong	.	HNRNPA1L2	20	.	NM_001011724	exon7	c.G39A	p.L13L	ACAGCTGAGGAAG	.	PASS	Atlas-SNP
PTGER3	5733	hgsc.bcm.edu	37	1	71512643	71512643	+	Silent	SNP	C	C	A	rs5671	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	68	32	57	1	0.470588	0.0175439	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	.	scavenged	Atlas-SNP
NOM1	64434	hgsc.bcm.edu	37	7	156762248	156762248	+	Missense_Mutation	SNP	G	G	A	rs12919	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	21	21	24	0	1	0	G|0.474;A|0.526	0.526	strong	NOM1,rectum,carcinoma,0,1	NOM1	73	1	NM_138400	exon11	c.G2434A	p.V812M	CTGGGGGTGTTAC	.	PASS	Atlas-SNP
CKM	1158	hgsc.bcm.edu	37	19	45815033	45815033	+	Silent	SNP	G	G	T	rs17875616	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	68	41	72	0	0.602941	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
C16orf45	89927	hgsc.bcm.edu	37	16	15661871	15661871	+	Missense_Mutation	SNP	A	A	G	rs149928639	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	109	74	127	0	0.678899	0	A|0.996;G|0.004	0.004	strong	.	C16orf45	24	.	NM_033201	exon3	c.A262G	p.M88V	GACATCATGGACT	.	PASS	Atlas-SNP
TOR1AIP1	26092	hgsc.bcm.edu	37	1	179877780	179877780	+	Missense_Mutation	SNP	A	A	C	rs17279712	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	203	98	269	0	0.482759	0	A|0.955;C|0.045	0.045	strong	.	TOR1AIP1	58	.	NM_001267578	exon8	c.A882C	p.Q294H	CCCACAAACTGCA	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105419234	105419234	+	Missense_Mutation	SNP	T	T	C	rs74090129	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	250	67	203	0	0.268	0	T|0.852;C|0.148	0.148	strong	.	AHNAK2	719	.	NM_138420	exon7	c.A2554G	p.M852V	CCTCCATGGACTT	.	PASS	Atlas-SNP
TMPRSS11F	389208	hgsc.bcm.edu	37	4	68930465	68930465	+	Missense_Mutation	SNP	G	G	A	rs143544573	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	51	102	0	0.586207	0	G|0.994;A|0.006	0.006	strong	TMPRSS11F,NS,carcinoma,0,1	TMPRSS11F	79	1	NM_207407	exon8	c.C953T	p.S318F	TTTATAGATGAGT	.	PASS	Atlas-SNP
MYO3B	140469	hgsc.bcm.edu	37	2	171260797	171260797	+	Missense_Mutation	SNP	A	A	G	rs33962844	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	31	112	0	0.397436	0	A|0.726;G|0.274	0.274	strong	MYO3B,neck,malignant_melanoma,+1,1	MYO3B	320	1	NM_001083615	exon20	c.A2318G	p.E773G	CCGTGGAATATGA	.	PASS	Atlas-SNP
A2ML1	144568	hgsc.bcm.edu	37	12	9009820	9009820	+	Missense_Mutation	SNP	G	G	A	rs1558526	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	176	79	194	0	0.448864	0	G|0.843;A|0.157	0.157	strong	.	A2ML1	199	.	NM_144670	exon24	c.G2909A	p.C970Y	GTGGCTGTGGCGA	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105417774	105417774	+	Silent	SNP	G	G	A	rs2013228	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	67	66	0	0	0.985075	.	G|0.700;A|0.300	0.300	strong	.	AHNAK2	719	.	NM_138420	exon7	c.C4014T	p.F1338F	CACCCCGAACGAC	.	PASS	Atlas-SNP
ELFN2	114794	hgsc.bcm.edu	37	22	37770066	37770066	+	Silent	SNP	G	G	T	rs8142615	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	66	41	73	1	0.621212	0.0136986	G|0.597;T|0.403	0.403	strong	ELFN2,colon,carcinoma,0,1	ELFN2	89	1	NM_052906	exon3	c.C1509A	p.I503I	CACCTCGATATAG	.	scavenged	Atlas-SNP
MMP3	4314	hgsc.bcm.edu	37	11	102713620	102713620	+	Missense_Mutation	SNP	T	T	C	rs679620	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	58	72	0	1	0	T|0.428;C|0.572	0.572	strong	MMP3,NS,carcinoma,0,1	MMP3	60	1	NM_002422	exon2	c.A133G	p.K45E	CTTTTTTGAGGTC	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	54	31	77	0	0.574074	0	C|0.708;T|0.292	0.292	strong	.	ABP1	92	.	NM_001091	exon2	c.C47T	p.T16M	TGCAGACGGCCAT	.	PASS	Atlas-SNP
XAB2	56949	hgsc.bcm.edu	37	19	7685843	7685843	+	Silent	SNP	G	G	A	rs794078	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	51	26	54	0	0.509804	0	A|0.158;C|0.007	0.158	strong	XAB2,NS,carcinoma,0,1	XAB2	69	1	NM_020196	exon14	c.C1860T	p.T620T	GGCCCTGGTGGCA	.	PASS	Atlas-SNP
OR2C1	4993	hgsc.bcm.edu	37	16	3405986	3405986	+	Missense_Mutation	SNP	G	G	A	rs1218762	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	147	118	175	0	0.802721	0	G|0.723;A|0.277	0.277	strong	.	OR2C1	38	.	NM_012368	exon1	c.G46A	p.G16S	CTGATGGGCATAT	.	PASS	Atlas-SNP
CANT1	124583	hgsc.bcm.edu	37	17	76993546	76993546	+	Silent	SNP	A	A	G	rs8077024	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	91	37	90	0	0.406593	0	A|0.572;G|0.428	0.428	strong	.	CANT1	39	.	NM_001159772	exon4	c.T159C	p.A53A	GATGGCAGCACCC	.	PASS	Atlas-SNP
NRCAM	4897	hgsc.bcm.edu	37	7	107872816	107872816	+	Silent	SNP	G	G	A	rs2072546	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	187	102	196	0	0.545455	0	G|0.834;A|0.166	0.166	strong	NRCAM_ENST00000379028,colon,carcinoma,0,2	NRCAM	267	2	NM_001037132	exon4	c.C381T	p.N127N	GCGTTCGTTCCTT	.	PASS	Atlas-SNP
AADACL3	126767	hgsc.bcm.edu	37	1	12785749	12785749	+	Missense_Mutation	SNP	C	C	T	rs11121969	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	162	87	164	0	0.537037	0	C|0.922;T|0.078	0.078	strong	.	AADACL3	84	.	NM_001103170	exon4	c.C839T	p.P280L	AGCTCCCGGAAAC	.	PASS	Atlas-SNP
GFRA2	2675	hgsc.bcm.edu	37	8	21550800	21550800	+	Missense_Mutation	SNP	A	A	T	rs1128397	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	60	58	0	0.769231	0	A|0.607;T|0.393	0.393	strong	.	GFRA2	23	.	NM_001495	exon9	c.T1385A	p.L462Q	AAGGCCAGTTTCA	.	PASS	Atlas-SNP
RECK	8434	hgsc.bcm.edu	37	9	36110063	36110063	+	Silent	SNP	T	T	A	rs10972727	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	142	84	183	0	0.591549	0	T|0.719;A|0.281	0.281	strong	.	RECK	73	.	NM_021111	exon15	c.T1875A	p.R625R	TGACCGTCGTACC	.	PASS	Atlas-SNP
FHL5	9457	hgsc.bcm.edu	37	6	97058553	97058553	+	Missense_Mutation	SNP	A	A	G	rs2273621	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	217	217	271	0	1	0	A|0.603;G|0.397	0.397	strong	.	FHL5	73	.	NM_020482	exon6	c.A610G	p.R204G	ATGTCCAGAGACG	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	89	89	130	0	1	0	A|0.847;G|0.153	0.153	strong	.	SEZ6	61	.	NM_001098635	exon12	c.T2417C	p.M806T	CTGCCCATCAGCA	.	PASS	Atlas-SNP
EFHB	151651	hgsc.bcm.edu	37	3	19975215	19975215	+	Missense_Mutation	SNP	C	C	A	rs17795400	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	266	133	331	0	0.5	0	C|0.797;A|0.202	0.202	strong	.	EFHB	186	.	NM_144715	exon1	c.G296T	p.G99V	TTTGTTCCCTGTG	.	PASS	Atlas-SNP
TUBB1	81027	hgsc.bcm.edu	37	20	57599402	57599402	+	Missense_Mutation	SNP	G	G	A	rs6070697	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	50	24	65	0	0.48	0	G|0.852;A|0.148	0.148	strong	.	TUBB1	42	.	NM_030773	exon4	c.G920A	p.R307H	TCCGCCGTGGCCG	.	PASS	Atlas-SNP
GALNS	2588	hgsc.bcm.edu	37	16	88902183	88902183	+	Silent	SNP	G	G	A	rs1064315	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	147	90	102	0	0.612245	0	G|0.715;A|0.285	0.285	strong	.	GALNS	37	.	NM_000512	exon7	c.C708T	p.H236H	GGGTGCGTGCGTG	.	PASS	Atlas-SNP
PTDSS2	81490	hgsc.bcm.edu	37	11	490035	490035	+	Missense_Mutation	SNP	C	C	T	rs61742833	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	45	33	62	0	0.733333	0	C|0.925;T|0.075	0.075	strong	PTDSS2,caecum,carcinoma,-1,3	PTDSS2	27	3	NM_030783	exon11	c.C1268T	p.A423V	TCCTGGCGCTCAC	.	PASS	Atlas-SNP
GPR18	2841	hgsc.bcm.edu	37	13	99907341	99907341	+	Silent	SNP	G	G	A	rs3742130	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	156	155	149	0	0.99359	0	G|0.849;A|0.151	0.151	strong	.	GPR18	23	.	NM_001098200	exon2	c.C786T	p.N262N	GTAACTGTTCTCC	.	PASS	Atlas-SNP
PSPH	5723	hgsc.bcm.edu	37	7	56087423	56087423	+	Missense_Mutation	SNP	G	G	A	rs79451216	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	28	4	31	0	0.142857	0	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
PPP1R1A	5502	hgsc.bcm.edu	37	12	54974803	54974803	+	Silent	SNP	C	C	T	rs8407	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	310	137	295	0	0.441935	0	C|0.825;T|0.175	0.175	strong	PPP1R1A_ENST00000257905,NS,carcinoma,-2,2	PPP1R1A	18	2	NM_006741	exon6	c.G435A	p.E145E	GCCTCTCTCGTGA	.	PASS	Atlas-SNP
MLX	6945	hgsc.bcm.edu	37	17	40722162	40722162	+	Silent	SNP	G	G	A	rs1474040	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	152	75	201	0	0.493421	0	G|0.827;A|0.173	0.173	strong	MLX,colon,carcinoma,+1,1	MLX	17	1	NM_170607	exon7	c.G801A	p.A267A	GTCAGCGTGTGTC	.	PASS	Atlas-SNP
GIPR	2696	hgsc.bcm.edu	37	19	46181392	46181392	+	Missense_Mutation	SNP	G	G	C	rs1800437	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	110	58	95	0	0.527273	0	G|0.836;C|0.164	0.164	strong	.	GIPR	36	.	NM_000164	exon12	c.G1060C	p.E354Q	GTCCACGAGGTGG	.	PASS	Atlas-SNP
PDXDC1	23042	hgsc.bcm.edu	37	16	15129970	15129970	+	Silent	SNP	A	A	G	rs7200543	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	43	35	65	0	0.813953	0	A|0.706;G|0.294	0.294	strong	.	PDXDC1	59	.	NM_015027	exon23	c.A2205G	p.L735L	GCGCCTATCCAGT	.	PASS	Atlas-SNP
LBP	3929	hgsc.bcm.edu	37	20	36979265	36979265	+	Silent	SNP	T	T	C	rs2232582	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	51	28	43	0	0.54902	0	T|0.792;C|0.208	0.208	strong	.	LBP	60	.	NM_004139	exon3	c.T291C	p.P97P	TGTCCCTGGCCAG	.	PASS	Atlas-SNP
DGKH	160851	hgsc.bcm.edu	37	13	42729463	42729463	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	206	42	205	0	0.203883	0	.	.	none	.	DGKH	106	.	NM_001204504	exon5	c.G421A	p.E141K	TGTGCTGAGAACA	.	PASS	Atlas-SNP
COL6A5	256076	hgsc.bcm.edu	37	3	130104062	130104062	+	Silent	SNP	T	T	C	rs10212241	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	89	44	113	0	0.494382	0	T|0.605;C|0.395	0.395	strong	.	COL6A5	205	.	NM_153264	exon5	c.T1716C	p.T572T	AATCACTGTTCAT	.	PASS	Atlas-SNP
BBS1	582	hgsc.bcm.edu	37	11	66297363	66297363	+	Silent	SNP	C	C	T	rs3816492	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	48	37	62	0	0.770833	0	C|0.843;T|0.157	0.157	strong	.	BBS1	58	.	NM_024649	exon14	c.C1413T	p.L471L	GGCCCTCGAGTCC	.	PASS	Atlas-SNP
ZNF676	163223	hgsc.bcm.edu	37	19	22363448	22363448	+	Silent	SNP	A	A	T	rs200452805	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	18	3	25	2	0.166667	0.08	.	.	weak	ZNF676,rectum,carcinoma,0,2	ZNF676	146	2	NM_001001411	exon3	c.T1071A	p.I357I	ATGAATAATCTTA	.	scavenged	Atlas-SNP
ADAM21	8747	hgsc.bcm.edu	37	14	70924696	70924696	+	Silent	SNP	G	G	A	rs77892318	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	64	13	88	0	0.203125	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	.	scavenged	Atlas-SNP
CLDN15	24146	hgsc.bcm.edu	37	7	100875772	100875772	+	Silent	SNP	T	T	G	rs1047319	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	52	21	56	0	0.403846	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
PTPN13	5783	hgsc.bcm.edu	37	4	87685796	87685796	+	Missense_Mutation	SNP	T	T	G	rs10033029	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	53	131	0	0.524752	0	T|0.934;G|0.066	0.066	strong	.	PTPN13	203	.	NM_080683	exon25	c.T4068G	p.F1356L	AACTTTTTCTTCA	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	137	134	234	1	0.978102	0.0042735	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
FBXO40	51725	hgsc.bcm.edu	37	3	121341019	121341019	+	Missense_Mutation	SNP	A	A	T	rs142436040	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	47	28	61	0	0.595745	0	A|0.997;T|0.003	0.003	strong	.	FBXO40	108	.	NM_016298	exon3	c.A743T	p.K248I	CCGAGAAAGAACA	.	PASS	Atlas-SNP
C9orf66	157983	hgsc.bcm.edu	37	9	214804	214804	+	Missense_Mutation	SNP	A	A	G	rs76707254	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	40	13	24	0	0.325	0	A|0.831;G|0.169	0.169	strong	C9orf66,colon,carcinoma,0,1	C9orf66	16	1	NM_152569	exon1	c.T593C	p.V198A	GCTCGGACCCTCC	.	PASS	Atlas-SNP
TFEB	7942	hgsc.bcm.edu	37	6	41652514	41652514	+	Silent	SNP	C	C	T	rs2073158	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	126	55	144	0	0.436508	0	C|0.832;T|0.168	0.168	strong	TFEB,NS,carcinoma,-1,1	TFEB	37	1	NM_001167827	exon9	c.G1296A	p.A432A	CCCCGGCGCCAGG	.	PASS	Atlas-SNP
ABCA7	10347	hgsc.bcm.edu	37	19	1045173	1045173	+	Missense_Mutation	SNP	G	G	A	rs3752233	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	24	64	0	0.413793	0	A|0.041;C|0.000;G|0.959	0.041	strong	ABCA7,NS,carcinoma,0,1	ABCA7	174	1	NM_019112	exon12	c.G1388A	p.R463H	ACGTGCGCATCAA	.	PASS	Atlas-SNP
USHBP1	83878	hgsc.bcm.edu	37	19	17361064	17361064	+	Silent	SNP	C	C	T	rs10415471	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	80	41	91	0	0.5125	0	C|0.828;T|0.172	0.172	strong	.	USHBP1	85	.	NM_031941	exon13	c.G2082A	p.P694P	GGGAGGCGGGAGG	.	PASS	Atlas-SNP
MRGPRX2	117194	hgsc.bcm.edu	37	11	19077765	19077765	+	Missense_Mutation	SNP	T	T	C	rs10833049	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	68	15	63	0	0.220588	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
MUC4	4585	hgsc.bcm.edu	37	3	195506597	195506597	+	Missense_Mutation	SNP	G	G	A	rs200685331		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	39	22	128	1	0.564103	0.0078125	.	.	weak	MUC4_ENST00000463781,NS,carcinoma,0,9	MUC4	1505	9	NM_018406	exon2	c.C11854T	p.P3952S	GAAGAGGGGTGGT	.	scavenged	Atlas-SNP
VILL	50853	hgsc.bcm.edu	37	3	38043904	38043904	+	Silent	SNP	T	T	C	rs9843296	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	50	27	47	0	0.54	0	T|0.803;C|0.197	0.197	strong	VILL,NS,carcinoma,0,1	VILL	61	1	NM_015873	exon13	c.T1497C	p.H499H	GCACCATGGAAAG	.	PASS	Atlas-SNP
WDR46	9277	hgsc.bcm.edu	37	6	33254665	33254665	+	Missense_Mutation	SNP	A	A	G	rs14398	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	90	41	81	0	0.455556	0	A|0.903;G|0.097	0.097	strong	.	WDR46	43	.	NM_005452	exon10	c.T1022C	p.V341A	AAAGACACAGTAC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195510149	195510149	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	79	11	42	2	0.139241	0.047619	.	.	none	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.C8302T	p.P2768S	GAAGAGGGGTGGC	.	scavenged	Atlas-SNP
GABBR2	9568	hgsc.bcm.edu	37	9	101340316	101340316	+	Silent	SNP	T	T	C	rs3750344	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	105	52	92	0	0.495238	0	T|0.809;C|0.191	0.191	strong	.	GABBR2	126	.	NM_005458	exon2	c.A360G	p.A120A	TTTTATTGCATCG	.	PASS	Atlas-SNP
ESPL1	9700	hgsc.bcm.edu	37	12	53682986	53682986	+	Silent	SNP	C	C	T	rs3214023	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	120	56	105	0	0.466667	0	C|0.499;T|0.501	0.501	strong	.	ESPL1	158	.	NM_012291	exon21	c.C4821T	p.C1607C	CTTGTGCCTGGGC	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29911319	29911319	+	Silent	SNP	G	G	T	rs41554520	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	125	51	126	0	0.408	0	G|0.885;T|0.115	0.115	strong	.	HLA-A	89	.	NM_001242758	exon3	c.G618T	p.T206T	GCGCACGGGTACC	.	PASS	Atlas-SNP
TAS2R42	353164	hgsc.bcm.edu	37	12	11338750	11338750	+	Missense_Mutation	SNP	T	T	C	rs1451772	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	34	82	0	0.435897	0	C|0.238;N|0.001	0.238	strong	.	TAS2R42	30	.	NM_181429	exon1	c.A794G	p.Y265C	TTTATGTACTTGT	.	PASS	Atlas-SNP
ARMS2	387715	hgsc.bcm.edu	37	10	124214448	124214448	+	Missense_Mutation	SNP	G	G	T	rs10490924	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	214	106	197	0	0.495327	0	G|0.712;T|0.288	0.288	strong	.	ARMS2	7	.	NM_001099667	exon1	c.G205T	p.A69S	CCAGCTGCTAAAA	.	PASS	Atlas-SNP
KIAA1549	57670	hgsc.bcm.edu	37	7	138596064	138596064	+	Silent	SNP	G	G	A	rs6969074	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	50	27	85	0	0.54	0	G|0.513;A|0.486	0.486	strong	.	KIAA1549	314	.	NM_020910	exon4	c.C2973T	p.Y991Y	TAGTTCGTAAACC	.	PASS	Atlas-SNP
CTSH	1512	hgsc.bcm.edu	37	15	79237247	79237247	+	Missense_Mutation	SNP	C	C	G	rs1036938	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	159	159	141	0	1	0	C|0.624;G|0.376	0.376	strong	.	CTSH	23	.	NM_004390	exon1	c.G77C	p.C26S	TTCACGCACAGTT	.	PASS	Atlas-SNP
ZNF804A	91752	hgsc.bcm.edu	37	2	185800768	185800768	+	Silent	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	20	106	0	0.28169	0	.	.	none	ZNF804A,colon,carcinoma,0,1	ZNF804A	322	1	NM_194250	exon4	c.T645C	p.S215S	CTTTTCTTTTGCA	.	PASS	Atlas-SNP
COQ5	84274	hgsc.bcm.edu	37	12	120966921	120966921	+	Silent	SNP	A	A	G	rs3742052	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	79	37	82	0	0.468354	0	A|0.748;G|0.252	0.252	strong	.	COQ5	26	.	NM_032314	exon1	c.T24C	p.A8A	CCATAGAGCACAG	.	PASS	Atlas-SNP
ATP8A2	51761	hgsc.bcm.edu	37	13	26043182	26043182	+	Silent	SNP	A	A	C	rs7317185	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	115	51	85	0	0.443478	0	A|0.790;C|0.210	0.210	strong	ATP8A2,colon,carcinoma,0,1	ATP8A2	181	1	NM_016529	exon2	c.A144C	p.G48G	TGTTGGAGACCAG	.	PASS	Atlas-SNP
OR10G3	26533	hgsc.bcm.edu	37	14	22038450	22038450	+	Silent	SNP	G	G	A	rs11626669	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	32	107	0	0.450704	0	G|0.547;A|0.453	0.453	strong	.	OR10G3	40	.	NM_001005465	exon1	c.C426T	p.S142S	CAAGGCGCTCAGC	.	PASS	Atlas-SNP
ALPPL2	251	hgsc.bcm.edu	37	2	233271669	233271669	+	Missense_Mutation	SNP	C	C	T	rs41415150		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	166	19	154	0	0.114458	0	C|1.000;|0.000	.	weak	.	ALPPL2	36	.	NM_031313	exon1	c.C65T	p.P22L	TCATCCCAGGTAA	.	PASS	Atlas-SNP
RNF144A	9781	hgsc.bcm.edu	37	2	7164578	7164578	+	Silent	SNP	A	A	G	rs376219	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	94	94	93	0	1	0	A|0.727;G|0.273	0.273	strong	.	RNF144A	38	.	NM_014746	exon7	c.A588G	p.E196E	AGACGAAGGCTGC	.	PASS	Atlas-SNP
BTN3A2	11118	hgsc.bcm.edu	37	6	26373150	26373150	+	Silent	SNP	C	C	T	rs12174631	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	74	73	79	0	0.986486	0	C|0.924;T|0.076	0.076	strong	.	BTN3A2	44	.	NM_001197246	exon4	c.C741T	p.P247P	CCAGCCCTGGATC	.	PASS	Atlas-SNP
CEACAM20	125931	hgsc.bcm.edu	37	19	45021252	45021252	+	Missense_Mutation	SNP	G	G	A	rs16959164	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	21	21	26	0	1	0	G|0.956;A|0.044	0.044	strong	.	CEACAM20	31	.	NM_001102600	exon6	c.C1064T	p.S355L	GATGCCGACTCCC	.	PASS	Atlas-SNP
ZNF415	55786	hgsc.bcm.edu	37	19	53612055	53612055	+	Missense_Mutation	SNP	T	T	C	rs10410030	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	43	19	30	0	0.44186	0	T|0.842;C|0.158	0.158	strong	.	ZNF415	68	.	NM_018355	exon4	c.A1243G	p.N415D	ATTCATTGCATTT	.	PASS	Atlas-SNP
AARS	16	hgsc.bcm.edu	37	16	70303580	70303580	+	Silent	SNP	G	G	A	rs2070203	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	77	45	57	0	0.584416	0	G|0.526;A|0.474	0.474	strong	.	AARS	62	.	NM_001605	exon7	c.C903T	p.H301H	CCGAGCGTGGTCA	.	PASS	Atlas-SNP
GAREM	64762	hgsc.bcm.edu	37	18	29972964	29972964	+	Silent	SNP	A	A	G	rs3786308	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	136	65	136	0	0.477941	0	A|0.855;G|0.145	0.145	strong	.	.	.	.	NM_022751	exon2	c.T156C	p.Y52Y	CAGCAGATAGTCA	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	29	69	0	0.371795	0	T|0.271;A|0.729	0.729	strong	.	KRTAP19-6	16	.	NM_181612	exon1	c.A153T	p.G51G	TCCATATCCTTCA	.	PASS	Atlas-SNP
TPRX1	284355	hgsc.bcm.edu	37	19	48305586	48305586	+	Missense_Mutation	SNP	G	G	A	rs145255760	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	24	5	19	0	0.208333	0	G|0.957;A|0.043	0.043	strong	.	TPRX1	46	.	NM_198479	exon2	c.C682T	p.P228S	GGCCTGGGATTGG	.	PASS	Atlas-SNP
SRSF4	6429	hgsc.bcm.edu	37	1	29475394	29475394	+	Missense_Mutation	SNP	C	C	G	rs2230677	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	66	66	86	0	1	0	C|0.377;G|0.623	0.623	strong	.	SRSF4	44	.	NM_005626	exon6	c.G1013C	p.G338A	CTGCCCCCTTTGC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195495916	195495916	+	Missense_Mutation	SNP	G	G	C	rs2550240	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	57	24	69	0	0.421053	0	G|0.607;C|0.393	0.393	strong	.	MUC4	1505	.	NM_018406	exon7	c.C13506G	p.N4502K	CACCGGGTTGCCT	.	PASS	Atlas-SNP
CPT1B	1375	hgsc.bcm.edu	37	22	51015838	51015838	+	Missense_Mutation	SNP	T	T	C	rs3213445	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	123	56	124	0	0.455285	0	T|0.882;C|0.118	0.118	strong	.	CPT1B	61	.	NM_001145135	exon3	c.A196G	p.I66V	CCATGATGACGAC	.	PASS	Atlas-SNP
FAHD1	81889	hgsc.bcm.edu	37	16	1877494	1877494	+	Silent	SNP	T	T	C	rs3743854	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	91	70	82	0	0.769231	0	T|0.840;C|0.160	0.160	strong	.	FAHD1	18	.	NM_031208	exon1	c.T264C	p.A88A	CGAGGCTGCGGCC	.	PASS	Atlas-SNP
CRTAP	10491	hgsc.bcm.edu	37	3	33161898	33161898	+	Silent	SNP	C	C	T	rs4076086	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	104	53	122	0	0.509615	0	C|0.764;T|0.236	0.236	strong	.	CRTAP	16	.	NM_006371	exon2	c.C534T	p.D178D	TGATGACGAAATG	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29912368	29912368	+	Silent	SNP	C	C	T	rs1141891	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	155	52	208	0	0.335484	0	C|0.359;T|0.641	0.641	strong	.	HLA-A	89	.	NM_001242758	exon5	c.C987T	p.A329A	CGCTGCCGTGATG	.	PASS	Atlas-SNP
ITPR3	3710	hgsc.bcm.edu	37	6	33658780	33658780	+	Silent	SNP	C	C	T	rs35506178	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	162	81	172	0	0.5	0	C|0.966;T|0.034	0.034	strong	.	ITPR3	409	.	NM_002224	exon52	c.C7119T	p.A2373A	GACAGCCCTGCTG	.	PASS	Atlas-SNP
ADAMTSL1	92949	hgsc.bcm.edu	37	9	18829952	18829952	+	Missense_Mutation	SNP	A	A	G	rs41304755	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	98	39	81	0	0.397959	0	A|0.852;G|0.148	0.148	strong	.	ADAMTSL1	306	.	NM_001040272	exon23	c.A4226G	p.D1409G	TCCTGGATCCTGG	.	PASS	Atlas-SNP
MYO7A	4647	hgsc.bcm.edu	37	11	76917220	76917220	+	Silent	SNP	A	A	G	rs2276293	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	91	70	90	0	0.769231	0	A|0.427;G|0.573	0.573	strong	.	MYO7A	164	.	NM_000260	exon41	c.A5715G	p.K1905K	CCACAAAGTCTAC	.	PASS	Atlas-SNP
OR10H5	284433	hgsc.bcm.edu	37	19	15905661	15905661	+	Missense_Mutation	SNP	C	C	A	rs67455341	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	150	88	151	0	0.586667	0	C|0.733;A|0.267	0.267	strong	.	OR10H5	49	.	NM_001004466	exon1	c.C803A	p.S268Y	CCCAGTCTCCGGA	.	PASS	Atlas-SNP
ZNF831	128611	hgsc.bcm.edu	37	20	57768743	57768743	+	Missense_Mutation	SNP	C	C	T	rs56057707	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	91	42	76	0	0.461538	0	C|0.821;T|0.179	0.179	strong	.	ZNF831	287	.	NM_178457	exon1	c.C2669T	p.A890V	CTGCTGCTTCTGT	.	PASS	Atlas-SNP
ZC3HAV1	56829	hgsc.bcm.edu	37	7	138732497	138732497	+	Missense_Mutation	SNP	G	G	A	rs3735007	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	88	88	103	0	1	0	G|0.444;N|0.000	.	strong	ZC3HAV1,colon,carcinoma,+1,1	ZC3HAV1	75	1	NM_020119	exon13	c.C2552T	p.T851I	CCTTCAGTAAACT	.	PASS	Atlas-SNP
POLR2B	5431	hgsc.bcm.edu	37	4	57889677	57889677	+	Silent	SNP	C	C	T	rs1056364	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	98	97	127	1	0.989796	0.00787402	C|0.436;T|0.564	0.564	strong	POLR2B,NS,carcinoma,0,1	POLR2B	108	1	NM_000938	exon19	c.C2697T	p.S899S	AACTAGCGAGACG	.	PASS	Atlas-SNP
ABCC5	10057	hgsc.bcm.edu	37	3	183685534	183685534	+	Silent	SNP	A	A	G	rs939336	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	38	88	0	0.413043	0	A|0.320;G|0.680	0.680	strong	.	ABCC5	142	.	NM_005688	exon12	c.T1782C	p.C594C	ACTGCCACAGATT	.	PASS	Atlas-SNP
HIST1H1E	3008	hgsc.bcm.edu	37	6	26157219	26157219	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	10	98	0	0.140845	0	.	.	none	.	HIST1H1E	69	.	NM_005321	exon1	c.C601T	p.P201S	GCTAAACCAAAGA	.	PASS	Atlas-SNP
SLC25A13	10165	hgsc.bcm.edu	37	7	95800820	95800820	+	Silent	SNP	T	T	C	rs2301629	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	136	74	176	0	0.544118	0	T|0.645;C|0.355	0.355	strong	SLC25A13,caecum,carcinoma,0,1	SLC25A13	131	1	NM_001160210	exon12	c.A1197G	p.L399L	TCCCAATAACTGT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195509784	195509784	+	Silent	SNP	C	C	T	rs61099195	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	93	53	65	1	0.569892	0.0153846	C|0.250;T|0.750	0.750	weak	MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	NM_018406	exon2	c.G8667A	p.V2889V	TGTGGACACTGAG	.	scavenged	Atlas-SNP
CSN3	1448	hgsc.bcm.edu	37	4	71115053	71115053	+	Silent	SNP	T	T	A	rs3775740	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	35	99	0	0.466667	0	T|0.896;A|0.104	0.104	strong	.	CSN3	43	.	NM_005212	exon4	c.T426A	p.P142P	TGAACCTACACCA	.	PASS	Atlas-SNP
PLCB2	5330	hgsc.bcm.edu	37	15	40589002	40589002	+	Silent	SNP	A	A	G	rs2229691	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	46	20	78	0	0.434783	0	A|0.697;G|0.303	0.303	strong	.	PLCB2	177	.	NM_004573	exon14	c.T1431C	p.T477T	CCCACCAGTATCC	.	PASS	Atlas-SNP
LETMD1	25875	hgsc.bcm.edu	37	12	51449729	51449729	+	Silent	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	2	132	0	0.025641	0	.	.	none	LETMD1,brain,glioma,+2,1	LETMD1	33	1	NM_001243689	exon5	c.T624C	p.I208I	AATTATTAGTTAT	.	scavenged	Atlas-SNP
AIM1	202	hgsc.bcm.edu	37	6	106999822	106999822	+	Missense_Mutation	SNP	G	G	A	rs2297970	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	141	59	171	0	0.41844	0	G|0.768;A|0.232	0.232	strong	AIM1,NS,carcinoma,0,1	AIM1	161	1	NM_001624	exon12	c.G4184A	p.C1395Y	AAAATTGTAAGAT	.	PASS	Atlas-SNP
RRP7A	27341	hgsc.bcm.edu	37	22	42912097	42912097	+	Missense_Mutation	SNP	C	C	T	rs11553441	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	68	32	78	0	0.470588	0	C|0.893;T|0.107	0.107	strong	.	RRP7A	25	.	NM_015703	exon3	c.G262A	p.V88I	ACTCTACAGACTG	.	PASS	Atlas-SNP
KIAA1967	57805	hgsc.bcm.edu	37	8	22471824	22471824	+	Silent	SNP	G	G	A	rs3736147	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	151	115	163	0	0.761589	0	G|0.741;A|0.259	0.259	strong	.	KIAA1967	72	.	NM_021174	exon9	c.G924A	p.S308S	TAGTTCGAAGGTA	.	PASS	Atlas-SNP
ADAMTSL3	57188	hgsc.bcm.edu	37	15	84706461	84706461	+	Missense_Mutation	SNP	C	C	T	rs950169	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	81	81	86	0	1	0	T|0.150;G|0.006	0.150	strong	.	ADAMTSL3	290	.	NM_207517	exon30	c.C4979T	p.T1660I	ACTGCACAGACAC	.	PASS	Atlas-SNP
GYG1	2992	hgsc.bcm.edu	37	3	148727133	148727133	+	Silent	SNP	G	G	A	rs4938	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	65	23	89	0	0.353846	0	G|0.703;A|0.297	0.297	strong	.	GYG1	29	.	NM_004130	exon5	c.G552A	p.P184P	CCTGCCGTTTATT	.	PASS	Atlas-SNP
KCNT1	57582	hgsc.bcm.edu	37	9	138669261	138669261	+	Silent	SNP	G	G	A	rs914428	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	153	79	190	0	0.51634	0	G|0.379;A|0.621	0.621	strong	.	KCNT1	139	.	NM_020822	exon21	c.G2427A	p.T809T	AGAGACGGCCGGC	.	PASS	Atlas-SNP
HEG1	57493	hgsc.bcm.edu	37	3	124732618	124732618	+	Missense_Mutation	SNP	A	A	G	rs6790837	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	148	64	190	0	0.432432	0	A|0.568;G|0.432	0.432	strong	.	HEG1	109	.	NM_020733	exon6	c.T1805C	p.F602S	GCATGAAAAAAGG	.	PASS	Atlas-SNP
TYW1	55253	hgsc.bcm.edu	37	7	66648157	66648157	+	Silent	SNP	C	C	T	rs4145350	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	81	33	113	0	0.407407	0	C|0.778;T|0.222	0.222	strong	.	TYW1	71	.	NM_018264	exon14	c.C1743T	p.N581N	ATGGAACGTGGAC	.	PASS	Atlas-SNP
IGLL5	100423062	hgsc.bcm.edu	37	22	23230407	23230407	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	110	22	122	0	0.2	0	.	.	none	.	IGLL5	26	.	NM_001178126	exon1	c.C174G	p.S58R	TGGAAGCAGCCGA	.	PASS	Atlas-SNP
ANXA13	312	hgsc.bcm.edu	37	8	124710664	124710664	+	Missense_Mutation	SNP	C	C	T	rs6995099	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	117	102	124	0	0.871795	0	C|0.936;T|0.064	0.064	strong	.	ANXA13	38	.	NM_001003954	exon5	c.G445A	p.V149I	TGAGGACGGACTC	.	PASS	Atlas-SNP
ESRRB	2103	hgsc.bcm.edu	37	14	76964655	76964655	+	Missense_Mutation	SNP	C	C	T	rs61742642	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	54	142	0	0.534653	0	C|0.945;T|0.055	0.055	strong	ESRRB_ENST00000380887,NS,carcinoma,0,3	ESRRB	114	3	NM_004452	exon9	c.C1156T	p.P386S	GAGGAGCCCTGGA	.	PASS	Atlas-SNP
C5	727	hgsc.bcm.edu	37	9	123776220	123776220	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	131	42	153	0	0.320611	0	.	.	none	.	C5	124	.	NM_001735	exon17	c.G2188A	p.E730K	AACATTCAGTGAA	.	PASS	Atlas-SNP
TMEM209	84928	hgsc.bcm.edu	37	7	129813738	129813738	+	Silent	SNP	T	T	C	rs3823482	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	44	108	0	0.505747	0	T|0.703;C|0.297	0.297	strong	.	TMEM209	31	.	NM_032842	exon12	c.A1386G	p.L462L	TGGAGGTAATCTG	.	PASS	Atlas-SNP
GIMAP1-GIMAP5	0	hgsc.bcm.edu	37	7	150440043	150440043	+	Silent	SNP	C	C	T	rs1046355	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	121	121	114	0	1	0	C|0.620;T|0.380	0.380	strong	.	.	.	.	NM_001199577	exon6	c.C1428T	p.L476L	GGCGCTCCTCAGA	.	PASS	Atlas-SNP
NRG3	10718	hgsc.bcm.edu	37	10	84745256	84745256	+	Silent	SNP	C	C	T	rs2295933	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	38	38	61	0	1	0	C|0.606;T|0.394	0.394	strong	.	NRG3	301	.	NM_001010848	exon9	c.C1986T	p.S662S	TGCAAGCGAAAAC	.	PASS	Atlas-SNP
ST14	6768	hgsc.bcm.edu	37	11	130068491	130068491	+	Silent	SNP	G	G	C	rs11827924	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	171	26	174	1	0.152047	0.00574713	G|0.868;C|0.132	0.132	strong	ST14,NS,malignant_melanoma,+1,1	ST14	82	1	NM_021978	exon14	c.G1659C	p.G553G	GGACGGGTCCGAC	.	scavenged	Atlas-SNP
DSC1	1823	hgsc.bcm.edu	37	18	28722039	28722039	+	Silent	SNP	G	G	A	rs2577075	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	225	107	248	0	0.475556	0	G|0.696;A|0.304	0.304	strong	.	DSC1	240	.	NM_004948	exon9	c.C1183T	p.L395L	CTTGTAGGATTTT	.	PASS	Atlas-SNP
IGLL5	100423062	hgsc.bcm.edu	37	22	23230317	23230317	+	Silent	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	158	33	153	0	0.208861	0	.	.	none	.	IGLL5	26	.	NM_001178126	exon1	c.G84A	p.L28L	GCTGCTGCTGGGT	.	PASS	Atlas-SNP
OR1F1	4992	hgsc.bcm.edu	37	16	3254470	3254470	+	Missense_Mutation	SNP	T	T	C	rs1834026	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	246	193	318	1	0.784553	0.00314465	T|0.581;G|0.003	.	strong	.	OR1F1	36	.	NM_012360	exon1	c.T224C	p.F75S	TCTCCTTCACCAC	.	PASS	Atlas-SNP
SLC2A11	66035	hgsc.bcm.edu	37	22	24224659	24224659	+	Silent	SNP	C	C	A	rs9612499	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	20	18	14	0	0.9	0	C|0.674;A|0.326	0.326	strong	.	SLC2A11	32	.	NM_030807	exon8	c.C720A	p.L240L	GCGGCTCCGGGGC	.	PASS	Atlas-SNP
JARID2	3720	hgsc.bcm.edu	37	6	15512616	15512616	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	44	13	59	0	0.295455	0	.	.	none	.	JARID2	135	.	NM_004973	exon14	c.G3130A	p.A1044T	GAGACCGCCAAGG	.	PASS	Atlas-SNP
C3	718	hgsc.bcm.edu	37	19	6702157	6702157	+	Silent	SNP	C	C	G	rs428453	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	33	33	61	0	1	0	C|0.332;G|0.668	0.668	strong	.	C3	192	.	NM_000064	exon19	c.G2421C	p.V807V	CATGCTCACAGCC	.	PASS	Atlas-SNP
RYR3	6263	hgsc.bcm.edu	37	15	34151901	34151901	+	Silent	SNP	C	C	T	rs79305633	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	149	79	186	0	0.530201	0	C|0.975;T|0.025	0.025	strong	.	RYR3	760	.	NM_001036	exon100	c.C14268T	p.F4756F	CTTCTTCGTCATT	.	PASS	Atlas-SNP
CCDC170	80129	hgsc.bcm.edu	37	6	151914265	151914265	+	Silent	SNP	T	T	C	rs17081470	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	50	152	0	0.714286	0	T|0.914;C|0.086	0.086	strong	.	.	.	.	NM_025059	exon8	c.T1317C	p.L439L	TCAGCTTTCTCAG	.	PASS	Atlas-SNP
MAN2A2	4122	hgsc.bcm.edu	37	15	91452595	91452595	+	Missense_Mutation	SNP	A	A	G	rs2106673	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	117	116	111	0	0.991453	0	A|0.596;G|0.404	0.404	strong	.	MAN2A2	99	.	NM_006122	exon8	c.A1235G	p.Q412R	AGTCCCAGCTGTT	.	PASS	Atlas-SNP
PAK2	5062	hgsc.bcm.edu	37	3	196529982	196529982	+	Missense_Mutation	SNP	A	A	G	rs78043821	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	110	8	109	1	0.0727273	0.00917431	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
CDC14A	8556	hgsc.bcm.edu	37	1	100949860	100949860	+	Silent	SNP	G	G	A	rs2270694	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	29	29	70	0	1	0	G|0.905;A|0.095	0.095	strong	.	CDC14A	65	.	NM_033313	exon11	c.G990A	p.S330S	AGCATCGTTGTGG	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	136	68	165	0	0.5	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
INTS3	65123	hgsc.bcm.edu	37	1	153701188	153701188	+	Silent	SNP	G	G	A	rs150819290	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	137	70	151	0	0.510949	0	G|0.994;A|0.006	0.006	strong	.	INTS3	83	.	NM_023015	exon1	c.G78A	p.A26A	AGGAGCGGGAGCA	.	PASS	Atlas-SNP
IRF7	3665	hgsc.bcm.edu	37	11	614318	614318	+	Missense_Mutation	SNP	T	T	C	rs1061502	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	55	62	0	0.785714	0	T|0.664;C|0.336	0.336	strong	.	IRF7	23	.	NM_004031	exon4	c.A574G	p.K192E	CCCCCTTGTCACC	.	PASS	Atlas-SNP
TRAK1	22906	hgsc.bcm.edu	37	3	42251329	42251329	+	Silent	SNP	C	C	T	rs2290133	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	29	71	0	0.39726	0	C|0.681;T|0.319	0.319	strong	.	TRAK1	188	.	NM_001265608	exon14	c.C1815T	p.P605P	CCGGCCCGGTGTG	.	PASS	Atlas-SNP
PTOV1	53635	hgsc.bcm.edu	37	19	50361353	50361353	+	Silent	SNP	C	C	T	rs2290286	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	54	20	75	0	0.37037	0	C|0.981;T|0.019	0.019	strong	.	PTOV1	41	.	NM_017432	exon9	c.C918T	p.L306L	GCAGCTCATCCCG	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29910693	29910693	+	Missense_Mutation	SNP	A	A	G	rs41559716	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	207	18	223	1	0.0869565	0.00448431	A|0.979;G|0.021	0.021	strong	HLA-A,bladder,carcinoma,0,8	HLA-A	89	8	NM_001242758	exon2	c.A233G	p.Q78R	TAGAGCAGGAGGG	.	scavenged	Atlas-SNP
LPL	4023	hgsc.bcm.edu	37	8	19810826	19810826	+	Silent	SNP	G	G	A	rs248	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	15	87	0	0.217391	0	G|0.944;A|0.056	0.056	strong	.	LPL	78	.	NM_000237	exon4	c.G435A	p.E145E	GGAGGAGTTTAAC	.	PASS	Atlas-SNP
TAX1BP1	8887	hgsc.bcm.edu	37	7	27827103	27827103	+	Missense_Mutation	SNP	T	T	A	rs11540483	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	127	28	162	0	0.220472	0	A|0.078;T|0.922	0.078	strong	TAX1BP1,NS,carcinoma,-1,1	TAX1BP1	71	1	NM_006024	exon8	c.T919A	p.L307I	AAAAATTTAGATG	.	PASS	Atlas-SNP
ITGB8	3696	hgsc.bcm.edu	37	7	20421490	20421490	+	Silent	SNP	T	T	C	rs2230398	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	52	9	48	0	0.173077	0	A|0.000;C|0.395;G|0.000;T|0.605	0.395	strong	ITGB8_ENST00000222573,NS,carcinoma,0,1	ITGB8	159	1	NM_002214	exon6	c.T942C	p.Y314Y	CGTCTATGTCAAA	.	PASS	Atlas-SNP
ADAT1	23536	hgsc.bcm.edu	37	16	75646576	75646576	+	Missense_Mutation	SNP	G	G	T	rs3743599	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	139	53	151	0	0.381295	0	G|0.860;T|0.140	0.140	strong	.	ADAT1	45	.	NM_012091	exon7	c.C608A	p.T203N	GCTGCAGTCCCAG	.	PASS	Atlas-SNP
DHX9	1660	hgsc.bcm.edu	37	1	182850520	182850520	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	117	62	134	0	0.529915	0	.	.	none	.	DHX9	114	.	NM_001357	exon23	c.G2746A	p.V916I	GATCACGTAGCCC	.	PASS	Atlas-SNP
PBX1	5087	hgsc.bcm.edu	37	1	164529120	164529120	+	Missense_Mutation	SNP	G	G	A	rs2275558	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	140	137	194	0	0.978571	0	G|0.695;A|0.305	0.305	strong	PBX1_ENST00000420696,colon,carcinoma,0,1	PBX1	60	1	NM_001204963	exon1	c.G61A	p.G21S	CACCCCGGCCTGT	.	PASS	Atlas-SNP
OR2T4	127074	hgsc.bcm.edu	37	1	248525640	248525640	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	296	12	357	9	0.0405405	0.0252101	.	.	none	OR2T4,brain,glioma,+1,1	OR2T4	126	1	NM_001004696	exon1	c.T758C	p.I253T	TACTCATCCTCCT	.	scavenged	Atlas-SNP
VILL	50853	hgsc.bcm.edu	37	3	38047954	38047954	+	Missense_Mutation	SNP	G	G	C	rs9816693	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	108	107	192	0	0.990741	0	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	.	PASS	Atlas-SNP
TMEM119	338773	hgsc.bcm.edu	37	12	108986031	108986031	+	Silent	SNP	C	C	T	rs74504010	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	24	11	9	0	0.458333	0	C|0.827;T|0.173	0.173	strong	TMEM119,NS,carcinoma,0,1	TMEM119	31	1	NM_181724	exon2	c.G129A	p.E43E	CTCGGCCTCCCCA	.	scavenged	Atlas-SNP
CCDC168	643677	hgsc.bcm.edu	37	13	103390386	103390386	+	Missense_Mutation	SNP	C	C	A	rs74471135	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	296	138	344	1	0.466216	0.00290698	C|0.931;A|0.069	0.069	strong	.	.	.	.	NM_001146197	exon4	c.G12661T	p.A4221S	GTCCTGCACCTCT	.	PASS	Atlas-SNP
CSMD1	64478	hgsc.bcm.edu	37	8	3200877	3200877	+	Silent	SNP	C	C	T	rs2161752	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	208	59	244	0	0.283654	0	C|0.853;T|0.147	0.147	strong	CSMD1_ENST00000537824,colon,carcinoma,0,4	CSMD1	1469	4	NM_033225	exon23	c.G3570A	p.L1190L	TAGCCACAGGTGA	.	PASS	Atlas-SNP
HSPG2	3339	hgsc.bcm.edu	37	1	22150118	22150118	+	Missense_Mutation	SNP	C	C	T	rs1138469	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	93	42	99	0	0.451613	0	C|0.949;T|0.051	0.051	strong	.	HSPG2	311	.	NM_005529	exon96	c.G12994A	p.V4332I	TGTAGACGCTGCC	.	PASS	Atlas-SNP
CLCA2	9635	hgsc.bcm.edu	37	1	86909582	86909582	+	Missense_Mutation	SNP	G	G	A	rs1413426	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	81	41	86	0	0.506173	0	G|0.904;A|0.096	0.096	strong	.	CLCA2	102	.	NM_006536	exon10	c.G1601A	p.G534D	CCAGTGGTCCTCC	.	PASS	Atlas-SNP
TRIM39	56658	hgsc.bcm.edu	37	6	30309508	30309508	+	Silent	SNP	T	T	C	rs2074474	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	50	29	57	0	0.58	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
PDE4DIP	9659	hgsc.bcm.edu	37	1	144856852	144856852	+	Silent	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	128	24	152	0	0.1875	0	.	.	none	PDE4DIP_ENST00000369356,NS,carcinoma,-1,3	PDE4DIP	817	3	NM_014644	exon40	c.G6633A	p.A2211A	GCTGCACGCTGAT	.	PASS	Atlas-SNP
SLC8A1	6546	hgsc.bcm.edu	37	2	40656756	40656756	+	Nonsense_Mutation	SNP	A	A	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	100	15	54	0	0.15	0	.	.	none	.	SLC8A1	221	.	NM_001252624	exon1	c.T665A	p.L222X	ACAGACAAAATAA	.	PASS	Atlas-SNP
OR5D14	219436	hgsc.bcm.edu	37	11	55563738	55563738	+	Missense_Mutation	SNP	G	G	A	rs67863827	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	175	125	196	0	0.714286	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
SEBOX	645832	hgsc.bcm.edu	37	17	26691916	26691916	+	Silent	SNP	T	T	C	rs2277667	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	106	46	122	0	0.433962	0	T|0.855;C|0.145	0.145	strong	.	SEBOX	20	.	NM_001080837	exon2	c.A171G	p.L57L	CTCCAGTAGCTGC	.	PASS	Atlas-SNP
RILPL1	353116	hgsc.bcm.edu	37	12	124017850	124017850	+	Silent	SNP	G	G	C	rs28492040	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	47	46	39	0	0.978723	0	G|0.882;C|0.118	0.118	strong	RILPL1,NS,carcinoma,0,1	RILPL1	23	1	NM_178314	exon1	c.C180G	p.V60V	CTCCAGGACGCGC	.	PASS	Atlas-SNP
HIST1H1B	3009	hgsc.bcm.edu	37	6	27835218	27835218	+	Silent	SNP	G	G	A	rs17763089	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	109	51	142	0	0.46789	0	G|0.945;A|0.055	0.055	strong	.	HIST1H1B	54	.	NM_005322	exon1	c.C90T	p.G30G	GCCGGCGCCGGCA	.	PASS	Atlas-SNP
FBXL13	222235	hgsc.bcm.edu	37	7	102462636	102462636	+	Silent	SNP	T	T	C	rs10279449	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	55	28	91	0	0.509091	0	T|0.517;C|0.483	0.483	strong	.	FBXL13	65	.	NM_145032	exon19	c.A1869G	p.A623A	CTCCATTGCTGAG	.	PASS	Atlas-SNP
SLC19A1	6573	hgsc.bcm.edu	37	21	46957794	46957794	+	Missense_Mutation	SNP	T	T	C	rs1051266	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	28	28	28	0	1	0	T|0.518;C|0.482	0.482	strong	.	SLC19A1	53	.	NM_001205206	exon2	c.A80G	p.H27R	ACGAGGTGCCGCC	.	PASS	Atlas-SNP
PGLYRP2	114770	hgsc.bcm.edu	37	19	15587345	15587345	+	Missense_Mutation	SNP	T	T	C	rs3813135	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	63	25	77	1	0.396825	0.012987	T|0.639;C|0.361	0.361	strong	PGLYRP2_ENST00000292609,NS,carcinoma,0,2	PGLYRP2	116	2	NM_052890	exon2	c.A136G	p.T46A	GTCTGGTCTTGGC	.	scavenged	Atlas-SNP
TMEM204	79652	hgsc.bcm.edu	37	16	1591962	1591962	+	Silent	SNP	G	G	A	rs2076443	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	29	45	0	0.353659	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
RAPGEF1	2889	hgsc.bcm.edu	37	9	134503415	134503415	+	Silent	SNP	C	C	T	rs371503343		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	45	23	46	0	0.511111	0	.	.	weak	.	RAPGEF1	126	.	NM_198679	exon9	c.G1089A	p.S363S	GCGGGGCGACTCT	.	PASS	Atlas-SNP
SHROOM3	57619	hgsc.bcm.edu	37	4	77675925	77675925	+	Missense_Mutation	SNP	G	G	A	rs61741104	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	184	92	224	1	0.5	0.00446429	G|0.965;A|0.035	0.035	strong	.	SHROOM3	134	.	NM_020859	exon7	c.G4289A	p.R1430Q	CTTCTCGAGCAAA	.	PASS	Atlas-SNP
ZNF417	147687	hgsc.bcm.edu	37	19	58420167	58420167	+	Silent	SNP	T	T	C	rs17852300	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	219	101	235	0	0.461187	0	T|0.773;C|0.227	0.227	strong	ZNF417,NS,carcinoma,0,1	ZNF417	44	1	NM_152475	exon3	c.A1479G	p.E493E	ATTGCATTCATAC	.	PASS	Atlas-SNP
VPS18	57617	hgsc.bcm.edu	37	15	41191184	41191184	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	46	24	70	0	0.521739	0	.	.	none	.	VPS18	67	.	NM_020857	exon3	c.C313T	p.L105F	ATGTTCCTTGACC	.	PASS	Atlas-SNP
MACF1	23499	hgsc.bcm.edu	37	1	39816626	39816626	+	Missense_Mutation	SNP	C	C	A	rs116162513	bycluster;byfrequency;by1000genomes;alternate_allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	57	14	80	0	0.245614	0	C|0.999;T|0.001	.	alt	.	MACF1	909	.	NM_012090	exon39	c.C4949A	p.T1650K	AAGAGACACGTGT	.	PASS	Atlas-SNP
ZNF880	400713	hgsc.bcm.edu	37	19	52887427	52887427	+	Missense_Mutation	SNP	A	A	C	rs8104808	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	66	66	84	0	1	0	A|0.652;C|0.348	0.348	strong	.	ZNF880	45	.	NM_001145434	exon4	c.A594C	p.R198S	TTCAAGACTTGCT	.	PASS	Atlas-SNP
TEK	7010	hgsc.bcm.edu	37	9	27206669	27206669	+	Silent	SNP	G	G	C	rs55789591	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	65	30	98	0	0.461538	0	G|0.989;C|0.011	0.011	strong	.	TEK	250	.	NM_000459	exon15	c.G2454C	p.V818V	TCCAGTGCTTGAC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195512597	195512597	+	Missense_Mutation	SNP	G	G	A	rs6799339	bycluster;byfrequency;by2hit2allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	112	25	53	0	0.223214	0	G|0.975;A|0.025	0.025	strong	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.C5854T	p.P1952S	GAAGAGGGGTGGT	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29913037	29913037	+	Missense_Mutation	SNP	G	G	A	rs1137631	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	127	43	215	0	0.338583	0	G|0.829;A|0.171	0.171	strong	HLA-A,caecum,carcinoma,0,1	HLA-A	89	1	NM_001242758	exon7	c.G1072A	p.V358M	TCTGATGTGTCCC	.	PASS	Atlas-SNP
OR6S1	341799	hgsc.bcm.edu	37	14	21109726	21109726	+	Missense_Mutation	SNP	G	G	A	rs11622794	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	52	83	0	0.597701	0	G|0.491;A|0.508	0.508	strong	.	OR6S1	49	.	NM_001001968	exon1	c.C125T	p.T42I	TTGCCTGTCAGAT	.	PASS	Atlas-SNP
FOXK2	3607	hgsc.bcm.edu	37	17	80529614	80529614	+	Silent	SNP	G	G	T	rs117692271	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	65	35	86	0	0.538462	0	G|0.996;T|0.004	0.004	strong	.	FOXK2	46	.	NM_004514	exon4	c.G777T	p.P259P	AAAGCCGCCTTAC	.	PASS	Atlas-SNP
ALMS1	7840	hgsc.bcm.edu	37	2	73677833	73677833	+	Silent	SNP	A	A	G	rs6546836	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	84	84	105	0	1	0	A|0.737;G|0.263	0.263	strong	ALMS1,colon,carcinoma,0,1	ALMS1	384	1	NM_015120	exon8	c.A4176G	p.Q1392Q	CTACCAACAGTCG	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	82	96	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
C7	730	hgsc.bcm.edu	37	5	40934471	40934471	+	Silent	SNP	G	G	A	rs34196526	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	268	162	266	0	0.604478	0	G|0.992;A|0.008	0.008	strong	.	C7	136	.	NM_000587	exon4	c.G183A	p.Q61Q	AGGCCAGCCTTGT	.	PASS	Atlas-SNP
ACAN	176	hgsc.bcm.edu	37	15	89398330	89398330	+	Silent	SNP	G	G	A	rs3743399	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	156	155	105	1	0.99359	0.00952381	G|0.244;A|0.756	0.756	strong	.	ACAN	220	.	NM_001135	exon12	c.G2514A	p.S838S	AGCCTCGGAAGAG	.	PASS	Atlas-SNP
ZC3HAV1L	92092	hgsc.bcm.edu	37	7	138713476	138713476	+	Missense_Mutation	SNP	C	C	T	rs17856272	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	95	95	138	0	1	0	C|0.925;T|0.075	0.075	strong	.	ZC3HAV1L	15	.	NM_080660	exon3	c.G732A	p.M244I	CAGCTTCATATGC	.	PASS	Atlas-SNP
SMG8	55181	hgsc.bcm.edu	37	17	57290383	57290383	+	Silent	SNP	G	G	A	rs3744383	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	109	108	135	0	0.990826	0	G|0.551;A|0.449	0.449	strong	.	SMG8	79	.	NM_018149	exon3	c.G2199A	p.R733R	GAAGAGGCCAAAC	.	PASS	Atlas-SNP
FER	2241	hgsc.bcm.edu	37	5	108133967	108133967	+	Silent	SNP	A	A	G	rs2229085	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	190	94	252	0	0.494737	0	A|0.801;G|0.199	0.199	strong	.	FER	100	.	NM_005246	exon3	c.A84G	p.V28V	AACAGTAAAGAAA	.	PASS	Atlas-SNP
PPAN-P2RY11	692312	hgsc.bcm.edu	37	19	10224637	10224637	+	Silent	SNP	C	C	T	rs79800334	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	30	20	32	0	0.666667	0	C|0.997;T|0.003	0.003	strong	.	PPAN-P2RY11	81	.	NM_001040664	exon13	c.C1608T	p.S536S	GGGCAGCGTCATC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195515038	195515038	+	Missense_Mutation	SNP	G	G	A	rs201206859		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	39	3	47	0	0.0769231	0	.	.	weak	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.C3413T	p.P1138L	GTGACAGGAAGAG	.	scavenged	Atlas-SNP
PDE4A	5141	hgsc.bcm.edu	37	19	10572271	10572271	+	Missense_Mutation	SNP	A	A	G	rs141379029	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	105	52	154	0	0.495238	0	A|1.000;G|0.000	0.000	strong	.	PDE4A	236	.	NM_001111307	exon12	c.A1535G	p.K512R	GCTTCAAGCTGCT	.	PASS	Atlas-SNP
VDR	7421	hgsc.bcm.edu	37	12	48238757	48238757	+	Silent	SNP	A	A	G	rs731236	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	129	54	169	1	0.418605	0.00591716	A|0.692;G|0.308	0.308	strong	VDR,NS,carcinoma,0,1	VDR	47	1	NM_001017536	exon10	c.T1206C	p.I402I	GGCCTCAATCAGC	.	scavenged	Atlas-SNP
NOTCH1	4851	hgsc.bcm.edu	37	9	139391636	139391636	+	Silent	SNP	G	G	A	rs2229974	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	125	56	121	0	0.448	0	G|0.341;A|0.659	0.659	strong	.	NOTCH1	1980	.	NM_017617	exon34	c.C6555T	p.D2185D	CTTGCCGTCCTGG	.	PASS	Atlas-SNP
C3orf30	152405	hgsc.bcm.edu	37	3	118865609	118865609	+	Silent	SNP	C	C	T	rs10934483	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	84	44	102	0	0.52381	0	C|0.855;T|0.145	0.145	strong	C3orf30,rectum,carcinoma,0,1	C3orf30	64	1	NM_152539	exon1	c.C573T	p.S191S	AGCTTCCGAGCAG	.	PASS	Atlas-SNP
MCM10	55388	hgsc.bcm.edu	37	10	13230950	13230950	+	Silent	SNP	C	C	T	rs2296222	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	90	49	117	0	0.544444	0	C|0.837;T|0.163	0.163	strong	.	MCM10	76	.	NM_182751	exon10	c.C1288T	p.L430L	GCGGATCTGCAGT	.	PASS	Atlas-SNP
PKHD1	5314	hgsc.bcm.edu	37	6	51491884	51491884	+	Missense_Mutation	SNP	T	T	C	rs4715227	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	129	127	172	0	0.984496	0	T|0.467;C|0.533	0.533	strong	.	PKHD1	927	.	NM_138694	exon66	c.A11696G	p.Q3899R	TTAGTCTGGGATT	.	PASS	Atlas-SNP
ULBP3	79465	hgsc.bcm.edu	37	6	150386752	150386752	+	Missense_Mutation	SNP	C	C	T	rs34547018	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	19	105	0	0.275362	0	C|0.997;T|0.003	0.003	strong	.	ULBP3	22	.	NM_024518	exon3	c.G410A	p.R137H	GATCCACGGATGT	.	PASS	Atlas-SNP
NLRP8	126205	hgsc.bcm.edu	37	19	56487603	56487603	+	Missense_Mutation	SNP	A	A	G	rs306481	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	186	186	220	1	1	0.00454545	A|0.474;G|0.526	0.526	strong	.	NLRP8	225	.	NM_176811	exon8	c.A2810G	p.K937R	GCCTGAAGGATGA	.	PASS	Atlas-SNP
RAD51AP2	729475	hgsc.bcm.edu	37	2	17697635	17697635	+	Missense_Mutation	SNP	T	T	C	rs181531922	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	84	50	113	0	0.595238	0	T|0.994;C|0.006	0.006	strong	.	RAD51AP2	134	.	NM_001099218	exon1	c.A2048G	p.E683G	TATGTTTCAAAAA	.	PASS	Atlas-SNP
ZNF91	7644	hgsc.bcm.edu	37	19	23542626	23542626	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	25	12	34	0	0.48	0	.	.	none	.	ZNF91	349	.	NM_003430	exon4	c.G3155A	p.C1052Y	TCTTCACACTTGT	.	PASS	Atlas-SNP
PPP1R3A	5506	hgsc.bcm.edu	37	7	113518434	113518434	+	Missense_Mutation	SNP	C	C	A	rs1799999	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	52	33	70	0	0.634615	0	C|0.769;N|0.000	.	strong	.	PPP1R3A	317	.	NM_002711	exon4	c.G2713T	p.D905Y	TAGTGTCTGAGTT	.	PASS	Atlas-SNP
ATP10D	57205	hgsc.bcm.edu	37	4	47514685	47514685	+	Missense_Mutation	SNP	C	C	T	rs33995001	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	100	43	136	0	0.43	0	C|0.623;T|0.377	0.377	strong	.	ATP10D	168	.	NM_020453	exon2	c.C128T	p.T43I	CTCAGACCCCTAA	.	PASS	Atlas-SNP
LRRC8A	56262	hgsc.bcm.edu	37	9	131670457	131670457	+	Silent	SNP	T	T	C	rs3750320	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	45	120	0	0.48913	0	T|0.745;C|0.255	0.255	strong	.	LRRC8A	69	.	NM_001127244	exon3	c.T1014C	p.Y338Y	CATGTATACACTG	.	PASS	Atlas-SNP
C5orf60	285679	hgsc.bcm.edu	37	5	179071893	179071893	+	Silent	SNP	A	A	G	rs4990388	bycluster;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	235	11	327	0	0.0468085	0	A|0.993;G|0.007	0.007	strong	C5orf60,NS,carcinoma,0,2	C5orf60	24	2	NM_001142306	exon1	c.T129C	p.F43F	CACAACAAAGAGG	.	scavenged	Atlas-SNP
C6	729	hgsc.bcm.edu	37	5	41155088	41155088	+	Missense_Mutation	SNP	T	T	C	rs41271067	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	107	38	95	0	0.35514	0	T|0.992;C|0.008	0.008	strong	.	C6	197	.	NM_001115131	exon14	c.A2087G	p.D696G	TCCACATCCCCTT	.	PASS	Atlas-SNP
OR5L2	26338	hgsc.bcm.edu	37	11	55595018	55595018	+	Silent	SNP	A	A	G	rs61745634	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	37	140	0	0.521127	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
MUC20	200958	hgsc.bcm.edu	37	3	195453244	195453244	+	Silent	SNP	G	G	A	rs140946665	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	135	46	139	0	0.340741	0	G|0.965;A|0.035	0.035	strong	.	MUC20	84	.	NM_152673	exon3	c.G1257A	p.P419P	GACACCGACCATG	.	PASS	Atlas-SNP
MST1R	4486	hgsc.bcm.edu	37	3	49936102	49936102	+	Missense_Mutation	SNP	T	T	C	rs2230590	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	76	53	97	0	0.697368	0	T|0.495;C|0.505	0.505	strong	.	MST1R	205	.	NM_001244937	exon4	c.A1568G	p.Q523R	GGGCCTTGGATAG	.	PASS	Atlas-SNP
TCN2	6948	hgsc.bcm.edu	37	22	31006860	31006860	+	Missense_Mutation	SNP	A	A	G	rs9606756	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	50	85	0	0.574713	0	A|0.885;G|0.115	0.115	strong	.	TCN2	44	.	NM_001184726	exon2	c.A67G	p.I23V	TAAGAAATACCAG	.	PASS	Atlas-SNP
MRGPRX4	117196	hgsc.bcm.edu	37	11	18195348	18195348	+	Missense_Mutation	SNP	C	C	T	rs11024532	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	115	24	106	0	0.208696	0	C|0.817;T|0.183	0.183	strong	.	MRGPRX4	68	.	NM_054032	exon1	c.C545T	p.A182V	CAGTCGCGTGGCT	.	PASS	Atlas-SNP
RP1L1	94137	hgsc.bcm.edu	37	8	10469292	10469292	+	Silent	SNP	C	C	T	rs62490857	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	74	81	0	0.762887	0	C|0.945;T|0.055	0.055	strong	.	RP1L1	453	.	NM_178857	exon4	c.G2316A	p.S772S	GGCCGGCGAGCAT	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179440029	179440029	+	Silent	SNP	G	G	A	rs12464787	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	124	61	128	0	0.491935	0	G|0.832;A|0.168	0.168	strong	.	TTN	18412	.	NM_001267550	exon326	c.C70830T	p.S23610S	CCCCGCGCTGTTC	.	PASS	Atlas-SNP
AP4B1	10717	hgsc.bcm.edu	37	1	114444444	114444444	+	Silent	SNP	T	T	G	rs34751342	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	132	60	157	0	0.454545	0	T|0.971;G|0.029	0.029	strong	.	AP4B1	72	.	NM_006594	exon4	c.A402C	p.S134S	GACATATGAAGCC	.	PASS	Atlas-SNP
BPIFC	254240	hgsc.bcm.edu	37	22	32831711	32831711	+	Missense_Mutation	SNP	C	C	G	rs5994570	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	23	13	28	0	0.565217	0	C|0.857;G|0.143	0.143	strong	.	.	.	.	NM_174932	exon8	c.G904C	p.V302L	GAGTGACATTGAA	.	PASS	Atlas-SNP
NBPF14	25832	hgsc.bcm.edu	37	1	148009510	148009510	+	Silent	SNP	G	G	A	rs1127394		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	53	7	45	0	0.132075	0	G|0.500;A|0.500	0.500	weak	NBPF14,NS,carcinoma,0,1	NBPF14	107	1	NM_015383	exon16	c.C1797T	p.S599S	CTCCCCGCTGAGC	.	PASS	Atlas-SNP
ADNP2	22850	hgsc.bcm.edu	37	18	77894844	77894844	+	Silent	SNP	G	G	A	rs3744877	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	140	47	214	0	0.335714	0	G|0.596;A|0.404	0.404	strong	.	ADNP2	102	.	NM_014913	exon4	c.G1548A	p.P516P	GGTCCCGTCTGGG	.	PASS	Atlas-SNP
PLEC	5339	hgsc.bcm.edu	37	8	145001588	145001588	+	Missense_Mutation	SNP	C	C	T	rs11136334	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	3	3	3	1	1	0.333333	C|0.706;T|0.294	0.294	strong	PLEC_ENST00000436759,NS,carcinoma,0,3	PLEC	1144	3	NM_201380	exon27	c.G4157A	p.R1386Q	TCCTGCCGCAGCT	.	scavenged	Atlas-SNP
HEG1	57493	hgsc.bcm.edu	37	3	124739892	124739892	+	Silent	SNP	G	G	A	rs6438874	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	195	97	223	0	0.497436	0	G|0.510;A|0.490	0.490	strong	.	HEG1	109	.	NM_020733	exon4	c.C996T	p.A332A	CACGGTGGCAACA	.	PASS	Atlas-SNP
NPHS1	4868	hgsc.bcm.edu	37	19	36322601	36322601	+	Missense_Mutation	SNP	T	T	C	rs4806213	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	31	13	36	0	0.419355	0	T|0.897;C|0.103	0.103	strong	.	NPHS1	165	.	NM_004646	exon24	c.A3230G	p.N1077S	GAGGCATTGGAGA	.	PASS	Atlas-SNP
TAOK2	9344	hgsc.bcm.edu	37	16	29994922	29994922	+	Silent	SNP	C	C	T	rs3814883	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	62	61	67	0	0.983871	0	C|0.622;T|0.378	0.378	strong	.	TAOK2	142	.	NM_004783	exon13	c.C1359T	p.S453S	CTCTTCCGCCCGC	.	PASS	Atlas-SNP
RPGR	6103	hgsc.bcm.edu	37	X	38158290	38158290	+	Silent	SNP	C	C	T	rs1801686	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	94	91	153	1	0.968085	0.00653595	C|0.887;T|0.113	0.113	strong	.	RPGR	175	.	NM_001034853	exon10	c.G1164A	p.A388A	AAAAGTCGCCACA	.	PASS	Atlas-SNP
DDX47	51202	hgsc.bcm.edu	37	12	12967127	12967127	+	Silent	SNP	C	C	T	rs1051374	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	165	163	230	0	0.987879	0	C|0.686;T|0.314	0.314	strong	.	DDX47	37	.	NM_201224	exon2	c.C150T	p.I50I	CAAGATCCAGATT	.	PASS	Atlas-SNP
NCAN	1463	hgsc.bcm.edu	37	19	19335135	19335135	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	88	20	111	0	0.227273	0	.	.	none	.	NCAN	277	.	NM_004386	exon5	c.G671A	p.R224H	AGTCCCGTCCTGG	.	PASS	Atlas-SNP
ARL13B	200894	hgsc.bcm.edu	37	3	93768268	93768268	+	Missense_Mutation	SNP	C	C	G	rs33944211	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	143	63	189	0	0.440559	0	C|0.914;G|0.086	0.086	strong	.	ARL13B	52	.	NM_182896	exon8	c.C1043G	p.T348S	AGAAAACTAAGAA	.	PASS	Atlas-SNP
MUC20	200958	hgsc.bcm.edu	37	3	195452783	195452783	+	Missense_Mutation	SNP	C	C	T	rs199620417	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	543	124	576	1	0.228361	0.00173611	C|0.955;T|0.045	0.045	strong	MUC20,caecum,carcinoma,0,1	MUC20	84	1	NM_152673	exon3	c.C796T	p.P266S	AGCATCCCTGGGG	.	PASS	Atlas-SNP
ACACB	32	hgsc.bcm.edu	37	12	109617728	109617728	+	Missense_Mutation	SNP	A	A	G	rs16940029	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	184	85	170	0	0.461957	0	A|0.917;G|0.083	0.083	strong	.	ACACB	330	.	NM_001093	exon10	c.A1654G	p.I552V	TGTGCCATCCGCC	.	PASS	Atlas-SNP
TBX5	6910	hgsc.bcm.edu	37	12	114793414	114793414	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	42	90	0	0.482759	0	.	.	none	.	TBX5	188	.	NM_000192	exon9	c.C1480T	p.P494S	TCCTTGGCACGCC	.	PASS	Atlas-SNP
SPAG7	9552	hgsc.bcm.edu	37	17	4864114	4864114	+	Silent	SNP	T	T	C	rs61749470	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	245	105	250	0	0.428571	0	T|0.975;C|0.025	0.025	strong	.	SPAG7	22	.	NM_004890	exon2	c.A120G	p.Q40Q	TTTCTCTTGCTCT	.	PASS	Atlas-SNP
LCE1E	353135	hgsc.bcm.edu	37	1	152760075	152760075	+	Silent	SNP	A	A	G	rs201660535	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	209	39	404	0	0.186603	0	A|0.995;G|0.005	0.005	strong	.	LCE1E	26	.	NM_178353	exon2	c.A300G	p.S100S	GCCCTCAGGGGGC	.	PASS	Atlas-SNP
KDR	3791	hgsc.bcm.edu	37	4	55972974	55972974	+	Missense_Mutation	SNP	T	T	A	rs1870377	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	139	66	164	0	0.47482	0	T|0.781;A|0.219	0.219	strong	KDR,NS,carcinoma,0,1	KDR	307	1	NM_002253	exon11	c.A1416T	p.Q472H	GACAGCTTGGCTA	.	PASS	Atlas-SNP
MYO9B	4650	hgsc.bcm.edu	37	19	17306074	17306074	+	Missense_Mutation	SNP	G	G	A	rs112900956	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	57	29	38	0	0.508772	0	G|0.994;A|0.006	0.006	strong	MYO9B_ENST00000319396,adrenal_gland,adrenal_cortical_adenoma,0,2	MYO9B	264	2	NM_001130065	exon22	c.G3838A	p.G1280S	CCATGTGGCAGCC	.	PASS	Atlas-SNP
LRPAP1	4043	hgsc.bcm.edu	37	4	3519762	3519762	+	Silent	SNP	A	A	G	rs13325	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	38	20	40	0	0.526316	0	A|0.853;G|0.147	0.147	strong	.	LRPAP1	29	.	NM_002337	exon5	c.T750C	p.A250A	CTCACCAGCCTCA	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	118	44	114	0	0.372881	0	G|0.780;C|0.220	0.220	strong	.	DCTN4	35	.	NM_001135643	exon12	c.C1047G	p.F349L	ACACTCGAAGAGA	.	PASS	Atlas-SNP
OR52E2	119678	hgsc.bcm.edu	37	11	5080337	5080337	+	Missense_Mutation	SNP	T	T	C	rs61746343	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	14	74	0	0.202899	0	T|0.770;C|0.230	0.230	strong	.	OR52E2	63	.	NM_001005164	exon1	c.A521G	p.H174R	ATTACATGATTCC	.	PASS	Atlas-SNP
RTP2	344892	hgsc.bcm.edu	37	3	187419816	187419816	+	Missense_Mutation	SNP	T	T	C	rs61754877	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	163	88	201	1	0.539877	0.00497512	T|0.832;C|0.168	0.168	strong	.	RTP2	38	.	NM_001004312	exon1	c.A101G	p.N34S	TTGAGGTTGGGGT	.	PASS	Atlas-SNP
SERPINB10	5273	hgsc.bcm.edu	37	18	61600384	61600384	+	Missense_Mutation	SNP	C	C	T	rs963075	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	84	38	105	0	0.452381	0	C|0.570;T|0.430	0.430	strong	SERPINB10,colon,carcinoma,0,1	SERPINB10	53	1	NM_005024	exon6	c.C736T	p.R246C	AAAAGCCGTGACC	.	PASS	Atlas-SNP
PKD1L1	168507	hgsc.bcm.edu	37	7	47874630	47874630	+	Missense_Mutation	SNP	G	G	A	rs66755489	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	56	38	61	0	0.678571	0	G|0.831;A|0.169	0.169	strong	PKD1L1,caecum,carcinoma,+1,1	PKD1L1	328	1	NM_138295	exon39	c.C6062T	p.P2021L	GACCCCGGGGCTT	.	PASS	Atlas-SNP
OR5L2	26338	hgsc.bcm.edu	37	11	55595012	55595012	+	Silent	SNP	A	A	T	rs35645945	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	68	39	138	0	0.573529	0	A|0.934;T|0.066	0.066	strong	.	OR5L2	135	.	NM_001004739	exon1	c.A318T	p.T106T	TTGCACATGTGGA	.	PASS	Atlas-SNP
BOC	91653	hgsc.bcm.edu	37	3	112991959	112991959	+	Silent	SNP	C	C	T	rs11710894	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	165	94	143	0	0.569697	0	C|0.773;T|0.227	0.227	strong	.	BOC	139	.	NM_033254	exon8	c.C1005T	p.P335P	CATCCCCTGGGGC	.	PASS	Atlas-SNP
CLEC18A	348174	hgsc.bcm.edu	37	16	69988463	69988463	+	Missense_Mutation	SNP	C	C	G	rs78531533	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	346	44	308	0	0.127168	0	C|0.997;G|0.003	0.003	strong	CLEC18A,NS,carcinoid-endocrine_tumour,0,1	CLEC18A	9	1	NM_001271197	exon4	c.C443G	p.T148S	CCTGCACCCACTA	.	scavenged	Atlas-SNP
ATP2B4	493	hgsc.bcm.edu	37	1	203669371	203669371	+	Silent	SNP	G	G	A	rs2228446	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	49	108	0	0.505155	0	G|0.987;A|0.013	0.013	strong	.	ATP2B4	226	.	NM_001001396	exon5	c.G687A	p.G229G	CCAAGGGAATGAT	.	PASS	Atlas-SNP
AQP12B	653437	hgsc.bcm.edu	37	2	241622195	241622195	+	Silent	SNP	T	T	C	rs184458523	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	150	71	147	0	0.473333	0	T|0.907;C|0.093	0.093	strong	.	AQP12B	33	.	NM_001102467	exon1	c.A60G	p.A20A	CCTGGCTGCCTCA	.	PASS	Atlas-SNP
CD22	933	hgsc.bcm.edu	37	19	35831986	35831986	+	Silent	SNP	C	C	T	rs25677	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	126	64	138	0	0.507937	0	A|0.015;C|0.932;T|0.053	0.053	strong	.	CD22	129	.	NM_001185100	exon7	c.C1452T	p.C484C	CGCCTGCGCAGCT	.	PASS	Atlas-SNP
KCNA2	3737	hgsc.bcm.edu	37	1	111144661	111144661	+	Silent	SNP	A	A	G	rs12407942	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	59	37	63	0	0.627119	0	A|0.800;G|0.200	0.200	strong	.	KCNA2	61	.	NM_001204269	exon4	c.T1026C	p.D342D	CCTGTCATCAGGA	.	PASS	Atlas-SNP
MEGF11	84465	hgsc.bcm.edu	37	15	66411441	66411441	+	Missense_Mutation	SNP	C	C	T	rs16949528	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	29	29	34	0	1	0	C|0.642;T|0.358	0.358	strong	.	MEGF11	70	.	NM_032445	exon4	c.G284A	p.S95N	TCTCCGCTCTCAT	.	PASS	Atlas-SNP
FBN3	84467	hgsc.bcm.edu	37	19	8196499	8196499	+	Silent	SNP	G	G	A	rs3813774	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	184	80	165	0	0.434783	0	G|0.878;A|0.122	0.122	strong	.	FBN3	300	.	NM_032447	exon14	c.C1929T	p.C643C	GGCACAGCAGCAC	.	PASS	Atlas-SNP
BFSP1	631	hgsc.bcm.edu	37	20	17475217	17475217	+	Silent	SNP	C	C	T	rs6136118	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	125	63	141	0	0.504	0	C|0.697;T|0.303	0.303	strong	.	BFSP1	55	.	NM_001195	exon8	c.G1500A	p.A500A	GTCTTCCGCAACA	.	PASS	Atlas-SNP
DIDO1	11083	hgsc.bcm.edu	37	20	61538601	61538601	+	Silent	SNP	C	C	T	rs34820000	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	224	109	267	1	0.486607	0.00374532	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
HLA-A	3105	hgsc.bcm.edu	37	6	29910759	29910759	+	Missense_Mutation	SNP	T	T	C	rs1071742	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	144	142	235	0	0.986111	0	A|0.129;C|0.082;T|0.790	0.082	strong	HLA-A,rectum,carcinoma,0,1	HLA-A	89	1	NM_001242758	exon2	c.T299C	p.V100A	ACCGAGTGGACCT	.	PASS	Atlas-SNP
SH3BP4	23677	hgsc.bcm.edu	37	2	235950284	235950284	+	Silent	SNP	A	A	C	rs3731648	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	41	97	1	0.445652	0.0103093	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	.	scavenged	Atlas-SNP
TRAPPC12	51112	hgsc.bcm.edu	37	2	3483205	3483205	+	Silent	SNP	C	C	T	rs6767	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	221	82	174	0	0.371041	0	C|0.531;T|0.469	0.469	strong	.	.	.	.	NM_016030	exon12	c.C2181T	p.F727F	CAGCTTCAACACA	.	PASS	Atlas-SNP
SLC22A4	6583	hgsc.bcm.edu	37	5	131676320	131676320	+	Missense_Mutation	SNP	C	C	T	rs1050152	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	153	71	190	1	0.464052	0.00526316	C|0.748;T|0.252	0.252	strong	SLC22A4,NS,carcinoma,-2,1	SLC22A4	45	1	NM_003059	exon9	c.C1507T	p.L503F	GGAATCCTCACCC	.	scavenged	Atlas-SNP
EFCAB4B	84766	hgsc.bcm.edu	37	12	3806147	3806147	+	Missense_Mutation	SNP	T	T	C	rs9788233	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	33	17	36	0	0.515152	0	T|0.870;C|0.130	0.130	strong	EFCAB4B_ENST00000444507,NS,carcinoma,+2,8	EFCAB4B	100	8	NM_001144958	exon4	c.A19G	p.R7G	CTACCCTCCCGTC	.	PASS	Atlas-SNP
DNAH8	1769	hgsc.bcm.edu	37	6	38980081	38980081	+	Missense_Mutation	SNP	A	A	G	rs10484847	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	126	67	121	0	0.531746	0	A|0.890;G|0.110	0.110	strong	DNAH8_ENST00000359357,NS,carcinoma,-1,2	DNAH8	1239	2	NM_001206927	exon90	c.A13462G	p.I4488V	ATTTCAATACTCC	.	PASS	Atlas-SNP
ACTL7B	10880	hgsc.bcm.edu	37	9	111618163	111618163	+	Silent	SNP	G	G	A	rs3750468	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	48	14	53	0	0.291667	0	G|0.783;A|0.217	0.217	strong	.	ACTL7B	57	.	NM_006686	exon1	c.C48T	p.D16D	TCCAGGGTCACCC	.	PASS	Atlas-SNP
OR2AG2	338755	hgsc.bcm.edu	37	11	6789492	6789492	+	Missense_Mutation	SNP	C	C	T	rs143018775	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	179	145	199	0	0.810056	0	C|0.999;T|0.001	0.001	strong	.	OR2AG2	55	.	NM_001004490	exon1	c.G697A	p.G233R	TCCTCCCCTCATT	.	PASS	Atlas-SNP
PRAMEF1	65121	hgsc.bcm.edu	37	1	12854428	12854428	+	Missense_Mutation	SNP	C	C	T	rs1769774	bycluster;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	355	156	482	1	0.439437	0.00207469	C|0.713;T|0.287	0.287	strong	.	PRAMEF1	78	.	NM_023013	exon3	c.C652T	p.P218S	TCCTGGCCACGTC	.	PASS	Atlas-SNP
FRRS1	391059	hgsc.bcm.edu	37	1	100181147	100181147	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	241	4	320	0	0.0165975	0	.	.	none	FRRS1,NS,carcinoma,0,1	FRRS1	50	1	NM_001013660	exon12	c.A1318T	p.S440C	CCCTACTCCAGCC	.	scavenged	Atlas-SNP
FBLN2	2199	hgsc.bcm.edu	37	3	13612936	13612936	+	Missense_Mutation	SNP	A	A	G	rs3732666	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	50	117	0	0.574713	0	A|0.603;G|0.397	0.397	strong	.	FBLN2	137	.	NM_001998	exon2	c.A1081G	p.S361G	GCACCGAGCCTGG	.	PASS	Atlas-SNP
OR52R1	119695	hgsc.bcm.edu	37	11	4825225	4825225	+	Missense_Mutation	SNP	A	A	G	rs7941731	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	76	16	70	0	0.210526	0	A|0.629;G|0.371	0.371	strong	.	OR52R1	81	.	NM_001005177	exon1	c.T386C	p.I129T	AAGCAGATAGCCA	.	PASS	Atlas-SNP
KCTD1	284252	hgsc.bcm.edu	37	18	24035788	24035788	+	Silent	SNP	G	G	A	rs3755	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	45	102	0	0.48913	0	G|0.889;A|0.111	0.111	strong	.	KCTD1	76	.	NM_001142730	exon5	c.C2517T	p.S839S	GTATTCGCTGAAC	.	PASS	Atlas-SNP
ITPR1	3708	hgsc.bcm.edu	37	3	4709131	4709131	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	117	2	104	0	0.017094	0	.	.	none	ITPR1,NS,carcinoma,-1,1	ITPR1	659	1	NM_001099952	exon18	c.T1784C	p.I595T	ACACTATCACTGC	.	scavenged	Atlas-SNP
PDE6C	5146	hgsc.bcm.edu	37	10	95372764	95372764	+	Silent	SNP	C	C	T	rs12781149	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	39	21	45	0	0.538462	0	C|0.939;T|0.061	0.061	strong	.	PDE6C	97	.	NM_006204	exon1	c.C282T	p.D94D	GGCTGACCGCTGC	.	PASS	Atlas-SNP
PIGG	54872	hgsc.bcm.edu	37	4	517376	517376	+	Silent	SNP	T	T	C	rs7666226	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	142	80	192	1	0.56338	0.00520833	T|0.780;C|0.220	0.220	strong	.	PIGG	86	.	NM_001127178	exon9	c.T1743C	p.L581L	CTTCCTTGTGAAC	.	PASS	Atlas-SNP
AXDND1	126859	hgsc.bcm.edu	37	1	179504043	179504043	+	Missense_Mutation	SNP	C	C	G	rs6658180	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	185	92	243	0	0.497297	0	C|0.671;G|0.329	0.329	strong	.	AXDND1	142	.	NM_144696	exon25	c.C2977G	p.Q993E	GAACAACAAGAAG	.	PASS	Atlas-SNP
NEK4	6787	hgsc.bcm.edu	37	3	52800284	52800284	+	Silent	SNP	T	T	C	rs2230535	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	272	271	309	1	0.996324	0.00323625	T|0.652;C|0.348	0.348	strong	.	NEK4	51	.	NM_003157	exon3	c.A468G	p.L156L	GTTCTCTAACACT	.	PASS	Atlas-SNP
GSDMC	56169	hgsc.bcm.edu	37	8	130774897	130774897	+	Silent	SNP	T	T	C	rs17190932	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	67	19	82	1	0.283582	0.0121951	C|0.125;N|0.000	0.125	strong	GSDMC,NS,carcinoma,0,1	GSDMC	71	1	NM_031415	exon5	c.A651G	p.R217R	CTGCTTTCTCTTA	.	scavenged	Atlas-SNP
FCRLA	84824	hgsc.bcm.edu	37	1	161683136	161683136	+	Missense_Mutation	SNP	G	G	A	rs11746	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	99	98	120	0	0.989899	0	G|0.661;A|0.339	0.339	strong	FCRLA,NS,carcinoma,0,1	FCRLA	101	1	NM_001184866	exon6	c.G1115A	p.R372Q	GCCACCGGAAGCC	.	PASS	Atlas-SNP
MYOF	26509	hgsc.bcm.edu	37	10	95082882	95082882	+	Silent	SNP	G	G	A	rs34048939	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	172	88	241	1	0.511628	0.00414938	G|0.958;A|0.042	0.042	strong	.	MYOF	177	.	NM_013451	exon48	c.C5409T	p.D1803D	TTTCTCGTCCAAG	.	PASS	Atlas-SNP
MYO3B	140469	hgsc.bcm.edu	37	2	171073887	171073887	+	Silent	SNP	G	G	A	rs2161916	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	219	106	271	0	0.484018	0	G|0.433;A|0.567	0.567	strong	.	MYO3B	320	.	NM_001083615	exon6	c.G585A	p.P195P	CACCCCGTTCTGG	.	PASS	Atlas-SNP
OGFOD3	79701	hgsc.bcm.edu	37	17	80352303	80352303	+	Missense_Mutation	SNP	G	G	A	rs62079523	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	32	87	0	0.450704	0	G|0.728;A|0.272	0.272	strong	.	.	.	.	NM_175902	exon9	c.C940T	p.P314S	TCTCGGGCGGGTG	.	PASS	Atlas-SNP
CCDC64B	146439	hgsc.bcm.edu	37	16	3085326	3085326	+	Missense_Mutation	SNP	C	C	T	rs71386699	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	132	17	132	0	0.128788	0	C|0.985;T|0.015	0.015	strong	.	CCDC64B	19	.	NM_001103175	exon1	c.G172A	p.E58K	CTTTCTCCTTCTG	.	PASS	Atlas-SNP
PDCD11	22984	hgsc.bcm.edu	37	10	105205260	105205260	+	Missense_Mutation	SNP	A	A	G	rs151054853	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	134	78	177	0	0.58209	0	A|0.998;G|0.002	0.002	strong	.	PDCD11	160	.	NM_014976	exon36	c.A5570G	p.K1857R	AGGCCAAGGCCCT	.	PASS	Atlas-SNP
ZC3H7B	23264	hgsc.bcm.edu	37	22	41752747	41752747	+	Silent	SNP	G	G	A	rs12484074	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	144	73	134	0	0.506944	0	G|0.810;A|0.190	0.190	strong	.	ZC3H7B	82	.	NM_017590	exon22	c.G2616A	p.T872T	CTTCACGTCCGAC	.	PASS	Atlas-SNP
PAXIP1	22976	hgsc.bcm.edu	37	7	154760666	154760666	+	Silent	SNP	C	C	T	rs61752011	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	31	85	0	0.413333	0	C|0.784;T|0.216	0.216	strong	PAXIP1_ENST00000397192,NS,carcinoma,0,2	PAXIP1	150	2	NM_007349	exon7	c.G1245A	p.P415P	TAAAACCGGGTGC	.	PASS	Atlas-SNP
TET1	80312	hgsc.bcm.edu	37	10	70332312	70332312	+	Missense_Mutation	SNP	C	C	T	rs138684329	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	43	100	0	0.443299	0	C|1.000;T|0.000	0.000	strong	.	TET1	255	.	NM_030625	exon2	c.C217T	p.L73F	AGAAGCCTTCTGA	.	PASS	Atlas-SNP
ABHD4	63874	hgsc.bcm.edu	37	14	23072905	23072905	+	Silent	SNP	C	C	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	183	91	198	0	0.497268	0	.	.	none	.	ABHD4	30	.	NM_022060	exon4	c.C561G	p.P187P	TGCACCCCCAGCC	.	PASS	Atlas-SNP
GMIP	51291	hgsc.bcm.edu	37	19	19745962	19745962	+	Missense_Mutation	SNP	G	G	A	rs372547969		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	94	6	122	0	0.0638298	0	.	.	weak	.	GMIP	55	.	NM_016573	exon16	c.C1621T	p.R541W	GGAGCCGCCTGTG	.	PASS	Atlas-SNP
LILRA2	11027	hgsc.bcm.edu	37	19	55086873	55086873	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	198	4	204	0	0.020202	0	.	.	none	LILRA2,NS,carcinoma,0,1	LILRA2	99	1	NM_001130917	exon5	c.G806A	p.W269X	CTGGTTGGCAGCC	.	scavenged	Atlas-SNP
PDE11A	50940	hgsc.bcm.edu	37	2	178528641	178528641	+	Missense_Mutation	SNP	G	G	C	rs61306957	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	34	111	0	0.485714	0	G|0.975;C|0.025	0.025	strong	.	PDE11A	283	.	NM_016953	exon19	c.C2599G	p.R867G	GCAACCGAGGCAG	.	PASS	Atlas-SNP
TMEM2	23670	hgsc.bcm.edu	37	9	74360395	74360395	+	Silent	SNP	T	T	C	rs76670837	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	78	84	0	1	0	T|0.926;C|0.074	0.074	strong	.	TMEM2	112	.	NM_001135820	exon4	c.A573G	p.A191A	TTTTTCTGCTCCA	.	PASS	Atlas-SNP
SEH1L	81929	hgsc.bcm.edu	37	18	12955467	12955467	+	Silent	SNP	T	T	C	rs2015378		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	132	7	141	0	0.0530303	0	.	.	weak	SEH1L,NS,carcinoma,0,3	SEH1L	33	3	NM_001013437	exon3	c.T168C	p.H56H	GACACATAGTGGA	.	PASS	Atlas-SNP
BCS1L	617	hgsc.bcm.edu	37	2	219527857	219527857	+	Silent	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	146	39	184	0	0.267123	0	.	.	none	.	BCS1L	22	.	NM_001257343	exon9	c.G1008A	p.R336R	TCTCAGGCTGGAC	.	PASS	Atlas-SNP
BTG2	7832	hgsc.bcm.edu	37	1	203274826	203274826	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	165	44	132	0	0.266667	0	.	.	none	.	BTG2	16	.	NM_006763	exon1	c.G92A	p.S31N	GCGTGAGCGAGCA	.	PASS	Atlas-SNP
ATE1	11101	hgsc.bcm.edu	37	10	123549691	123549691	+	Silent	SNP	T	T	G	rs35350755	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	79	78	86	0	0.987342	0	T|0.544;G|0.456	0.456	strong	.	ATE1	67	.	NM_001001976	exon11	c.A1371C	p.P457P	TGCTTCTGGGTCC	.	PASS	Atlas-SNP
PSAPL1	768239	hgsc.bcm.edu	37	4	7436486	7436486	+	Missense_Mutation	SNP	C	C	A	rs11548325	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	132	66	187	0	0.5	0	C|0.820;A|0.180	0.180	strong	.	PSAPL1	51	.	NM_001085382	exon1	c.G121T	p.A41S	ACCTGGCAGCTGT	.	PASS	Atlas-SNP
SAMSN1	64092	hgsc.bcm.edu	37	21	15954528	15954528	+	Missense_Mutation	SNP	G	G	A	rs2822785	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	121	120	117	0	0.991736	0	G|0.692;A|0.307	0.307	strong	.	SAMSN1	112	.	NM_001256370	exon2	c.C190T	p.H64Y	AGCAGTGGTCCCA	.	PASS	Atlas-SNP
CEACAM19	56971	hgsc.bcm.edu	37	19	45176003	45176003	+	Missense_Mutation	SNP	A	A	G	rs201929208		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	151	76	124	0	0.503311	0	.	.	weak	.	CEACAM19	27	.	NM_001127893	exon2	c.A191G	p.N64S	ACTTCAACTGGTA	.	PASS	Atlas-SNP
C9orf84	158401	hgsc.bcm.edu	37	9	114454544	114454544	+	Missense_Mutation	SNP	T	T	C	rs7869279	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	124	48	130	0	0.387097	0	T|0.528;C|0.472	0.472	strong	.	C9orf84	207	.	NM_173521	exon25	c.A3521G	p.E1174G	GAGATTTCTTTTA	.	PASS	Atlas-SNP
SCRIB	23513	hgsc.bcm.edu	37	8	144874554	144874554	+	Silent	SNP	T	T	C	rs6991873	bycluster;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	2	2	2	1	1	0.5	T|0.010;C|0.990	0.990	strong	SCRIB_ENST00000356994,colon,carcinoma,-2,2	SCRIB	192	2	NM_015356	exon32	c.A4350G	p.P1450P	CAGGGGTGGGGGG	.	scavenged	Atlas-SNP
ARHGAP44	9912	hgsc.bcm.edu	37	17	12888086	12888086	+	Silent	SNP	G	G	A	rs143756943	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	103	51	109	0	0.495146	0	G|0.998;A|0.002	0.002	strong	ARHGAP44,NS,carcinoma,+1,1	ARHGAP44	55	1	NM_014859	exon20	c.G2178A	p.S726S	CAAATCGCGGCCC	.	PASS	Atlas-SNP
DCLK2	166614	hgsc.bcm.edu	37	4	151141918	151141918	+	Missense_Mutation	SNP	A	A	C	rs148315360	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	134	71	215	0	0.529851	0	A|0.998;C|0.002	0.002	strong	.	DCLK2	168	.	NM_001040261	exon7	c.A1171C	p.I391L	CGTTGCATAAGTC	.	PASS	Atlas-SNP
JAKMIP2	9832	hgsc.bcm.edu	37	5	147051334	147051334	+	Silent	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	152	3	178	0	0.0197368	0	.	.	none	JAKMIP2,right_upper_lobe,carcinoma,0,1	JAKMIP2	154	1	NM_001270941	exon2	c.C36T	p.P12P	TGCCTCGGGCTTC	.	scavenged	Atlas-SNP
ZNF17	7565	hgsc.bcm.edu	37	19	57931553	57931553	+	Silent	SNP	C	C	T	rs10417533	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	89	89	69	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
ULK1	8408	hgsc.bcm.edu	37	12	132401058	132401058	+	Missense_Mutation	SNP	C	C	T	rs55815560	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	61	30	60	0	0.491803	0	C|0.998;T|0.002	0.002	strong	.	ULK1	92	.	NM_003565	exon20	c.C1994T	p.S665L	ACCTCTCGGAGGT	.	PASS	Atlas-SNP
MYO3B	140469	hgsc.bcm.edu	37	2	171070912	171070912	+	Silent	SNP	T	T	C	rs13385825	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	115	55	151	0	0.478261	0	T|0.608;C|0.392	0.392	strong	.	MYO3B	320	.	NM_001083615	exon4	c.T345C	p.T115T	AGTCACTGAGCTT	.	PASS	Atlas-SNP
ANKRD30A	91074	hgsc.bcm.edu	37	10	37486235	37486235	+	Missense_Mutation	SNP	G	G	A	rs201775035	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	292	18	328	1	0.0616438	0.00304878	.	.	weak	ANKRD30A,NS,carcinoma,0,1	ANKRD30A	448	1	NM_052997	exon28	c.G2473A	p.E825K	GCCTTCGAGGTAT	.	scavenged	Atlas-SNP
DOCK1	1793	hgsc.bcm.edu	37	10	129160458	129160458	+	Silent	SNP	G	G	A	rs2296635	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	81	40	91	0	0.493827	0	G|0.808;A|0.192	0.192	strong	.	DOCK1	188	.	NM_001380	exon33	c.G3351A	p.S1117S	CCATTCGACCCGA	.	PASS	Atlas-SNP
FAM205A	259308	hgsc.bcm.edu	37	9	34726671	34726671	+	Missense_Mutation	SNP	G	G	A	rs41318950	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	44	118	0	0.517647	0	G|0.708;A|0.292	0.292	strong	.	FAM205A	45	.	NM_001141917	exon4	c.C566T	p.T189M	GCATACGTTGACT	.	PASS	Atlas-SNP
PPAP2C	8612	hgsc.bcm.edu	37	19	282753	282753	+	Missense_Mutation	SNP	G	G	A	rs1138439	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	41	20	65	0	0.487805	0	T|0.071;G|0.466;C|0.124;A|0.339	0.339	strong	PPAP2C_ENST00000269812,caecum,carcinoma,0,5	PPAP2C	38	5	NM_177543	exon4	c.C602T	p.A201V	CTCACCGCCAAGA	.	PASS	Atlas-SNP
OR52I1	390037	hgsc.bcm.edu	37	11	4615508	4615508	+	Silent	SNP	C	C	G	rs2010719	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	335	52	336	0	0.155224	0	C|0.416;G|0.584	0.584	strong	OR52I1,NS,carcinoma,+1,1	OR52I1	29	1	NM_001005169	exon1	c.C240G	p.S80S	CTCCTCCGTGGTA	.	PASS	Atlas-SNP
LILRA6	79168	hgsc.bcm.edu	37	19	54744210	54744210	+	Missense_Mutation	SNP	A	A	G	rs8104206	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	188	54	294	0	0.287234	0	A|0.830;G|0.170	0.170	strong	.	LILRA6	75	.	NM_024318	exon6	c.T1198C	p.Y400H	AGCTGTATGAGCC	.	PASS	Atlas-SNP
KANK2	25959	hgsc.bcm.edu	37	19	11305161	11305161	+	Silent	SNP	A	A	G	rs754529	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	47	22	43	0	0.468085	0	A|0.932;G|0.068	0.068	strong	.	KANK2	47	.	NM_015493	exon1	c.T27C	p.A9A	GAAGGGAGCAGGC	.	PASS	Atlas-SNP
PCDHB7	56129	hgsc.bcm.edu	37	5	140553919	140553919	+	Silent	SNP	C	C	A	rs17844456	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	100	50	143	0	0.5	0	C|0.826;A|0.174	0.174	strong	.	PCDHB7	231	.	NM_018940	exon1	c.C1503A	p.A501A	CCTCGCCTCCCTG	.	PASS	Atlas-SNP
JHDM1D	80853	hgsc.bcm.edu	37	7	139797431	139797431	+	Missense_Mutation	SNP	G	G	T	rs6950119	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	106	45	140	0	0.424528	0	A|0.000;G|0.670;T|0.330	0.330	strong	JHDM1D,NS,carcinoma,0,1	JHDM1D	54	1	NM_030647	exon15	c.C1930A	p.R644S	TCACACGTGTAAA	.	PASS	Atlas-SNP
AKAP6	9472	hgsc.bcm.edu	37	14	33015397	33015397	+	Missense_Mutation	SNP	G	G	T	rs45477296	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	79	78	122	0	0.987342	0	G|0.952;T|0.048	0.048	strong	.	AKAP6	308	.	NM_004274	exon4	c.G1538T	p.R513L	CTAAACGGGGGAC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195511390	195511390	+	Missense_Mutation	SNP	T	T	G	rs75692609	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	49	26	106	0	0.530612	0	T|0.928;G|0.072	0.072	strong	MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	NM_018406	exon2	c.A7061C	p.H2354P	GTGACATGAAGAG	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	115	51	125	0	0.443478	0	A|0.785;G|0.214	0.214	strong	.	CR1	354	.	NM_000651	exon30	c.A4973G	p.H1658R	GTGAGCATACCCC	.	PASS	Atlas-SNP
CARD10	29775	hgsc.bcm.edu	37	22	37900771	37900771	+	Silent	SNP	A	A	G	rs3817806	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	29	87	0	0.5	0	A|0.934;G|0.066	0.066	strong	.	CARD10	55	.	NM_014550	exon8	c.T1389C	p.C463C	GGAGGCACAGGCC	.	PASS	Atlas-SNP
PPAN	56342	hgsc.bcm.edu	37	19	10221642	10221642	+	Missense_Mutation	SNP	A	A	G	rs11559188	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	35	17	40	0	0.485714	0	A|0.943;G|0.057	0.057	strong	.	PPAN	43	.	NM_020230	exon12	c.A1223G	p.Q408R	CCAAGCAGAAACG	.	PASS	Atlas-SNP
PCCB	5096	hgsc.bcm.edu	37	3	136012637	136012637	+	Nonsense_Mutation	SNP	A	A	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	17	83	0	0.293103	0	.	.	none	.	PCCB	52	.	NM_001178014	exon8	c.A754T	p.K252X	GTTGTGAAGTCTG	.	PASS	Atlas-SNP
TMC6	11322	hgsc.bcm.edu	37	17	76117136	76117136	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	129	71	117	0	0.550388	0	.	.	none	.	TMC6	42	.	NM_001127198	exon12	c.C1493T	p.P498L	TCATGCGGCTCCA	.	PASS	Atlas-SNP
GRM6	2916	hgsc.bcm.edu	37	5	178410151	178410151	+	Silent	SNP	C	C	T	rs2071247	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	96	59	107	0	0.614583	0	C|0.792;T|0.208	0.208	strong	.	GRM6	149	.	NM_000843	exon9	c.G2196A	p.T732T	GTCCACCGTCCGC	.	PASS	Atlas-SNP
ASCC3	10973	hgsc.bcm.edu	37	6	101166095	101166095	+	Silent	SNP	G	G	A	rs41288423	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	67	67	63	0	1	0	G|0.528;A|0.472	0.472	strong	ASCC3,NS,carcinoma,0,2	ASCC3	205	2	NM_006828	exon12	c.C1935T	p.L645L	CAGTCCGAGAATC	.	PASS	Atlas-SNP
SLC38A8	146167	hgsc.bcm.edu	37	16	84050209	84050209	+	Silent	SNP	G	G	A	rs77876966	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	62	30	52	0	0.483871	0	G|0.954;A|0.046	0.046	strong	.	SLC38A8	60	.	NM_001080442	exon8	c.C1077T	p.L359L	CATGGCGAGCGTC	.	PASS	Atlas-SNP
CTH	1491	hgsc.bcm.edu	37	1	70904800	70904800	+	Missense_Mutation	SNP	G	G	T	rs1021737	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	172	73	176	0	0.424419	0	G|0.779;T|0.221	0.221	strong	.	CTH	48	.	NM_001902	exon12	c.G1208T	p.S403I	GTGGAAGTCACAG	.	PASS	Atlas-SNP
OR51B6	390058	hgsc.bcm.edu	37	11	5372863	5372863	+	Silent	SNP	T	T	A	rs10837882	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	350	276	282	0	0.788571	0	T|0.871;A|0.129	0.129	strong	.	OR51B6	53	.	NM_001004750	exon1	c.T126A	p.T42T	TGGCACTCTTCTC	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	51	93	0	0.6	0	C|0.810;T|0.190	0.190	strong	.	KCNG4	71	.	NM_172347	exon3	c.G973A	p.G325R	AGCTCCCGCTCGG	.	PASS	Atlas-SNP
OR4M2	390538	hgsc.bcm.edu	37	15	22369290	22369290	+	Missense_Mutation	SNP	A	A	G	rs75045725		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	328	86	242	0	0.262195	0	.	.	weak	OR4M2,NS,carcinoma,0,1	OR4M2	140	1	NM_001004719	exon1	c.A715G	p.M239V	AGGGCCATGTCCA	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	54	29	75	0	0.537037	0	G|0.674;A|0.326	0.326	strong	.	DVL2	49	.	NM_004422	exon3	c.C405T	p.S135S	CTGGAAGGATGGA	.	PASS	Atlas-SNP
MOXD1	26002	hgsc.bcm.edu	37	6	132636820	132636820	+	Missense_Mutation	SNP	C	C	G	rs36075540	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	57	35	127	0	0.614035	0	C|0.971;G|0.029	0.029	strong	.	MOXD1	136	.	NM_015529	exon10	c.G1462C	p.E488Q	GTTGTTCCATAAT	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	98	135	0	0.970297	0	G|0.520;N|0.000	0.520	strong	.	UNC5C	141	.	NM_003728	exon13	c.T2162C	p.M721T	CCTCCCATCTGTC	.	PASS	Atlas-SNP
RTP4	64108	hgsc.bcm.edu	37	3	187088812	187088812	+	Missense_Mutation	SNP	C	C	T	rs3821812	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	118	67	124	0	0.567797	0	C|0.657;N|0.000	.	strong	.	RTP4	20	.	NM_022147	exon2	c.C392T	p.T131M	ATGGCACGAGGAA	.	PASS	Atlas-SNP
NFATC4	4776	hgsc.bcm.edu	37	14	24838953	24838953	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	4	65	0	0.0571429	0	.	.	none	.	NFATC4	115	.	NM_001198967	exon3	c.C538T	p.R180C	AGCATCCGCATCA	.	PASS	Atlas-SNP
OPLAH	26873	hgsc.bcm.edu	37	8	145114844	145114844	+	Missense_Mutation	SNP	C	C	T	rs7004867	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	76	75	93	0	0.986842	0	C|0.921;T|0.079	0.079	strong	OPLAH,NS,carcinoma,0,2	OPLAH	78	2	NM_017570	exon2	c.G92A	p.R31Q	AAGACCCGCACGT	.	PASS	Atlas-SNP
ARID4B	51742	hgsc.bcm.edu	37	1	235392546	235392546	+	Silent	SNP	T	T	C	rs12731746	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	103	103	168	0	1	0	T|0.545;C|0.455	0.455	strong	.	ARID4B	142	.	NM_016374	exon11	c.A897G	p.E299E	ACTTACTTCTTCT	.	PASS	Atlas-SNP
MTOR	2475	hgsc.bcm.edu	37	1	11181327	11181327	+	Silent	SNP	C	C	T	rs11121691	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	64	39	58	0	0.609375	0	C|0.721;T|0.279	0.279	strong	.	MTOR	327	.	NM_004958	exon49	c.G6909A	p.L2303L	CAGCCACAGCAGC	.	PASS	Atlas-SNP
ZNF598	90850	hgsc.bcm.edu	37	16	2049728	2049728	+	Missense_Mutation	SNP	C	C	T	rs11248905	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	53	41	37	0	0.773585	0	C|0.890;T|0.110	0.110	strong	ZNF598,NS,carcinoma,0,1	ZNF598	55	1	NM_178167	exon11	c.G1822A	p.A608T	AGGTAGCGGGCGG	.	PASS	Atlas-SNP
TMEM86B	255043	hgsc.bcm.edu	37	19	55738746	55738746	+	Silent	SNP	G	G	A	rs4374298	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	56	27	36	0	0.482143	0	G|0.828;A|0.172	0.172	strong	.	TMEM86B	12	.	NM_173804	exon3	c.C484T	p.L162L	GCCACAGCATGGC	.	PASS	Atlas-SNP
UNC5C	8633	hgsc.bcm.edu	37	4	96123981	96123981	+	Silent	SNP	C	C	T	rs3733212	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	154	61	159	0	0.396104	0	C|0.347;T|0.653	0.653	strong	.	UNC5C	141	.	NM_003728	exon12	c.G2037A	p.A679A	GCGCTTCGCAGCC	.	PASS	Atlas-SNP
TNC	3371	hgsc.bcm.edu	37	9	117797597	117797597	+	Silent	SNP	T	T	C	rs12347433	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	43	19	54	0	0.44186	0	T|0.813;C|0.187	0.187	strong	TNC,NS,carcinoma,0,1	TNC	282	1	NM_002160	exon22	c.A5673G	p.R1891R	CAAGTCTCTTGGA	.	PASS	Atlas-SNP
IFITM2	10581	hgsc.bcm.edu	37	11	308314	308314	+	Missense_Mutation	SNP	T	T	C	rs55900504		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	151	109	134	1	0.721854	0.00746269	.	.	weak	IFITM2,rectum,carcinoma,0,1	IFITM2	21	1	NM_006435	exon1	c.T122C	p.M41T	CCCCGATGTCCAC	.	scavenged	Atlas-SNP
TTC7B	145567	hgsc.bcm.edu	37	14	91161862	91161862	+	Silent	SNP	C	C	T	rs10146731	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	121	120	127	0	0.991736	0	C|0.384;T|0.616	0.616	strong	.	TTC7B	93	.	NM_001010854	exon6	c.G759A	p.T253T	TTGAGTCGTTCTT	.	PASS	Atlas-SNP
KIAA0226	9711	hgsc.bcm.edu	37	3	197427557	197427557	+	Silent	SNP	A	A	G	rs28394098	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	168	83	200	0	0.494048	0	A|0.885;G|0.115	0.115	strong	.	KIAA0226	136	.	NM_014687	exon7	c.T1188C	p.T396T	GGTGACAGTGAGT	.	PASS	Atlas-SNP
AZI1	22994	hgsc.bcm.edu	37	17	79164488	79164488	+	Missense_Mutation	SNP	C	C	T	rs117616373	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	39	28	25	0	0.717949	0	C|0.979;T|0.021	0.021	strong	.	AZI1	145	.	NM_014984	exon24	c.G3058A	p.A1020T	GCGTGGCCAGCTC	.	PASS	Atlas-SNP
RAI1	10743	hgsc.bcm.edu	37	17	17700573	17700573	+	Silent	SNP	T	T	C	rs4925112	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	38	18	50	0	0.473684	0	T|0.888;C|0.112	0.112	strong	.	RAI1	121	.	NM_030665	exon3	c.T4311C	p.P1437P	GCAGCCTGGGGGG	.	PASS	Atlas-SNP
ELN	2006	hgsc.bcm.edu	37	7	73470714	73470714	+	Missense_Mutation	SNP	G	G	A	rs2071307	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	131	51	153	0	0.389313	0	G|0.704;A|0.296	0.296	strong	ELN,NS,carcinoma,0,1	ELN	81	1	NM_001081753	exon20	c.G1279A	p.G427S	GTCCCTGGTGTCG	.	PASS	Atlas-SNP
BABAM1	29086	hgsc.bcm.edu	37	19	17389704	17389704	+	Silent	SNP	G	G	A	rs8170	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	61	26	72	0	0.42623	0	G|0.869;A|0.131	0.131	strong	C19orf62,NS,carcinoma,0,2	BABAM1	14	2	NM_014173	exon9	c.G837A	p.K279K	CTACAAGTATGAG	.	PASS	Atlas-SNP
NAT2	10	hgsc.bcm.edu	37	8	18257795	18257795	+	Silent	SNP	C	C	T	rs1041983	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	129	32	110	0	0.248062	0	C|0.637;T|0.363	0.363	strong	.	NAT2	34	.	NM_000015	exon2	c.C282T	p.Y94Y	TTTTTACATCCCT	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9013905	9013905	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	83	18	103	0	0.216867	0	.	.	none	.	MUC16	4315	.	NM_024690	exon33	c.G38485C	p.G12829R	AGGTCCCAGGAGC	.	PASS	Atlas-SNP
LRRC4B	94030	hgsc.bcm.edu	37	19	51022073	51022073	+	Silent	SNP	G	G	A	rs61745055	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	108	61	138	0	0.564815	0	G|0.993;A|0.007	0.007	strong	.	LRRC4B	89	.	NM_001080457	exon3	c.C897T	p.P299P	GTGCAGGGGCGTG	.	PASS	Atlas-SNP
CCDC168	643677	hgsc.bcm.edu	37	13	103392562	103392562	+	Missense_Mutation	SNP	C	C	A	rs12585626	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	60	29	72	0	0.483333	0	C|0.905;A|0.095	0.095	strong	.	.	.	.	NM_001146197	exon4	c.G10485T	p.M3495I	TGATTTCATTCCT	.	PASS	Atlas-SNP
KANK2	25959	hgsc.bcm.edu	37	19	11303618	11303618	+	Missense_Mutation	SNP	G	G	A	rs144821191	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	131	65	165	0	0.496183	0	G|0.999;A|0.001	0.001	strong	.	KANK2	47	.	NM_015493	exon2	c.C1138T	p.R380C	GGCTGCGGAACAC	.	PASS	Atlas-SNP
OR51F1	256892	hgsc.bcm.edu	37	11	4790482	4790482	+	Silent	SNP	T	T	C	rs12792898	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	181	39	172	0	0.21547	0	T|0.909;C|0.091	0.091	strong	OR51F1,NS,carcinoma,-2,1	OR51F1	60	1	NM_001004752	exon1	c.A666G	p.L222L	AATAATTAAGATA	.	PASS	Atlas-SNP
CCDC27	148870	hgsc.bcm.edu	37	1	3669205	3669205	+	Missense_Mutation	SNP	C	C	G	rs10910021	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	95	67	174	1	0.705263	0.00574713	C|0.625;G|0.375	0.375	strong	.	CCDC27	79	.	NM_152492	exon1	c.C160G	p.Q54E	CCATCTCAGAGGC	.	PASS	Atlas-SNP
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057720	46057720	+	Missense_Mutation	SNP	A	A	C	rs4818949	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	165	50	121	0	0.30303	0	A|0.711;C|0.289	0.289	strong	.	KRTAP10-10	37	.	NM_181688	exon1	c.A386C	p.Q129P	GCCAGCAGTCTAG	.	PASS	Atlas-SNP
BPHL	670	hgsc.bcm.edu	37	6	3123983	3123983	+	Missense_Mutation	SNP	C	C	T	rs372718817		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	230	3	226	0	0.0130435	0	.	.	weak	BPHL,NS,carcinoma,0,1	BPHL	32	1	NM_004332	exon2	c.C200T	p.P67L	TACTTCCTGGGAT	.	scavenged	Atlas-SNP
DYNC2LI1	51626	hgsc.bcm.edu	37	2	44021826	44021826	+	Missense_Mutation	SNP	T	T	A	rs9309107	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	404	402	250	0	0.995049	0	A|0.389;N|0.001	0.389	strong	.	DYNC2LI1	46	.	NM_015522	exon6	c.T551A	p.F184Y	TCCCATTTATAGT	.	PASS	Atlas-SNP
RFTN2	130132	hgsc.bcm.edu	37	2	198460748	198460748	+	Silent	SNP	T	T	G	rs77442629	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	65	30	83	0	0.461538	0	T|0.995;G|0.005	0.005	strong	.	RFTN2	68	.	NM_144629	exon8	c.A1200C	p.P400P	CATAACTGGCCTC	.	PASS	Atlas-SNP
SETX	23064	hgsc.bcm.edu	37	9	135172412	135172412	+	Silent	SNP	A	A	G	rs2296869	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	95	44	115	0	0.463158	0	A|0.628;G|0.372	0.372	strong	.	SETX	234	.	NM_015046	exon14	c.T5811C	p.D1937D	CTTTTGATCTTCA	.	PASS	Atlas-SNP
OR13C9	286362	hgsc.bcm.edu	37	9	107379895	107379895	+	Missense_Mutation	SNP	G	G	T	rs10761054	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	166	77	205	0	0.463855	0	G|0.786;T|0.214	0.214	strong	.	OR13C9	42	.	NM_001001956	exon1	c.C591A	p.F197L	CATGAGGAACTCA	.	PASS	Atlas-SNP
STOX1	219736	hgsc.bcm.edu	37	10	70645376	70645376	+	Missense_Mutation	SNP	A	A	C	rs10509305	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	90	39	112	0	0.433333	0	A|0.858;C|0.142	0.142	strong	.	STOX1	75	.	NM_152709	exon3	c.A1824C	p.E608D	ATATGAAGTGTAT	.	PASS	Atlas-SNP
NT5DC3	51559	hgsc.bcm.edu	37	12	104186995	104186995	+	Silent	SNP	G	G	A	rs61748068	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	225	108	239	0	0.48	0	G|0.908;A|0.092	0.092	strong	.	NT5DC3	113	.	NM_001031701	exon9	c.C966T	p.F322F	CACATCGAACAGG	.	PASS	Atlas-SNP
ZNF416	55659	hgsc.bcm.edu	37	19	58084605	58084605	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	174	108	178	0	0.62069	0	.	.	none	.	ZNF416	50	.	NM_017879	exon4	c.G667C	p.E223Q	TGGACTCTCTCCT	.	PASS	Atlas-SNP
DNA2	1763	hgsc.bcm.edu	37	10	70191970	70191970	+	Silent	SNP	A	A	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	150	6	177	0	0.04	0	.	.	none	.	DNA2	76	.	NM_001080449	exon12	c.T1866C	p.I622I	CTTTAGAATGCAG	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	212	99	263	1	0.466981	0.00380228	G|0.597;N|0.001	0.597	strong	.	CAND2	138	.	NM_001162499	exon8	c.A1223G	p.Q408R	AAACACAGCCCCC	.	PASS	Atlas-SNP
TTLL12	23170	hgsc.bcm.edu	37	22	43576904	43576904	+	Silent	SNP	G	G	A	rs2071723	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	112	53	111	0	0.473214	0	A|0.339;C|0.000;G|0.661	0.339	strong	TTLL12,NS,carcinoma,0,1	TTLL12	50	1	NM_015140	exon3	c.C390T	p.H130H	GCGCGCGTGCTCC	.	PASS	Atlas-SNP
CCDC176	80127	hgsc.bcm.edu	37	14	74523949	74523949	+	Silent	SNP	G	G	A	rs3742808	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	108	53	124	0	0.490741	0	G|0.755;A|0.245	0.245	strong	.	.	.	.	NM_025057	exon11	c.G1566A	p.Q522Q	ACCTCAGGAGTCT	.	PASS	Atlas-SNP
DIDO1	11083	hgsc.bcm.edu	37	20	61512185	61512185	+	Missense_Mutation	SNP	G	G	C	rs41282984	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	100	49	136	0	0.49	0	G|0.921;C|0.079	0.079	strong	.	DIDO1	321	.	NM_001193369	exon16	c.C5123G	p.S1708C	CCAGCAGAATGAA	.	PASS	Atlas-SNP
IGSF8	93185	hgsc.bcm.edu	37	1	160064697	160064697	+	Missense_Mutation	SNP	C	C	T	rs200550632	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	54	69	0	0.627907	0	C|1.000;T|0.000	0.000	strong	.	IGSF8	59	.	NM_052868	exon2	c.G404A	p.R135H	AGGTAGCGGGTAT	.	PASS	Atlas-SNP
APLF	200558	hgsc.bcm.edu	37	2	68765205	68765205	+	Missense_Mutation	SNP	C	C	T	rs13404469	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	187	94	203	1	0.502674	0.00492611	C|0.910;T|0.090	0.090	strong	.	APLF	69	.	NM_173545	exon7	c.C1006T	p.L336F	GACTCACTTCAGG	.	PASS	Atlas-SNP
SIGLEC6	946	hgsc.bcm.edu	37	19	52034469	52034469	+	Silent	SNP	C	C	T	rs1993462	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	40	16	63	0	0.4	0	C|0.860;N|0.000	.	strong	.	SIGLEC6	142	.	NM_001177549	exon2	c.G372A	p.K124K	TTTGGACTTCAAC	.	PASS	Atlas-SNP
RELN	5649	hgsc.bcm.edu	37	7	103251161	103251161	+	Missense_Mutation	SNP	G	G	C	rs362691	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	54	28	61	0	0.518519	0	C|0.101;G|0.899;N|0.000	0.101	strong	.	RELN	593	.	NM_173054	exon22	c.C2989G	p.L997V	GAAGAAGCACTAT	.	PASS	Atlas-SNP
HIST1H2BF	8343	hgsc.bcm.edu	37	6	26199822	26199822	+	Silent	SNP	A	A	G	rs41266807	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	167	110	191	1	0.658683	0.0052356	A|0.844;G|0.156	0.156	strong	.	HIST1H2BF	25	.	NM_003522	exon1	c.A36G	p.K12K	TCCAAAAAAGGGC	.	PASS	Atlas-SNP
LYSMD3	116068	hgsc.bcm.edu	37	5	89820984	89820984	+	Silent	SNP	T	T	C	rs10069050	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	183	66	183	0	0.360656	0	T|0.410;C|0.590	0.590	strong	.	LYSMD3	25	.	NM_198273	exon2	c.A123G	p.E41E	TCGAAGTTCATAC	.	PASS	Atlas-SNP
CALU	813	hgsc.bcm.edu	37	7	128394606	128394606	+	Missense_Mutation	SNP	C	C	T	rs2307040	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	117	57	157	0	0.487179	0	C|0.785;T|0.215	0.215	strong	CALU_ENST00000542996,NS,carcinoma,0,1	CALU	42	1	NM_001199672	exon4	c.C269T	p.A90V	TAGACGCGGATAA	.	PASS	Atlas-SNP
CNTN6	27255	hgsc.bcm.edu	37	3	1424850	1424850	+	Silent	SNP	T	T	G	rs2291100	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	177	87	214	0	0.491525	0	T|0.724;G|0.276	0.276	strong	.	CNTN6	245	.	NM_014461	exon18	c.T2391G	p.S797S	CTACTCTGGGGAA	.	PASS	Atlas-SNP
TDG	6996	hgsc.bcm.edu	37	12	104376700	104376700	+	Missense_Mutation	SNP	A	A	C	rs61937630	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	242	14	212	0	0.0578512	0	.	.	weak	TDG,extremity,malignant_melanoma,0,1	TDG	43	1	NM_003211	exon5	c.A602C	p.K201T	GCAGCAAAGATCT	.	PASS	Atlas-SNP
CENPQ	55166	hgsc.bcm.edu	37	6	49439805	49439805	+	Missense_Mutation	SNP	G	G	A	rs4267943	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	46	26	50	0	0.565217	0	G|0.653;A|0.347	0.347	strong	.	CENPQ	23	.	NM_018132	exon4	c.G187A	p.G63R	AAACACGGAAAGA	.	PASS	Atlas-SNP
MLF1IP	79682	hgsc.bcm.edu	37	4	185634144	185634144	+	Missense_Mutation	SNP	T	T	C	rs4616798	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	39	22	69	0	0.564103	0	T|0.826;C|0.174	0.174	strong	.	MLF1IP	33	.	NM_024629	exon7	c.A642G	p.I214M	ATGAGATATCTTC	.	PASS	Atlas-SNP
E2F1	1869	hgsc.bcm.edu	37	20	32266134	32266134	+	Missense_Mutation	SNP	C	C	T	rs35385772	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	98	45	115	0	0.459184	0	C|0.980;T|0.020	0.020	strong	.	E2F1	41	.	NM_005225	exon4	c.G598A	p.G200S	GTCCGCCGACGCC	.	PASS	Atlas-SNP
IRX1	79192	hgsc.bcm.edu	37	5	3600136	3600136	+	Silent	SNP	G	G	A	rs61746094	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	125	116	112	0	0.928	0	G|0.920;A|0.080	0.080	strong	.	IRX1	106	.	NM_024337	exon2	c.G1074A	p.L358L	CTTCCTGCCTAGC	.	PASS	Atlas-SNP
TRAPPC10	7109	hgsc.bcm.edu	37	21	45502844	45502844	+	Missense_Mutation	SNP	T	T	G	rs915877	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	136	41	145	0	0.301471	0	T|0.954;G|0.046	0.046	strong	.	TRAPPC10	109	.	NM_003274	exon14	c.T1899G	p.I633M	CAGCATTGAGAAA	.	PASS	Atlas-SNP
ADRA1A	148	hgsc.bcm.edu	37	8	26628028	26628028	+	Missense_Mutation	SNP	A	A	G	rs1048101	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	24	100	0	0.282353	0	T|0.003;G|0.595	0.595	strong	.	ADRA1A	337	.	NM_033303	exon2	c.T1039C	p.C347R	TTCTGCAGAGACA	.	PASS	Atlas-SNP
PCNT	5116	hgsc.bcm.edu	37	21	47808679	47808679	+	Missense_Mutation	SNP	C	C	T	rs7279204	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	89	27	78	0	0.303371	0	C|0.883;T|0.117	0.117	strong	PCNT,face,carcinoma,-1,1	PCNT	283	1	NM_006031	exon18	c.C3487T	p.R1163C	GCCCTGCGCAGGC	.	PASS	Atlas-SNP
CEP72	55722	hgsc.bcm.edu	37	5	640705	640705	+	Missense_Mutation	SNP	A	A	G	rs868649	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	42	62	0	0.591549	0	T|0.001;G|0.251	0.251	strong	.	CEP72	53	.	NM_018140	exon9	c.A1525G	p.T509A	CACCACACACACA	.	PASS	Atlas-SNP
SLC9C1	285335	hgsc.bcm.edu	37	3	111985107	111985107	+	Missense_Mutation	SNP	T	T	C	rs9872691	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	208	207	246	0	0.995192	0	T|0.705;C|0.295	0.295	strong	.	.	.	.	NM_183061	exon8	c.A856G	p.I286V	CTTCAATTGCTGC	.	PASS	Atlas-SNP
ZNF750	79755	hgsc.bcm.edu	37	17	80789468	80789468	+	Missense_Mutation	SNP	G	G	A	rs35653278	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	171	85	207	1	0.497076	0.00483092	G|0.934;A|0.066	0.066	strong	.	ZNF750	60	.	NM_024702	exon2	c.C863T	p.P288L	GGCCCCGGGTGAG	.	PASS	Atlas-SNP
MANSC1	54682	hgsc.bcm.edu	37	12	12483030	12483030	+	Silent	SNP	C	C	T	rs75750739	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	80	38	72	0	0.475	0	C|0.995;T|0.005	0.005	strong	.	MANSC1	38	.	NM_018050	exon4	c.G1227A	p.S409S	TGATTCCGAGAGG	.	PASS	Atlas-SNP
WWP2	11060	hgsc.bcm.edu	37	16	69963355	69963355	+	Silent	SNP	G	G	A	rs1566452	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	150	150	156	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
MUC4	4585	hgsc.bcm.edu	37	3	195508115	195508115	+	Missense_Mutation	SNP	T	T	G	rs77145082	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	13	65	2	0.158537	0.0307692	G|1.000;|0.000	1.000	weak	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.A10336C	p.T3446P	AGGAAGTGCTGGT	.	scavenged	Atlas-SNP
NDRG4	65009	hgsc.bcm.edu	37	16	58542901	58542901	+	Silent	SNP	G	G	A	rs867583	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	107	43	90	0	0.401869	0	G|0.696;A|0.304	0.304	strong	.	NDRG4	29	.	NM_001130487	exon13	c.G921A	p.T307T	CACTACGACCTTC	.	PASS	Atlas-SNP
SFSWAP	6433	hgsc.bcm.edu	37	12	132237750	132237750	+	Silent	SNP	C	C	T	rs1051219	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	155	90	196	0	0.580645	0	C|0.832;T|0.168	0.168	strong	.	SFSWAP	69	.	NM_001261411	exon8	c.C1164T	p.D388D	AATCGACGTGACT	.	PASS	Atlas-SNP
PPP1R21	129285	hgsc.bcm.edu	37	2	48687054	48687054	+	Silent	SNP	A	A	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	334	33	166	0	0.0988024	0	.	.	none	.	PPP1R21	47	.	NM_152994	exon5	c.A537C	p.L179L	TAAACTAGAAGTA	.	PASS	Atlas-SNP
METTL11B	149281	hgsc.bcm.edu	37	1	170135669	170135669	+	Silent	SNP	C	C	T	rs6427234	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	50	31	60	0	0.62	0	C|0.725;T|0.275	0.275	strong	.	METTL11B	18	.	NM_001136107	exon3	c.C357T	p.C119C	AGACTGCGCCTTG	.	PASS	Atlas-SNP
FBN3	84467	hgsc.bcm.edu	37	19	8145928	8145928	+	Missense_Mutation	SNP	C	C	T	rs3848570	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	23	9	28	0	0.391304	0	C|0.971;T|0.029	0.029	strong	.	FBN3	300	.	NM_032447	exon58	c.G7412A	p.R2471H	GGACAGCGGCAGG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195507228	195507228	+	Missense_Mutation	SNP	G	G	C	rs375915811	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	19	65	0	0.24359	0	.	.	weak	MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	NM_018406	exon2	c.C11223G	p.H3741Q	GGTGACGTGACCT	.	PASS	Atlas-SNP
ITPR2	3709	hgsc.bcm.edu	37	12	26648092	26648092	+	Silent	SNP	C	C	T	rs2230381	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	50	129	0	0.574713	0	C|0.868;T|0.132	0.132	strong	.	ITPR2	270	.	NM_002223	exon38	c.G5175A	p.Q1725Q	TCCCACCTGTGCA	.	PASS	Atlas-SNP
COL9A1	1297	hgsc.bcm.edu	37	6	70984436	70984436	+	Missense_Mutation	SNP	A	A	G	rs592121	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	28	12	50	0	0.428571	0	A|0.531;G|0.469	0.469	strong	COL9A1_ENST00000320755,NS,adenoma,0,2	COL9A1	228	2	NM_001851	exon11	c.T1015C	p.S339P	CCTTTGACCCAAT	.	PASS	Atlas-SNP
TSPAN17	26262	hgsc.bcm.edu	37	5	176081907	176081907	+	Silent	SNP	C	C	T	rs11267007	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	218	119	207	1	0.545872	0.00483092	C|0.791;G|0.000;N|0.001;T|0.208	0.208	strong	TSPAN17,NS,carcinoma,0,1	TSPAN17	33	1	NM_001006616	exon5	c.C468T	p.C156C	TTGCTGCGGAGCC	.	PASS	Atlas-SNP
TLN2	83660	hgsc.bcm.edu	37	15	63102153	63102153	+	Silent	SNP	C	C	T	rs150114385	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	201	123	180	0	0.61194	0	C|0.997;T|0.003	0.003	strong	.	TLN2	253	.	NM_015059	exon49	c.C6693T	p.D2231D	CAGTGACGAGGTG	.	PASS	Atlas-SNP
OPLAH	26873	hgsc.bcm.edu	37	8	145113241	145113241	+	Missense_Mutation	SNP	T	T	G	rs3935209	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	28	28	30	1	1	0.0333333	T|0.812;G|0.188	0.188	strong	OPLAH,NS,carcinoma,0,1	OPLAH	78	1	NM_017570	exon7	c.A850C	p.S284R	CAGCACTGGAGCC	.	scavenged	Atlas-SNP
TOP2A	7153	hgsc.bcm.edu	37	17	38547868	38547868	+	Missense_Mutation	SNP	C	C	T	rs34300454	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	136	60	134	0	0.441176	0	C|0.955;T|0.045	0.045	strong	.	TOP2A	124	.	NM_001067	exon33	c.G4157A	p.G1386D	ACACTGCCCTTAA	.	PASS	Atlas-SNP
ABP1	26	hgsc.bcm.edu	37	7	150555915	150555915	+	Silent	SNP	A	A	G	rs10893	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	154	69	146	0	0.448052	0	A|0.571;G|0.429	0.429	strong	.	ABP1	92	.	NM_001091	exon3	c.A1635G	p.P545P	GAGCCCAAGACAC	.	PASS	Atlas-SNP
ITGAM	3684	hgsc.bcm.edu	37	16	31343005	31343005	+	Missense_Mutation	SNP	C	C	T	rs1143678	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	157	86	111	0	0.547771	0	C|0.864;T|0.136	0.136	strong	.	ITGAM	137	.	NM_001145808	exon30	c.C3439T	p.P1147S	GGGGGTCCCCCGG	.	PASS	Atlas-SNP
ZNF462	58499	hgsc.bcm.edu	37	9	109691676	109691676	+	Missense_Mutation	SNP	A	A	G	rs3814538	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	60	26	69	0	0.433333	0	G|0.519;N|0.001	0.519	strong	.	ZNF462	322	.	NM_021224	exon3	c.A5483G	p.N1828S	GAGGCAACTTTGA	.	PASS	Atlas-SNP
CYP4F12	66002	hgsc.bcm.edu	37	19	15784377	15784377	+	Missense_Mutation	SNP	C	C	T	rs16995376	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	90	49	83	0	0.544444	0	C|0.775;T|0.225	0.225	strong	.	CYP4F12	89	.	NM_023944	exon2	c.C38T	p.P13L	TCAGACCGGTGGC	.	PASS	Atlas-SNP
NUMB	8650	hgsc.bcm.edu	37	14	73753886	73753886	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	396	4	419	0	0.010101	0	.	.	none	NUMB,NS,lymphoid_neoplasm,0,1	NUMB	56	1	NM_001005744	exon9	c.G587A	p.R196H	GTGACACGGAATG	.	scavenged	Atlas-SNP
BTN3A2	11118	hgsc.bcm.edu	37	6	26370572	26370572	+	Silent	SNP	C	C	T	rs34878490	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	81	80	90	0	0.987654	0	C|0.923;T|0.077	0.077	strong	.	BTN3A2	44	.	NM_001197246	exon3	c.C456T	p.V152V	TCACGTCGAAGTG	.	PASS	Atlas-SNP
MFAP3	4238	hgsc.bcm.edu	37	5	153432970	153432970	+	Silent	SNP	C	C	T	rs2255493	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	94	52	99	0	0.553191	0	C|0.346;T|0.654	0.654	strong	.	MFAP3	20	.	NM_005927	exon3	c.C786T	p.D262D	AGTGGACGACCCT	.	PASS	Atlas-SNP
IL27RA	9466	hgsc.bcm.edu	37	19	14142705	14142705	+	Silent	SNP	C	C	T	rs113593439	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	68	42	69	0	0.617647	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
MRPL28	10573	hgsc.bcm.edu	37	16	420140	420140	+	Missense_Mutation	SNP	G	G	A	rs3194151	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	40	40	52	0	1	0	G|0.896;A|0.104	0.104	strong	.	MRPL28	15	.	NM_006428	exon2	c.C79T	p.H27Y	GGTAGTGGCCGGG	.	PASS	Atlas-SNP
SNRNP48	154007	hgsc.bcm.edu	37	6	7590624	7590624	+	Missense_Mutation	SNP	C	C	T	rs2757594	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	100	58	101	0	0.58	0	C|0.778;T|0.222	0.222	strong	.	SNRNP48	32	.	NM_152551	exon1	c.C134T	p.P45L	TGGATCCCGGGGA	.	PASS	Atlas-SNP
ZNF426	79088	hgsc.bcm.edu	37	19	9641722	9641722	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	111	27	113	0	0.243243	0	.	.	none	.	ZNF426	56	.	NM_024106	exon7	c.C347T	p.T116I	CACTGGGTTTCAA	.	PASS	Atlas-SNP
DYSF	8291	hgsc.bcm.edu	37	2	71795152	71795152	+	Silent	SNP	A	A	T	rs2288355	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	247	117	245	0	0.473684	0	A|0.354;T|0.646	0.646	strong	.	DYSF	536	.	NM_001130982	exon26	c.A2679T	p.S893S	GCTCTCAGTGGAT	.	PASS	Atlas-SNP
MUC6	4588	hgsc.bcm.edu	37	11	1016851	1016851	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	1061	37	754	22	0.0348728	0.0291777	.	.	none	MUC6_ENST00000421673,NS,carcinoma,+2,2	MUC6	408	2	NM_005961	exon31	c.A5950G	p.M1984V	CAGTCATAGGACC	.	scavenged	Atlas-SNP
TTLL4	9654	hgsc.bcm.edu	37	2	219602499	219602499	+	Missense_Mutation	SNP	G	G	C	rs3731877	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	144	144	141	0	1	0	G|0.525;C|0.475	0.475	strong	TTLL4,brain,glioma,0,1	TTLL4	96	1	NM_014640	exon3	c.G100C	p.E34Q	CCACCTGAGAAAC	.	PASS	Atlas-SNP
KIAA0226	9711	hgsc.bcm.edu	37	3	197432029	197432029	+	Silent	SNP	C	C	A	rs60457064	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	54	32	62	0	0.592593	0	C|0.877;A|0.123	0.123	strong	.	KIAA0226	136	.	NM_014687	exon3	c.G237T	p.T79T	GTAATCCGTCTGG	.	PASS	Atlas-SNP
OR2D3	120775	hgsc.bcm.edu	37	11	6942628	6942628	+	Silent	SNP	A	A	C	rs11605995	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	268	223	283	0	0.83209	0	A|0.655;C|0.345	0.345	strong	.	OR2D3	51	.	NM_001004684	exon1	c.A396C	p.A132A	GCTGGCAGTGATG	.	PASS	Atlas-SNP
CHRNA3	1136	hgsc.bcm.edu	37	15	78911181	78911181	+	Silent	SNP	T	T	C	rs8040868	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	90	90	93	0	1	0	T|0.616;C|0.384	0.384	strong	.	CHRNA3	56	.	NM_000743	exon2	c.A159G	p.V53V	GTTGGCTACAGGC	.	PASS	Atlas-SNP
WDFY4	57705	hgsc.bcm.edu	37	10	49998824	49998824	+	Silent	SNP	C	C	T	rs10857644	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	161	79	165	1	0.490683	0.00606061	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
UGT2B7	7364	hgsc.bcm.edu	37	4	69964337	69964337	+	Silent	SNP	A	A	T	rs7438284	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	138	90	137	0	0.652174	0	A|0.452;T|0.548	0.548	strong	UGT2B7,NS,carcinoma,0,1	UGT2B7	79	1	NM_001074	exon2	c.A801T	p.P267P	GTTTCCATATCCA	.	PASS	Atlas-SNP
CDH23	64072	hgsc.bcm.edu	37	10	73434888	73434888	+	Missense_Mutation	SNP	G	G	C	rs1227049	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	26	89	0	0.448276	0	G|0.821;C|0.179	0.179	strong	.	CDH23	365	.	NM_022124	exon14	c.G1469C	p.G490A	ATGCAGGCACCTT	.	PASS	Atlas-SNP
OR5P2	120065	hgsc.bcm.edu	37	11	7817852	7817852	+	Missense_Mutation	SNP	C	C	G	rs76615008	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	178	141	197	0	0.792135	0	C|0.738;G|0.262	0.262	strong	.	OR5P2	68	.	NM_153444	exon1	c.G638C	p.C213S	ATGTAGCAGACGG	.	PASS	Atlas-SNP
OR2T4	127074	hgsc.bcm.edu	37	1	248525639	248525639	+	Missense_Mutation	SNP	A	A	T	rs76878172	alternate_allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	508	225	662	312	0.442913	0.471299	.	.	alt	OR2T4,brain,glioma,0,1	OR2T4	126	1	NM_001004696	exon1	c.A757T	p.I253F	TTACTCATCCTCC	.	scavenged	Atlas-SNP
KCTD16	57528	hgsc.bcm.edu	37	5	143853421	143853421	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	198	3	190	0	0.0151515	0	.	.	none	KCTD16,NS,carcinoma,+1,3	KCTD16	70	3	NM_020768	exon4	c.G1031A	p.R344H	TGGACCGTCCCAT	.	scavenged	Atlas-SNP
IL12RB1	3594	hgsc.bcm.edu	37	19	18188408	18188408	+	Missense_Mutation	SNP	C	C	T	rs11575926	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	94	47	121	0	0.5	0	C|0.900;T|0.100	0.100	strong	.	IL12RB1	92	.	NM_153701	exon5	c.G467A	p.R156H	TCCATACGCAGCT	.	PASS	Atlas-SNP
OR1S2	219958	hgsc.bcm.edu	37	11	57970981	57970981	+	Missense_Mutation	SNP	C	C	T	rs11229278	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	103	24	120	0	0.23301	0	C|0.931;T|0.069	0.069	strong	.	OR1S2	119	.	NM_001004459	exon1	c.G673A	p.V225I	TGAGTACAAAGGG	.	PASS	Atlas-SNP
UBR2	23304	hgsc.bcm.edu	37	6	42627430	42627430	+	Silent	SNP	C	C	T	rs6916713	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	77	40	80	0	0.519481	0	C|0.739;T|0.261	0.261	strong	.	UBR2	134	.	NM_015255	exon30	c.C3279T	p.G1093G	ACTGGGCCCCGCA	.	PASS	Atlas-SNP
LTN1	26046	hgsc.bcm.edu	37	21	30339120	30339120	+	Missense_Mutation	SNP	C	C	A	rs34191159	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	25	69	0	0.333333	0	C|0.836;A|0.164	0.164	strong	.	LTN1	141	.	NM_015565	exon10	c.G1831T	p.G611C	CCCAGCCTTCAAT	.	PASS	Atlas-SNP
ROBO1	6091	hgsc.bcm.edu	37	3	78717343	78717343	+	Silent	SNP	C	C	T	rs2271151	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	96	52	99	0	0.541667	0	C|0.699;T|0.301	0.301	strong	.	ROBO1	833	.	NM_002941	exon13	c.G1740A	p.S580S	TTGCCACGATAAT	.	PASS	Atlas-SNP
PGLYRP2	114770	hgsc.bcm.edu	37	19	15580658	15580658	+	Missense_Mutation	SNP	G	G	A	rs2304200	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	33	25	30	0	0.757576	0	G|0.952;A|0.048	0.048	strong	.	PGLYRP2	116	.	NM_052890	exon4	c.C1426T	p.R476W	AGCCCCGGGAGTT	.	PASS	Atlas-SNP
ANKRD27	84079	hgsc.bcm.edu	37	19	33096786	33096786	+	Silent	SNP	G	G	A	rs7247420	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	122	47	220	0	0.385246	0	G|0.792;A|0.208	0.208	strong	.	ANKRD27	86	.	NM_032139	exon24	c.C2448T	p.Y816Y	GCAGGCGTAAATG	.	PASS	Atlas-SNP
CHRNA9	55584	hgsc.bcm.edu	37	4	40339250	40339250	+	Silent	SNP	T	T	C	rs55998310	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	156	70	137	0	0.448718	0	T|0.993;C|0.007	0.007	strong	.	CHRNA9	53	.	NM_017581	exon3	c.T234C	p.T78T	TCTGACTGCTTAT	.	PASS	Atlas-SNP
SLC5A10	125206	hgsc.bcm.edu	37	17	18855611	18855611	+	Silent	SNP	T	T	C	rs2076562	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	190	92	176	0	0.484211	0	T|0.605;C|0.395	0.395	strong	SLC5A10,NS,carcinoma,0,1	SLC5A10	55	1	NM_001042450	exon1	c.T93C	p.N31N	TCTGAATGTGGCC	.	PASS	Atlas-SNP
ATAD5	79915	hgsc.bcm.edu	37	17	29187497	29187497	+	Silent	SNP	A	A	G	rs9896095	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	150	78	217	0	0.52	0	A|0.862;G|0.138	0.138	strong	.	ATAD5	150	.	NM_024857	exon10	c.A3003G	p.V1001V	ACTCGTAGAAGCA	.	PASS	Atlas-SNP
CTDP1	9150	hgsc.bcm.edu	37	18	77455227	77455227	+	Missense_Mutation	SNP	C	C	T	rs115044443	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	119	40	193	0	0.336134	0	C|0.977;T|0.023	0.023	strong	.	CTDP1	67	.	NM_004715	exon2	c.C317T	p.A106V	GTAGAGCGGTTCT	.	PASS	Atlas-SNP
PTPRG	5793	hgsc.bcm.edu	37	3	61975382	61975382	+	Missense_Mutation	SNP	T	T	C	rs62620047	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	127	63	125	0	0.496063	0	T|0.887;C|0.113	0.113	strong	.	PTPRG	153	.	NM_002841	exon3	c.T274C	p.Y92H	GACCAGTATGCGC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195513812	195513812	+	Missense_Mutation	SNP	T	T	A	rs201142885	byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	21	2	49	0	0.0952381	0	T|0.976;A|0.023	0.023	strong	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.A4639T	p.T1547S	CACCTGTGGATGC	.	scavenged	Atlas-SNP
FUT5	2527	hgsc.bcm.edu	37	19	5867154	5867154	+	Missense_Mutation	SNP	G	G	A	rs61744945	byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	49	158	0	0.505155	0	G|0.900;A|0.100	0.100	strong	.	FUT5	29	.	NM_002034	exon2	c.C583T	p.P195S	GCGGTGGGTGGGC	.	PASS	Atlas-SNP
SMYD4	114826	hgsc.bcm.edu	37	17	1690752	1690752	+	Missense_Mutation	SNP	G	G	A	rs11549830	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	126	125	178	0	0.992063	0	G|0.609;A|0.391	0.391	strong	.	SMYD4	50	.	NM_052928	exon6	c.C1684T	p.R562W	TAATCCGCTGTGA	.	PASS	Atlas-SNP
COL4A3	1285	hgsc.bcm.edu	37	2	228131752	228131752	+	Silent	SNP	G	G	A	rs34019152	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	47	24	65	0	0.510638	0	G|0.905;A|0.095	0.095	strong	.	COL4A3	293	.	NM_000091	exon23	c.G1452A	p.G484G	CCCAGGGCCTCCC	.	PASS	Atlas-SNP
MMP3	4314	hgsc.bcm.edu	37	11	102709425	102709425	+	Silent	SNP	A	A	G	rs520540	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	62	62	73	0	1	0	A|0.461;G|0.539	0.539	strong	.	MMP3	60	.	NM_002422	exon8	c.T1086C	p.A362A	TCTGATAGCCCAG	.	PASS	Atlas-SNP
TMEM25	84866	hgsc.bcm.edu	37	11	118404804	118404804	+	Silent	SNP	G	G	A	rs6589664	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	108	75	130	0	0.694444	0	G|0.738;A|0.262	0.262	strong	TMEM25,NS,carcinoma,0,1	TMEM25	24	1	NM_032780	exon7	c.G897A	p.P299P	CCTCCCGTCCAAC	.	PASS	Atlas-SNP
GCNT1	2650	hgsc.bcm.edu	37	9	79118329	79118329	+	Silent	SNP	G	G	A	rs1057406	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	210	91	273	0	0.433333	0	G|0.774;A|0.226	0.226	strong	.	GCNT1	52	.	NM_001490	exon4	c.G1032A	p.L344L	TGATCTGTCTGAC	.	PASS	Atlas-SNP
OR7D4	125958	hgsc.bcm.edu	37	19	9324863	9324863	+	Silent	SNP	G	G	A	rs8109935	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	39	71	0	0.52	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
FDXACB1	91893	hgsc.bcm.edu	37	11	111747297	111747297	+	Silent	SNP	A	A	G	rs7124696	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	99	28	139	0	0.282828	0	A|0.738;G|0.262	0.262	strong	.	FDXACB1	74	.	NM_138378	exon4	c.T600C	p.F200F	ACCTTCAAAAGGT	.	PASS	Atlas-SNP
HEMGN	55363	hgsc.bcm.edu	37	9	100692648	100692648	+	Silent	SNP	G	G	T	rs35527067	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	214	114	268	1	0.53271	0.00373134	G|0.992;T|0.008	0.008	strong	.	HEMGN	55	.	NM_197978	exon3	c.C1029A	p.I343I	TTCTTGGATTGTT	.	PASS	Atlas-SNP
HJURP	55355	hgsc.bcm.edu	37	2	234749258	234749258	+	Missense_Mutation	SNP	T	T	C	rs10511	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	124	57	146	0	0.459677	0	A|0.153;C|0.110	0.110	strong	.	HJURP	72	.	NM_018410	exon8	c.A2168G	p.E723G	TACCTCTCTTCTG	.	PASS	Atlas-SNP
HLA-G	3135	hgsc.bcm.edu	37	6	29795993	29795993	+	Silent	SNP	G	G	A	rs1130355	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	98	85	0	0.970297	0	G|0.500;A|0.500	0.500	strong	.	HLA-G	90	.	NM_002127	exon3	c.G243A	p.P81P	GGGGCCGGAGTAT	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	47	21	85	0	0.446809	0	T|0.541;C|0.459	0.459	strong	.	GPATCH1	79	.	NM_018025	exon11	c.T1427C	p.L476P	CCCAGCTCTCCCC	.	PASS	Atlas-SNP
PBRM1	55193	hgsc.bcm.edu	37	3	52643685	52643685	+	Silent	SNP	T	T	C	rs3755806	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	181	179	187	0	0.98895	0	T|0.658;C|0.342	0.342	strong	PBRM1_ENST00000356770,rectum,carcinoma,0,3	PBRM1	1252	3	NM_018313	exon17	c.A2211G	p.T737T	ATTGTATGTACAG	.	PASS	Atlas-SNP
SLC2A11	66035	hgsc.bcm.edu	37	22	24224655	24224655	+	Missense_Mutation	SNP	G	G	A	rs9608213	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	21	19	15	0	0.904762	0	G|0.678;A|0.322	0.322	strong	.	SLC2A11	32	.	NM_030807	exon8	c.G716A	p.R239Q	TACGGCGGCTCCG	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29910742	29910742	+	Missense_Mutation	SNP	G	G	C	rs78306866	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	170	165	261	0	0.970588	0	C|0.643;G|0.357	0.643	strong	HLA-A,NS,carcinoma,0,1	HLA-A	89	1	NM_001242758	exon2	c.G282C	p.Q94H	GGCCCAGTCACAG	.	PASS	Atlas-SNP
ABCG5	64240	hgsc.bcm.edu	37	2	44040401	44040401	+	Missense_Mutation	SNP	G	G	C	rs6720173	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	213	213	128	0	1	0	G|0.792;C|0.208	0.208	strong	.	ABCG5	72	.	NM_022436	exon13	c.C1810G	p.Q604E	TTCCTTGAGTGAA	.	PASS	Atlas-SNP
C19orf21	126353	hgsc.bcm.edu	37	19	757234	757234	+	Silent	SNP	C	C	T	rs34384654	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	63	31	111	0	0.492063	0	C|0.986;T|0.014	0.014	strong	C19orf21,NS,carcinoma,+2,1	C19orf21	56	1	NM_173481	exon2	c.C288T	p.R96R	TTACCGCCTGGGC	.	PASS	Atlas-SNP
CCDC168	643677	hgsc.bcm.edu	37	13	103390322	103390322	+	Missense_Mutation	SNP	T	T	C	rs112442443	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	245	124	301	1	0.506122	0.00332226	T|0.995;C|0.005	0.005	strong	.	.	.	.	NM_001146197	exon4	c.A12725G	p.E4242G	TGTTGCTCTTCAA	.	PASS	Atlas-SNP
ARHGAP42	143872	hgsc.bcm.edu	37	11	100814570	100814570	+	Silent	SNP	A	A	G	rs543146	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	43	7	57	0	0.162791	0	A|0.643;G|0.357	0.357	strong	.	ARHGAP42	32	.	NM_152432	exon10	c.A1014G	p.R338R	CAAACGATTCTGC	.	PASS	Atlas-SNP
WRAP53	55135	hgsc.bcm.edu	37	17	7606722	7606722	+	Missense_Mutation	SNP	C	C	G	rs7640	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	23	68	0	0.396552	0	C|0.591;G|0.409	0.409	strong	WRAP53,NS,carcinoma,0,1	WRAP53	35	1	NM_001143991	exon11	c.C1565G	p.A522G	GGGGGGCGCCAGA	.	PASS	Atlas-SNP
FAM86C1	55199	hgsc.bcm.edu	37	11	71507158	71507158	+	Silent	SNP	A	A	G	rs138882787	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	187	39	178	0	0.208556	0	A|0.998;G|0.002	0.002	strong	.	FAM86C1	27	.	NM_018172	exon4	c.A357G	p.T119T	TTCTACATGGCCC	.	PASS	Atlas-SNP
GDPGP1	390637	hgsc.bcm.edu	37	15	90784930	90784930	+	Missense_Mutation	SNP	C	C	A	rs10152994	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	119	47	70	0	0.394958	0	C|0.833;A|0.167	0.167	strong	.	.	.	.	NM_001013657	exon4	c.C790A	p.P264T	CCAGGGCCTGACT	.	PASS	Atlas-SNP
CCDC53	51019	hgsc.bcm.edu	37	12	102455729	102455729	+	Silent	SNP	G	G	A	rs3751129	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	38	20	41	0	0.526316	0	G|0.694;A|0.306	0.306	strong	.	CCDC53	14	.	NM_016053	exon1	c.C12T	p.D4D	AAGCCCGTCCTCA	.	PASS	Atlas-SNP
F2R	2149	hgsc.bcm.edu	37	5	76028669	76028669	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	250	49	249	0	0.196	0	.	.	none	.	F2R	58	.	NM_001992	exon2	c.C619T	p.P207S	GTGTATCCCATGC	.	PASS	Atlas-SNP
CMYA5	202333	hgsc.bcm.edu	37	5	79032562	79032562	+	Silent	SNP	A	A	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	106	3	128	1	0.0283019	0.0078125	.	.	none	CMYA5_ENST00000446378,lower_third,carcinoma,0,2	CMYA5	643	2	NM_153610	exon2	c.A7974G	p.V2658V	TCTAGTATTAGAA	.	scavenged	Atlas-SNP
DTX2	113878	hgsc.bcm.edu	37	7	76111938	76111938	+	Missense_Mutation	SNP	G	G	A	rs12534498	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	136	68	182	0	0.5	0	G|0.988;A|0.012	0.012	strong	.	DTX2	64	.	NM_001102596	exon2	c.G382A	p.V128I	GCCAGCGTCTGTG	.	PASS	Atlas-SNP
ADAMTS18	170692	hgsc.bcm.edu	37	16	77328990	77328990	+	Missense_Mutation	SNP	C	C	A	rs12935394	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	104	35	90	0	0.336538	0	C|0.893;A|0.107	0.107	strong	.	ADAMTS18	270	.	NM_199355	exon19	c.G2836T	p.A946S	CACAGGCCTTGCT	.	PASS	Atlas-SNP
KLHL1	57626	hgsc.bcm.edu	37	13	70293616	70293616	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	15	106	0	0.182927	0	.	.	none	.	KLHL1	164	.	NM_020866	exon9	c.T1900A	p.C634S	TCTTACACATGGG	.	PASS	Atlas-SNP
CCDC67	159989	hgsc.bcm.edu	37	11	93129483	93129483	+	Missense_Mutation	SNP	G	G	C	rs12288277	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	116	115	154	0	0.991379	0	C|0.236;G|0.764	0.236	strong	.	CCDC67	57	.	NM_181645	exon11	c.G1318C	p.E440Q	CCCGGAGAATACA	.	PASS	Atlas-SNP
PARL	55486	hgsc.bcm.edu	37	3	183560195	183560195	+	Silent	SNP	A	A	G	rs13091	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	64	32	86	0	0.5	0	A|0.512;G|0.488	0.488	strong	PARL,NS,carcinoma,0,1	PARL	32	1	NM_018622	exon6	c.T648C	p.H216H	GGAGAAATGACTG	.	PASS	Atlas-SNP
CINP	51550	hgsc.bcm.edu	37	14	102815042	102815042	+	Missense_Mutation	SNP	C	C	T	rs7011	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	84	42	111	0	0.5	0	C|0.795;N|0.000	.	strong	CINP,NS,carcinoma,-1,1	CINP	17	1	NM_001177611	exon5	c.G536A	p.R179H	ACCGTGCGCTTCA	.	PASS	Atlas-SNP
CALB2	794	hgsc.bcm.edu	37	16	71411636	71411636	+	Missense_Mutation	SNP	G	G	A	rs11545954	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	91	54	69	0	0.593407	0	G|0.867;A|0.133	0.133	strong	.	CALB2	46	.	NM_007088	exon4	c.G328A	p.A110T	TCCAGCGCCGAGT	.	PASS	Atlas-SNP
LRRK2	120892	hgsc.bcm.edu	37	12	40677936	40677936	+	Splice_Site	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	43	13	39	0	0.302326	0	.	.	none	.	LRRK2	763	.	NM_198578	exon19	c.2500+1G>A	.	AAACAAGTAAGTA	.	PASS	Atlas-SNP
GAS2L2	246176	hgsc.bcm.edu	37	17	34072555	34072555	+	Missense_Mutation	SNP	G	G	A	rs3744374	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	48	19	80	0	0.395833	0	G|0.753;A|0.247	0.247	strong	GAS2L2,NS,carcinoma,0,1	GAS2L2	94	1	NM_139285	exon6	c.C1961T	p.A654V	TGGATGGCTTTGT	.	PASS	Atlas-SNP
FAM120B	84498	hgsc.bcm.edu	37	6	170627761	170627761	+	Missense_Mutation	SNP	A	A	G	rs6900199	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	36	15	49	0	0.416667	0	A|0.862;G|0.138	0.138	strong	.	FAM120B	108	.	NM_032448	exon2	c.A1283G	p.Y428C	CCATGTATACAGA	.	PASS	Atlas-SNP
CHST10	9486	hgsc.bcm.edu	37	2	101009869	101009869	+	Silent	SNP	C	C	T	rs148920749	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	249	117	296	0	0.46988	0	C|0.993;T|0.007	0.007	strong	.	CHST10	42	.	NM_004854	exon7	c.G909A	p.V303V	GTATGACACCAGG	.	PASS	Atlas-SNP
TRIM31	11074	hgsc.bcm.edu	37	6	30080231	30080231	+	Missense_Mutation	SNP	G	G	A	rs3734838	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	109	71	130	0	0.651376	0	A|0.078;G|0.922	0.078	strong	.	TRIM31	40	.	NM_007028	exon2	c.C352T	p.R118C	ATTCACGACACAC	.	PASS	Atlas-SNP
SYNE1	23345	hgsc.bcm.edu	37	6	152668215	152668215	+	Silent	SNP	C	C	T	rs144596829	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	96	70	124	0	0.729167	0	C|0.991;T|0.009	0.009	strong	SYNE1_ENST00000423061,right_upper_lobe,carcinoma,0,3	SYNE1	3227	3	NM_182961	exon73	c.G12057A	p.A4019A	GCAGATCGCTGAG	.	PASS	Atlas-SNP
PSPH	5723	hgsc.bcm.edu	37	7	56088789	56088789	+	Silent	SNP	G	G	A	rs199851385	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	165	27	140	0	0.163636	0	G|0.750;A|0.250	0.250	strong	.	PSPH	23	.	NM_004577	exon4	c.C117T	p.G39G	CTCAACGCCACAG	.	PASS	Atlas-SNP
C11orf82	220042	hgsc.bcm.edu	37	11	82643760	82643760	+	Missense_Mutation	SNP	G	G	T	rs7947780	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	38	10	44	0	0.263158	0	G|0.697;N|0.000	.	strong	.	C11orf82	71	.	NM_145018	exon6	c.G1380T	p.R460S	CAGCAGGTTATCT	.	PASS	Atlas-SNP
PPP1R26	9858	hgsc.bcm.edu	37	9	138376649	138376649	+	Missense_Mutation	SNP	T	T	C	rs3748192	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	35	19	34	0	0.542857	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
MTMR3	8897	hgsc.bcm.edu	37	22	30403996	30403996	+	Silent	SNP	C	C	T	rs2074204	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	159	81	180	0	0.509434	0	C|0.678;T|0.322	0.322	strong	.	MTMR3	106	.	NM_021090	exon11	c.C984T	p.A328A	CCGAGCCAAAGGA	.	PASS	Atlas-SNP
SEL1L2	80343	hgsc.bcm.edu	37	20	13912309	13912309	+	Missense_Mutation	SNP	G	G	A	rs41275404	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	117	66	165	0	0.564103	0	G|0.910;A|0.090	0.090	strong	SEL1L2,colon,carcinoma,0,1	SEL1L2	103	1	NM_001271539	exon3	c.C223T	p.R75C	TTTTACGTTGATT	.	PASS	Atlas-SNP
CYP8B1	1582	hgsc.bcm.edu	37	3	42915878	42915878	+	Silent	SNP	C	C	T	rs735320	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	109	58	143	0	0.53211	0	C|0.861;T|0.139	0.139	strong	.	CYP8B1	59	.	NM_004391	exon1	c.G1431A	p.P477P	GCGCTGCGGGTCA	.	PASS	Atlas-SNP
CCDC73	493860	hgsc.bcm.edu	37	11	32624405	32624405	+	Silent	SNP	C	C	T	rs201893	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	87	137	1	1	0.00729927	C|0.791;T|0.209	0.209	strong	.	CCDC73	136	.	NM_001008391	exon18	c.A3192A	p.R1064R	TCTTTTCTTTGGC	.	PASS	Atlas-SNP
MAP3K6	9064	hgsc.bcm.edu	37	1	27687466	27687466	+	Missense_Mutation	SNP	G	G	T	rs35659744	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	65	35	85	2	0.538462	0.0235294	G|0.846;T|0.154	0.154	strong	MAP3K6_ENST00000493901,brain,glioma,0,16	MAP3K6	134	16	NM_004672	exon14	c.C1866A	p.N622K	ATCCGGGTTCGTC	.	scavenged	Atlas-SNP
UNC13D	201294	hgsc.bcm.edu	37	17	73827205	73827205	+	Missense_Mutation	SNP	T	T	C	rs1135688	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	66	33	59	0	0.5	0	T|0.510;C|0.490	0.490	strong	.	UNC13D	68	.	NM_199242	exon27	c.A2599G	p.K867E	GGGCCTTGGGTGG	.	PASS	Atlas-SNP
CUL9	23113	hgsc.bcm.edu	37	6	43182906	43182906	+	Silent	SNP	C	C	T	rs76552409	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	89	39	98	0	0.438202	0	C|0.981;T|0.019	0.019	strong	.	CUL9	248	.	NM_015089	exon30	c.C5778T	p.V1926V	AGATGTCCTCTCT	.	PASS	Atlas-SNP
CCDC90A	63933	hgsc.bcm.edu	37	6	13801615	13801615	+	Missense_Mutation	SNP	T	T	C	rs3180196	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	57	29	66	0	0.508772	0	T|0.880;C|0.120	0.120	strong	CCDC90A,NS,carcinoma,0,1	CCDC90A	15	1	NM_001031713	exon4	c.A646G	p.T216A	GAAAAGTGATTTC	.	PASS	Atlas-SNP
CPS1	1373	hgsc.bcm.edu	37	2	211540507	211540507	+	Missense_Mutation	SNP	C	C	A	rs1047891	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	127	66	175	0	0.519685	0	C|0.699;A|0.301	0.301	strong	.	CPS1	485	.	NM_001122633	exon37	c.C4235A	p.T1412N	CTGCCACCCCAGT	.	PASS	Atlas-SNP
PEX6	5190	hgsc.bcm.edu	37	6	42932200	42932200	+	Missense_Mutation	SNP	G	G	T	rs1129187	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	103	101	132	0	0.980583	0	G|0.617;T|0.383	0.383	strong	PEX6,colon,carcinoma,0,1	PEX6	44	1	NM_000287	exon17	c.C2816A	p.P939Q	CTACCTGGCTCCA	.	PASS	Atlas-SNP
RFX3	5991	hgsc.bcm.edu	37	9	3247895	3247895	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	22	13	25	0	0.590909	0	.	.	none	.	RFX3	156	.	NM_002919	exon16	c.T2105C	p.V702A	GCAATAACTCCAC	.	PASS	Atlas-SNP
NOTCH1	4851	hgsc.bcm.edu	37	9	139407932	139407932	+	Silent	SNP	A	A	G	rs2229971	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	113	51	129	0	0.451327	0	A|0.484;G|0.516	0.516	strong	.	NOTCH1	1980	.	NM_017617	exon14	c.T2265C	p.N755N	ACACTCATTGTTG	.	PASS	Atlas-SNP
MYO5A	4644	hgsc.bcm.edu	37	15	52611451	52611451	+	Silent	SNP	A	A	G	rs2290332	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	250	249	217	0	0.996	0	A|0.716;G|0.284	0.284	strong	.	MYO5A	145	.	NM_000259	exon38	c.T4965C	p.D1655D	GCCCTCATCGGCG	.	PASS	Atlas-SNP
COL4A4	1286	hgsc.bcm.edu	37	2	227917090	227917090	+	Missense_Mutation	SNP	T	T	C	rs80243096	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	123	57	135	0	0.463415	0	T|0.988;C|0.012	0.012	strong	.	COL4A4	215	.	NM_000092	exon32	c.A2899G	p.I967V	AAATGATAGCCAT	.	PASS	Atlas-SNP
OR4N4	283694	hgsc.bcm.edu	37	15	22383189	22383189	+	Silent	SNP	G	G	A	rs1820851	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	141	71	72	0	0.503546	0	G|0.536;A|0.464	0.464	strong	OR4N4,NS,carcinoma,0,2	OR4N4	108	2	NM_001005241	exon1	c.G717A	p.T239T	GTCCACGTGCACC	.	PASS	Atlas-SNP
PCDHB16	57717	hgsc.bcm.edu	37	5	140563173	140563173	+	Missense_Mutation	SNP	G	G	T	rs28664170	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	94	46	118	0	0.489362	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
TSNARE1	203062	hgsc.bcm.edu	37	8	143427178	143427178	+	Missense_Mutation	SNP	C	C	G	rs33970858	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	149	24	148	0	0.161074	0	C|0.671;G|0.329	0.329	strong	TSNARE1,NS,carcinoma,0,1	TSNARE1	59	1	NM_145003	exon3	c.G164C	p.R55P	ACACAGCGGTTCT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195509689	195509689	+	Missense_Mutation	SNP	G	G	A	rs59620726	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	126	62	56	1	0.492063	0.0178571	G|0.997;A|0.003	0.003	weak	MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	NM_018406	exon2	c.C8762T	p.A2921V	GTGGATGCTGAGG	.	scavenged	Atlas-SNP
NCAM1	4684	hgsc.bcm.edu	37	11	113146033	113146033	+	Missense_Mutation	SNP	C	C	T	rs17174409	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	65	52	62	0	0.8	0	C|0.995;T|0.005	0.005	strong	.	NCAM1	372	.	NM_001242607	exon21	c.C2579T	p.T860M	CAGAAACGAAGCC	.	PASS	Atlas-SNP
FMNL2	114793	hgsc.bcm.edu	37	2	153378487	153378487	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	107	21	127	0	0.196262	0	.	.	none	.	FMNL2	75	.	NM_052905	exon2	c.A148T	p.R50W	AAAGCCAGGTTAC	.	PASS	Atlas-SNP
PDGFRB	5159	hgsc.bcm.edu	37	5	149511636	149511636	+	Silent	SNP	C	C	G	rs2228439	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	151	68	153	0	0.450331	0	C|0.992;G|0.008	0.008	strong	.	PDGFRB	142	.	NM_002609	exon8	c.G1149C	p.L383L	GCGAACCAGTGTC	.	PASS	Atlas-SNP
KRTAP4-6	81871	hgsc.bcm.edu	37	17	39296152	39296152	+	Silent	SNP	A	A	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	148	7	140	1	0.0472973	0.00714286	.	.	none	KRTAP4-6,NS,carcinoma,0,1	KRTAP4-6	46	1	NM_030976	exon1	c.T588C	p.R196R	CAAGGGACGGGGG	.	scavenged	Atlas-SNP
ESPNL	339768	hgsc.bcm.edu	37	2	239039075	239039075	+	Missense_Mutation	SNP	G	G	T	rs13006204	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	47	26	56	0	0.553191	0	G|0.611;T|0.389	0.389	strong	.	ESPNL	63	.	NM_194312	exon9	c.G1720T	p.A574S	GAGCCCGCAGGGT	.	PASS	Atlas-SNP
DERL1	79139	hgsc.bcm.edu	37	8	124031541	124031541	+	Missense_Mutation	SNP	T	T	C	rs2272722	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	100	67	94	0	0.67	0	T|0.926;C|0.074	0.074	strong	.	DERL1	27	.	NM_024295	exon7	c.A511G	p.I171V	CATTGATTACCCT	.	PASS	Atlas-SNP
SGK1	6446	hgsc.bcm.edu	37	6	134495159	134495159	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	15	82	0	0.258621	0	.	.	none	SGK1_ENST00000528577,NS,lymphoid_neoplasm,0,5	SGK1	387	5	NM_001143676	exon5	c.C497G	p.A166G	GGGTTGGCATTCA	.	PASS	Atlas-SNP
MTBP	27085	hgsc.bcm.edu	37	8	121530190	121530190	+	Silent	SNP	A	A	G	rs13258848	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	86	88	0	1	0	A|0.493;G|0.507	0.507	strong	.	MTBP	77	.	NM_022045	exon19	c.A2346G	p.E782E	AACAGAACGGTCC	.	PASS	Atlas-SNP
CATSPER1	117144	hgsc.bcm.edu	37	11	65793797	65793797	+	Silent	SNP	G	G	A	rs1893316	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	73	120	0	0.848837	0	G|0.825;A|0.175	0.175	strong	.	CATSPER1	101	.	NM_053054	exon1	c.C54T	p.N18N	ATCTGCGTTATTG	.	PASS	Atlas-SNP
CENPE	1062	hgsc.bcm.edu	37	4	104061993	104061993	+	Missense_Mutation	SNP	C	C	G	rs1381657	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	177	79	227	0	0.446328	0	C|0.816;G|0.184	0.184	strong	.	CENPE	253	.	NM_001813	exon36	c.G5732C	p.S1911T	TGCAGGCTTTCCT	.	PASS	Atlas-SNP
ALPI	248	hgsc.bcm.edu	37	2	233322286	233322286	+	Silent	SNP	C	C	T	rs139371546	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	228	129	240	1	0.565789	0.00416667	C|0.999;T|0.001	0.001	strong	.	ALPI	64	.	NM_001631	exon6	c.C660T	p.G220G	CCTTGGCGGAGGC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195513442	195513442	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	160	34	169	0	0.2125	0	.	.	none	.	MUC4	1505	.	NM_018406	exon2	c.C5009A	p.T1670N	GAGGAAGTGCTGG	.	PASS	Atlas-SNP
ANKRD13A	88455	hgsc.bcm.edu	37	12	110474070	110474070	+	Missense_Mutation	SNP	T	T	C	rs2287174	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	167	81	196	0	0.48503	0	T|0.923;C|0.077	0.077	strong	.	ANKRD13A	39	.	NM_033121	exon14	c.T1514C	p.L505P	AGGAACTTTCAGG	.	PASS	Atlas-SNP
MYH7B	57644	hgsc.bcm.edu	37	20	33578899	33578899	+	Silent	SNP	T	T	C	rs2425009	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	39	39	53	0	1	0	T|0.217;C|0.783	0.783	strong	.	MYH7B	145	.	NM_020884	exon24	c.T2284C	p.L762L	AACAGGTTGCTCT	.	PASS	Atlas-SNP
DYNC2H1	79659	hgsc.bcm.edu	37	11	103057048	103057048	+	Silent	SNP	A	A	G	rs658804	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	74	74	86	0	1	0	A|0.420;G|0.580	0.580	strong	.	DYNC2H1	246	.	NM_001377	exon42	c.A6711G	p.R2237R	GGGTCGATTAGCA	.	PASS	Atlas-SNP
LILRA6	79168	hgsc.bcm.edu	37	19	54744387	54744387	+	Missense_Mutation	SNP	C	C	T	rs71263238	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	209	96	124	0	0.45933	0	C|0.659;T|0.341	0.341	strong	.	LILRA6	75	.	NM_024318	exon6	c.G1021A	p.V341M	GGGTCACGTTCTC	.	PASS	Atlas-SNP
METTL11B	149281	hgsc.bcm.edu	37	1	170135760	170135760	+	Missense_Mutation	SNP	T	T	C	rs6427235	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	132	74	138	0	0.560606	0	T|0.719;C|0.281	0.281	strong	.	METTL11B	18	.	NM_001136107	exon3	c.T448C	p.S150P	ATGGAATCCTTTC	.	PASS	Atlas-SNP
PIGZ	80235	hgsc.bcm.edu	37	3	196674916	196674916	+	Silent	SNP	A	A	C	rs1147240	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	50	49	72	0	0.98	0	A|0.479;C|0.521	0.521	strong	.	PIGZ	34	.	NM_025163	exon3	c.T852G	p.A284A	GGATGTAGCGGGG	.	PASS	Atlas-SNP
EMC10	284361	hgsc.bcm.edu	37	19	50983930	50983930	+	Silent	SNP	C	C	T	rs10409679	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	60	33	40	0	0.55	0	C|0.493;T|0.507	0.507	strong	C19orf63_ENST00000376918,rectum,carcinoma,0,2	.	.	2	NM_175063	exon5	c.C495T	p.P165P	GCACCCCGGGGGC	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	91	91	90	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
MOCS1	4337	hgsc.bcm.edu	37	6	39881568	39881568	+	Missense_Mutation	SNP	C	C	A	rs377241570	alternate_allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	66	16	96	0	0.242424	0	.	.	alt	.	MOCS1	87	.	NM_005943	exon4	c.G595T	p.V199F	CCATGACCTTGTG	.	PASS	Atlas-SNP
LY75	4065	hgsc.bcm.edu	37	2	160732019	160732019	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	99	58	123	0	0.585859	0	.	.	none	.	LY75	151	.	NM_002349	exon12	c.C1910G	p.P637R	GGCTTAGGGGATG	.	PASS	Atlas-SNP
ULK4	54986	hgsc.bcm.edu	37	3	41952852	41952852	+	Missense_Mutation	SNP	T	T	C	rs35263917	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	237	138	265	0	0.582278	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
ZNF30	90075	hgsc.bcm.edu	37	19	35435069	35435069	+	Missense_Mutation	SNP	A	A	G	rs765746	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	50	82	0	0.588235	0	A|0.758;G|0.242	0.242	strong	.	ZNF30	44	.	NM_001099438	exon5	c.A1202G	p.Y401C	AGCCCTATGAATG	.	PASS	Atlas-SNP
KRTAP10-11	386678	hgsc.bcm.edu	37	21	46066764	46066764	+	Missense_Mutation	SNP	C	C	T	rs4818952	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	239	236	189	0	0.987448	0	C|0.241;T|0.759	0.759	strong	.	KRTAP10-11	36	.	NM_198692	exon1	c.C389T	p.S130F	GGCAGTCTAGCTG	.	PASS	Atlas-SNP
MEP1B	4225	hgsc.bcm.edu	37	18	29772759	29772759	+	Silent	SNP	G	G	A	rs2289544	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	65	35	96	0	0.538462	0	G|0.924;A|0.076	0.076	strong	.	MEP1B	54	.	NM_005925	exon4	c.G150A	p.E50E	TTTTGAGGGTGAC	.	PASS	Atlas-SNP
KLK11	11012	hgsc.bcm.edu	37	19	51527942	51527942	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	65	25	78	0	0.384615	0	.	.	none	.	KLK11	28	.	NM_144947	exon3	c.C245T	p.T82M	ATGAGCGTCGCCC	.	PASS	Atlas-SNP
DOCK1	1793	hgsc.bcm.edu	37	10	129249676	129249676	+	Silent	SNP	C	C	T	rs2229604	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	22	15	17	0	0.681818	0	C|0.571;T|0.429	0.429	strong	.	DOCK1	188	.	NM_001380	exon52	c.C5583T	p.S1861S	GGACTCCGGGATC	.	PASS	Atlas-SNP
ARHGAP5	394	hgsc.bcm.edu	37	14	32561340	32561340	+	Missense_Mutation	SNP	G	G	A	rs78337553	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	102	15	101	0	0.147059	0	G|0.999;A|0.001	0.001	weak	ARHGAP5,NS,carcinoma,0,1	ARHGAP5	166	1	NM_001173	exon2	c.G1465A	p.E489K	AAAGAAGAGTTTC	.	scavenged	Atlas-SNP
PATE2	399967	hgsc.bcm.edu	37	11	125647286	125647286	+	Silent	SNP	C	C	T	rs76476146	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	118	87	114	0	0.737288	0	C|0.936;T|0.064	0.064	strong	.	PATE2	14	.	NM_212555	exon4	c.G333A	p.E111E	AACTCCCTCAGGG	.	PASS	Atlas-SNP
SERHL2	253190	hgsc.bcm.edu	37	22	42970004	42970004	+	Silent	SNP	G	G	C	rs147451679	byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	502	78	477	0	0.155378	0	G|0.998;C|0.002	0.002	strong	SERHL2,NS,carcinoma,0,3	SERHL2	23	3	NM_014509	exon12	c.G888C	p.V296V	GCACGTGGCCAGT	.	scavenged	Atlas-SNP
HLX	3142	hgsc.bcm.edu	37	1	221053545	221053545	+	Missense_Mutation	SNP	T	T	C	rs12141189	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	57	57	51	1	1	0.0196078	T|0.782;C|0.218	0.218	strong	HLX,NS,carcinoma,0,1	HLX	67	1	NM_021958	exon1	c.T346C	p.S116P	CCGCTCTCAGCCG	.	scavenged	Atlas-SNP
ASAP3	55616	hgsc.bcm.edu	37	1	23767669	23767669	+	Silent	SNP	A	A	G	rs12117542	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	100	48	113	0	0.48	0	A|0.967;G|0.033	0.033	strong	.	ASAP3	65	.	NM_017707	exon10	c.T870C	p.Y290Y	GATGCTATAGCCA	.	PASS	Atlas-SNP
MDGA1	266727	hgsc.bcm.edu	37	6	37623626	37623626	+	Silent	SNP	C	C	T	rs13204070	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	102	57	109	0	0.558824	0	C|0.847;T|0.153	0.153	strong	.	MDGA1	104	.	NM_153487	exon4	c.G429A	p.V143V	GCCTCGCACATCG	.	PASS	Atlas-SNP
PSG8	440533	hgsc.bcm.edu	37	19	43269705	43269705	+	Missense_Mutation	SNP	G	G	A	rs7245423	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	15	10	24	0	0.666667	0	G|0.635;A|0.365	0.365	strong	.	PSG8	101	.	NM_001130168	exon1	c.C29T	p.T10I	CGCTGTGTGCAGG	.	PASS	Atlas-SNP
ITPKC	80271	hgsc.bcm.edu	37	19	41243671	41243671	+	Silent	SNP	C	C	T	rs145921796	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	103	49	120	0	0.475728	0	C|1.000;T|0.000	0.000	strong	.	ITPKC	36	.	NM_025194	exon6	c.C1845T	p.H615H	GACCCACGAGGTG	.	PASS	Atlas-SNP
KIAA1524	57650	hgsc.bcm.edu	37	3	108303958	108303958	+	Silent	SNP	T	T	G	rs79888562	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	112	57	138	0	0.508929	0	T|0.976;G|0.024	0.024	strong	.	KIAA1524	82	.	NM_020890	exon2	c.A204C	p.I68I	AGCACTTATGTTG	.	PASS	Atlas-SNP
DEPTOR	64798	hgsc.bcm.edu	37	8	120940652	120940652	+	Silent	SNP	C	C	T	rs16893299	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	19	66	0	0.327586	0	C|0.743;T|0.257	0.257	strong	.	DEPTOR	41	.	NM_022783	exon2	c.C135T	p.H45H	GCTGCACGAAGAA	.	PASS	Atlas-SNP
SHC3	53358	hgsc.bcm.edu	37	9	91690082	91690082	+	Missense_Mutation	SNP	C	C	T	rs35046724	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	133	67	102	0	0.503759	0	C|0.987;T|0.013	0.013	strong	.	SHC3	66	.	NM_016848	exon4	c.G671A	p.S224N	GAGATGCTCATTC	.	PASS	Atlas-SNP
OR5L1	219437	hgsc.bcm.edu	37	11	55578987	55578987	+	Silent	SNP	T	T	C	rs67727364	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	61	42	76	0	0.688525	0	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	.	PASS	Atlas-SNP
OR13C2	392376	hgsc.bcm.edu	37	9	107367132	107367132	+	Silent	SNP	G	G	A	rs10820679	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	136	69	210	0	0.507353	0	G|0.791;A|0.209	0.209	strong	.	OR13C2	46	.	NM_001004481	exon1	c.C777T	p.Y259Y	CTTCATGTACATG	.	PASS	Atlas-SNP
FYCO1	79443	hgsc.bcm.edu	37	3	46007825	46007825	+	Missense_Mutation	SNP	T	T	C	rs13059238	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	185	72	187	0	0.389189	0	T|0.928;C|0.072	0.072	strong	.	FYCO1	115	.	NM_024513	exon8	c.A3001G	p.N1001D	GGGTGTTGAGCTC	.	PASS	Atlas-SNP
IGHMBP2	3508	hgsc.bcm.edu	37	11	68704264	68704264	+	Silent	SNP	C	C	T	rs546382	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	84	20	111	0	0.238095	0	C|0.761;T|0.239	0.239	strong	.	IGHMBP2	83	.	NM_002180	exon13	c.C2316T	p.S772S	CAGTTCCGGGGAA	.	PASS	Atlas-SNP
TLE1	7088	hgsc.bcm.edu	37	9	84200529	84200529	+	Silent	SNP	T	T	C	rs2228172	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	37	52	0	0.513889	0	T|0.948;C|0.052	0.052	strong	.	TLE1	81	.	NM_005077	exon18	c.A2019G	p.A673A	GCCCACTGCCAGC	.	PASS	Atlas-SNP
PCDHB4	56131	hgsc.bcm.edu	37	5	140502344	140502344	+	Missense_Mutation	SNP	C	C	T	rs377479392	alternate_allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	107	50	145	0	0.46729	0	.	.	alt	.	PCDHB4	177	.	NM_018938	exon1	c.C764T	p.P255L	ACAGCCCCCTAGA	.	PASS	Atlas-SNP
CHD5	26038	hgsc.bcm.edu	37	1	6196869	6196869	+	Silent	SNP	A	A	G	rs2250358	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	20	88	0	0.285714	0	A|0.550;G|0.450	0.450	strong	.	CHD5	267	.	NM_015557	exon16	c.T2493C	p.I831I	CTGGTCAATGGTG	.	PASS	Atlas-SNP
LOXHD1	125336	hgsc.bcm.edu	37	18	44137400	44137400	+	Missense_Mutation	SNP	C	C	T	rs118174674	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	344	174	377	1	0.505814	0.00265252	C|0.986;T|0.014	0.014	strong	LOXHD1_ENST00000398722,NS,carcinoma,-1,2	LOXHD1	367	2	NM_144612	exon21	c.G3269A	p.R1090Q	CGAATCCGAATCT	.	PASS	Atlas-SNP
OR1S2	219958	hgsc.bcm.edu	37	11	57970980	57970980	+	Missense_Mutation	SNP	A	A	G	rs34249289	bycluster;alternate_allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	104	24	121	0	0.230769	0	AC|0.500;GT|0.500	.	alt	.	OR1S2	119	.	NM_001004459	exon1	c.T674C	p.V225A	ATGAGTACAAAGG	.	PASS	Atlas-SNP
PKHD1L1	93035	hgsc.bcm.edu	37	8	110416813	110416813	+	Silent	SNP	C	C	T	rs1457286	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	156	95	180	0	0.608974	0	C|0.434;T|0.566	0.566	strong	.	PKHD1L1	522	.	NM_177531	exon15	c.C1404T	p.Y468Y	GGAGTACAGATTA	.	PASS	Atlas-SNP
SNED1	25992	hgsc.bcm.edu	37	2	241991875	241991875	+	Silent	SNP	G	G	A	rs57214830	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	65	36	68	0	0.553846	0	G|0.756;A|0.244	0.244	strong	.	SNED1	76	.	NM_001080437	exon15	c.G2073A	p.R691R	ACGCCGGTGCCAG	.	PASS	Atlas-SNP
USP53	54532	hgsc.bcm.edu	37	4	120214030	120214030	+	Missense_Mutation	SNP	T	T	G	rs3749591	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	83	82	74	1	0.987952	0.0135135	T|0.725;G|0.275	0.275	strong	USP53,NS,carcinoma,0,1	USP53	69	1	NM_019050	exon18	c.T2886G	p.S962R	GCACAGTTTAAGT	.	scavenged	Atlas-SNP
RP1L1	94137	hgsc.bcm.edu	37	8	10467604	10467604	+	Missense_Mutation	SNP	C	C	A	rs74366179	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	118	24	127	0	0.20339	0	C|0.824;A|0.176	0.176	strong	RP1L1,NS,carcinoma,0,1	RP1L1	453	1	NM_178857	exon4	c.G4004T	p.G1335V	TGCACCCCCTCTT	.	PASS	Atlas-SNP
WDR93	56964	hgsc.bcm.edu	37	15	90246336	90246336	+	Silent	SNP	A	A	G	rs16974175	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	252	93	195	0	0.369048	0	A|0.575;G|0.425	0.425	strong	.	WDR93	63	.	NM_020212	exon3	c.A459G	p.L153L	AGATTTAGGGAAT	.	PASS	Atlas-SNP
KAZN	23254	hgsc.bcm.edu	37	1	15382667	15382667	+	Silent	SNP	T	T	C	rs2076570	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	199	101	252	0	0.507538	0	T|0.984;C|0.016	0.016	strong	.	KAZN	57	.	NM_015209	exon5	c.T807C	p.N269N	GCTCAATGGCAAC	.	PASS	Atlas-SNP
EPS8L2	64787	hgsc.bcm.edu	37	11	721570	721570	+	Silent	SNP	C	C	T	rs7635	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	109	22	82	0	0.201835	0	C|0.687;T|0.313	0.313	strong	EPS8L2,colon,carcinoma,0,1	EPS8L2	42	1	NM_022772	exon10	c.C774T	p.I258I	GCAAATCCTCAAC	.	PASS	Atlas-SNP
HRH3	11255	hgsc.bcm.edu	37	20	60791422	60791422	+	Silent	SNP	C	C	T	rs3787430	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	83	43	109	0	0.518072	0	C|0.833;T|0.167	0.167	strong	.	HRH3	25	.	NM_007232	exon3	c.G978A	p.P326P	CGCCGACGGCTTG	.	PASS	Atlas-SNP
ALMS1	7840	hgsc.bcm.edu	37	2	73746923	73746923	+	Silent	SNP	C	C	T	rs11884776	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	124	124	180	0	1	0	C|0.742;T|0.258	0.258	strong	.	ALMS1	384	.	NM_015120	exon11	c.C9558T	p.T3186T	GAAGACCCCACTT	.	PASS	Atlas-SNP
OR10H4	126541	hgsc.bcm.edu	37	19	16060021	16060021	+	Silent	SNP	C	C	T	rs16980821	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	223	108	226	0	0.484305	0	C|0.723;T|0.277	0.277	strong	.	OR10H4	48	.	NM_001004465	exon1	c.C204T	p.S68S	CCTCTCCGTCTCT	.	PASS	Atlas-SNP
TMEM173	340061	hgsc.bcm.edu	37	5	138861078	138861078	+	Missense_Mutation	SNP	C	C	T	rs11554776	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	116	52	151	0	0.448276	0	C|0.867;T|0.133	0.133	strong	TMEM173,NS,carcinoma,0,1	TMEM173	19	1	NM_198282	exon3	c.G212A	p.R71H	ATGTGGCGCAGCT	.	PASS	Atlas-SNP
SNX30	401548	hgsc.bcm.edu	37	9	115600827	115600827	+	Silent	SNP	C	C	T	rs41280189	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	119	63	142	0	0.529412	0	C|0.922;T|0.078	0.078	strong	.	SNX30	32	.	NM_001012994	exon6	c.C864T	p.S288S	ATGGAGCGCCTTG	.	PASS	Atlas-SNP
BOC	91653	hgsc.bcm.edu	37	3	112991312	112991312	+	Silent	SNP	C	C	T	rs3814398	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	116	64	140	0	0.551724	0	C|0.788;T|0.212	0.212	strong	.	BOC	139	.	NM_033254	exon7	c.C723T	p.I241I	CATCATCGTCACC	.	PASS	Atlas-SNP
ZNF761	388561	hgsc.bcm.edu	37	19	53959804	53959804	+	Silent	SNP	T	T	C	rs4803129	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	18	12	32	0	0.666667	0	T|0.823;C|0.177	0.177	strong	ZNF761,NS,carcinoma,0,1	ZNF761	104	1	NM_001008401	exon7	c.T2043C	p.H681H	CCATCATAGACTT	.	PASS	Atlas-SNP
LCE1D	353134	hgsc.bcm.edu	37	1	152770589	152770589	+	Missense_Mutation	SNP	A	A	G	rs11485496	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	560	368	500	1	0.657143	0.002	A|0.659;G|0.341	0.341	strong	.	LCE1D	19	.	NM_178352	exon2	c.A319G	p.S107G	GGCAGCAGCCAGC	.	PASS	Atlas-SNP
AFF2	2334	hgsc.bcm.edu	37	X	148048494	148048494	+	Missense_Mutation	SNP	A	A	C	rs149653283	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	91	89	147	0	0.978022	0	A|1.000;C|0.000	0.000	strong	.	AFF2	679	.	NM_002025	exon14	c.A3088C	p.I1030L	TCTACCATCACTA	.	PASS	Atlas-SNP
MCC	4163	hgsc.bcm.edu	37	5	112406862	112406862	+	Silent	SNP	G	G	A	rs2227950	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	222	99	222	0	0.445946	0	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
CFLAR	8837	hgsc.bcm.edu	37	2	202006096	202006096	+	Splice_Site	SNP	G	G	A	rs10190751	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	165	73	193	0	0.442424	0	G|0.764;A|0.236	0.236	strong	.	CFLAR	37	.	NM_001127184	exon6	c.607-1G>A	.	TCTACAGATGATA	.	PASS	Atlas-SNP
DMBT1	1755	hgsc.bcm.edu	37	10	124345796	124345796	+	Missense_Mutation	SNP	C	C	G	rs143892520	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	134	64	159	0	0.477612	0	C|0.989;G|0.011	0.011	strong	DMBT1_ENST00000368915,caecum,carcinoma,0,13	DMBT1	677	13	NM_007329	exon16	c.C1680G	p.D560E	GGATGACGTGCGC	.	PASS	Atlas-SNP
CEL	1056	hgsc.bcm.edu	37	9	135945997	135945997	+	Missense_Mutation	SNP	C	C	T	rs201677850	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	244	9	174	0	0.0368852	0	C|0.998;T|0.002	0.002	strong	CEL,NS,carcinoma,+1,1	CEL	71	1	NM_001807	exon10	c.C1445T	p.T482I	ACAGGACAGTCTC	.	scavenged	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29911240	29911240	+	Missense_Mutation	SNP	T	T	G	rs9260156	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	130	107	257	2	0.823077	0.0077821	A|0.250;G|0.070;T|0.680	0.070	strong	HLA-A,mouth,carcinoma,0,1	HLA-A	89	1	NM_001242758	exon3	c.T539G	p.L180W	AGCAGTTGAGAGC	.	PASS	Atlas-SNP
STT3A	3703	hgsc.bcm.edu	37	11	125465862	125465862	+	Silent	SNP	T	T	C	rs10082632	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	168	117	234	0	0.696429	0	T|0.885;C|0.115	0.115	strong	.	STT3A	52	.	NM_152713	exon2	c.T52C	p.L18L	ACACTTTTGAAGC	.	PASS	Atlas-SNP
CEACAM20	125931	hgsc.bcm.edu	37	19	45033485	45033485	+	Silent	SNP	A	A	G	rs62116895	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	83	83	129	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
SH2D3A	10045	hgsc.bcm.edu	37	19	6763718	6763718	+	Silent	SNP	A	A	G	rs2305805	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	46	19	53	0	0.413043	0	A|0.742;G|0.258	0.258	strong	.	SH2D3A	53	.	NM_005490	exon2	c.T42C	p.P14P	GTACCAAGGTTGG	.	PASS	Atlas-SNP
TDRD9	122402	hgsc.bcm.edu	37	14	104452640	104452640	+	Silent	SNP	G	G	A	rs10143389	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	119	52	132	0	0.436975	0	G|0.674;A|0.326	0.326	strong	TDRD9_ENST00000409874,NS,carcinoma,0,2	TDRD9	175	2	NM_153046	exon8	c.G1098A	p.L366L	TGACTTGGATATG	.	PASS	Atlas-SNP
MFGE8	4240	hgsc.bcm.edu	37	15	89450587	89450587	+	Missense_Mutation	SNP	G	G	T	rs1878326	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	203	202	186	0	0.995074	0	G|0.336;T|0.658	0.658	strong	MFGE8,NS,carcinoma,0,2	MFGE8	60	2	NM_001114614	exon3	c.C226A	p.L76M	TCTCCAGGCCCAG	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	177	177	266	0	1	0	G|0.530;C|0.470	0.470	strong	.	ERO1LB	48	.	NM_019891	exon16	c.C1395G	p.H465Q	CCTACTGTGTTGT	.	PASS	Atlas-SNP
SYNE1	23345	hgsc.bcm.edu	37	6	152772264	152772264	+	Missense_Mutation	SNP	A	A	G	rs214976	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	79	79	125	0	1	0	G|0.567;N|0.000	0.567	strong	.	SYNE1	3227	.	NM_033071	exon26	c.T3125C	p.V1042A	TCTTCTACAGAGG	.	PASS	Atlas-SNP
GLYATL3	389396	hgsc.bcm.edu	37	6	49494241	49494241	+	Missense_Mutation	SNP	A	A	G	rs9367359	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	166	75	211	0	0.451807	0	A|0.510;G|0.490	0.490	strong	.	GLYATL3	19	.	NM_001010904	exon6	c.A481G	p.N161D	GTTGCCAATGCGG	.	PASS	Atlas-SNP
ZNF880	400713	hgsc.bcm.edu	37	19	52888245	52888245	+	Missense_Mutation	SNP	A	A	G	rs55748277	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	32	32	56	0	1	0	A|0.631;G|0.369	0.369	strong	.	ZNF880	45	.	NM_001145434	exon4	c.A1412G	p.K471R	GTGGCAAGGACTT	.	PASS	Atlas-SNP
WNK1	65125	hgsc.bcm.edu	37	12	993930	993930	+	Silent	SNP	C	C	T	rs7300444	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	278	135	289	1	0.485611	0.00346021	C|0.597;T|0.403	0.403	strong	.	WNK1	403	.	NM_001184985	exon19	c.C4740T	p.N1580N	ACCCAACACAGCA	.	PASS	Atlas-SNP
TMEM82	388595	hgsc.bcm.edu	37	1	16070912	16070912	+	Silent	SNP	T	T	C	rs7525747	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	34	16	40	0	0.470588	0	T|0.848;C|0.152	0.152	strong	.	TMEM82	30	.	NM_001013641	exon4	c.T594C	p.H198H	TGCACATGGCCTC	.	PASS	Atlas-SNP
SART1	9092	hgsc.bcm.edu	37	11	65735174	65735174	+	Missense_Mutation	SNP	G	G	C	rs660118	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	66	65	111	0	0.984848	0	G|0.591;C|0.409	0.409	strong	.	SART1	41	.	NM_005146	exon12	c.G1454C	p.G485A	CGCCGGGGTCCCC	.	PASS	Atlas-SNP
SPATA17	128153	hgsc.bcm.edu	37	1	217856626	217856626	+	Silent	SNP	G	G	A	rs12068167	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	169	68	187	0	0.402367	0	G|0.826;A|0.174	0.174	strong	.	SPATA17	59	.	NM_138796	exon5	c.G318A	p.R106R	CTATAGGGTTCGG	.	PASS	Atlas-SNP
STXBP2	6813	hgsc.bcm.edu	37	19	7712277	7712277	+	Missense_Mutation	SNP	A	A	G	rs6791	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	36	35	57	0	0.972222	0	A|0.305;C|0.008	.	strong	STXBP2,NS,carcinoma,0,1	STXBP2	63	1	NM_001272034	exon18	c.A1609G	p.I537V	GCTGGCATAGAAG	.	PASS	Atlas-SNP
RGMA	56963	hgsc.bcm.edu	37	15	93588264	93588264	+	Silent	SNP	G	G	C	rs4299103	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	30	14	18	0	0.466667	0	G|0.523;C|0.477	0.477	strong	.	RGMA	49	.	NM_001166283	exon4	c.C1341G	p.L447L	CGGGACGAGGGCG	.	PASS	Atlas-SNP
DCC	1630	hgsc.bcm.edu	37	18	49867246	49867246	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	190	37	247	0	0.194737	0	.	.	none	.	DCC	360	.	NM_005215	exon1	c.C89T	p.T30I	AAGTAACCGGTAA	.	PASS	Atlas-SNP
SLC35B1	10237	hgsc.bcm.edu	37	17	47783663	47783663	+	Missense_Mutation	SNP	C	C	T	rs1135034	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	84	36	97	0	0.428571	0	C|0.928;T|0.072	0.072	strong	.	SLC35B1	21	.	NM_005827	exon3	c.G242A	p.R81H	CGGGTACGATCCA	.	PASS	Atlas-SNP
UNC5C	8633	hgsc.bcm.edu	37	4	96166270	96166270	+	Silent	SNP	C	C	T	rs35120448	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	41	62	0	0.5	0	C|0.961;T|0.039	0.039	strong	UNC5C,NS,carcinoma,-1,1	UNC5C	141	1	NM_003728	exon6	c.G801A	p.T267T	CCACTCCGTCCAG	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179396573	179396573	+	Silent	SNP	T	T	G	rs56375087	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	126	57	143	0	0.452381	0	T|0.993;G|0.007	0.007	strong	.	TTN	18412	.	NM_001267550	exon358	c.A104769C	p.T34923T	TTCTGATGTCTTC	.	PASS	Atlas-SNP
ACSM4	341392	hgsc.bcm.edu	37	12	7463241	7463241	+	Silent	SNP	A	A	T	rs7968241	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	67	29	88	0	0.432836	0	A|0.570;T|0.430	0.430	strong	.	ACSM4	98	.	NM_001080454	exon3	c.A519T	p.P173P	GGCCCCAGCGGTG	.	PASS	Atlas-SNP
IL31	386653	hgsc.bcm.edu	37	12	122657271	122657271	+	Silent	SNP	G	G	C	rs7974857	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	163	160	173	1	0.981595	0.00578035	G|0.882;C|0.118	0.118	strong	.	IL31	23	.	NM_001014336	exon3	c.C183G	p.G61G	GAGCACGCCCTTC	.	PASS	Atlas-SNP
ACOT4	122970	hgsc.bcm.edu	37	14	74060508	74060508	+	Missense_Mutation	SNP	C	C	A	rs35724886	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	23	99	0	0.270588	0	C|0.889;A|0.111	0.111	strong	.	ACOT4	25	.	NM_152331	exon2	c.C560A	p.A187D	CGTTGGCTCTAGC	.	PASS	Atlas-SNP
ATP13A4	84239	hgsc.bcm.edu	37	3	193180592	193180592	+	Silent	SNP	G	G	A	rs59451116	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	45	118	0	0.48913	0	G|0.762;A|0.238	0.238	strong	.	ATP13A4	154	.	NM_032279	exon13	c.C1482T	p.D494D	CAAGCCGTCCCTT	.	PASS	Atlas-SNP
TCEB3B	51224	hgsc.bcm.edu	37	18	44560300	44560300	+	Missense_Mutation	SNP	C	C	T	rs79620461		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	60	24	93	0	0.4	0	.	.	weak	.	TCEB3B	141	.	NM_016427	exon1	c.G1336A	p.A446T	AATCAGCGCCGGC	.	PASS	Atlas-SNP
ADGB	79747	hgsc.bcm.edu	37	6	146993445	146993445	+	Missense_Mutation	SNP	T	T	C	rs9497606	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	42	105	0	0.608696	0	T|0.734;C|0.266	0.266	strong	.	ADGB	93	.	NM_024694	exon8	c.T929C	p.I310T	GCAAAATAGCAGT	.	PASS	Atlas-SNP
SKA3	221150	hgsc.bcm.edu	37	13	21729267	21729267	+	Missense_Mutation	SNP	G	G	A	rs11147977	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	81	15	91	0	0.185185	0	G|0.905;A|0.095	0.095	strong	.	SKA3	76	.	NM_001166017	exon8	c.C1142T	p.T381I	TTCTGTGTTGGAT	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	228	117	258	1	0.513158	0.00387597	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
ARHGEF28	64283	hgsc.bcm.edu	37	5	73205337	73205337	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	270	108	198	0	0.4	0	.	.	none	.	.	.	.	NM_001080479	exon34	c.C4262A	p.P1421H	GCGGCCCCTTGCA	.	PASS	Atlas-SNP
TNFRSF13B	23495	hgsc.bcm.edu	37	17	16842991	16842991	+	Missense_Mutation	SNP	G	G	A	rs34562254	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	168	167	164	0	0.994048	0	G|0.865;A|0.135	0.135	strong	.	TNFRSF13B	34	.	NM_012452	exon5	c.C752T	p.P251L	GGGTCGGGGGTCC	.	PASS	Atlas-SNP
OPLAH	26873	hgsc.bcm.edu	37	8	145107915	145107915	+	Missense_Mutation	SNP	G	G	A	rs200620019	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	103	26	129	0	0.252427	0	.	.	weak	.	OPLAH	78	.	NM_017570	exon21	c.C2989T	p.R997C	GGAGGCGGATGGG	.	PASS	Atlas-SNP
PANK1	53354	hgsc.bcm.edu	37	10	91405044	91405044	+	Missense_Mutation	SNP	C	C	T	rs61853459	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	42	104	0	0.494118	0	C|0.967;T|0.033	0.033	strong	.	PANK1	35	.	NM_148977	exon1	c.G16A	p.G6S	CGCCACCGACGAG	.	PASS	Atlas-SNP
CHIA	27159	hgsc.bcm.edu	37	1	111862042	111862042	+	Missense_Mutation	SNP	T	T	C	rs36011905	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	137	65	139	0	0.474453	0	T|0.971;C|0.029	0.029	strong	.	CHIA	115	.	NM_201653	exon11	c.T1129C	p.F377L	GGCAAGTTTCCCC	.	PASS	Atlas-SNP
SPTBN1	6711	hgsc.bcm.edu	37	2	54844790	54844790	+	Silent	SNP	C	C	T	rs2229506	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	480	115	186	0	0.239583	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
KANK2	25959	hgsc.bcm.edu	37	19	11304404	11304404	+	Missense_Mutation	SNP	C	C	T	rs755237	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	28	14	45	0	0.5	0	C|0.936;T|0.064	0.064	strong	.	KANK2	47	.	NM_015493	exon2	c.G352A	p.G118S	AGCCACCGCGGGT	.	PASS	Atlas-SNP
JARID2	3720	hgsc.bcm.edu	37	6	15513482	15513482	+	Silent	SNP	G	G	A	rs2235258	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	62	62	76	0	1	0	G|0.410;A|0.590	0.590	strong	JARID2,NS,carcinoma,0,1	JARID2	135	1	NM_004973	exon16	c.G3279A	p.L1093L	AGAGCTGCGGCAG	.	PASS	Atlas-SNP
SCARF1	8578	hgsc.bcm.edu	37	17	1538714	1538714	+	Missense_Mutation	SNP	T	T	G	rs61738531	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	77	22	88	0	0.285714	0	T|0.984;G|0.016	0.016	strong	.	SCARF1	46	.	NM_003693	exon11	c.A1831C	p.S611R	GCGGGCTGGAGAG	.	PASS	Atlas-SNP
UMODL1	89766	hgsc.bcm.edu	37	21	43543098	43543098	+	Silent	SNP	C	C	T	rs58867895	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	93	35	95	0	0.376344	0	C|0.985;T|0.015	0.015	strong	.	UMODL1	186	.	NM_173568	exon16	c.C3369T	p.I1123I	TGAGATCGAGAAG	.	PASS	Atlas-SNP
PTCH1	5727	hgsc.bcm.edu	37	9	98209594	98209594	+	Missense_Mutation	SNP	G	G	A	rs357564	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	40	19	35	0	0.475	0	G|0.661;A|0.339	0.339	strong	PTCH1_ENST00000430669,NS,NS,0,4	PTCH1	1850	4	NM_000264	exon23	c.C3944T	p.P1315L	CTGTAGGGGGGTG	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29911124	29911124	+	Silent	SNP	C	C	T	rs3173418	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	166	67	263	0	0.403614	0	C|0.930;T|0.070	0.070	strong	.	HLA-A	89	.	NM_001242758	exon3	c.C423T	p.A141A	GGACGCCTACGAC	.	PASS	Atlas-SNP
RIPPLY2	134701	hgsc.bcm.edu	37	6	84563147	84563147	+	Silent	SNP	G	G	A	rs9353143	bycluster;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	20	10	11	0	0.5	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
RFX7	64864	hgsc.bcm.edu	37	15	56387142	56387142	+	Silent	SNP	G	G	A	rs34361729	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	109	69	101	0	0.633027	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
DOC2A	8448	hgsc.bcm.edu	37	16	30018500	30018500	+	Silent	SNP	C	C	T	rs3935873	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	58	53	0	1	0	C|0.660;T|0.340	0.340	strong	.	DOC2A	40	.	NM_003586	exon6	c.G648A	p.Q216Q	CGGGACCTGGCGC	.	PASS	Atlas-SNP
CNR1	1268	hgsc.bcm.edu	37	6	88853635	88853635	+	Silent	SNP	C	C	T	rs1049353	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	146	77	142	0	0.527397	0	C|0.840;T|0.160	0.160	strong	CNR1,NS,carcinoma,-1,1	CNR1	91	1	NM_001160258	exon4	c.G1359A	p.T453T	CTTGACCGTGCTC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195507324	195507324	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	95	12	80	0	0.126316	0	.	.	none	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.C11127G	p.H3709Q	GGTGGTGTGACCT	.	PASS	Atlas-SNP
RECK	8434	hgsc.bcm.edu	37	9	36105264	36105264	+	Silent	SNP	A	A	G	rs11788747	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	166	66	204	0	0.39759	0	A|0.721;G|0.279	0.279	strong	.	RECK	73	.	NM_021111	exon13	c.A1560G	p.P520P	TCTTCCATACTTT	.	PASS	Atlas-SNP
OR51F1	256892	hgsc.bcm.edu	37	11	4790575	4790575	+	Silent	SNP	A	A	G	rs12788102	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	289	58	244	0	0.200692	0	A|0.911;G|0.089	0.089	strong	.	OR51F1	60	.	NM_001004752	exon1	c.T573C	p.C191C	GTCTGAACATGCT	.	PASS	Atlas-SNP
SLC20A2	6575	hgsc.bcm.edu	37	8	42294592	42294592	+	Missense_Mutation	SNP	C	C	T	rs79577461	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	17	4	32	0	0.235294	0	C|0.985;T|0.015	0.015	strong	.	SLC20A2	64	.	NM_001257181	exon8	c.G1438A	p.A480T	CGGGTGCGTCCTT	.	PASS	Atlas-SNP
TMPRSS11A	339967	hgsc.bcm.edu	37	4	68829109	68829109	+	Missense_Mutation	SNP	C	C	T	rs977728	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	95	45	120	1	0.473684	0.00833333	C|0.829;T|0.171	0.171	strong	TMPRSS11A,NS,carcinoma,0,1	TMPRSS11A	74	1	NM_001114387	exon1	c.G3A	p.M1I	ATACATCATGTAC	.	scavenged	Atlas-SNP
ZNF611	81856	hgsc.bcm.edu	37	19	53209554	53209554	+	Missense_Mutation	SNP	G	G	T	rs76627659		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	37	93	0	0.402174	0	.	.	weak	ZNF611,NS,carcinoma,+1,1	ZNF611	72	1	NM_030972	exon7	c.C754A	p.P252T	AATGGGGTATCTG	.	PASS	Atlas-SNP
ITPR1	3708	hgsc.bcm.edu	37	3	4842231	4842231	+	Silent	SNP	C	C	T	rs2291862	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	103	50	100	0	0.485437	0	C|0.722;T|0.278	0.278	strong	.	ITPR1	659	.	NM_001168272	exon53	c.C7009T	p.L2337L	CTACGACTGATAT	.	PASS	Atlas-SNP
LCA5	167691	hgsc.bcm.edu	37	6	80196848	80196848	+	Missense_Mutation	SNP	C	C	T	rs1875845	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	177	77	249	1	0.435028	0.00401606	C|0.626;T|0.374	0.374	strong	.	LCA5	71	.	NM_001122769	exon8	c.G1967A	p.G656D	AAAAAGCCTTCAT	.	PASS	Atlas-SNP
DPYS	1807	hgsc.bcm.edu	37	8	105478933	105478933	+	Silent	SNP	G	G	A	rs2298840	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	17	17	20	0	1	0	G|0.763;A|0.237	0.237	strong	.	DPYS	107	.	NM_001385	exon1	c.C216T	p.F72F	GAAGGGGAACTGC	.	PASS	Atlas-SNP
FCGBP	8857	hgsc.bcm.edu	37	19	40408532	40408532	+	Missense_Mutation	SNP	G	G	A	rs36106401	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	294	141	363	0	0.479592	0	G|0.853;A|0.147	0.147	strong	FCGBP,NS,carcinoma,0,1	FCGBP	416	1	NM_003890	exon8	c.C4307T	p.P1436L	CTCCCCGGCGGGC	.	PASS	Atlas-SNP
SPTAN1	6709	hgsc.bcm.edu	37	9	131379998	131379998	+	Silent	SNP	C	C	A	rs3750333	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	47	89	0	0.552941	0	C|0.977;A|0.023	0.023	strong	.	SPTAN1	266	.	NM_001130438	exon42	c.C5437A	p.R1813R	CACAAGCGGCTGG	.	PASS	Atlas-SNP
KDELR3	11015	hgsc.bcm.edu	37	22	38877461	38877461	+	Missense_Mutation	SNP	T	T	G	rs12004	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	178	86	237	1	0.483146	0.00421941	A|0.004;C|0.002	.	strong	.	KDELR3	39	.	NM_016657	exon4	c.T596G	p.V199G	TGTATGTGACCAA	.	PASS	Atlas-SNP
ALOX15B	247	hgsc.bcm.edu	37	17	7950009	7950009	+	Nonsense_Mutation	SNP	C	C	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	61	31	86	0	0.508197	0	.	.	none	.	ALOX15B	66	.	NM_001141	exon9	c.C1224G	p.Y408X	CCGATACACCCTG	.	PASS	Atlas-SNP
DAPL1	92196	hgsc.bcm.edu	37	2	159660870	159660870	+	Silent	SNP	C	C	T	rs17810398	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	36	115	0	0.371134	0	C|0.916;T|0.084	0.084	strong	.	DAPL1	11	.	NM_001017920	exon2	c.C135T	p.F45F	AGGATTCGAGAAA	.	PASS	Atlas-SNP
PPWD1	23398	hgsc.bcm.edu	37	5	64863426	64863426	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	454	5	400	0	0.0110132	0	.	.	none	PPWD1,NS,carcinoma,-2,1	PPWD1	47	1	NM_015342	exon2	c.C283T	p.H95Y	ATCACCCATGTGG	.	scavenged	Atlas-SNP
TRIM2	23321	hgsc.bcm.edu	37	4	154197234	154197234	+	Silent	SNP	T	T	G	rs2289409	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	81	41	95	0	0.506173	0	T|0.783;G|0.217	0.217	strong	.	TRIM2	105	.	NM_015271	exon3	c.T405G	p.T135T	AGTCACTGCTGTG	.	PASS	Atlas-SNP
CYP4F12	66002	hgsc.bcm.edu	37	19	15793235	15793235	+	Missense_Mutation	SNP	T	T	C	rs79526533		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	174	171	158	0	0.982759	0	.	.	weak	.	CYP4F12	89	.	NM_023944	exon6	c.T562C	p.C188R	AGCAGTTGTCTGG	.	PASS	Atlas-SNP
RCAN3	11123	hgsc.bcm.edu	37	1	24859617	24859617	+	Silent	SNP	G	G	A	rs196429	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	48	19	76	0	0.395833	0	G|0.669;A|0.331	0.331	strong	.	RCAN3	22	.	NM_001251979	exon4	c.G414A	p.P138P	CCTGCCGCCCCAG	.	PASS	Atlas-SNP
CNOT4	4850	hgsc.bcm.edu	37	7	135123060	135123060	+	Missense_Mutation	SNP	G	G	C	rs17480616	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	98	39	163	0	0.397959	0	G|0.983;C|0.017	0.017	strong	.	CNOT4	146	.	NM_001190850	exon2	c.C20G	p.A7G	TCCTTCGCATCAG	.	PASS	Atlas-SNP
OR5AR1	219493	hgsc.bcm.edu	37	11	56431834	56431834	+	Missense_Mutation	SNP	A	A	G	rs56067375	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	136	103	190	0	0.757353	0	A|0.952;G|0.048	0.048	strong	OR5AR1,NS,carcinoma,0,1	OR5AR1	68	1	NM_001004730	exon1	c.A673G	p.I225V	GTTGCAATCATCA	.	PASS	Atlas-SNP
ALMS1	7840	hgsc.bcm.edu	37	2	73679280	73679280	+	Missense_Mutation	SNP	A	A	G	rs6546838	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	66	66	85	0	1	0	A|0.663;G|0.337	0.337	strong	.	ALMS1	384	.	NM_015120	exon8	c.A5623G	p.I1875V	AAAGCAATAGGGG	.	PASS	Atlas-SNP
BTBD16	118663	hgsc.bcm.edu	37	10	124096061	124096061	+	Missense_Mutation	SNP	A	A	C	rs1048347	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	68	34	111	0	0.5	0	A|0.608;C|0.392	0.392	strong	.	BTBD16	44	.	NM_144587	exon15	c.A1316C	p.H439P	ACAACCACGTCAG	.	PASS	Atlas-SNP
TAF1L	138474	hgsc.bcm.edu	37	9	32630472	32630472	+	Silent	SNP	T	T	C	rs10758145	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	216	117	227	0	0.541667	0	T|0.672;C|0.328	0.328	strong	.	TAF1L	382	.	NM_153809	exon1	c.A5106G	p.K1702K	CATCTGTTTTTCT	.	PASS	Atlas-SNP
TOM1	10043	hgsc.bcm.edu	37	22	35717988	35717988	+	Silent	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	145	2	142	0	0.0137931	0	.	.	none	TOM1,NS,carcinoma,0,1	TOM1	43	1	NM_001135732	exon3	c.C174T	p.I58I	GAGAATCGTGGGG	.	scavenged	Atlas-SNP
SLC35E2	9906	hgsc.bcm.edu	37	1	1663960	1663960	+	Silent	SNP	G	G	A	rs147265331	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	61	147	0	0.743902	0	G|0.987;A|0.013	0.013	strong	.	SLC35E2	13	.	NM_182838	exon6	c.C735T	p.V245V	CTGCGGGACCTGC	.	PASS	Atlas-SNP
CSGALNACT1	55790	hgsc.bcm.edu	37	8	19316086	19316086	+	Silent	SNP	G	G	A	rs12155539	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	285	211	317	0	0.740351	0	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
TPTE2	93492	hgsc.bcm.edu	37	13	20067011	20067011	+	Missense_Mutation	SNP	A	A	C	rs76437836	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	174	20	160	0	0.114943	0	A|0.375;C|0.625	0.625	strong	TPTE2_ENST00000400230,adrenal_gland,adrenal_cortical_adenoma,0,3	TPTE2	225	3	NM_199254	exon4	c.T98G	p.L33R	GACACCAGGGCTG	.	scavenged	Atlas-SNP
DTX1	1840	hgsc.bcm.edu	37	12	113496182	113496182	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	12	59	0	0.206897	0	.	.	none	.	DTX1	83	.	NM_004416	exon1	c.T185G	p.L62R	TGGTCCTGGGGCA	.	PASS	Atlas-SNP
GRIN3A	116443	hgsc.bcm.edu	37	9	104385712	104385712	+	Silent	SNP	A	A	G	rs10989564	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	140	138	184	0	0.985714	0	A|0.501;G|0.499	0.499	strong	.	GRIN3A	186	.	NM_133445	exon5	c.T2502C	p.N834N	TGGATCATTCCTA	.	PASS	Atlas-SNP
OR4M1	441670	hgsc.bcm.edu	37	14	20248828	20248828	+	Missense_Mutation	SNP	C	C	T	rs2635535	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	308	93	310	0	0.301948	0	C|0.736;T|0.264	0.264	strong	.	OR4M1	104	.	NM_001005500	exon1	c.C347T	p.T116I	TGCTCACAGTGAT	.	PASS	Atlas-SNP
FAM205A	259308	hgsc.bcm.edu	37	9	34725112	34725112	+	Missense_Mutation	SNP	C	C	T	rs200209883	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	395	126	473	0	0.318987	0	C|0.978;T|0.022	0.022	strong	FAM205A_ENST00000378788,NS,haematopoietic_neoplasm,0,2	FAM205A	45	2	NM_001141917	exon4	c.G2125A	p.A709T	CCACTGCCAGGAC	.	PASS	Atlas-SNP
C2orf83	56918	hgsc.bcm.edu	37	2	228493211	228493211	+	Missense_Mutation	SNP	G	G	A	rs28739019	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	28	93	0	0.358974	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
PTPRH	5794	hgsc.bcm.edu	37	19	55715309	55715309	+	Missense_Mutation	SNP	C	C	T	rs45535035	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	115	55	146	0	0.478261	0	C|0.840;T|0.160	0.160	strong	.	PTPRH	139	.	NM_002842	exon5	c.G727A	p.V243I	ACTGAACGCAGTA	.	PASS	Atlas-SNP
WDR87	83889	hgsc.bcm.edu	37	19	38376103	38376103	+	Silent	SNP	A	A	G	rs73027454	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	28	65	0	0.482759	0	A|0.775;G|0.225	0.225	strong	.	WDR87	191	.	NM_031951	exon6	c.T8091C	p.F2697F	ATCCTTAAAATCC	.	PASS	Atlas-SNP
FAM179A	165186	hgsc.bcm.edu	37	2	29240060	29240060	+	Missense_Mutation	SNP	A	A	G	rs11127202	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	379	227	316	0	0.598945	0	A|0.778;G|0.222	0.222	strong	.	FAM179A	106	.	NM_199280	exon9	c.A1085G	p.Q362R	AGATGCAGCTGAA	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	201	102	237	1	0.507463	0.00421941	A|0.592;T|0.408	0.408	strong	.	CYP39A1	41	.	NM_016593	exon8	c.T972A	p.N324K	AAGGAGATTCTCC	.	PASS	Atlas-SNP
NDUFA7	4701	hgsc.bcm.edu	37	19	8376431	8376431	+	Silent	SNP	G	G	A	rs561	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	117	65	129	0	0.555556	0	G|0.844;A|0.156	0.156	strong	.	NDUFA7	11	.	NM_005001	exon4	c.C300T	p.P100P	CTTTATGGGAGGA	.	PASS	Atlas-SNP
OR51F1	256892	hgsc.bcm.edu	37	11	4790410	4790410	+	Silent	SNP	A	A	G	rs1030724	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	171	42	168	0	0.245614	0	A|0.707;G|0.293	0.293	strong	OR51F1,right_upper_lobe,carcinoma,-2,1	OR51F1	60	1	NM_001004752	exon1	c.T738C	p.H246H	TCCCACATGGGAG	.	PASS	Atlas-SNP
GABRB3	2562	hgsc.bcm.edu	37	15	26806154	26806154	+	Silent	SNP	G	G	A	rs74907974	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	129	53	159	0	0.410853	0	G|0.991;A|0.009	0.009	strong	GABRB3_ENST00000541819,right_upper_lobe,carcinoma,-2,6	GABRB3	338	6	NM_021912	exon8	c.C1005T	p.G335G	TTGAGGGCCTCTT	.	PASS	Atlas-SNP
LINGO1	84894	hgsc.bcm.edu	37	15	77907775	77907775	+	Silent	SNP	T	T	C	rs2271397	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	182	181	189	0	0.994505	0	T|0.292;C|0.708	0.708	strong	.	LINGO1	76	.	NM_032808	exon2	c.A474G	p.L158L	GTCCAGTAGGATA	.	PASS	Atlas-SNP
SLFN13	146857	hgsc.bcm.edu	37	17	33772550	33772550	+	Silent	SNP	C	C	T	rs76192030	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	141	80	168	0	0.567376	0	C|0.930;T|0.070	0.070	strong	SLFN13,rectum,carcinoma,-2,1	SLFN13	79	1	NM_144682	exon3	c.G150A	p.A50A	AGCACACGCGGCC	.	PASS	Atlas-SNP
COL6A2	1292	hgsc.bcm.edu	37	21	47552130	47552130	+	Silent	SNP	A	A	G	rs9977394	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	59	28	45	0	0.474576	0	A|0.879;G|0.121	0.121	strong	.	COL6A2	351	.	NM_001849	exon28	c.A2724G	p.T908T	GACCACACAATAC	.	PASS	Atlas-SNP
HELB	92797	hgsc.bcm.edu	37	12	66704225	66704225	+	Missense_Mutation	SNP	A	A	G	rs75770066	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	118	50	128	0	0.423729	0	A|0.975;G|0.025	0.025	strong	.	HELB	90	.	NM_033647	exon4	c.A1517G	p.D506G	GTGAAGATTTTGA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195506007	195506007	+	Silent	SNP	G	G	A	rs71635085		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	112	2	79	0	0.0178571	0	G|1.000;|0.000	.	weak	MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	NM_018406	exon2	c.C12444T	p.T4148T	AGGGATGGTGACA	.	scavenged	Atlas-SNP
MACF1	23499	hgsc.bcm.edu	37	1	39816546	39816546	+	Silent	SNP	G	G	A	rs41270815	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	91	40	86	0	0.43956	0	G|0.947;A|0.053	0.053	strong	.	MACF1	909	.	NM_012090	exon39	c.G4869A	p.K1623K	GACCAAGCTGAGC	.	PASS	Atlas-SNP
FMO1	2326	hgsc.bcm.edu	37	1	171252287	171252287	+	Silent	SNP	A	A	G	rs1126692	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	293	165	279	0	0.56314	0	A|0.769;C|0.000;G|0.231	0.231	strong	FMO1,left_upper_lobe,carcinoma,+2,1	FMO1	79	1	NM_002021	exon8	c.A1188G	p.V396V	AGGTGTAAATAAG	.	PASS	Atlas-SNP
NLRP2	55655	hgsc.bcm.edu	37	19	55494262	55494262	+	Missense_Mutation	SNP	C	C	T	rs142821233	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	117	3	141	0	0.025641	0	C|1.000;T|0.000	0.000	weak	NLRP2_ENST00000543010,caecum,carcinoma,0,1	NLRP2	161	1	NM_017852	exon6	c.C1196T	p.A399V	CCCCCGCGGTGTG	.	scavenged	Atlas-SNP
MYH4	4622	hgsc.bcm.edu	37	17	10355371	10355371	+	Missense_Mutation	SNP	C	C	T	rs11651295	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	43	118	0	0.5	0	C|0.616;T|0.384	0.384	strong	.	MYH4	349	.	NM_017533	exon27	c.G3625A	p.E1209K	TCTGCTCCCCAAG	.	PASS	Atlas-SNP
PPM1E	22843	hgsc.bcm.edu	37	17	56833612	56833612	+	Missense_Mutation	SNP	C	C	G	rs116991234	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	57	25	46	0	0.438596	0	C|0.993;G|0.007	0.007	strong	.	PPM1E	97	.	NM_014906	exon1	c.C254G	p.P85R	AAGACCCGGAGCC	.	PASS	Atlas-SNP
MTA1	9112	hgsc.bcm.edu	37	14	105936204	105936204	+	Silent	SNP	C	C	T	rs373034822		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	53	102	0	0.546392	0	.	.	weak	.	MTA1	61	.	NM_004689	exon20	c.C1872T	p.N624N	GCTCAACGGGAAG	.	PASS	Atlas-SNP
WNK1	65125	hgsc.bcm.edu	37	12	999632	999632	+	Missense_Mutation	SNP	C	C	A	rs371264719	alternate_allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	249	55	312	0	0.220884	0	.	.	alt	.	WNK1	403	.	NM_001184985	exon22	c.C6242A	p.A2081E	CCATGGCGGCTCC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195513461	195513461	+	Missense_Mutation	SNP	G	G	A	rs199513183	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	207	23	168	0	0.111111	0	.	.	weak	.	MUC4	1505	.	NM_018406	exon2	c.C4990T	p.P1664S	GAAGAGGGGTGGC	.	PASS	Atlas-SNP
RNASE11	122651	hgsc.bcm.edu	37	14	21052259	21052259	+	Silent	SNP	T	T	C	rs1429539	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	229	229	242	0	1	0	T|0.613;C|0.387	0.387	strong	.	RNASE11	44	.	NM_145250	exon3	c.A375G	p.T125T	CACTTCTGTGGAG	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179659912	179659912	+	Missense_Mutation	SNP	G	G	A	rs16866538	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	42	89	0	0.538462	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
CACNA2D4	93589	hgsc.bcm.edu	37	12	1902905	1902905	+	Silent	SNP	G	G	A	rs33912216	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	184	94	147	0	0.51087	0	G|0.891;A|0.109	0.109	strong	.	CACNA2D4	220	.	NM_172364	exon38	c.C3330T	p.G1110G	GGCGCCGCCGCAG	.	PASS	Atlas-SNP
CCT2	10576	hgsc.bcm.edu	37	12	69986788	69986788	+	Silent	SNP	A	A	G	rs1043434	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	61	24	58	0	0.393443	0	A|0.800;G|0.200	0.200	strong	.	CCT2	49	.	NM_006431	exon9	c.A783G	p.T261T	CTCTACAGCAAAG	.	PASS	Atlas-SNP
WDFY4	57705	hgsc.bcm.edu	37	10	50183042	50183042	+	Missense_Mutation	SNP	G	G	A	rs61733240	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	118	58	118	0	0.491525	0	G|0.901;A|0.099	0.099	strong	.	WDFY4	205	.	NM_020945	exon58	c.G9064A	p.A3022T	CTGCCCGCCCATC	.	PASS	Atlas-SNP
TSEN54	283989	hgsc.bcm.edu	37	17	73520435	73520435	+	Missense_Mutation	SNP	G	G	A	rs200275380		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	150	83	180	0	0.553333	0	G|0.999;A|0.001	0.001	weak	.	TSEN54	27	.	NM_207346	exon11	c.G1523A	p.G508D	ATCATGGTGACAT	.	PASS	Atlas-SNP
PIEZO1	9780	hgsc.bcm.edu	37	16	88783521	88783521	+	Silent	SNP	T	T	C	rs6500491	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	97	95	0	1	0	C|0.901;G|0.000;T|0.099	0.901	strong	.	PIEZO1	79	.	NM_001142864	exon45	c.A6570G	p.P2190P	GAGCAGTGGGAAC	.	PASS	Atlas-SNP
LCA5L	150082	hgsc.bcm.edu	37	21	40800368	40800368	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	124	23	89	0	0.185484	0	.	.	none	.	LCA5L	57	.	NM_152505	exon4	c.G52A	p.V18M	ATGCCACGCCGAA	.	PASS	Atlas-SNP
CARD10	29775	hgsc.bcm.edu	37	22	37906262	37906262	+	Missense_Mutation	SNP	C	C	T	rs9610775	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	16	9	32	0	0.5625	0	C|0.806;T|0.194	0.194	strong	.	CARD10	55	.	NM_014550	exon4	c.G866A	p.R289Q	GTCAGCCGCTGGT	.	PASS	Atlas-SNP
PKHD1	5314	hgsc.bcm.edu	37	6	51524681	51524681	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	167	42	189	0	0.251497	0	.	.	none	PKHD1,NS,carcinoma,0,1	PKHD1	927	1	NM_138694	exon61	c.C10243T	p.L3415F	TATCAAGAATTAG	.	PASS	Atlas-SNP
KIAA0226	9711	hgsc.bcm.edu	37	3	197401952	197401952	+	Silent	SNP	T	T	C	rs28562770	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	31	86	0	0.442857	0	T|0.811;C|0.189	0.189	strong	.	KIAA0226	136	.	NM_014687	exon20	c.A2856G	p.S952S	GTAGTCTGACAGG	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1263776	1263776	+	Missense_Mutation	SNP	C	C	T	rs2943510	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	204	38	213	0	0.186275	0	C|0.873;T|0.127	0.127	strong	.	MUC5B	473	.	NM_002458	exon31	c.C5666T	p.P1889L	GTACCCCAGCCAC	.	PASS	Atlas-SNP
GPER	2852	hgsc.bcm.edu	37	7	1132153	1132153	+	Silent	SNP	G	G	A	rs3808352	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	24	10	36	0	0.416667	0	G|0.875;A|0.125	0.125	strong	.	GPER	25	.	NM_001505	exon2	c.G789A	p.A263A	CCTCGCGGTGGTG	.	PASS	Atlas-SNP
KRT77	374454	hgsc.bcm.edu	37	12	53086645	53086645	+	Missense_Mutation	SNP	G	G	A	rs3782489	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	172	74	210	0	0.430233	0	G|0.631;A|0.369	0.369	strong	.	KRT77	58	.	NM_175078	exon6	c.C1100T	p.T367M	CCTGCCGTGATCT	.	PASS	Atlas-SNP
SLC35A1	10559	hgsc.bcm.edu	37	6	88218282	88218282	+	Missense_Mutation	SNP	A	A	G	rs188216651	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	52	31	59	0	0.596154	0	A|1.000;G|0.000	0.000	strong	.	SLC35A1	29	.	NM_006416	exon6	c.A719G	p.Y240C	TTTTCTATGGTTA	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	40	96	0	0.412371	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
FANCE	2178	hgsc.bcm.edu	37	6	35426175	35426175	+	Silent	SNP	C	C	T	rs3823434	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	96	38	110	0	0.395833	0	C|0.960;T|0.040	0.040	strong	.	FANCE	45	.	NM_021922	exon5	c.C1071T	p.L357L	CAGCCTCAGCAAT	.	PASS	Atlas-SNP
CD33	945	hgsc.bcm.edu	37	19	51728641	51728641	+	Missense_Mutation	SNP	A	A	G	rs2455069	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	140	73	149	1	0.521429	0.00671141	A|0.596;G|0.404	0.404	strong	CD33,NS,carcinoma,0,1	CD33	55	1	NM_001772	exon2	c.A205G	p.R69G	ATATCCAGGGACT	.	scavenged	Atlas-SNP
CWF19L2	143884	hgsc.bcm.edu	37	11	107224415	107224415	+	Silent	SNP	A	A	G	rs35543671	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	100	27	90	0	0.27	0	A|0.983;G|0.017	0.017	strong	.	CWF19L2	135	.	NM_152434	exon13	c.T1920C	p.F640F	GGAGACAAACATG	.	PASS	Atlas-SNP
TRPM1	4308	hgsc.bcm.edu	37	15	31327779	31327779	+	Silent	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	93	5	89	0	0.0537634	0	.	.	none	.	TRPM1	183	.	NM_001252020	exon20	c.C2721T	p.I907I	GCTCACGATGTAG	.	PASS	Atlas-SNP
FAM109B	150368	hgsc.bcm.edu	37	22	42473860	42473860	+	Missense_Mutation	SNP	C	C	G	rs1807493	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	37	37	56	0	1	0	C|0.837;G|0.163	0.163	strong	.	FAM109B	22	.	NM_001002034	exon3	c.C563G	p.A188G	AAGAAGCGGGCAG	.	PASS	Atlas-SNP
MAP4K1	11184	hgsc.bcm.edu	37	19	39092142	39092142	+	Silent	SNP	C	C	T	rs35423612	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	43	22	40	0	0.511628	0	C|0.990;T|0.010	0.010	strong	.	MAP4K1	165	.	NM_007181	exon20	c.G1470A	p.L490L	ATTGAACAACTTT	.	PASS	Atlas-SNP
FRZB	2487	hgsc.bcm.edu	37	2	183699584	183699584	+	Missense_Mutation	SNP	G	G	C	rs7775	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	160	62	169	0	0.3875	0	G|0.865;C|0.135	0.135	strong	FRZB,NS,carcinoma,+1,1	FRZB	42	1	NM_001463	exon6	c.C970G	p.R324G	AGTTGCGTGCTTG	.	PASS	Atlas-SNP
GPR4	2828	hgsc.bcm.edu	37	19	46094597	46094597	+	Silent	SNP	G	G	A	rs3745820	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	96	93	117	0	0.96875	0	G|0.820;A|0.180	0.180	strong	.	GPR4	54	.	NM_005282	exon2	c.C528T	p.G176G	CACCCAGCCTTCC	.	PASS	Atlas-SNP
GCNT2	2651	hgsc.bcm.edu	37	6	10586727	10586727	+	Missense_Mutation	SNP	G	G	A	rs56106312	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	163	111	165	0	0.680982	0	G|0.996;A|0.004	0.004	strong	.	GCNT2	123	.	NM_145655	exon1	c.G505A	p.A169T	CTCCAGGCTGACC	.	PASS	Atlas-SNP
D2HGDH	728294	hgsc.bcm.edu	37	2	242690770	242690770	+	Silent	SNP	T	T	C	rs141343442	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	81	34	93	0	0.419753	0	T|0.973;C|0.027	0.027	strong	.	D2HGDH	39	.	NM_152783	exon8	c.T1107C	p.D369D	GACCGATGGGACC	.	PASS	Atlas-SNP
SLC25A27	9481	hgsc.bcm.edu	37	6	46632594	46632594	+	Missense_Mutation	SNP	T	T	C	rs35884480	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	64	39	76	0	0.609375	0	T|0.951;C|0.049	0.049	strong	.	SLC25A27	22	.	NM_001204051	exon5	c.T590C	p.I197T	CCAATATACAAAG	.	PASS	Atlas-SNP
PER3	8863	hgsc.bcm.edu	37	1	7890026	7890026	+	Missense_Mutation	SNP	A	A	G	rs199947375	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	18	154	1	0.209302	0.00649351	.	.	weak	PER3,NS,carcinoma,0,4	PER3	95	4	NM_016831	exon18	c.A2992G	p.K998E	CCCATGAAGAATC	.	scavenged	Atlas-SNP
ELSPBP1	64100	hgsc.bcm.edu	37	19	48519244	48519244	+	Silent	SNP	A	A	G	rs35792818	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	90	50	108	0	0.555556	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
FUT2	2524	hgsc.bcm.edu	37	19	49206603	49206603	+	Silent	SNP	C	C	T	rs281377	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	48	25	62	0	0.520833	0	C|0.559;T|0.441	0.441	strong	.	FUT2	30	.	NM_001097638	exon2	c.C390T	p.N130N	CCTGAACGACTGG	.	PASS	Atlas-SNP
ZAN	7455	hgsc.bcm.edu	37	7	100377373	100377373	+	Splice_Site	SNP	G	G	A	rs482308	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	20	12	32	0	0.6	0	G|0.690;T|0.002	.	strong	.	ZAN	658	.	NM_003386	exon35	c.6621+1G>A	.	TCTGCCGTGAGTG	.	PASS	Atlas-SNP
WDR78	79819	hgsc.bcm.edu	37	1	67327894	67327894	+	Silent	SNP	A	A	G	rs34182923	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	316	159	424	1	0.503165	0.00235849	A|0.982;G|0.018	0.018	strong	.	WDR78	102	.	NM_207014	exon7	c.T1032C	p.S344S	TTTACTACTTGAC	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	9	9	22	0	1	0	T|0.588;C|0.412	0.412	strong	.	ZNF737	50	.	NM_001159293	exon4	c.A1546G	p.K516E	AGCCTTTGCCACA	.	PASS	Atlas-SNP
FAT1	2195	hgsc.bcm.edu	37	4	187525020	187525020	+	Missense_Mutation	SNP	A	A	C	rs2637777	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	117	57	149	0	0.487179	0	T|0.007;G|0.007	.	strong	.	FAT1	500	.	NM_005245	exon19	c.T10660G	p.S3554A	CAGAAGAGGTGAT	.	PASS	Atlas-SNP
OR1S1	219959	hgsc.bcm.edu	37	11	57983162	57983162	+	Missense_Mutation	SNP	A	A	G	rs7103026	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	104	67	117	0	0.644231	0	A|0.817;G|0.183	0.183	strong	OR1S1,NS,carcinoma,0,2	OR1S1	139	2	NM_001004458	exon1	c.A946G	p.K316E	CTGAGAAAGCTCA	.	PASS	Atlas-SNP
MAGEA12	4111	hgsc.bcm.edu	37	X	151899913	151899913	+	Silent	SNP	T	T	C	rs2233055	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	336	335	555	2	0.997024	0.0036036	T|0.627;C|0.373	0.373	strong	.	MAGEA12	125	.	NM_005367	exon2	c.A888G	p.G296G	GTGAGGTCCTCCA	.	PASS	Atlas-SNP
KRTAP10-11	386678	hgsc.bcm.edu	37	21	46067193	46067193	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	107	4	89	1	0.0373832	0.011236	.	.	none	KRTAP10-11,NS,carcinoma,-1,1	KRTAP10-11	36	1	NM_198692	exon1	c.G818C	p.C273S	CCTCCTGCGTGTC	.	scavenged	Atlas-SNP
PITPNM3	83394	hgsc.bcm.edu	37	17	6441376	6441376	+	Missense_Mutation	SNP	G	G	A	rs28493751	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	175	78	218	1	0.445714	0.00458716	G|0.926;A|0.074	0.074	strong	PITPNM3,brain,glioma,0,1	PITPNM3	91	1	NM_031220	exon2	c.C49T	p.P17S	GCCAGGGGGCACC	.	scavenged	Atlas-SNP
CEP68	23177	hgsc.bcm.edu	37	2	65299298	65299298	+	Missense_Mutation	SNP	C	C	A	rs2723088	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	205	153	107	0	0.746341	0	C|0.905;A|0.095	0.095	strong	.	CEP68	69	.	NM_015147	exon3	c.C1068A	p.N356K	CCCCAACTGCCCA	.	PASS	Atlas-SNP
TMEM8A	58986	hgsc.bcm.edu	37	16	427516	427516	+	Silent	SNP	T	T	C	rs11649031	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	76	152	1	0.974359	0.00657895	T|0.429;C|0.571	0.571	strong	TMEM8A,colon,carcinoma,0,2	TMEM8A	49	2	NM_021259	exon3	c.A369G	p.V123V	GGGCTGTACCGCG	.	PASS	Atlas-SNP
CDH17	1015	hgsc.bcm.edu	37	8	95186382	95186382	+	Silent	SNP	G	G	A	rs3214050	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	135	31	124	1	0.22963	0.00806452	G|0.634;A|0.366	0.366	strong	CDH17,NS,carcinoma,0,1	CDH17	119	1	NM_004063	exon6	c.C531T	p.V177V	GTACATGACATTG	.	scavenged	Atlas-SNP
FAM13A	10144	hgsc.bcm.edu	37	4	89668859	89668859	+	Missense_Mutation	SNP	C	C	T	rs7657817	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	174	80	213	0	0.45977	0	C|0.745;T|0.255	0.255	strong	.	FAM13A	181	.	NM_014883	exon18	c.G2305A	p.V769I	CTTCAACACTGGG	.	PASS	Atlas-SNP
RAD21L1	642636	hgsc.bcm.edu	37	20	1224774	1224774	+	Missense_Mutation	SNP	A	A	C	rs17717241	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	81	39	112	0	0.481481	0	A|0.928;C|0.072	0.072	strong	.	RAD21L1	51	.	NM_001136566	exon11	c.A1268C	p.H423P	CTCAGCATAGCTC	.	PASS	Atlas-SNP
NLRP7	199713	hgsc.bcm.edu	37	19	55451797	55451797	+	Silent	SNP	C	C	T	rs775883	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	117	50	167	0	0.42735	0	C|0.623;T|0.377	0.377	strong	.	NLRP7	411	.	NM_001127255	exon4	c.G390A	p.Q130Q	CAAAGACTGTTTC	.	PASS	Atlas-SNP
LAMB2	3913	hgsc.bcm.edu	37	3	49162284	49162284	+	Missense_Mutation	SNP	C	C	T	rs34759087	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	83	49	110	0	0.590361	0	C|0.920;T|0.080	0.080	strong	.	LAMB2	156	.	NM_002292	exon21	c.G2959A	p.E987K	TGCACTCACACAG	.	PASS	Atlas-SNP
PAMR1	25891	hgsc.bcm.edu	37	11	35463043	35463043	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	129	65	129	0	0.503876	0	.	.	none	.	PAMR1	85	.	NM_015430	exon8	c.C1070T	p.P357L	CAGATGGGCTGTT	.	PASS	Atlas-SNP
ZFPM1	161882	hgsc.bcm.edu	37	16	88599023	88599023	+	Silent	SNP	A	A	G	rs56041036	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	196	194	179	0	0.989796	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
DNAH8	1769	hgsc.bcm.edu	37	6	38800209	38800209	+	Silent	SNP	T	T	C	rs1678729	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	76	35	82	0	0.460526	0	T|0.758;C|0.242	0.242	strong	.	DNAH8	1239	.	NM_001206927	exon31	c.T4300C	p.L1434L	TATGAATTGGTAA	.	PASS	Atlas-SNP
HYPK	25764	hgsc.bcm.edu	37	15	44093927	44093927	+	Missense_Mutation	SNP	T	T	C	rs12702	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	30	72	0	0.352941	0	T|0.812;C|0.188	0.188	strong	.	.	.	.	NM_016400	exon4	c.T313C	p.S105P	GAGATATCTCGAG	.	PASS	Atlas-SNP
HYAL4	23553	hgsc.bcm.edu	37	7	123514896	123514896	+	Missense_Mutation	SNP	G	G	T	rs6949082	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	59	59	81	0	1	0	G|0.852;T|0.148	0.148	strong	.	HYAL4	65	.	NM_012269	exon4	c.G1036T	p.A346S	TTAACTGCATCCA	.	PASS	Atlas-SNP
YTHDF1	54915	hgsc.bcm.edu	37	20	61834695	61834695	+	Silent	SNP	G	G	A	rs6122103	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	51	23	53	0	0.45098	0	G|0.680;A|0.320	0.320	strong	.	YTHDF1	66	.	NM_017798	exon4	c.C597T	p.A199A	CTTGACGGCGGAG	.	PASS	Atlas-SNP
SLC16A8	23539	hgsc.bcm.edu	37	22	38477930	38477930	+	Silent	SNP	G	G	A	rs2235573	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	208	85	229	1	0.408654	0.00436681	G|0.551;A|0.449	0.449	strong	SLC16A8,NS,carcinoma,0,1	SLC16A8	13	1	NM_013356	exon3	c.C324T	p.L108L	CTCCAGGAGGCGC	.	scavenged	Atlas-SNP
FAM13A	10144	hgsc.bcm.edu	37	4	89772321	89772321	+	Missense_Mutation	SNP	C	C	T	rs115194267	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	60	28	50	0	0.466667	0	C|0.990;T|0.010	0.010	strong	.	FAM13A	181	.	NM_014883	exon7	c.G857A	p.R286K	TCACTCCTGGATT	.	PASS	Atlas-SNP
DMRTC2	63946	hgsc.bcm.edu	37	19	42354629	42354629	+	Silent	SNP	T	T	C	rs2305809	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	27	25	26	0	0.925926	0	T|0.398;C|0.602	0.602	strong	.	DMRTC2	31	.	NM_001040283	exon8	c.T852C	p.G284G	ATCTGGTCCCTCA	.	PASS	Atlas-SNP
FREM1	158326	hgsc.bcm.edu	37	9	14801725	14801725	+	Missense_Mutation	SNP	C	C	G	rs61744094	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	221	97	238	0	0.438914	0	C|0.889;G|0.111	0.111	strong	.	FREM1	261	.	NM_144966	exon21	c.G3619C	p.E1207Q	TATTCTCAGAGAA	.	PASS	Atlas-SNP
JAK1	3716	hgsc.bcm.edu	37	1	65335095	65335095	+	Silent	SNP	T	T	C	rs11585932	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	106	46	134	0	0.433962	0	T|0.963;C|0.037	0.037	strong	.	JAK1	209	.	NM_002227	exon6	c.A546G	p.G182G	ATCATGTCCATCC	.	PASS	Atlas-SNP
NUP62CL	54830	hgsc.bcm.edu	37	X	106396455	106396455	+	Silent	SNP	A	A	G	rs1285590	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	214	212	349	0	0.990654	0	A|0.553;G|0.447	0.447	strong	.	NUP62CL	10	.	NM_017681	exon7	c.T477C	p.R159R	CTGGTCACGCGTA	.	PASS	Atlas-SNP
LHB	3972	hgsc.bcm.edu	37	19	49519873	49519873	+	Silent	SNP	G	G	C	rs72626226		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	253	34	362	0	0.134387	0	.	.	weak	.	LHB	20	.	NM_000894	exon2	c.C114G	p.V38V	CTTCTCGACAGCC	.	PASS	Atlas-SNP
HSD17B14	51171	hgsc.bcm.edu	37	19	49318380	49318380	+	Missense_Mutation	SNP	G	G	A	rs35299026	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	36	15	51	0	0.416667	0	G|0.966;A|0.034	0.034	strong	.	HSD17B14	25	.	NM_016246	exon6	c.C388T	p.R130W	TCTTCCGCAGGTA	.	PASS	Atlas-SNP
CDON	50937	hgsc.bcm.edu	37	11	125851055	125851055	+	Silent	SNP	A	A	G	rs564214	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	109	18	141	1	0.165138	0.0070922	A|0.698;G|0.302	0.302	strong	CDON,brain,glioma,0,1	CDON	137	1	NM_016952	exon17	c.T3165C	p.N1055N	GACTGCATTGGGG	.	scavenged	Atlas-SNP
LAMA3	3909	hgsc.bcm.edu	37	18	21437931	21437931	+	Silent	SNP	G	G	C	rs867449	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	91	41	116	0	0.450549	0	G|0.488;C|0.512	0.512	strong	.	LAMA3	397	.	NM_001127717	exon33	c.G4260C	p.G1420G	CCCAGGGACCGGG	.	PASS	Atlas-SNP
PALLD	23022	hgsc.bcm.edu	37	4	169433333	169433333	+	Silent	SNP	C	C	T	rs7673220	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	60	60	80	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
EXO5	64789	hgsc.bcm.edu	37	1	40980731	40980731	+	Missense_Mutation	SNP	G	G	T	rs11208299	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	87	137	0	1	0	G|0.508;T|0.492	0.492	strong	.	.	.	.	NM_022774	exon3	c.G515T	p.G172V	GGGAAGGGGAGGG	.	PASS	Atlas-SNP
SMEK1	55671	hgsc.bcm.edu	37	14	91948043	91948043	+	Silent	SNP	T	T	C	rs17127374	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	266	127	360	0	0.477444	0	T|0.932;C|0.068	0.068	strong	.	SMEK1	94	.	NM_032560	exon5	c.A792G	p.T264T	TCTGTATGTCTGA	.	PASS	Atlas-SNP
SPEG	10290	hgsc.bcm.edu	37	2	220353532	220353532	+	Missense_Mutation	SNP	C	C	A	rs13026308	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	193	104	221	0	0.53886	0	C|0.913;A|0.087	0.087	strong	.	SPEG	272	.	NM_005876	exon34	c.C8059A	p.P2687T	GAGGTACCCCAGA	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	37	71	0	0.521127	0	G|0.373;C|0.627	0.627	strong	.	DUSP27	235	.	NM_001080426	exon5	c.G795C	p.E265D	CAATGAGGGCTTC	.	PASS	Atlas-SNP
MAPKAPK2	9261	hgsc.bcm.edu	37	1	206905043	206905043	+	Silent	SNP	C	C	T	rs4073250	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	152	80	192	0	0.526316	0	C|0.820;T|0.180	0.180	strong	.	MAPKAPK2	45	.	NM_004759	exon8	c.C951T	p.T317T	CATCACCGAGTTT	.	PASS	Atlas-SNP
ZNF695	57116	hgsc.bcm.edu	37	1	247151035	247151035	+	Missense_Mutation	SNP	T	T	G	rs2642993	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	128	63	144	0	0.492188	0	T|0.936;G|0.064	0.064	strong	.	ZNF695	55	.	NM_020394	exon4	c.A782C	p.N261T	GTATGATTTTTCT	.	PASS	Atlas-SNP
ACAN	176	hgsc.bcm.edu	37	15	89401615	89401615	+	Silent	SNP	T	T	G	rs3825994	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	148	147	137	0	0.993243	0	T|0.431;G|0.569	0.569	strong	.	ACAN	220	.	NM_001135	exon12	c.T5799G	p.T1933T	CCCCACTGTCTCT	.	PASS	Atlas-SNP
TCN1	6947	hgsc.bcm.edu	37	11	59623433	59623433	+	Silent	SNP	G	G	A	rs1042613	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	159	117	144	2	0.735849	0.0138889	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	.	scavenged	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	102	101	125	0	0.990196	0	G|0.522;A|0.478	0.478	strong	.	MAN2B2	80	.	NM_015274	exon7	c.G958A	p.V320M	GTCTCGGTGCAGT	.	PASS	Atlas-SNP
SESN1	27244	hgsc.bcm.edu	37	6	109322554	109322554	+	Silent	SNP	C	C	T	rs12214121	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	124	54	163	0	0.435484	0	C|0.915;T|0.085	0.085	strong	.	SESN1	29	.	NM_014454	exon3	c.G483A	p.Q161Q	ATAGTGCTGAGTT	.	PASS	Atlas-SNP
DDIT4L	115265	hgsc.bcm.edu	37	4	101109161	101109161	+	Silent	SNP	G	G	C	rs3749604	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	76	32	77	0	0.421053	0	G|0.813;C|0.187	0.187	strong	DDIT4L,NS,carcinoma,-1,1	DDIT4L	33	1	NM_145244	exon3	c.C255G	p.T85T	TCTCTGGGTCAGT	.	PASS	Atlas-SNP
ZNF516	9658	hgsc.bcm.edu	37	18	74155000	74155000	+	Missense_Mutation	SNP	T	T	C	rs3752097	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	14	14	30	0	1	0	T|0.920;C|0.080	0.080	strong	.	ZNF516	102	.	NM_014643	exon3	c.A11G	p.N4S	TCTCTGTTGCGAT	.	PASS	Atlas-SNP
MMS19	64210	hgsc.bcm.edu	37	10	99219885	99219885	+	Silent	SNP	G	G	A	rs2152092	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	128	127	134	0	0.992188	0	G|0.506;A|0.494	0.494	strong	.	MMS19	36	.	NM_022362	exon26	c.C2574T	p.A858A	CACTTCGGCATGG	.	PASS	Atlas-SNP
ZFHX3	463	hgsc.bcm.edu	37	16	72993397	72993397	+	Silent	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	100	38	96	0	0.38	0	.	.	none	.	ZFHX3	404	.	NM_006885	exon2	c.G648A	p.P216P	GGTATTCGGGAAA	.	PASS	Atlas-SNP
C1S	716	hgsc.bcm.edu	37	12	7175762	7175762	+	Missense_Mutation	SNP	G	G	C	rs150549869	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	120	56	137	0	0.466667	0	G|1.000;C|0.000	0.000	strong	.	C1S	93	.	NM_201442	exon11	c.G1198C	p.E400Q	CCAGGGGAGTATC	.	PASS	Atlas-SNP
TDRD6	221400	hgsc.bcm.edu	37	6	46658905	46658905	+	Missense_Mutation	SNP	C	C	G	rs9381472	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	53	17	81	0	0.320755	0	C|0.649;G|0.351	0.351	strong	.	TDRD6	205	.	NM_001168359	exon1	c.C3040G	p.Q1014E	TTAGAACAGTTGT	.	PASS	Atlas-SNP
OR5T2	219464	hgsc.bcm.edu	37	11	56000079	56000079	+	Missense_Mutation	SNP	C	C	T	rs77295387	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	207	157	264	0	0.758454	0	C|0.981;T|0.019	0.019	strong	.	OR5T2	107	.	NM_001004746	exon1	c.G583A	p.A195T	TAGTAGCATGTAA	.	PASS	Atlas-SNP
ESYT2	57488	hgsc.bcm.edu	37	7	158590740	158590740	+	Missense_Mutation	SNP	A	A	T	rs13233513	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	29	67	0	0.42029	0	A|0.887;T|0.113	0.113	strong	.	ESYT2	70	.	NM_020728	exon3	c.T544A	p.C182S	ATTGGCAAATGAA	.	PASS	Atlas-SNP
C1orf65	164127	hgsc.bcm.edu	37	1	223566876	223566876	+	Missense_Mutation	SNP	G	G	A	rs75945379	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	11	8	23	0	0.727273	0	G|0.937;A|0.063	0.063	strong	C1orf65,NS,carcinoma,0,1	C1orf65	71	1	NM_152610	exon1	c.G59A	p.R20Q	CCCCGCGGCCCGG	.	PASS	Atlas-SNP
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32609094	32609094	+	Silent	SNP	C	C	T	rs1129737	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	126	82	153	0	0.650794	0	C|0.706;T|0.294	0.294	strong	.	HLA-DQA1	52	.	NM_002122	exon2	c.C90T	p.H30H	TGACCACGTTGCC	.	PASS	Atlas-SNP
DYNC1I1	1780	hgsc.bcm.edu	37	7	95668664	95668664	+	Silent	SNP	C	C	A	rs1048666	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	159	158	199	1	0.993711	0.00502513	C|0.760;A|0.240	0.240	strong	.	DYNC1I1	111	.	NM_004411	exon14	c.C1491A	p.G497G	AGTGGGCCCAATC	.	PASS	Atlas-SNP
RGL3	57139	hgsc.bcm.edu	37	19	11516007	11516007	+	Silent	SNP	T	T	G	rs10416704	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	55	31	59	0	0.563636	0	T|0.794;G|0.206	0.206	strong	.	RGL3	100	.	NM_001035223	exon8	c.A1092C	p.A364A	GCTCACTGCCCCC	.	PASS	Atlas-SNP
APOBEC3F	200316	hgsc.bcm.edu	37	22	39441203	39441203	+	Silent	SNP	C	C	T	rs4821862	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	51	135	1	0.504951	0.00740741	C|0.439;T|0.561	0.561	strong	APOBEC3F,NS,carcinoma,+2,2	APOBEC3F	37	2	NM_145298	exon3	c.C429T	p.R143R	GGCCCGCGTGAAG	.	scavenged	Atlas-SNP
TMPRSS6	164656	hgsc.bcm.edu	37	22	37466565	37466565	+	Silent	SNP	G	G	A	rs145814440	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	153	67	207	0	0.437909	0	G|0.992;A|0.008	0.008	strong	.	TMPRSS6	99	.	NM_153609	exon15	c.C1827T	p.D609D	CCAGCGGTCAGCG	.	PASS	Atlas-SNP
TTLL6	284076	hgsc.bcm.edu	37	17	46894377	46894377	+	Missense_Mutation	SNP	A	A	C	rs3959442	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	25	15	28	0	0.6	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
ACO2	50	hgsc.bcm.edu	37	22	41903813	41903813	+	Silent	SNP	A	A	C	rs137831	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	96	56	145	0	0.583333	0	A|0.669;C|0.331	0.331	strong	.	ACO2	58	.	NM_001098	exon3	c.A192C	p.T64T	GCTGACACTCTCG	.	PASS	Atlas-SNP
ALB	213	hgsc.bcm.edu	37	4	74285263	74285263	+	Silent	SNP	A	A	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	22	91	0	0.217822	0	.	.	none	.	ALB	132	.	NM_000477	exon13	c.A1692G	p.T564T	GGCAACAAAAGAG	.	PASS	Atlas-SNP
TCP11	6954	hgsc.bcm.edu	37	6	35090097	35090097	+	Silent	SNP	T	T	C	rs2234044	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	345	153	409	0	0.443478	0	T|0.808;C|0.192	0.192	strong	.	TCP11	94	.	NM_001093728	exon5	c.A414G	p.L138L	TGGTAATAGCAGT	.	PASS	Atlas-SNP
CHSY3	337876	hgsc.bcm.edu	37	5	129520679	129520679	+	Missense_Mutation	SNP	G	G	A	rs10068403	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	49	86	0	0.653333	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
GPRIN1	114787	hgsc.bcm.edu	37	5	176026143	176026143	+	Silent	SNP	C	C	T	rs77245696	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	134	44	167	0	0.328358	0	C|0.778;T|0.222	0.222	strong	.	GPRIN1	77	.	NM_052899	exon2	c.G693A	p.R231R	CTCCTTCCTCGGT	.	PASS	Atlas-SNP
ASPM	259266	hgsc.bcm.edu	37	1	197094030	197094030	+	Silent	SNP	C	C	T	rs6676084	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	142	142	213	0	1	0	C|0.754;N|0.000	.	strong	.	ASPM	444	.	NM_001206846	exon12	c.G3138A	p.R1046R	AAGCAACCTGAGA	.	PASS	Atlas-SNP
IFT81	28981	hgsc.bcm.edu	37	12	110618235	110618235	+	Silent	SNP	A	A	G	rs16940805	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	30	77	0	0.517241	0	A|0.963;G|0.037	0.037	strong	IFT81_ENST00000242591,caecum,carcinoma,+2,1	IFT81	86	1	NM_014055	exon12	c.A1197G	p.R399R	CAAACGATATGTC	.	PASS	Atlas-SNP
COL6A2	1292	hgsc.bcm.edu	37	21	47552385	47552385	+	Silent	SNP	C	C	T	rs6652	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	85	53	81	0	0.623529	0	C|0.863;T|0.137	0.137	strong	.	COL6A2	351	.	NM_001849	exon28	c.C2979T	p.R993R	TGACCGCGCCGCC	.	PASS	Atlas-SNP
KRT14	3861	hgsc.bcm.edu	37	17	39742921	39742921	+	Missense_Mutation	SNP	G	G	A	rs117484558	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	25	10	22	0	0.4	0	G|0.994;A|0.006	0.006	strong	KRT14,NS,carcinoma,+1,1	KRT14	65	1	NM_000526	exon1	c.C166T	p.R56C	AGAAGCGGGAGGA	.	PASS	Atlas-SNP
FKBP15	23307	hgsc.bcm.edu	37	9	115931703	115931703	+	Silent	SNP	G	G	A	rs3810910	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	196	98	207	0	0.5	0	G|0.712;A|0.288	0.288	strong	.	FKBP15	128	.	NM_015258	exon26	c.C3286T	p.L1096L	GGGACAGTCTTGT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195505874	195505874	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	84	6	64	1	0.0714286	0.015625	.	.	none	MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	NM_018406	exon2	c.C12577G	p.L4193V	CAGGAAGAGGGGT	.	scavenged	Atlas-SNP
PABPC1L	80336	hgsc.bcm.edu	37	20	43547677	43547677	+	Missense_Mutation	SNP	T	T	G	rs2075960	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	106	102	112	0	0.962264	0	T|0.781;G|0.219	0.219	strong	.	PABPC1L	59	.	NM_001124756	exon4	c.T634G	p.S212A	CTCTTCTCCCAGT	.	PASS	Atlas-SNP
ABCA4	24	hgsc.bcm.edu	37	1	94544233	94544233	+	Silent	SNP	G	G	A	rs4147831	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	155	64	163	0	0.412903	0	G|0.896;A|0.104	0.104	strong	ABCA4,NS,carcinoma,-2,2	ABCA4	275	2	NM_000350	exon10	c.C1269T	p.H423H	CCTAACGTGTTCC	.	PASS	Atlas-SNP
CPSF1	29894	hgsc.bcm.edu	37	8	145624578	145624578	+	Silent	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	89	40	95	0	0.449438	0	.	.	none	.	CPSF1	92	.	NM_013291	exon15	c.C1407T	p.I469I	GTTCAGGATGCTG	.	PASS	Atlas-SNP
PTPRR	5801	hgsc.bcm.edu	37	12	71286606	71286606	+	Silent	SNP	G	G	A	rs149684669	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	295	139	371	0	0.471186	0	G|0.997;A|0.003	0.003	strong	.	PTPRR	109	.	NM_002849	exon2	c.C210T	p.S70S	AGCTTCGGAAGAG	.	PASS	Atlas-SNP
KIAA0355	9710	hgsc.bcm.edu	37	19	34843761	34843761	+	Silent	SNP	C	C	A	rs397414	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	112	58	120	0	0.517857	0	C|0.378;A|0.622	0.622	strong	.	KIAA0355	105	.	NM_014686	exon14	c.C3114A	p.P1038P	CCCACCCCAGCCC	.	PASS	Atlas-SNP
ATG13	9776	hgsc.bcm.edu	37	11	46690413	46690413	+	Missense_Mutation	SNP	G	G	A	rs35619591	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	24	19	26	0	0.791667	0	G|0.994;A|0.006	0.006	strong	.	ATG13	60	.	NM_001205119	exon16	c.G1399A	p.G467R	TCCAGCGGGGGCA	.	PASS	Atlas-SNP
PRPS1L1	221823	hgsc.bcm.edu	37	7	18066569	18066569	+	Missense_Mutation	SNP	C	C	A	rs3800962	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	197	197	204	1	1	0.00490196	C|0.709;A|0.291	0.291	strong	.	PRPS1L1	90	.	NM_175886	exon1	c.G837T	p.E279D	CATCTTCTCATCT	.	PASS	Atlas-SNP
ADAM18	8749	hgsc.bcm.edu	37	8	39525607	39525607	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	323	4	303	0	0.0123839	0	.	.	none	ADAM18,NS,carcinoma,0,1	ADAM18	169	1	NM_014237	exon14	c.C1417T	p.P473S	TGTGTTCCTGACA	.	scavenged	Atlas-SNP
TBX10	347853	hgsc.bcm.edu	37	11	67402362	67402362	+	Missense_Mutation	SNP	T	T	G	rs3758938	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	66	109	0	0.758621	0	T|0.753;G|0.247	0.247	strong	.	TBX10	25	.	NM_005995	exon3	c.A302C	p.K101T	AGGATCTTCACCT	.	PASS	Atlas-SNP
ZNF625	90589	hgsc.bcm.edu	37	19	12256358	12256358	+	Silent	SNP	T	T	G	rs12972621	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	26	64	0	0.448276	0	G|0.365;N|0.000	0.365	strong	ZNF625,trunk,malignant_melanoma,-2,1	ZNF625	37	1	NM_145233	exon4	c.A873C	p.R291R	ATGATATCGAACG	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	25	73	0	0.342466	0	G|0.849;A|0.151	0.151	strong	.	CEP85	61	.	NM_022778	exon9	c.G1624A	p.A542T	AGAGAAGCAGAAT	.	PASS	Atlas-SNP
SEH1L	81929	hgsc.bcm.edu	37	18	12984144	12984144	+	Missense_Mutation	SNP	C	C	A	rs6505776	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	193	96	231	0	0.497409	0	C|0.252;A|0.748	0.748	strong	.	SEH1L	33	.	NM_001013437	exon8	c.C1025A	p.T342N	GTTCAACTATTCC	.	PASS	Atlas-SNP
TEX101	83639	hgsc.bcm.edu	37	19	43922061	43922061	+	Silent	SNP	A	A	G	rs3816438	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	345	152	375	0	0.44058	0	A|0.783;G|0.217	0.217	strong	.	TEX101	28	.	NM_031451	exon8	c.A477G	p.P159P	TTGTCCAACCTGT	.	PASS	Atlas-SNP
PTCH1	5727	hgsc.bcm.edu	37	9	98238358	98238358	+	Silent	SNP	G	G	A	rs2066836	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	31	12	35	0	0.387097	0	G|0.865;A|0.135	0.135	strong	.	PTCH1	1850	.	NM_000264	exon12	c.C1686T	p.A562A	TAACGCGGCCATG	.	PASS	Atlas-SNP
CYP4F12	66002	hgsc.bcm.edu	37	19	15807884	15807884	+	Missense_Mutation	SNP	A	A	G	rs593818	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	137	137	135	0	1	0	A|0.395;G|0.605	0.605	strong	.	CYP4F12	89	.	NM_023944	exon13	c.A1564G	p.S522G	AATGTAAGCTTGC	.	PASS	Atlas-SNP
CES1	1066	hgsc.bcm.edu	37	16	55862836	55862836	+	Silent	SNP	G	G	A	rs3826191	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	13	130	0	0.166667	0	G|0.500;A|0.500	0.500	strong	CES1_ENST00000360526,colon,carcinoma,0,1	CES1	78	1	NM_001025195	exon2	c.C103T	p.L35L	TCCCCAGCACTTT	.	PASS	Atlas-SNP
SLC2A14	144195	hgsc.bcm.edu	37	12	7966958	7966958	+	Missense_Mutation	SNP	C	C	T	rs10845981	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	201	88	180	0	0.437811	0	C|0.760;T|0.240	0.240	strong	SLC2A14,NS,carcinoma,0,1	SLC2A14	78	1	NM_153449	exon12	c.G1517A	p.G506E	TTCATCCCCATGA	.	PASS	Atlas-SNP
TIPIN	54962	hgsc.bcm.edu	37	15	66641732	66641732	+	Missense_Mutation	SNP	G	G	C	rs2063690	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	118	64	112	0	0.542373	0	G|0.877;C|0.123	0.123	strong	.	TIPIN	23	.	NM_017858	exon5	c.C332G	p.A111G	CTATGTGCCCAGT	.	PASS	Atlas-SNP
OR10H5	284433	hgsc.bcm.edu	37	19	15905002	15905002	+	Silent	SNP	T	T	C	rs56548474		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	187	88	208	0	0.470588	0	.	.	weak	.	OR10H5	49	.	NM_001004466	exon1	c.T144C	p.T48T	GGCCACTGTCTGG	.	PASS	Atlas-SNP
IPO13	9670	hgsc.bcm.edu	37	1	44415415	44415415	+	Silent	SNP	C	C	T	rs2240447	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	117	116	144	0	0.991453	0	C|0.416;T|0.584	0.584	strong	.	IPO13	86	.	NM_014652	exon2	c.C411T	p.D137D	GCCTGACGCTTGG	.	PASS	Atlas-SNP
ARSH	347527	hgsc.bcm.edu	37	X	2942109	2942109	+	Silent	SNP	T	T	C	rs5939407	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	209	207	273	0	0.990431	0	T|0.346;C|0.654	0.654	strong	.	ARSH	72	.	NM_001011719	exon6	c.T949C	p.L317L	CACACCTTGGTGT	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228482010	228482010	+	Silent	SNP	C	C	T	rs449133	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	174	99	185	1	0.568965	0.00540541	C|0.595;T|0.405	0.405	strong	.	OBSCN	2142	.	NM_001271223	exon47	c.C12576T	p.D4192D	GCAGGACGGGTCC	.	PASS	Atlas-SNP
KIRREL3	84623	hgsc.bcm.edu	37	11	126391297	126391297	+	Silent	SNP	T	T	G	rs12269776	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	112	26	104	0	0.232143	0	T|0.764;G|0.236	0.236	strong	.	KIRREL3	183	.	NM_032531	exon4	c.A346C	p.R116R	CTGCCCTCAGGAT	.	PASS	Atlas-SNP
CUX1	1523	hgsc.bcm.edu	37	7	101921292	101921292	+	Missense_Mutation	SNP	A	A	C	rs118010189	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	244	120	282	0	0.491803	0	A|0.993;C|0.007	0.007	strong	.	CUX1	253	.	NM_001913	exon18	c.A1636C	p.K546Q	AACATCAAGCTCT	.	PASS	Atlas-SNP
KIAA1751	85452	hgsc.bcm.edu	37	1	1916890	1916890	+	Silent	SNP	C	C	T	rs3795280	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	91	28	166	0	0.307692	0	C|0.606;T|0.394	0.394	strong	.	KIAA1751	92	.	NM_001080484	exon6	c.G435A	p.L145L	TGCAAACAGGCGT	.	PASS	Atlas-SNP
DNAH17	8632	hgsc.bcm.edu	37	17	76472768	76472768	+	Silent	SNP	G	G	A	rs7405830	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	211	113	263	0	0.535545	0	G|0.641;A|0.359	0.359	strong	.	DNAH17	347	.	NM_173628	exon52	c.C8040T	p.L2680L	GCGGACGAGGTCC	.	PASS	Atlas-SNP
BTN3A2	11118	hgsc.bcm.edu	37	6	26370659	26370659	+	Silent	SNP	C	C	T	rs9393711	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	115	114	138	0	0.991304	0	C|0.923;T|0.077	0.077	strong	.	BTN3A2	44	.	NM_001197246	exon3	c.C543T	p.N181N	GAGCAACGCCAAG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195506076	195506076	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	48	20	105	4	0.416667	0.0380952	.	.	none	MUC4_ENST00000463781,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	MUC4	1505	1	NM_018406	exon2	c.G12375C	p.Q4125H	GGTGGCCTGACCT	.	scavenged	Atlas-SNP
MMAB	326625	hgsc.bcm.edu	37	12	109994870	109994870	+	Missense_Mutation	SNP	A	A	T	rs9593	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	119	53	123	0	0.445378	0	A|0.431;T|0.569	0.569	strong	MMAB,rectum,carcinoma,+1,1	MMAB	16	1	NM_052845	exon9	c.T716A	p.M239K	TTTTTCATGTATA	.	PASS	Atlas-SNP
SLITRK1	114798	hgsc.bcm.edu	37	13	84455214	84455214	+	Silent	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	61	14	67	0	0.229508	0	.	.	none	.	SLITRK1	196	.	NM_052910	exon1	c.A429G	p.R143R	TATATCTCGTAAT	.	PASS	Atlas-SNP
FAM194B	220081	hgsc.bcm.edu	37	13	46170621	46170621	+	Missense_Mutation	SNP	A	A	T	rs17066954	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	95	51	134	0	0.536842	0	A|0.833;T|0.167	0.167	strong	.	FAM194B	42	.	NM_182542	exon3	c.T520A	p.S174T	GATATGATTTCTT	.	PASS	Atlas-SNP
NLRP6	171389	hgsc.bcm.edu	37	11	284257	284257	+	Silent	SNP	G	G	A	rs11246050	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	111	18	105	0	0.162162	0	G|0.866;A|0.134	0.134	strong	.	NLRP6	4	.	NM_138329	exon6	c.G2229A	p.A743A	TGACGCGGTCTGC	.	PASS	Atlas-SNP
CTDP1	9150	hgsc.bcm.edu	37	18	77474921	77474921	+	Silent	SNP	G	G	A	rs2126082	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	17	4	29	0	0.235294	0	G|0.813;A|0.187	0.187	strong	.	CTDP1	67	.	NM_004715	exon8	c.G1461A	p.P487P	GAAGCCGAAGGCT	.	PASS	Atlas-SNP
PCDHB8	56128	hgsc.bcm.edu	37	5	140559148	140559148	+	Silent	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	423	50	305	0	0.118203	0	.	.	none	.	PCDHB8	199	.	NM_019120	exon1	c.C1533T	p.N511N	AGACAACGGCCAC	.	PASS	Atlas-SNP
TAF3	83860	hgsc.bcm.edu	37	10	8007559	8007559	+	Missense_Mutation	SNP	G	G	C	rs10795583	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	34	18	42	0	0.529412	0	G|0.471;C|0.529	0.529	strong	.	TAF3	93	.	NM_031923	exon3	c.G2086C	p.V696L	GAGAAGGTGAAGG	.	PASS	Atlas-SNP
CCL4	6351	hgsc.bcm.edu	37	17	34432664	34432664	+	Missense_Mutation	SNP	T	T	A	rs1719152	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	386	205	412	0	0.531088	0	T|0.845;A|0.155	0.155	strong	.	CCL4	14	.	NM_002984	exon3	c.T238A	p.S80T	AGTGAATCCTGGG	.	PASS	Atlas-SNP
ASCC3	10973	hgsc.bcm.edu	37	6	101100745	101100745	+	Silent	SNP	C	C	T	rs41288409	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	90	49	130	0	0.544444	0	C|0.970;T|0.030	0.030	strong	.	ASCC3	205	.	NM_006828	exon18	c.G2844A	p.K948K	TCGATGCTTTCTT	.	PASS	Atlas-SNP
ZBED1	9189	hgsc.bcm.edu	37	X	2408437	2408437	+	Silent	SNP	G	G	A	rs3752331	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	164	164	160	0	1	0	G|0.779;A|0.221	0.221	strong	.	ZBED1	64	.	NM_001171135	exon2	c.C324T	p.D108D	CAGCGCGTCCTGC	.	PASS	Atlas-SNP
AKNA	80709	hgsc.bcm.edu	37	9	117110046	117110046	+	Missense_Mutation	SNP	C	C	T	rs3748178	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	77	44	44	0	0.571429	0	C|0.891;T|0.109	0.109	strong	.	AKNA	119	.	NM_030767	exon16	c.G3356A	p.R1119Q	GCTGGCCGGCCGC	.	PASS	Atlas-SNP
GLT6D1	360203	hgsc.bcm.edu	37	9	138516190	138516190	+	Missense_Mutation	SNP	T	T	C	rs35762223	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	48	23	77	1	0.479167	0.012987	T|0.870;C|0.130	0.130	strong	GLT6D1,NS,carcinoma,0,3	GLT6D1	56	3	NM_182974	exon5	c.A584G	p.H195R	CAGGCGTGGAGCT	.	scavenged	Atlas-SNP
ITGA1	3672	hgsc.bcm.edu	37	5	52157374	52157374	+	Silent	SNP	T	T	C	rs2447867	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	129	128	173	0	0.992248	0	T|0.204;C|0.796	0.796	strong	.	ITGA1	112	.	NM_181501	exon3	c.T276C	p.C92C	ACCTTGTGTAAAG	.	PASS	Atlas-SNP
TCHP	84260	hgsc.bcm.edu	37	12	110341933	110341933	+	Missense_Mutation	SNP	A	A	G	rs10774978	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	55	25	41	0	0.454545	0	A|0.700;G|0.300	0.300	strong	.	TCHP	45	.	NM_001143852	exon3	c.A380G	p.K127R	CAGCCAAAGAAGA	.	PASS	Atlas-SNP
CPN1	1369	hgsc.bcm.edu	37	10	101808540	101808540	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	113	26	137	0	0.230089	0	.	.	none	.	CPN1	62	.	NM_001308	exon8	c.C1205T	p.T402I	CCCACGGTCACAG	.	PASS	Atlas-SNP
STT3A	3703	hgsc.bcm.edu	37	11	125488404	125488404	+	Silent	SNP	C	C	T	rs17140116	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	83	65	86	0	0.783133	0	C|0.878;T|0.122	0.122	strong	.	STT3A	52	.	NM_152713	exon16	c.C1911T	p.C637C	CAACTGCCTCATG	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	40	9	48	0	0.225	0	T|0.675;C|0.325	0.325	strong	.	OR8B4	60	.	NM_001005196	exon1	c.A65G	p.E22G	TGGAGCTCTGGCT	.	PASS	Atlas-SNP
ACAN	176	hgsc.bcm.edu	37	15	89398407	89398407	+	Missense_Mutation	SNP	C	C	T	rs3743398	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	49	61	0	0.653333	0	C|0.871;T|0.129	0.129	strong	.	ACAN	220	.	NM_001135	exon12	c.C2591T	p.P864L	GGGCCCCTGATGT	.	PASS	Atlas-SNP
CPA4	51200	hgsc.bcm.edu	37	7	129938598	129938598	+	Missense_Mutation	SNP	G	G	T	rs34587586	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	237	110	236	0	0.464135	0	G|0.630;T|0.370	0.370	strong	.	CPA4	47	.	NM_016352	exon2	c.G81T	p.L27F	AGTTTTGAGGATT	.	PASS	Atlas-SNP
ZNF812	729648	hgsc.bcm.edu	37	19	9801257	9801257	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	24	116	0	0.275862	0	.	.	none	.	ZNF812	27	.	NM_001199814	exon6	c.A922G	p.K308E	ATTCCTTACATTC	.	PASS	Atlas-SNP
TNN	63923	hgsc.bcm.edu	37	1	175049379	175049379	+	Missense_Mutation	SNP	G	G	A	rs16847812	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	83	36	99	0	0.433735	0	G|0.872;A|0.128	0.128	strong	.	TNN	297	.	NM_022093	exon4	c.G865A	p.D289N	CAGGTGGATCACT	.	PASS	Atlas-SNP
FUT10	84750	hgsc.bcm.edu	37	8	33246685	33246685	+	Silent	SNP	G	G	A	rs16880852	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	289	287	318	1	0.99308	0.00314465	G|0.768;A|0.232	0.232	strong	FUT10,NS,carcinoma,0,1	FUT10	62	1	NM_032664	exon4	c.C1008T	p.Y336Y	TCTGATGTAACTT	.	PASS	Atlas-SNP
PRKRIR	5612	hgsc.bcm.edu	37	11	76072085	76072085	+	Missense_Mutation	SNP	C	C	T	rs76214254	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	106	8	115	1	0.0754717	0.00869565	C|0.999;T|0.001	0.001	strong	PRKRIR,caecum,adenoma,0,1	PRKRIR	65	1	NM_004705	exon3	c.G233A	p.R78Q	TTATCTCGAAGAA	.	scavenged	Atlas-SNP
PKHD1	5314	hgsc.bcm.edu	37	6	51890754	51890754	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	103	27	114	0	0.262136	0	.	.	none	.	PKHD1	927	.	NM_170724	exon32	c.G3854A	p.S1285N	ACCAAGCTTGGTG	.	PASS	Atlas-SNP
WDR82	80335	hgsc.bcm.edu	37	3	52293859	52293859	+	Silent	SNP	A	A	G	rs3210487	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	59	26	56	0	0.440678	0	A|0.888;G|0.112	0.112	strong	WDR82_ENST00000296490,NS,adenoma,-2,1	WDR82	19	1	NM_025222	exon6	c.T573C	p.Y191Y	TCGATCATACTGC	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	120	49	130	0	0.408333	0	C|0.840;G|0.160	0.160	strong	.	KRTAP21-2	16	.	NM_181617	exon1	c.G26C	p.C9S	CCACAGCAGTTTC	.	PASS	Atlas-SNP
BIN1	274	hgsc.bcm.edu	37	2	127826533	127826533	+	Silent	SNP	A	A	G	rs1060743	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	106	46	144	0	0.433962	0	A|0.702;G|0.298	0.298	strong	.	BIN1	85	.	NM_139346	exon6	c.T486C	p.T162T	TTTGGCAGTTTGA	.	PASS	Atlas-SNP
PRKCH	5583	hgsc.bcm.edu	37	14	61857969	61857969	+	Silent	SNP	A	A	G	rs2230499	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	54	20	47	0	0.37037	0	A|0.743;G|0.257	0.257	strong	.	PRKCH	89	.	NM_006255	exon2	c.A390G	p.V130V	GAAAGTATTTGTG	.	PASS	Atlas-SNP
TPR	7175	hgsc.bcm.edu	37	1	186321242	186321242	+	Missense_Mutation	SNP	C	C	T	rs61744267	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	41	18	72	0	0.439024	0	C|0.871;T|0.129	0.129	strong	TPR_ENST00000367478,NS,carcinoma,0,3	TPR	441	3	NM_003292	exon19	c.G2335A	p.V779I	CTCTTACCTAAAC	.	PASS	Atlas-SNP
DSPP	1834	hgsc.bcm.edu	37	4	88536448	88536448	+	Silent	SNP	C	C	T	rs142168734		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	12	108	0	0.164384	0	.	.	weak	.	DSPP	174	.	NM_014208	exon5	c.C2634T	p.D878D	CAGTGACAGCAGT	.	PASS	Atlas-SNP
BPIFB4	149954	hgsc.bcm.edu	37	20	31671599	31671599	+	Missense_Mutation	SNP	A	A	G	rs4339026	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	68	40	85	0	0.588235	0	A|0.777;G|0.223	0.223	strong	.	.	.	.	NM_182519	exon3	c.A596G	p.D199G	TTGGTGATGGAGG	.	PASS	Atlas-SNP
IL16	3603	hgsc.bcm.edu	37	15	81584925	81584925	+	Silent	SNP	C	C	T	rs61752774	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	52	15	64	0	0.288462	0	C|0.881;T|0.119	0.119	strong	IL16_ENST00000302987,caecum,carcinoma,0,2	IL16	254	2	NM_001172128	exon12	c.C1449T	p.H483H	TTGGCACGGGCGG	.	PASS	Atlas-SNP
ISYNA1	51477	hgsc.bcm.edu	37	19	18546678	18546678	+	Silent	SNP	T	T	C	rs2303697	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	116	116	148	0	1	0	T|0.535;C|0.465	0.465	strong	.	ISYNA1	31	.	NM_016368	exon8	c.A1029G	p.L343L	CGCCGATAGGTTC	.	PASS	Atlas-SNP
WDR35	57539	hgsc.bcm.edu	37	2	20133221	20133221	+	Missense_Mutation	SNP	C	C	T	rs2293669	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	100	29	90	0	0.29	0	C|0.942;G|0.000;T|0.058	0.058	strong	.	WDR35	92	.	NM_001006657	exon23	c.G2632A	p.A878T	AAAATGCAGTCAC	.	PASS	Atlas-SNP
GRIA2	2891	hgsc.bcm.edu	37	4	158242630	158242630	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	131	29	162	0	0.221374	0	.	.	none	.	GRIA2	358	.	NM_000826	exon6	c.G761T	p.G254V	TTGGAGGTGCAAA	.	PASS	Atlas-SNP
C6orf15	29113	hgsc.bcm.edu	37	6	31079644	31079644	+	Silent	SNP	G	G	A	rs2233980	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	83	30	97	0	0.361446	0	G|0.926;A|0.074	0.074	strong	.	C6orf15	29	.	NM_014070	exon2	c.C492T	p.P164P	AGCCTTGGGTGAG	.	PASS	Atlas-SNP
AATK	9625	hgsc.bcm.edu	37	17	79100340	79100340	+	Silent	SNP	C	C	T	rs139267162	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	59	31	60	0	0.525424	0	C|0.994;T|0.006	0.006	strong	.	AATK	102	.	NM_001080395	exon7	c.G642A	p.L214L	GCTCCGCAGGTAG	.	PASS	Atlas-SNP
CACNB2	783	hgsc.bcm.edu	37	10	18828371	18828371	+	Silent	SNP	C	C	T	rs2228645	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	112	51	114	0	0.455357	0	C|0.810;T|0.190	0.190	strong	CACNB2_ENST00000352115,NS,carcinoma,+2,3	CACNB2	220	3	NM_201596	exon14	c.C1701T	p.Y567Y	TGCCTACGTAGAG	.	PASS	Atlas-SNP
CAMTA1	23261	hgsc.bcm.edu	37	1	7723957	7723957	+	Silent	SNP	G	G	A	rs12128526	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	63	31	71	0	0.492063	0	G|0.581;A|0.419	0.419	strong	.	CAMTA1	226	.	NM_015215	exon9	c.G1350A	p.S450S	CAGCTCGGAGAGC	.	PASS	Atlas-SNP
TBC1D29	26083	hgsc.bcm.edu	37	17	28890361	28890361	+	Missense_Mutation	SNP	G	G	A	rs372824382	alternate_allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	166	4	137	0	0.0240964	0	.	.	alt	TBC1D29,NS,carcinoma,0,3	TBC1D29	19	3	NM_015594	exon5	c.G371A	p.R124Q	TGAGCCGGGGAGA	.	scavenged	Atlas-SNP
KRTAP3-1	83896	hgsc.bcm.edu	37	17	39165174	39165174	+	Silent	SNP	G	G	A	rs112432710	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	156	79	182	0	0.50641	0	G|0.925;A|0.075	0.075	strong	.	KRTAP3-1	11	.	NM_031958	exon1	c.C153T	p.C51C	TGGGGGGCAGGTG	.	PASS	Atlas-SNP
FGFR3	2261	hgsc.bcm.edu	37	4	1801511	1801511	+	Silent	SNP	C	C	T	rs3135867	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	156	78	196	0	0.5	0	C|0.965;T|0.035	0.035	strong	.	FGFR3	3320	.	NM_001163213	exon4	c.C417T	p.D139D	GGAGGACGAGGCT	.	PASS	Atlas-SNP
OR10G2	26534	hgsc.bcm.edu	37	14	22102745	22102745	+	Missense_Mutation	SNP	C	C	A	rs41314525	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	212	104	218	0	0.490566	0	C|0.782;A|0.218	0.218	strong	.	OR10G2	35	.	NM_001005466	exon1	c.G254T	p.R85L	ATAAGCCGAGGAA	.	PASS	Atlas-SNP
SLC25A22	79751	hgsc.bcm.edu	37	11	792692	792692	+	Missense_Mutation	SNP	G	G	C	rs111277421	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	20	12	13	0	0.6	0	G|0.963;C|0.037	0.037	strong	.	SLC25A22	19	.	NM_001191061	exon7	c.C448G	p.L150V	CCGAGAGCTGGCC	.	PASS	Atlas-SNP
P2RY2	5029	hgsc.bcm.edu	37	11	72946204	72946204	+	Missense_Mutation	SNP	C	C	T	rs1626154	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	34	27	43	0	0.794118	0	C|0.873;T|0.127	0.127	strong	.	P2RY2	54	.	NM_176071	exon3	c.C1000T	p.R334C	GCTCGCCGCAGGC	.	PASS	Atlas-SNP
OR5P2	120065	hgsc.bcm.edu	37	11	7817665	7817665	+	Silent	SNP	T	T	C	rs72484720	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	228	185	201	0	0.811404	0	T|0.738;C|0.262	0.262	strong	.	OR5P2	68	.	NM_153444	exon1	c.A825G	p.T275T	CACCACTGTGTAC	.	PASS	Atlas-SNP
LCE1D	353134	hgsc.bcm.edu	37	1	152770533	152770533	+	Missense_Mutation	SNP	G	G	A	rs41268494	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	257	102	241	0	0.396887	0	G|0.806;A|0.194	0.194	strong	.	LCE1D	19	.	NM_178352	exon2	c.G263A	p.S88N	CCCAGAGCTCTGA	.	PASS	Atlas-SNP
DNAH17	8632	hgsc.bcm.edu	37	17	76446872	76446872	+	Silent	SNP	A	A	G	rs35957404	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	67	24	90	0	0.358209	0	A|0.971;G|0.029	0.029	strong	.	DNAH17	347	.	NM_173628	exon67	c.T10791C	p.D3597D	GAGCGAATCTTCC	.	PASS	Atlas-SNP
CR2	1380	hgsc.bcm.edu	37	1	207653364	207653364	+	Missense_Mutation	SNP	A	A	G	rs17618	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	183	182	228	1	0.994536	0.00438596	A|0.932;G|0.068	0.068	strong	.	CR2	164	.	NM_001006658	exon18	c.A3154G	p.I1052V	ATTGTCATTACCT	.	PASS	Atlas-SNP
AEBP1	165	hgsc.bcm.edu	37	7	44147485	44147485	+	Missense_Mutation	SNP	C	C	A	rs2537188	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	157	108	152	0	0.687898	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
CEP164	22897	hgsc.bcm.edu	37	11	117266312	117266312	+	Missense_Mutation	SNP	C	C	G	rs2305830	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	18	134	0	0.178218	0	C|0.709;G|0.291	0.291	strong	.	CEP164	121	.	NM_001271933	exon23	c.C2972G	p.T991S	AGCACACCCACCT	.	PASS	Atlas-SNP
MUC21	394263	hgsc.bcm.edu	37	6	30954873	30954873	+	Silent	SNP	G	G	A	rs1625781	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	64	31	84	0	0.484375	0	G|0.774;A|0.226	0.226	strong	.	MUC21	98	.	NM_001010909	exon2	c.G921A	p.T307T	CAGTACGACCTCC	.	PASS	Atlas-SNP
ATP9B	374868	hgsc.bcm.edu	37	18	76870397	76870397	+	Silent	SNP	G	G	A	rs492657	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	48	18	77	0	0.375	0	G|0.862;A|0.138	0.138	strong	.	ATP9B	96	.	NM_198531	exon3	c.G336A	p.E112E	GAAAGAGCTGAAA	.	PASS	Atlas-SNP
CLEC1B	51266	hgsc.bcm.edu	37	12	10150961	10150961	+	Missense_Mutation	SNP	G	G	A	rs2273987	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	48	105	0	0.475248	0	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
OSCP1	127700	hgsc.bcm.edu	37	1	36888462	36888462	+	Missense_Mutation	SNP	A	A	G	rs1416840	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	152	67	208	0	0.440789	0	A|0.882;G|0.118	0.118	strong	.	OSCP1	48	.	NM_145047	exon6	c.T656C	p.I219T	AATTCTATCCTCT	.	PASS	Atlas-SNP
MYH8	4626	hgsc.bcm.edu	37	17	10312472	10312472	+	Missense_Mutation	SNP	G	G	A	rs34693726	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	104	53	181	0	0.509615	0	G|0.944;A|0.056	0.056	strong	MYH8,NS,carcinoma,+1,1	MYH8	346	1	NM_002472	exon17	c.C1907T	p.A636V	TTCTTCGCGCTGC	.	PASS	Atlas-SNP
SEMA5A	9037	hgsc.bcm.edu	37	5	9154659	9154659	+	Silent	SNP	G	G	C	rs1806151	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	135	133	190	1	0.985185	0.00526316	G|0.619;C|0.381	0.381	strong	SEMA5A,lymph_node,lymphoid_neoplasm,-1,1	SEMA5A	236	1	NM_003966	exon12	c.C1422G	p.G474G	CCGCAGGCCCACG	.	PASS	Atlas-SNP
MDN1	23195	hgsc.bcm.edu	37	6	90499502	90499502	+	Silent	SNP	G	G	A	rs1036853	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	95	44	112	0	0.463158	0	G|0.905;A|0.095	0.095	strong	.	MDN1	478	.	NM_014611	exon7	c.C1227T	p.D409D	TACCACGTCTAAG	.	PASS	Atlas-SNP
MKI67	4288	hgsc.bcm.edu	37	10	129900858	129900858	+	Silent	SNP	C	C	T	rs3191122	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	127	74	151	0	0.582677	0	C|0.803;T|0.197	0.197	strong	MKI67,NS,carcinoma,0,1	MKI67	363	1	NM_002417	exon13	c.G9246A	p.S3082S	AGGGACCGAGTCT	.	PASS	Atlas-SNP
COL4A1	1282	hgsc.bcm.edu	37	13	110827574	110827574	+	Silent	SNP	T	T	A	rs874203	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	94	48	119	0	0.510638	0	T|0.665;A|0.335	0.335	strong	COL4A1_ENST00000375815,NS,carcinoma,-1,2	COL4A1	372	2	NM_001845	exon37	c.A3189T	p.R1063R	TTCACCTCGCAGC	.	PASS	Atlas-SNP
FAM188B	84182	hgsc.bcm.edu	37	7	30818142	30818142	+	Missense_Mutation	SNP	T	T	G	rs201946407	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	209	47	226	0	0.22488	0	T|0.998;G|0.002	0.002	strong	.	FAM188B	62	.	NM_032222	exon2	c.T158G	p.L53R	TGCATCTTGAATT	.	PASS	Atlas-SNP
PKHD1L1	93035	hgsc.bcm.edu	37	8	110476993	110476993	+	Silent	SNP	A	A	G	rs1673398	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	109	86	159	0	0.788991	0	A|0.525;G|0.475	0.475	strong	.	PKHD1L1	522	.	NM_177531	exon49	c.A7932G	p.A2644A	GCCTGCACCTGCA	.	PASS	Atlas-SNP
AXIN1	8312	hgsc.bcm.edu	37	16	348222	348222	+	Silent	SNP	C	C	T	rs214250	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	40	14	26	0	0.35	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
ENGASE	64772	hgsc.bcm.edu	37	17	77078069	77078069	+	Missense_Mutation	SNP	G	G	A	rs12937557	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	218	89	269	0	0.408257	0	G|0.943;A|0.057	0.057	strong	.	ENGASE	55	.	NM_001042573	exon7	c.G962A	p.R321H	GGGAGCGCCGGGC	.	PASS	Atlas-SNP
KIAA1522	57648	hgsc.bcm.edu	37	1	33236824	33236824	+	Missense_Mutation	SNP	C	C	T	rs199566536	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	36	77	0	0.507042	0	C|0.997;T|0.003	0.003	strong	.	KIAA1522	68	.	NM_020888	exon6	c.C2044T	p.P682S	CCTAACCCAGCTG	.	PASS	Atlas-SNP
C18orf56	494514	hgsc.bcm.edu	37	18	658064	658064	+	Missense_Mutation	SNP	G	G	C	rs2853533	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	16	13	20	0	0.8125	0	G|0.684;C|0.316	0.316	strong	.	C18orf56	2	.	NM_001012716	exon1	c.C184G	p.R62G	TCCTGCGAGGGAG	.	PASS	Atlas-SNP
MED25	81857	hgsc.bcm.edu	37	19	50339548	50339548	+	Silent	SNP	G	G	A	rs57854058	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	60	37	51	0	0.616667	0	G|0.991;A|0.009	0.009	strong	MED25,NS,lymphoid_neoplasm,0,1	MED25	98	1	NM_030973	exon17	c.G2031A	p.A677A	TCCTGCGCTGCTG	.	PASS	Atlas-SNP
PAPLN	89932	hgsc.bcm.edu	37	14	73720604	73720604	+	Missense_Mutation	SNP	C	C	A	rs146030488	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	116	55	106	0	0.474138	0	C|0.996;A|0.004	0.004	strong	.	PAPLN	180	.	NM_173462	exon11	c.C1156A	p.P386T	GGGAAGCCCCCTG	.	PASS	Atlas-SNP
KNTC1	9735	hgsc.bcm.edu	37	12	123057792	123057792	+	Missense_Mutation	SNP	A	A	G	rs61751322	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	117	53	109	0	0.452991	0	A|0.962;G|0.038	0.038	strong	.	KNTC1	182	.	NM_014708	exon26	c.A2243G	p.H748R	GAGAACATGACTT	.	PASS	Atlas-SNP
VPS13A	23230	hgsc.bcm.edu	37	9	79986057	79986057	+	Silent	SNP	A	A	G	rs3737289	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	43	97	0	0.597222	0	A|0.606;G|0.394	0.394	strong	.	VPS13A	735	.	NM_001018038	exon67	c.A9069G	p.G3023G	TCAGGGAATAAAA	.	PASS	Atlas-SNP
CALML5	51806	hgsc.bcm.edu	37	10	5541183	5541183	+	Silent	SNP	C	C	T	rs10904517	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	29	68	0	0.5	0	C|0.622;T|0.378	0.378	strong	CALML5,rectum,carcinoma,0,1	CALML5	25	1	NM_017422	exon1	c.G219A	p.A73A	CTTCTTCGCCGCC	.	PASS	Atlas-SNP
TBC1D9	23158	hgsc.bcm.edu	37	4	141583176	141583176	+	Silent	SNP	C	C	T	rs28465061	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	182	90	175	0	0.494505	0	C|0.945;T|0.055	0.055	strong	.	TBC1D9	198	.	NM_015130	exon10	c.G1674A	p.E558E	AATCTCCTCCGTG	.	PASS	Atlas-SNP
BTBD6	90135	hgsc.bcm.edu	37	14	105716034	105716034	+	Silent	SNP	C	C	T	rs2816606	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	76	41	78	0	0.539474	0	C|0.776;T|0.224	0.224	strong	.	BTBD6	24	.	NM_033271	exon5	c.C483T	p.Y161Y	TCTGTACGCTGCT	.	PASS	Atlas-SNP
DSPP	1834	hgsc.bcm.edu	37	4	88535830	88535830	+	Silent	SNP	T	T	C	rs202057495		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	113	16	116	0	0.141593	0	.	.	weak	.	DSPP	174	.	NM_014208	exon5	c.T2016C	p.S672S	CAGCAGTGATAGC	.	PASS	Atlas-SNP
FRY	10129	hgsc.bcm.edu	37	13	32776153	32776153	+	Silent	SNP	T	T	C	rs9567420	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	37	114	0	0.451219	0	T|0.918;C|0.082	0.082	strong	.	FRY	312	.	NM_023037	exon30	c.T3822C	p.Y1274Y	GATTTATGAAATC	.	PASS	Atlas-SNP
MS4A6E	245802	hgsc.bcm.edu	37	11	60102384	60102384	+	Missense_Mutation	SNP	A	A	G	rs2304935	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	172	119	180	0	0.69186	0	A|0.705;G|0.295	0.295	strong	.	MS4A6E	22	.	NM_139249	exon1	c.A16G	p.I6V	CAACCTATTTCCA	.	PASS	Atlas-SNP
OR10H3	26532	hgsc.bcm.edu	37	19	15852223	15852223	+	Missense_Mutation	SNP	A	A	C	rs1966357	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	78	124	0	1	0	A|0.300;C|0.700	0.700	strong	OR10H3,colon,carcinoma,0,3	OR10H3	53	3	NM_013938	exon1	c.A21C	p.R7S	CTACAGAACCATA	.	PASS	Atlas-SNP
KIR3DL3	115653	hgsc.bcm.edu	37	19	55246731	55246731	+	Missense_Mutation	SNP	C	C	A	rs77241525	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	84	84	114	0	1	0	A|0.254;C|0.746	0.254	strong	KIR3DL3,NS,carcinoma,0,1	KIR3DL3	46	1	NM_153443	exon6	c.C961A	p.H321N	TCCAGACACCTGC	.	PASS	Atlas-SNP
MYH15	22989	hgsc.bcm.edu	37	3	108189627	108189627	+	Missense_Mutation	SNP	C	C	T	rs4299484	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	37	129	0	0.402174	0	C|0.833;T|0.167	0.167	strong	MYH15,NS,carcinoma,0,1	MYH15	223	1	NM_014981	exon14	c.G1361A	p.R454Q	TTGATCCGTGCCA	.	PASS	Atlas-SNP
ABCA7	10347	hgsc.bcm.edu	37	19	1047002	1047002	+	Silent	SNP	A	A	G	rs3752234	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	38	11	39	0	0.289474	0	A|0.401;G|0.599	0.599	strong	ABCA7,NS,carcinoma,0,1	ABCA7	174	1	NM_019112	exon14	c.A1824G	p.A608A	CGCCGCACTGCTG	.	PASS	Atlas-SNP
VCX	26609	hgsc.bcm.edu	37	X	7811760	7811760	+	Silent	SNP	C	C	A	rs202230674	alternate_allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	77	18	127	0	0.233766	0	.	.	alt	.	VCX	28	.	NM_013452	exon3	c.C324A	p.A108A	GGAGGCCGAGCTG	.	PASS	Atlas-SNP
SUN2	25777	hgsc.bcm.edu	37	22	39134715	39134715	+	Silent	SNP	T	T	C	rs1062687	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	63	30	77	0	0.47619	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
KPRP	448834	hgsc.bcm.edu	37	1	152732436	152732436	+	Silent	SNP	G	G	C	rs4845480	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	236	108	281	0	0.457627	0	G|0.490;C|0.510	0.510	strong	KPRP,NS,carcinoma,+1,1	KPRP	152	1	NM_001025231	exon2	c.G372C	p.A124A	CGAAGCGTCACAA	.	PASS	Atlas-SNP
SORCS3	22986	hgsc.bcm.edu	37	10	106907440	106907440	+	Silent	SNP	C	C	T	rs791125	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	178	178	179	0	1	0	C|0.497;T|0.503	0.503	strong	.	SORCS3	282	.	NM_014978	exon9	c.C1368T	p.N456N	CCAGAACGACACG	.	PASS	Atlas-SNP
MAPRE1	22919	hgsc.bcm.edu	37	20	31427635	31427635	+	Silent	SNP	C	C	T	rs2070090	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	32	94	0	0.390244	0	C|0.738;T|0.261	0.261	strong	.	MAPRE1	17	.	NM_012325	exon5	c.C570T	p.D190D	CGGAGACGACGAG	.	PASS	Atlas-SNP
MYCBPAP	84073	hgsc.bcm.edu	37	17	48594691	48594691	+	Missense_Mutation	SNP	G	G	A	rs61749930	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	47	113	0	0.465347	0	G|0.980;A|0.020	0.020	strong	.	MYCBPAP	135	.	NM_032133	exon3	c.G371A	p.R124H	ATAAACGTGTCAT	.	PASS	Atlas-SNP
PAX5	5079	hgsc.bcm.edu	37	9	37033983	37033983	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	98	29	72	0	0.295918	0	.	.	none	.	PAX5	250	.	NM_016734	exon1	c.G46C	p.G16R	TCCTACCTGTCCT	.	PASS	Atlas-SNP
BANK1	55024	hgsc.bcm.edu	37	4	102839287	102839287	+	Missense_Mutation	SNP	G	G	A	rs3733197	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	135	60	193	0	0.444444	0	G|0.725;A|0.275	0.275	strong	.	BANK1	95	.	NM_017935	exon7	c.G1147A	p.A383T	GACCCCGCACATA	.	PASS	Atlas-SNP
ARMC9	80210	hgsc.bcm.edu	37	2	232072912	232072912	+	Silent	SNP	T	T	C	rs11558174	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	227	116	303	0	0.511013	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
ENPP7	339221	hgsc.bcm.edu	37	17	77709339	77709339	+	Silent	SNP	C	C	G	rs11657217	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	36	100	0	0.514286	0	C|0.672;G|0.328	0.328	strong	.	ENPP7	63	.	NM_178543	exon3	c.C897G	p.A299A	CGATGCCCTCAAG	.	PASS	Atlas-SNP
IGSF22	283284	hgsc.bcm.edu	37	11	18729367	18729367	+	Silent	SNP	G	G	T	rs57253324	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	65	22	65	0	0.338462	0	G|0.901;T|0.099	0.099	strong	.	IGSF22	211	.	NM_173588	exon20	c.C3264A	p.I1088I	CACATGGATGTCA	.	PASS	Atlas-SNP
MRPL22	29093	hgsc.bcm.edu	37	5	154346259	154346259	+	Silent	SNP	A	A	G	rs14922	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	127	44	153	0	0.346457	0	T|0.168;G|0.092	0.092	strong	.	MRPL22	18	.	NM_014180	exon7	c.A423G	p.S141S	CACCTCAGGACGA	.	PASS	Atlas-SNP
RTEL1	51750	hgsc.bcm.edu	37	20	62294236	62294236	+	Missense_Mutation	SNP	G	G	A	rs184051277	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	83	29	69	0	0.349398	0	G|1.000;A|0.000	0.000	strong	.	RTEL1	114	.	NM_032957	exon6	c.G604A	p.V202I	AACAACGTAGAAG	.	PASS	Atlas-SNP
TAAR6	319100	hgsc.bcm.edu	37	6	132892253	132892253	+	Missense_Mutation	SNP	G	G	A	rs8192624	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	42	42	102	0	1	0	G|0.937;A|0.063	0.063	strong	.	TAAR6	68	.	NM_175067	exon1	c.G793A	p.V265I	ACAGTGGTAGCAT	.	PASS	Atlas-SNP
ATRNL1	26033	hgsc.bcm.edu	37	10	117075140	117075140	+	Silent	SNP	A	A	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	121	27	111	0	0.22314	0	.	.	none	.	ATRNL1	219	.	NM_207303	exon18	c.A2931C	p.S977S	TTCTTCACGGGGA	.	PASS	Atlas-SNP
C17orf77	146723	hgsc.bcm.edu	37	17	72588778	72588778	+	Missense_Mutation	SNP	C	C	T	rs58253413	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	44	70	0	0.619718	0	C|0.928;T|0.072	0.072	strong	C17orf77,NS,carcinoma,0,1	C17orf77	31	1	NM_152460	exon3	c.C593T	p.T198I	GACTCACACCCAG	.	PASS	Atlas-SNP
UBXN11	91544	hgsc.bcm.edu	37	1	26608883	26608883	+	Silent	SNP	A	A	G	rs1134580	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	26	9	31	0	0.346154	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	.	scavenged	Atlas-SNP
PRDM7	11105	hgsc.bcm.edu	37	16	90141355	90141355	+	Missense_Mutation	SNP	A	A	C	rs12925933	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	348	211	276	1	0.606322	0.00362319	A|0.605;C|0.395	0.395	strong	.	PRDM7	53	.	NM_001098173	exon3	c.T270G	p.D90E	ATCGGAATCTTCT	.	PASS	Atlas-SNP
FGD3	89846	hgsc.bcm.edu	37	9	95782667	95782667	+	Silent	SNP	C	C	T	rs11790517	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	27	77	0	0.369863	0	C|0.684;T|0.316	0.316	strong	.	FGD3	116	.	NM_001083536	exon13	c.C1455T	p.F485F	CGCCTTCAGCCAG	.	PASS	Atlas-SNP
DSP	1832	hgsc.bcm.edu	37	6	7585967	7585967	+	Silent	SNP	G	G	C	rs2744380	bycluster;byfrequency;bysubmitter;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	41	24	41	0	0.585366	0	G|0.303;C|0.697	0.697	strong	.	DSP	306	.	NM_004415	exon24	c.G8472C	p.G2824G	TCCGGGGTCCCGC	.	PASS	Atlas-SNP
FAM160B2	64760	hgsc.bcm.edu	37	8	21960096	21960096	+	Missense_Mutation	SNP	C	C	T	rs117802113	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	70	86	0	1	0	C|0.945;T|0.055	0.055	strong	.	FAM160B2	35	.	NM_022749	exon16	c.C2050T	p.L684F	AAGCTGCTCCTGG	.	PASS	Atlas-SNP
FGFR2	2263	hgsc.bcm.edu	37	10	123279643	123279643	+	Silent	SNP	C	C	T	rs138315382	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	63	18	78	0	0.285714	0	C|1.000;T|0.000	0.000	strong	.	FGFR2	758	.	NM_022970	exon7	c.G789A	p.P263P	ATTTGCCGGCAGT	.	PASS	Atlas-SNP
STIP1	10963	hgsc.bcm.edu	37	11	63970625	63970625	+	Silent	SNP	G	G	A	rs2070232	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	49	35	46	0	0.714286	0	A|0.052;C|0.008	0.052	strong	STIP1,NS,carcinoma,+1,1	STIP1	63	1	NM_006819	exon12	c.G1311A	p.A437A	CGCTGCGCTGGAA	.	PASS	Atlas-SNP
SPPL2C	162540	hgsc.bcm.edu	37	17	43922640	43922640	+	Missense_Mutation	SNP	G	G	A	rs17763658	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	102	47	103	0	0.460784	0	G|0.922;A|0.078	0.078	strong	.	.	.	.	NM_175882	exon1	c.G368A	p.R123Q	TGAGCCGGGTCAG	.	PASS	Atlas-SNP
B3GNT8	374907	hgsc.bcm.edu	37	19	41932063	41932063	+	Silent	SNP	A	A	G	rs45563938	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	34	95	0	0.435897	0	A|0.905;G|0.095	0.095	strong	.	B3GNT8	20	.	NM_198540	exon3	c.T621C	p.S207S	CAGGTCACTGTAG	.	PASS	Atlas-SNP
ZNF280D	54816	hgsc.bcm.edu	37	15	56959028	56959028	+	Missense_Mutation	SNP	C	C	T	rs28620278	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	313	169	328	0	0.539936	0	C|0.495;T|0.505	0.505	strong	.	ZNF280D	82	.	NM_017661	exon15	c.G1702A	p.V568I	ATTTGACTGTATT	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	60	26	63	0	0.433333	0	G|0.583;C|0.417	0.417	strong	.	C9orf114	28	.	NM_016390	exon5	c.C389G	p.T130R	ACTCCTGTGAATT	.	PASS	Atlas-SNP
ITIH1	3697	hgsc.bcm.edu	37	3	52821011	52821011	+	Missense_Mutation	SNP	A	A	G	rs1042779	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	111	110	143	0	0.990991	0	A|0.564;G|0.436	0.436	strong	.	ITIH1	108	.	NM_002215	exon14	c.A1784G	p.Q595R	CCCTGCAGATGTC	.	PASS	Atlas-SNP
SIRPD	128646	hgsc.bcm.edu	37	20	1538249	1538249	+	Silent	SNP	C	C	T	rs2250055	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	59	22	80	0	0.372881	0	C|0.856;T|0.144	0.144	strong	.	SIRPD	34	.	NM_178460	exon1	c.G51A	p.L17L	CAGATACAGCAGT	.	PASS	Atlas-SNP
ARHGEF19	128272	hgsc.bcm.edu	37	1	16532803	16532803	+	Silent	SNP	G	G	A	rs221050	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	107	48	141	0	0.448598	0	G|0.786;A|0.214	0.214	strong	.	ARHGEF19	49	.	NM_153213	exon7	c.C1170T	p.S390S	GATGTAGGAGGCC	.	PASS	Atlas-SNP
KIAA1522	57648	hgsc.bcm.edu	37	1	33235651	33235651	+	Missense_Mutation	SNP	A	A	G	rs12730560	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	124	67	107	0	0.540323	0	A|0.838;G|0.162	0.162	strong	KIAA1522,colon,carcinoma,0,1	KIAA1522	68	1	NM_020888	exon6	c.A871G	p.M291V	GAGGCCATGCTGC	.	PASS	Atlas-SNP
CRIPAK	285464	hgsc.bcm.edu	37	4	1388697	1388697	+	Missense_Mutation	SNP	C	C	T	rs113316888	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	25	8	42	1	0.32	0.0238095	C|0.500;T|0.500	0.500	weak	CRIPAK,NS,carcinoma,0,1	CRIPAK	185	1	NM_175918	exon1	c.C398T	p.A133V	CCCATGCGGAGTG	.	scavenged	Atlas-SNP
SOAT1	6646	hgsc.bcm.edu	37	1	179310439	179310439	+	Silent	SNP	C	C	T	rs7547733	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	83	42	100	0	0.506024	0	C|0.881;T|0.119	0.119	strong	.	SOAT1	53	.	NM_003101	exon7	c.C774T	p.F258F	TATATTCGAGCAG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195513433	195513433	+	Missense_Mutation	SNP	G	G	A	rs74419078	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	159	67	183	1	0.421384	0.00546448	G|0.986;A|0.014	0.014	strong	MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	NM_018406	exon2	c.C5018T	p.A1673V	GTGGATGCTGAGG	.	scavenged	Atlas-SNP
RAVER2	55225	hgsc.bcm.edu	37	1	65243466	65243466	+	Silent	SNP	A	A	G	rs41285400	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	237	120	249	0	0.506329	0	A|0.994;G|0.006	0.006	strong	.	RAVER2	56	.	NM_018211	exon3	c.A477G	p.E159E	GTTTGAAGAACTT	.	PASS	Atlas-SNP
MAT1A	4143	hgsc.bcm.edu	37	10	82033594	82033594	+	Silent	SNP	G	G	A	rs2993763	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	131	60	169	0	0.458015	0	G|0.458;A|0.542	0.542	strong	.	MAT1A	52	.	NM_000429	exon9	c.C1131T	p.Y377Y	ATGGCCGTAGCAT	.	PASS	Atlas-SNP
AKD1	221264	hgsc.bcm.edu	37	6	109894773	109894773	+	Missense_Mutation	SNP	T	T	A	rs12175588	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	119	115	117	0	0.966387	0	T|0.780;A|0.220	0.220	strong	.	AKD1	223	.	NM_001145128	exon21	c.A2216T	p.D739V	TCTTCATCCTCAT	.	PASS	Atlas-SNP
DFNA5	1687	hgsc.bcm.edu	37	7	24758753	24758753	+	Silent	SNP	C	C	T	rs754555	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	15	110	0	0.182927	0	C|0.802;T|0.198	0.198	strong	.	DFNA5	51	.	NM_001127453	exon4	c.G489A	p.T163T	CATCGTCGTGATC	.	PASS	Atlas-SNP
SLC6A19	340024	hgsc.bcm.edu	37	5	1208964	1208964	+	Silent	SNP	T	T	C	rs60992377	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	88	39	104	1	0.443182	0.00961538	T|0.608;C|0.392	0.392	strong	SLC6A19,NS,carcinoma,+2,2	SLC6A19	99	2	NM_001003841	exon2	c.T306C	p.G102G	CCTGGGTGTGTGG	.	scavenged	Atlas-SNP
OR5P2	120065	hgsc.bcm.edu	37	11	7818056	7818056	+	Missense_Mutation	SNP	T	T	C	rs73406604	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	48	62	0	0.827586	0	T|0.738;C|0.262	0.262	strong	OR5P2,brain,glioma,0,2	OR5P2	68	2	NM_153444	exon1	c.A434G	p.Y145C	GCTATGTAAACTA	.	PASS	Atlas-SNP
TMEM63B	55362	hgsc.bcm.edu	37	6	44117664	44117664	+	Silent	SNP	C	C	T	rs4714762	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	127	60	162	0	0.472441	0	C|0.910;G|0.000;T|0.089	0.089	strong	TMEM63B,NS,carcinoma,0,1	TMEM63B	77	1	NM_018426	exon16	c.C1482T	p.I494I	CACCATCGTCTAC	.	PASS	Atlas-SNP
LRRC43	254050	hgsc.bcm.edu	37	12	122674780	122674780	+	Missense_Mutation	SNP	C	C	A	rs11060094	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	149	73	154	0	0.489933	0	C|0.865;A|0.135	0.135	strong	.	LRRC43	105	.	NM_001098519	exon5	c.C766A	p.Q256K	GTGCTGCAGGGAA	.	PASS	Atlas-SNP
TLR6	10333	hgsc.bcm.edu	37	4	38830012	38830012	+	Silent	SNP	G	G	C	rs3821985	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	74	38	100	0	0.513514	0	G|0.583;C|0.417	0.417	strong	.	TLR6	67	.	NM_006068	exon2	c.C1083G	p.T361T	GTTCTGGGTAAAG	.	PASS	Atlas-SNP
OPN4	94233	hgsc.bcm.edu	37	10	88414569	88414569	+	Missense_Mutation	SNP	C	C	T	rs2675703	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	76	76	81	0	1	0	C|0.900;T|0.100	0.100	strong	OPN4,NS,carcinoma,0,1	OPN4	61	1	NM_033282	exon1	c.C29T	p.P10L	GAGTCCCGCCCAG	.	PASS	Atlas-SNP
TBC1D2B	23102	hgsc.bcm.edu	37	15	78369815	78369815	+	Silent	SNP	G	G	A	rs9047	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	39	21	41	0	0.538462	0	G|0.810;A|0.190	0.190	strong	.	TBC1D2B	104	.	NM_144572	exon1	c.C180T	p.F60F	CGCGTCGAACACG	.	PASS	Atlas-SNP
COL6A5	256076	hgsc.bcm.edu	37	3	130103709	130103709	+	Missense_Mutation	SNP	G	G	A	rs1453241	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	105	53	130	0	0.504762	0	G|0.619;A|0.381	0.381	strong	.	COL6A5	205	.	NM_153264	exon5	c.G1363A	p.E455K	ATCCAGGAGAAAC	.	PASS	Atlas-SNP
CR1	1378	hgsc.bcm.edu	37	1	207787831	207787831	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	202	4	200	2	0.019802	0.01	.	.	none	CR1_ENST00000367049,NS,carcinoma,0,12	CR1	354	12	NM_000651	exon40	c.G6658T	p.E2220X	GTGTGTGAACGTG	.	scavenged	Atlas-SNP
DAAM2	23500	hgsc.bcm.edu	37	6	39847197	39847197	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	169	2	172	0	0.0118343	0	.	.	none	DAAM2,rectum,carcinoma,-1,2	DAAM2	101	2	NM_015345	exon14	c.C1789T	p.R597C	AAAAAGCGTGTCC	.	scavenged	Atlas-SNP
SLIT3	6586	hgsc.bcm.edu	37	5	168098235	168098235	+	Silent	SNP	A	A	G	rs2277933	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	93	32	66	0	0.344086	0	A|0.689;G|0.311	0.311	strong	.	SLIT3	224	.	NM_001271946	exon34	c.T4116C	p.D1372D	CTCCTGATCGCAG	.	PASS	Atlas-SNP
OR1F1	4992	hgsc.bcm.edu	37	16	3254972	3254972	+	Silent	SNP	T	T	C	rs2075851	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	139	105	207	1	0.755396	0.00483092	T|0.618;C|0.382	0.382	strong	.	OR1F1	36	.	NM_012360	exon1	c.T726C	p.G242G	CTGTGGTTCTCAC	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29910358	29910358	+	Missense_Mutation	SNP	C	C	G	rs1143146	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	141	61	135	0	0.432624	0	C|0.511;G|0.489	0.489	strong	.	HLA-A	89	.	NM_001242758	exon1	c.C28G	p.L10V	ACCCTCCTCCTGC	.	PASS	Atlas-SNP
ATP6V0A1	535	hgsc.bcm.edu	37	17	40665913	40665913	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	193	58	210	0	0.300518	0	.	.	none	.	ATP6V0A1	67	.	NM_001130020	exon19	c.T2168C	p.I723T	AGGCCATCCACAC	.	PASS	Atlas-SNP
ZNF133	7692	hgsc.bcm.edu	37	20	18295730	18295730	+	Missense_Mutation	SNP	C	C	T	rs34099160	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	80	29	84	0	0.3625	0	C|0.894;T|0.106	0.106	strong	ZNF133,NS,carcinoma,0,1	ZNF133	63	1	NM_001083330	exon4	c.C232T	p.L78F	CCAGAGCTCTACC	.	PASS	Atlas-SNP
USP45	85015	hgsc.bcm.edu	37	6	99893878	99893878	+	Silent	SNP	T	T	C	rs12203426	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	27	63	0	0.465517	0	T|0.876;C|0.124	0.124	strong	.	USP45	56	.	NM_001080481	exon14	c.A1770G	p.L590L	CCCCTCTAAAAAA	.	PASS	Atlas-SNP
ZNF516	9658	hgsc.bcm.edu	37	18	74091766	74091766	+	Silent	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	89	26	135	0	0.292135	0	.	.	none	.	ZNF516	102	.	NM_014643	exon4	c.G2304A	p.K768K	GTAGGTCTTGTGG	.	PASS	Atlas-SNP
ZNF749	388567	hgsc.bcm.edu	37	19	57956186	57956186	+	Missense_Mutation	SNP	T	T	C	rs2240040	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	147	62	125	0	0.421769	0	T|0.982;C|0.018	0.018	strong	.	ZNF749	75	.	NM_001023561	exon3	c.T1670C	p.V557A	CTTATGTGTGTAG	.	PASS	Atlas-SNP
OTUD3	23252	hgsc.bcm.edu	37	1	20233086	20233086	+	Missense_Mutation	SNP	G	G	A	rs10916668	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	103	48	100	0	0.466019	0	G|0.948;A|0.052	0.052	strong	OTUD3,NS,carcinoma,-2,1	OTUD3	25	1	NM_015207	exon7	c.G997A	p.A333T	AACAAAGCAAATA	.	PASS	Atlas-SNP
C7orf31	136895	hgsc.bcm.edu	37	7	25181912	25181912	+	Missense_Mutation	SNP	T	T	C	rs2285738	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	76	59	69	0	0.776316	0	T|0.428;C|0.572	0.572	strong	.	C7orf31	53	.	NM_138811	exon9	c.A899G	p.H300R	TTTTCATGGTAAT	.	PASS	Atlas-SNP
ZNF343	79175	hgsc.bcm.edu	37	20	2464353	2464353	+	Silent	SNP	A	A	G	rs73085334	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	43	77	0	0.597222	0	A|0.989;G|0.011	0.011	strong	.	ZNF343	47	.	NM_024325	exon6	c.T1254C	p.F418F	CTGGCTAAAGCCT	.	PASS	Atlas-SNP
PRAMEF2	65122	hgsc.bcm.edu	37	1	12921137	12921137	+	Missense_Mutation	SNP	T	T	A	rs17039283		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	119	4	134	1	0.0336134	0.00746269	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
PTPRU	10076	hgsc.bcm.edu	37	1	29606589	29606589	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	239	53	277	0	0.221757	0	.	.	none	.	PTPRU	374	.	NM_001195001	exon11	c.G1804C	p.G602R	CCCCTGGGCGAGT	.	PASS	Atlas-SNP
TRAF3IP1	26146	hgsc.bcm.edu	37	2	239306268	239306268	+	Missense_Mutation	SNP	A	A	C	rs3739070	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	99	41	96	0	0.414141	0	A|0.944;C|0.056	0.056	strong	.	TRAF3IP1	58	.	NM_015650	exon16	c.A1858C	p.M620L	CTGCAGATGTGGC	.	PASS	Atlas-SNP
VSX1	30813	hgsc.bcm.edu	37	20	25059442	25059442	+	Missense_Mutation	SNP	C	C	T	rs6138482	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	163	78	214	0	0.478528	0	C|0.759;T|0.241	0.241	strong	.	VSX1	20	.	NM_199425	exon3	c.G650A	p.R217H	TTGGAGCGGAGAA	.	PASS	Atlas-SNP
PITRM1	10531	hgsc.bcm.edu	37	10	3180298	3180298	+	Silent	SNP	C	C	T	rs10175	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	77	34	83	0	0.441558	0	C|0.756;T|0.244	0.244	strong	.	PITRM1	109	.	NM_001242307	exon27	c.G3042A	p.K1014K	TGTGCTCTTCCCA	.	PASS	Atlas-SNP
TMCO3	55002	hgsc.bcm.edu	37	13	114154419	114154419	+	Silent	SNP	G	G	A	rs2260159	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	141	76	133	0	0.539007	0	G|0.796;A|0.204	0.204	strong	.	TMCO3	77	.	NM_017905	exon4	c.G771A	p.K257K	GACCAAGCCCAGA	.	PASS	Atlas-SNP
PRRT4	401399	hgsc.bcm.edu	37	7	127999645	127999645	+	Missense_Mutation	SNP	C	C	T	rs56272205	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	63	39	77	0	0.619048	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
UGT2B7	7364	hgsc.bcm.edu	37	4	69964338	69964338	+	Missense_Mutation	SNP	T	T	C	rs7439366	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	140	91	138	0	0.65	0	T|0.443;C|0.557	0.557	strong	.	UGT2B7	79	.	NM_001074	exon2	c.T802C	p.Y268H	TTTCCATATCCAC	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	77	23	153	0	0.298701	0	G|0.811;A|0.189	0.189	strong	.	FSCB	173	.	NM_032135	exon1	c.C1225T	p.P409S	TAGCTGGGGCCTC	.	PASS	Atlas-SNP
DDR1	780	hgsc.bcm.edu	37	6	30864829	30864829	+	Silent	SNP	T	T	C	rs1049623	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	168	86	208	0	0.511905	0	T|0.539;C|0.461	0.461	strong	DDR1_ENST00000376575,NS,adenoma,0,3	DDR1	213	3	NM_013994	exon13	c.T1908C	p.V636V	TCTGGTTAGTCTT	.	PASS	Atlas-SNP
C10orf120	399814	hgsc.bcm.edu	37	10	124459139	124459139	+	Silent	SNP	T	T	C	rs11813597	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	111	54	114	0	0.486486	0	C|0.427;N|0.000	0.427	strong	C10orf120,NS,carcinoma,0,1	C10orf120	55	1	NM_001010912	exon1	c.A168G	p.S56S	CAACGGTGAAGCA	.	PASS	Atlas-SNP
MMP13	4322	hgsc.bcm.edu	37	11	102825227	102825227	+	Silent	SNP	G	G	A	rs368161332		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	108	70	137	0	0.648148	0	.	.	weak	MMP13,NS,malignant_melanoma,-2,1	MMP13	75	1	NM_002427	exon3	c.C471T	p.H157H	GCCATCGTGAAGT	.	PASS	Atlas-SNP
JMJD1C	221037	hgsc.bcm.edu	37	10	64927823	64927823	+	Missense_Mutation	SNP	C	C	G	rs1935	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	100	55	154	0	0.55	0	C|0.570;G|0.430	0.430	strong	JMJD1C_ENST00000399262,NS,carcinoma,0,2	JMJD1C	347	2	NM_032776	exon26	c.G7605C	p.E2535D	CATATCCTCTACT	.	PASS	Atlas-SNP
OR2G2	81470	hgsc.bcm.edu	37	1	247752161	247752161	+	Missense_Mutation	SNP	T	T	C	rs10925085	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	163	71	197	0	0.435583	0	T|0.676;C|0.324	0.324	strong	.	OR2G2	88	.	NM_001001915	exon1	c.T500C	p.L167P	TCACCCTGCAGCT	.	PASS	Atlas-SNP
DOCK8	81704	hgsc.bcm.edu	37	9	340230	340230	+	Missense_Mutation	SNP	G	G	A	rs373187839		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	91	37	81	1	0.406593	0.0123457	.	.	weak	DOCK8_ENST00000453981,NS,carcinoma,-2,2	DOCK8	401	2	NM_203447	exon14	c.G1588A	p.V530M	CTGCCCGTGAAAC	.	scavenged	Atlas-SNP
FBP1	2203	hgsc.bcm.edu	37	9	97369151	97369151	+	Silent	SNP	G	G	A	rs1042144	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	153	72	193	0	0.470588	0	T|0.000;G|0.682;A|0.318	0.318	strong	.	FBP1	13	.	NM_000507	exon5	c.C651T	p.A217A	GTCCCTGGCGTAG	.	PASS	Atlas-SNP
ALPK3	57538	hgsc.bcm.edu	37	15	85383640	85383640	+	Missense_Mutation	SNP	G	G	A	rs3803405	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	64	36	68	0	0.5625	0	G|0.815;A|0.185	0.185	strong	.	ALPK3	289	.	NM_020778	exon5	c.G1736A	p.G579E	CACGGGGGCCTGG	.	PASS	Atlas-SNP
GNL3	26354	hgsc.bcm.edu	37	3	52721305	52721305	+	Missense_Mutation	SNP	G	G	A	rs11177	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	127	126	168	0	0.992126	0	G|0.658;A|0.342	0.342	strong	.	GNL3	37	.	NM_014366	exon3	c.G116A	p.R39Q	AAAAGCGGGGTCA	.	PASS	Atlas-SNP
ZNF578	147660	hgsc.bcm.edu	37	19	53014752	53014752	+	Missense_Mutation	SNP	G	G	A	rs61739625	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	45	24	57	0	0.533333	0	G|0.995;A|0.005	0.005	strong	.	.	.	.	NM_001099694	exon6	c.G1118A	p.C373Y	ACAAGTGTAATGA	.	PASS	Atlas-SNP
VWA3A	146177	hgsc.bcm.edu	37	16	22144377	22144377	+	Silent	SNP	C	C	A	rs371670962	alternate_allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	27	91	0	0.380282	0	.	.	alt	.	VWA3A	115	.	NM_173615	exon20	c.C2029A	p.R677R	GTCACCCGGGCTG	.	PASS	Atlas-SNP
EAPP	55837	hgsc.bcm.edu	37	14	34993982	34993982	+	Missense_Mutation	SNP	G	G	C	rs17352411	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	138	62	159	0	0.449275	0	G|0.947;C|0.053	0.053	strong	.	EAPP	28	.	NM_018453	exon5	c.C502G	p.Q168E	GTTGTTGACGTGA	.	PASS	Atlas-SNP
FCGBP	8857	hgsc.bcm.edu	37	19	40405999	40405999	+	Missense_Mutation	SNP	C	C	A	rs7248839	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	448	48	721	18	0.107143	0.0249653	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
ARAP2	116984	hgsc.bcm.edu	37	4	36069805	36069805	+	Silent	SNP	G	G	A	rs7657166	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	104	103	99	0	0.990385	0	G|0.777;A|0.223	0.223	strong	.	ARAP2	210	.	NM_015230	exon33	c.C4839T	p.A1613A	GCAGTGGGCCACC	.	PASS	Atlas-SNP
CYP39A1	51302	hgsc.bcm.edu	37	6	46620252	46620252	+	Missense_Mutation	SNP	C	C	G	rs12192544	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	79	40	84	0	0.506329	0	C|0.846;G|0.154	0.154	strong	.	CYP39A1	41	.	NM_016593	exon1	c.G68C	p.R23P	TTCTTCCGCTGAA	.	PASS	Atlas-SNP
AGAP11	119385	hgsc.bcm.edu	37	10	88768253	88768253	+	Missense_Mutation	SNP	A	A	G	rs2641563	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	109	53	151	0	0.486239	0	A|0.215;G|0.785	0.785	strong	.	.	.	.	NM_133447	exon12	c.A244G	p.I82V	ACGCCCATTTGCA	.	PASS	Atlas-SNP
PLEC	5339	hgsc.bcm.edu	37	8	145002070	145002070	+	Silent	SNP	G	G	A	rs145376880	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	26	84	0	0.333333	0	G|0.996;A|0.004	0.004	strong	.	PLEC	1144	.	NM_201380	exon26	c.C3762T	p.A1254A	CGGCACGGCCTGG	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	251	247	232	0	0.984064	0	A|0.493;G|0.507	0.507	strong	.	OR52J3	77	.	NM_001001916	exon1	c.A229G	p.T77A	CTTTCTACAACCT	.	PASS	Atlas-SNP
THBD	7056	hgsc.bcm.edu	37	20	23028724	23028724	+	Missense_Mutation	SNP	G	G	A	rs1042579	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	56	30	57	0	0.535714	0	G|0.846;A|0.154	0.154	strong	.	THBD	26	.	NM_000361	exon1	c.C1418T	p.A473V	TGGCGGGCAAGGG	.	PASS	Atlas-SNP
PRX	57716	hgsc.bcm.edu	37	19	40901604	40901604	+	Silent	SNP	A	A	G	rs268672	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	63	26	74	0	0.412698	0	A|0.457;G|0.543	0.543	strong	.	PRX	151	.	NM_181882	exon7	c.T2655C	p.P885P	CACCTCAGGGCCC	.	PASS	Atlas-SNP
PCNX	22990	hgsc.bcm.edu	37	14	71443816	71443816	+	Silent	SNP	T	T	G	rs35702999	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	218	94	227	0	0.431193	0	T|0.991;G|0.009	0.009	strong	.	PCNX	198	.	NM_014982	exon6	c.T762G	p.S254S	TCAGTCTCTGTCC	.	PASS	Atlas-SNP
BAZ2B	29994	hgsc.bcm.edu	37	2	160182302	160182302	+	Missense_Mutation	SNP	C	C	T	rs415793	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	173	173	226	0	1	0	T|0.249;G|0.012	0.249	strong	.	BAZ2B	196	.	NM_013450	exon35	c.G6071A	p.S2024N	AGTGAACTACTTG	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	182	82	179	0	0.450549	0	A|0.323;C|0.008	0.323	strong	.	LRRC38	12	.	NM_001010847	exon2	c.C762T	p.S254S	CACACCGGAGAAA	.	PASS	Atlas-SNP
APOPT1	84334	hgsc.bcm.edu	37	14	104029449	104029449	+	Silent	SNP	G	G	A	rs2274267	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	18	11	11	0	0.611111	0	G|0.747;A|0.253	0.253	strong	.	.	.	.	NM_032374	exon1	c.G150A	p.T50T	GGATACGGCGCCC	.	PASS	Atlas-SNP
PRSS55	203074	hgsc.bcm.edu	37	8	10396123	10396123	+	Silent	SNP	C	C	T	rs73195184	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	139	27	158	0	0.194245	0	C|0.985;T|0.015	0.015	strong	PRSS55,NS,carcinoma,+2,2	PRSS55	67	2	NM_198464	exon5	c.C879T	p.L293L	CAACCTCTGGATC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195512568	195512568	+	Silent	SNP	T	T	C	rs71254296	alternate_allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	117	21	55	1	0.179487	0.0181818	GT|0.500;AC|0.500	.	alt	MUC4_ENST00000463781,bladder,carcinoma,0,2	MUC4	1505	2	NM_018406	exon2	c.A5883G	p.V1961V	TGTGGGTACTGAG	.	scavenged	Atlas-SNP
NPSR1	387129	hgsc.bcm.edu	37	7	34874038	34874038	+	Missense_Mutation	SNP	C	C	G	rs727162	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	178	120	220	0	0.674157	0	C|0.744;G|0.256	0.256	strong	.	NPSR1	134	.	NM_207172	exon6	c.C723G	p.S241R	TAAAAGCAAAACC	.	PASS	Atlas-SNP
TREX2	11219	hgsc.bcm.edu	37	X	152710185	152710185	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	50	18	139	0	0.36	0	.	.	none	.	TREX2	36	.	NM_080701	exon2	c.A704C	p.E235A	CAGGCCTCCAGGC	.	PASS	Atlas-SNP
NLRP5	126206	hgsc.bcm.edu	37	19	56552456	56552456	+	Silent	SNP	G	G	T	rs61732213	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	146	83	147	0	0.568493	0	G|0.815;T|0.185	0.185	strong	.	NLRP5	217	.	NM_153447	exon11	c.G2955T	p.L985L	GAGGCTGATGTGA	.	PASS	Atlas-SNP
C10orf54	64115	hgsc.bcm.edu	37	10	73521371	73521371	+	Silent	SNP	C	C	T	rs3747867	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	46	29	56	0	0.630435	0	C|0.779;T|0.221	0.221	strong	.	C10orf54	29	.	NM_022153	exon2	c.G495A	p.E165E	CTGCAGCTCCATG	.	PASS	Atlas-SNP
EGFR	1956	hgsc.bcm.edu	37	7	55238087	55238087	+	Silent	SNP	C	C	T	rs10258429	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	145	66	152	0	0.455172	0	C|0.889;T|0.111	0.111	strong	.	EGFR	20426	.	NM_201284	exon16	c.C1968T	p.H656H	GTCCCACCAGAGC	.	PASS	Atlas-SNP
RABL6	55684	hgsc.bcm.edu	37	9	139731969	139731969	+	Silent	SNP	C	C	T	rs2811742	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	26	9	15	0	0.346154	0	C|0.236;T|0.764	0.764	strong	C9orf86_ENST00000371663,NS,carcinoma,0,2	.	.	2	NM_001173988	exon9	c.C984T	p.A328A	CAATGCCGCCCCA	.	PASS	Atlas-SNP
GALNT8	26290	hgsc.bcm.edu	37	12	4830000	4830000	+	Missense_Mutation	SNP	T	T	G	rs10849133	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	118	70	148	0	0.59322	0	G|0.410;N|0.000	0.410	strong	GALNT8,NS,carcinoma,0,2	GALNT8	89	2	NM_017417	exon1	c.T157G	p.Y53D	AAACGCTACGGGG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195515449	195515449	+	Missense_Mutation	SNP	A	A	T	rs200672669	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	88	12	71	0	0.136364	0	A|0.956;G|0.036;T|0.008	0.008	strong	MUC4_ENST00000463781,NS,carcinoma,0,12	MUC4	1505	12	NM_018406	exon2	c.T3002A	p.V1001E	GTGGATACTGAGG	.	PASS	Atlas-SNP
C6orf70	55780	hgsc.bcm.edu	37	6	170162537	170162537	+	Silent	SNP	C	C	T	rs11966349	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	57	12	126	0	0.210526	0	C|0.838;T|0.162	0.162	strong	.	C6orf70	63	.	NM_018341	exon9	c.C870T	p.C290C	TGACTGCGCCATA	.	PASS	Atlas-SNP
CXCR4	7852	hgsc.bcm.edu	37	2	136873084	136873084	+	Silent	SNP	G	G	A	rs2228014	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	44	19	56	0	0.431818	0	G|0.955;A|0.045	0.045	strong	CXCR4,NS,carcinoma,0,1	CXCR4	51	1	NM_001008540	exon1	c.C426T	p.I142I	GTGGACGATGGCC	.	PASS	Atlas-SNP
PML	5371	hgsc.bcm.edu	37	15	74328116	74328116	+	Missense_Mutation	SNP	A	A	G	rs743580	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	63	84	0	0.732558	0	A|0.492;C|0.000;G|0.508	0.508	strong	.	PML	169	.	NM_033239	exon8	c.A2314G	p.S772G	GGGGAAAGCAGAG	.	PASS	Atlas-SNP
THSD1	55901	hgsc.bcm.edu	37	13	52971893	52971893	+	Silent	SNP	G	G	A	rs3803264	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	57	57	46	0	1	0	G|0.397;A|0.603	0.603	strong	.	THSD1	89	.	NM_199263	exon3	c.C495T	p.I165I	CACTACGATGTTG	.	PASS	Atlas-SNP
COLEC12	81035	hgsc.bcm.edu	37	18	346821	346821	+	Silent	SNP	C	C	T	rs3826628	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	89	41	105	0	0.460674	0	C|0.763;T|0.237	0.237	strong	COLEC12,colon,carcinoma,0,1	COLEC12	121	1	NM_130386	exon5	c.G801A	p.T267T	AGCCAGCGTCTGC	.	PASS	Atlas-SNP
ADAM32	203102	hgsc.bcm.edu	37	8	39068684	39068684	+	Silent	SNP	T	T	A	rs61753544	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	56	89	0	0.788732	0	T|0.999;A|0.001	0.001	strong	.	ADAM32	70	.	NM_145004	exon12	c.T1074A	p.T358T	GAAGACTTTTAGC	.	PASS	Atlas-SNP
FAM135A	57579	hgsc.bcm.edu	37	6	71195892	71195892	+	Silent	SNP	A	A	G	rs142935920	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	201	94	232	0	0.467662	0	A|0.999;G|0.001	0.001	strong	.	FAM135A	181	.	NM_020819	exon9	c.A717G	p.L239L	GCTCCTATATGAG	.	PASS	Atlas-SNP
TRPA1	8989	hgsc.bcm.edu	37	8	72958799	72958799	+	Silent	SNP	G	G	A	rs61757563	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	44	32	39	0	0.727273	0	G|0.958;A|0.042	0.042	strong	.	TRPA1	256	.	NM_007332	exon17	c.C2010T	p.T670T	TTTTTTGGTGAAT	.	PASS	Atlas-SNP
WRN	7486	hgsc.bcm.edu	37	8	31024638	31024638	+	Silent	SNP	C	C	T	rs1801196	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	159	117	212	0	0.735849	0	C|0.728;T|0.272	0.272	strong	.	WRN	116	.	NM_000553	exon34	c.C4083T	p.S1361S	TGACAGCGGACTT	.	PASS	Atlas-SNP
PDILT	204474	hgsc.bcm.edu	37	16	20370810	20370810	+	Missense_Mutation	SNP	C	C	T	rs9652588	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	279	103	233	0	0.369176	0	C|0.575;T|0.425	0.425	strong	.	PDILT	120	.	NM_174924	exon12	c.G1586A	p.G529E	GGTAACCCTTTCC	.	PASS	Atlas-SNP
MTMR2	8898	hgsc.bcm.edu	37	11	95571347	95571347	+	Missense_Mutation	SNP	C	C	G	rs61735578	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	80	15	86	0	0.1875	0	C|0.960;G|0.040	0.040	strong	.	MTMR2	79	.	NM_016156	exon13	c.G1504C	p.E502Q	AATACTCATTGAA	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	103	11	120	0	0.106796	0	C|0.724;T|0.276	0.276	strong	.	ZDHHC11	97	.	NM_024786	exon8	c.G1022A	p.R341Q	CTTACCCGTGCCG	.	PASS	Atlas-SNP
TEX35	84066	hgsc.bcm.edu	37	1	178492447	178492447	+	Silent	SNP	T	T	A	rs7527160	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	11	11	17	0	1	0	T|0.409;A|0.591	0.591	strong	.	TEX35	15	.	NM_001170722	exon9	c.T621A	p.A207A	ATACGCTGCAGTG	.	PASS	Atlas-SNP
RADIL	55698	hgsc.bcm.edu	37	7	4843307	4843307	+	Missense_Mutation	SNP	T	T	C	rs187128776	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	116	26	111	1	0.224138	0.00900901	T|0.985;C|0.015	0.015	strong	RADIL,brain,glioma,0,1	RADIL	110	1	NM_018059	exon11	c.A2369G	p.N790S	AGGCAGTTGGCTT	.	scavenged	Atlas-SNP
ASXL1	171023	hgsc.bcm.edu	37	20	31024274	31024274	+	Silent	SNP	T	T	C	rs4911231	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	57	25	67	0	0.438596	0	T|0.653;C|0.347	0.347	strong	.	ASXL1	1114	.	NM_015338	exon12	c.T3759C	p.S1253S	GGACAGTAATTCA	.	PASS	Atlas-SNP
FCGR3B	2215	hgsc.bcm.edu	37	1	161599693	161599693	+	Missense_Mutation	SNP	T	T	C	rs76714703	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	277	273	165	1	0.98556	0.00606061	T|0.338;C|0.662	0.662	strong	.	FCGR3B	35	.	NM_001244753	exon3	c.A302G	p.N101S	ATGAGGTTCTCAT	.	PASS	Atlas-SNP
SLC12A6	9990	hgsc.bcm.edu	37	15	34551082	34551082	+	Silent	SNP	G	G	A	rs7164902	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	298	297	366	2	0.996644	0.00546448	G|0.751;A|0.249	0.249	strong	.	SLC12A6	205	.	NM_133647	exon4	c.C475T	p.L159L	GAGTCAGATTAGT	.	PASS	Atlas-SNP
DSC1	1823	hgsc.bcm.edu	37	18	28722103	28722103	+	Silent	SNP	T	T	C	rs2577074	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	198	102	209	0	0.515152	0	T|0.690;C|0.310	0.310	strong	.	DSC1	240	.	NM_004948	exon9	c.A1119G	p.L373L	CATTCGTAAAATC	.	PASS	Atlas-SNP
TOR2A	27433	hgsc.bcm.edu	37	9	130495633	130495633	+	Missense_Mutation	SNP	C	C	G	rs564754	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	57	26	76	0	0.45614	0	C|0.370;G|0.630	0.630	strong	.	TOR2A	26	.	NM_130459	exon3	c.G624C	p.W208C	GCCCCCCCACTGT	.	PASS	Atlas-SNP
TMEM132E	124842	hgsc.bcm.edu	37	17	32962064	32962064	+	Missense_Mutation	SNP	C	C	A	rs111689642	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	30	74	0	0.517241	0	C|0.985;A|0.015	0.015	strong	.	TMEM132E	122	.	NM_207313	exon8	c.C1665A	p.S555R	GGACAGCAGCACG	.	PASS	Atlas-SNP
OR8D1	283159	hgsc.bcm.edu	37	11	124180282	124180282	+	Missense_Mutation	SNP	A	A	C	rs7107539	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	49	14	69	0	0.285714	0	A|0.693;C|0.307	0.307	strong	.	OR8D1	53	.	NM_001002917	exon1	c.T381G	p.C127W	TGGGCTACAGATG	.	PASS	Atlas-SNP
KRTAP12-2	353323	hgsc.bcm.edu	37	21	46086757	46086757	+	Missense_Mutation	SNP	G	G	A	rs7275298	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	114	113	83	0	0.991228	0	G|0.314;A|0.686	0.686	strong	.	KRTAP12-2	10	.	NM_181684	exon1	c.C47T	p.A16V	CTGGGCGCGCAGC	.	PASS	Atlas-SNP
PCDHGC5	56097	hgsc.bcm.edu	37	5	140870949	140870949	+	Silent	SNP	G	G	T	rs918558	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	193	190	219	0	0.984456	0	G|0.820;T|0.180	0.180	strong	.	PCDHGC5	199	.	NM_018929	exon1	c.G2142T	p.A714A	GTCAGCGAAGTGC	.	PASS	Atlas-SNP
MOGS	7841	hgsc.bcm.edu	37	2	74692191	74692191	+	Missense_Mutation	SNP	C	C	T	rs79181168	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	9	7	6	0	0.777778	0	C|0.971;T|0.029	0.029	strong	.	MOGS	58	.	NM_006302	exon1	c.G184A	p.V62M	CCAGCACCCAGCG	.	PASS	Atlas-SNP
BAALC	79870	hgsc.bcm.edu	37	8	104153137	104153137	+	Silent	SNP	C	C	T	rs3736043	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	34	27	24	0	0.794118	0	C|0.958;T|0.042	0.042	strong	.	BAALC	15	.	NM_001024372	exon1	c.C12T	p.G4G	CTGCGGCGGGAGC	.	PASS	Atlas-SNP
DPPA4	55211	hgsc.bcm.edu	37	3	109052732	109052732	+	Missense_Mutation	SNP	T	T	C	rs3762648	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	109	108	156	0	0.990826	0	T|0.557;C|0.443	0.443	strong	DPPA4,NS,carcinoma,+2,1	DPPA4	56	1	NM_018189	exon2	c.A163G	p.I55V	CTTTGATAGACAT	.	PASS	Atlas-SNP
GPLD1	2822	hgsc.bcm.edu	37	6	24445829	24445829	+	Silent	SNP	G	G	A	rs9358767	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	99	52	108	0	0.525253	0	G|0.859;A|0.140	0.140	strong	.	GPLD1	91	.	NM_001503	exon20	c.C1965T	p.H655H	CAGTACGTGGCCA	.	PASS	Atlas-SNP
ENTPD6	955	hgsc.bcm.edu	37	20	25187213	25187213	+	Missense_Mutation	SNP	G	G	A	rs2076559	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	96	51	94	0	0.53125	0	G|0.702;A|0.298	0.298	strong	.	ENTPD6	57	.	NM_001247	exon2	c.G41A	p.S14N	AAACGAGCTACAT	.	PASS	Atlas-SNP
RNF213	57674	hgsc.bcm.edu	37	17	78263486	78263486	+	Missense_Mutation	SNP	T	T	C	rs17853989	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	102	50	117	1	0.490196	0.00854701	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	.	scavenged	Atlas-SNP
ULK3	25989	hgsc.bcm.edu	37	15	75130093	75130093	+	Missense_Mutation	SNP	T	T	C	rs12898397	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	89	89	85	0	1	0	T|0.596;C|0.404	0.404	strong	.	ULK3	30	.	NM_001099436	exon14	c.A1334G	p.K445R	CCCACCTTGACCT	.	PASS	Atlas-SNP
PRKAR1B	5575	hgsc.bcm.edu	37	7	618938	618938	+	Silent	SNP	A	A	G	rs3211362	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	140	103	121	0	0.735714	0	A|0.585;G|0.415	0.415	strong	.	PRKAR1B	32	.	NM_001164760	exon9	c.T846C	p.I282I	GACCACAATTTTC	.	PASS	Atlas-SNP
PREX2	80243	hgsc.bcm.edu	37	8	69058521	69058521	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	106	4	132	0	0.0377358	0	.	.	none	PREX2,back,malignant_melanoma,0,1	PREX2	614	1	NM_024870	exon34	c.G4165T	p.E1389X	CATTTTGAACAAC	.	scavenged	Atlas-SNP
C10orf25	220979	hgsc.bcm.edu	37	10	45496120	45496120	+	Missense_Mutation	SNP	A	A	T	rs12269028	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	85	104	0	0.988372	0	A|0.475;T|0.525	0.525	strong	.	C10orf25	11	.	NM_001039380	exon1	c.T188A	p.I63N	CTCAAAATTTGTG	.	PASS	Atlas-SNP
C6orf170	221322	hgsc.bcm.edu	37	6	121577370	121577370	+	Missense_Mutation	SNP	T	T	C	rs7745023	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	65	64	94	0	0.984615	0	T|0.674;C|0.326	0.326	strong	C6orf170,NS,carcinoma,0,1	C6orf170	146	1	NM_152730	exon16	c.A1795G	p.I599V	AAAATATAGAAAT	.	PASS	Atlas-SNP
GPR32	2854	hgsc.bcm.edu	37	19	51274836	51274836	+	Missense_Mutation	SNP	T	T	C	rs1864011	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	91	46	106	0	0.505495	0	T|0.976;C|0.024	0.024	strong	.	GPR32	68	.	NM_001506	exon1	c.T979C	p.F327L	GAAAAGTTTTTCC	.	PASS	Atlas-SNP
CHRND	1144	hgsc.bcm.edu	37	2	233390937	233390937	+	Silent	SNP	A	A	G	rs2245601	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	215	100	200	0	0.465116	0	A|0.542;G|0.458	0.458	strong	CHRND,NS,carcinoma,0,1	CHRND	67	1	NM_000751	exon1	c.A12G	p.P4P	GGGGCCAGTGCTG	.	PASS	Atlas-SNP
ZKSCAN2	342357	hgsc.bcm.edu	37	16	25268368	25268368	+	Silent	SNP	A	A	G	rs4787310	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	116	35	111	0	0.301724	0	A|0.562;G|0.438	0.438	strong	ZKSCAN2,NS,carcinoma,0,1	ZKSCAN2	90	1	NM_001012981	exon1	c.T81C	p.P27P	CCACTCAGGGTCC	.	PASS	Atlas-SNP
UBXN11	91544	hgsc.bcm.edu	37	1	26612460	26612460	+	Silent	SNP	G	G	A	rs11247900	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	152	68	151	0	0.447368	0	G|0.862;A|0.138	0.138	strong	.	UBXN11	54	.	NM_183008	exon10	c.C628T	p.L210L	CCACCAGCTCACT	.	PASS	Atlas-SNP
KIAA2026	158358	hgsc.bcm.edu	37	9	5921844	5921844	+	Missense_Mutation	SNP	G	G	T	rs117286418	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	42	124	0	0.488372	0	A|0.001;G|0.937;T|0.062	0.062	strong	KIAA2026_ENST00000399933,NS,carcinoma,0,2	KIAA2026	231	2	NM_001017969	exon8	c.C4152A	p.H1384Q	TATCACGTGGCCC	.	PASS	Atlas-SNP
PDE5A	8654	hgsc.bcm.edu	37	4	120474859	120474859	+	Silent	SNP	A	A	G	rs11947234	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	174	174	203	0	1	0	A|0.732;G|0.268	0.268	strong	.	PDE5A	83	.	NM_001083	exon8	c.T1242C	p.Y414Y	TTTGACATACTGA	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	273	272	223	0	0.996337	0	G|0.493;A|0.507	0.507	strong	.	OR52J3	77	.	NM_001001916	exon1	c.G382A	p.V128I	GTGGCCGTCTGTG	.	PASS	Atlas-SNP
ESYT2	57488	hgsc.bcm.edu	37	7	158536345	158536345	+	Missense_Mutation	SNP	A	A	G	rs2305475	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	29	100	0	0.371795	0	A|0.737;C|0.000;G|0.262;T|0.000	0.262	strong	.	ESYT2	70	.	NM_020728	exon16	c.T1750C	p.S584P	CCAGGGAACACTG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195508249	195508249	+	Missense_Mutation	SNP	A	A	G	rs71187729		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	90	8	83	0	0.0888889	0	A|0.500;G|0.500	0.500	weak	MUC4_ENST00000463781,NS,carcinoma,0,7	MUC4	1505	7	NM_018406	exon2	c.T10202C	p.V3401A	GTGGATACTGAGG	.	scavenged	Atlas-SNP
ELSPBP1	64100	hgsc.bcm.edu	37	19	48525507	48525507	+	Missense_Mutation	SNP	G	G	A	rs2303690	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	167	80	209	0	0.479042	0	G|0.365;A|0.635	0.635	strong	ELSPBP1,NS,adenoma,0,1	ELSPBP1	29	1	NM_022142	exon6	c.G595A	p.E199K	ACTAACGAAGGAT	.	PASS	Atlas-SNP
DYNC2H1	79659	hgsc.bcm.edu	37	11	103116000	103116000	+	Silent	SNP	T	T	C	rs192003811	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	51	8	62	0	0.156863	0	T|0.997;C|0.003	0.003	strong	.	DYNC2H1	246	.	NM_001080463	exon66	c.T9960C	p.A3320A	CACAGCTCTTGAA	.	PASS	Atlas-SNP
ELF4	2000	hgsc.bcm.edu	37	X	129201179	129201179	+	Silent	SNP	C	C	T	rs2181440	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	96	95	97	0	0.989583	0	C|0.813;T|0.187	0.187	strong	.	ELF4	67	.	NM_001421	exon9	c.G1509A	p.T503T	TGTGACCGTGGGT	.	PASS	Atlas-SNP
CCDC168	643677	hgsc.bcm.edu	37	13	103394239	103394239	+	Silent	SNP	C	C	T	rs16960471	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	162	83	188	0	0.512346	0	C|0.924;T|0.076	0.076	strong	.	.	.	.	NM_001146197	exon4	c.G8808A	p.P2936P	CCTTAACGGTCCA	.	PASS	Atlas-SNP
DOCK4	9732	hgsc.bcm.edu	37	7	111375211	111375211	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	37	11	44	0	0.297297	0	.	.	none	.	DOCK4	365	.	NM_014705	exon50	c.C5291G	p.T1764S	CTAGGGGTGGGGT	.	PASS	Atlas-SNP
TAT	6898	hgsc.bcm.edu	37	16	71609856	71609856	+	Silent	SNP	C	C	T	rs78302875	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	115	80	105	1	0.695652	0.00952381	C|0.928;T|0.072	0.072	strong	TAT,colon,carcinoma,-1,1	TAT	80	1	NM_000353	exon3	c.G309A	p.S103S	TTTGCCCGAGTCC	.	scavenged	Atlas-SNP
TDRD9	122402	hgsc.bcm.edu	37	14	104436931	104436931	+	Silent	SNP	C	C	T	rs11851097	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	64	30	87	0	0.46875	0	C|0.648;T|0.352	0.352	strong	TDRD9_ENST00000409874,NS,carcinoma,0,1	TDRD9	175	1	NM_153046	exon6	c.C819T	p.L273L	CAAACTCTTAAGA	.	PASS	Atlas-SNP
OGFRL1	79627	hgsc.bcm.edu	37	6	72006512	72006512	+	Silent	SNP	T	T	C	rs2273888	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	114	57	118	0	0.5	0	T|0.820;C|0.180	0.180	strong	.	OGFRL1	44	.	NM_024576	exon6	c.T684C	p.H228H	TCAGCATCTGAAT	.	PASS	Atlas-SNP
TBC1D25	4943	hgsc.bcm.edu	37	X	48418659	48418659	+	Missense_Mutation	SNP	G	G	A	rs235836	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	158	157	189	0	0.993671	0	G|0.441;A|0.559	0.559	strong	.	TBC1D25	70	.	NM_002536	exon6	c.G1363A	p.A455T	GCAGACGCTGGTT	.	PASS	Atlas-SNP
STON1	11037	hgsc.bcm.edu	37	2	48807976	48807976	+	Silent	SNP	T	T	C	rs3828340	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	269	64	146	0	0.237918	0	T|0.674;C|0.326	0.326	strong	.	STON1	100	.	NM_001198595	exon3	c.T204C	p.D68D	TGTAGATTTTTAT	.	PASS	Atlas-SNP
PPL	5493	hgsc.bcm.edu	37	16	4933907	4933907	+	Silent	SNP	T	T	C	rs17137389	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	125	84	162	0	0.672	0	T|0.902;C|0.098	0.098	strong	.	PPL	168	.	NM_002705	exon22	c.A4749G	p.Q1583Q	TTCCGATTGGAGC	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	127	43	162	0	0.338583	0	G|0.831;C|0.169	0.169	strong	.	IFNAR1	44	.	NM_000629	exon4	c.G502C	p.V168L	AGCTTAGTTATCT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195505955	195505955	+	Missense_Mutation	SNP	C	C	T	rs55789594	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	65	17	47	1	0.261538	0.0212766	.	.	weak	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.G12496A	p.A4166T	AGGAAGCGTCGGT	.	scavenged	Atlas-SNP
ALMS1	7840	hgsc.bcm.edu	37	2	73651967	73651967	+	Missense_Mutation	SNP	C	C	T	rs3813227	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	215	213	283	0	0.990698	0	C|0.661;T|0.339	0.339	strong	.	ALMS1	384	.	NM_015120	exon5	c.C1174T	p.R392C	GCTGCTCGTTCAT	.	PASS	Atlas-SNP
CNTN5	53942	hgsc.bcm.edu	37	11	99690450	99690450	+	Silent	SNP	T	T	C	rs12222337	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	109	21	129	0	0.192661	0	C|0.101;T|0.899	0.101	strong	.	CNTN5	324	.	NM_001243270	exon3	c.T231C	p.Y77Y	TTATTATTCCCCC	.	PASS	Atlas-SNP
FAM170B	170370	hgsc.bcm.edu	37	10	50341954	50341954	+	Missense_Mutation	SNP	A	A	G	rs34110351	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	173	86	202	1	0.49711	0.00495049	A|0.759;G|0.241	0.241	strong	.	FAM170B	20	.	NM_001164484	exon1	c.T10C	p.Y4H	TGAAGTAGCATTT	.	PASS	Atlas-SNP
ZFP69B	65243	hgsc.bcm.edu	37	1	40923019	40923019	+	Missense_Mutation	SNP	G	G	A	rs2272994	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	110	39	150	0	0.354545	0	G|0.815;A|0.185	0.185	strong	.	.	.	.	NM_023070	exon4	c.G344A	p.C115Y	CAGGATGTCAGCT	.	PASS	Atlas-SNP
OR1A2	26189	hgsc.bcm.edu	37	17	3101691	3101691	+	Missense_Mutation	SNP	G	G	T	rs12150427	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	89	89	117	0	1	0	G|0.697;N|0.000	.	strong	OR1A2,NS,carcinoma,0,1	OR1A2	52	1	NM_012352	exon1	c.G879T	p.W293C	AAATTGGGATATG	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	143	42	159	0	0.293706	0	C|0.553;T|0.447	0.447	strong	.	RIMS2	1357	.	NM_001100117	exon24	c.C3981T	p.A1327A	CTTGGCCCCTCTG	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179393691	179393691	+	Missense_Mutation	SNP	G	G	A	rs55842557	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	202	80	229	0	0.39604	0	G|0.993;A|0.007	0.007	strong	.	TTN	18412	.	NM_001267550	exon360	c.C106787T	p.T35596I	TGTGATGTTTTAG	.	PASS	Atlas-SNP
NOM1	64434	hgsc.bcm.edu	37	7	156762224	156762224	+	Missense_Mutation	SNP	G	G	C	rs2302443	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	15	15	22	0	1	0	G|0.498;C|0.502	0.502	strong	.	NOM1	73	.	NM_138400	exon11	c.G2410C	p.V804L	TCCAGAGTATCTG	.	PASS	Atlas-SNP
CACNA1S	779	hgsc.bcm.edu	37	1	201047062	201047062	+	Silent	SNP	G	G	A	rs4915476	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	165	161	203	1	0.975758	0.00492611	G|0.776;A|0.224	0.224	strong	.	CACNA1S	249	.	NM_000069	exon11	c.C1564T	p.L522L	TGCCCAGGGGTGT	.	PASS	Atlas-SNP
ELFN2	114794	hgsc.bcm.edu	37	22	37771158	37771158	+	Silent	SNP	G	G	A	rs2071857	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	93	46	111	0	0.494624	0	G|0.569;A|0.431	0.431	strong	.	ELFN2	89	.	NM_052906	exon3	c.C417T	p.I139I	CACCTCGATGAGG	.	PASS	Atlas-SNP
FAM193A	8603	hgsc.bcm.edu	37	4	2702115	2702115	+	Missense_Mutation	SNP	A	A	G	rs17681870	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	39	148	0	0.402062	0	A|0.965;G|0.035	0.035	strong	.	FAM193A	103	.	NM_001256667	exon18	c.A3409G	p.I1137V	AACCACATCAAGG	.	PASS	Atlas-SNP
TUBB4A	10382	hgsc.bcm.edu	37	19	6495199	6495199	+	Silent	SNP	C	C	T	rs369467354		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	49	18	54	0	0.367347	0	.	.	weak	.	.	.	.	NM_006087	exon4	c.G1311A	p.E437E	CGCCTCCTCCTCG	.	PASS	Atlas-SNP
OR5H1	26341	hgsc.bcm.edu	37	3	97851645	97851645	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	369	9	450	1	0.0243902	0.00222222	.	.	none	OR5H1,NS,carcinoma,+1,1	OR5H1	71	1	NM_001005338	exon1	c.A104G	p.Y35C	TAATATATCTCAT	.	scavenged	Atlas-SNP
FAT4	79633	hgsc.bcm.edu	37	4	126336348	126336348	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	107	7	126	0	0.0654206	0	.	.	none	.	FAT4	1752	.	NM_024582	exon5	c.C6230G	p.P2077R	CTGACCCAGATAG	.	PASS	Atlas-SNP
SMO	6608	hgsc.bcm.edu	37	7	128843277	128843277	+	Silent	SNP	C	C	T	rs45571737	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	103	40	99	0	0.38835	0	C|0.993;T|0.007	0.007	strong	.	SMO	145	.	NM_005631	exon2	c.C384T	p.A128A	GTGTGCCGTATAC	.	PASS	Atlas-SNP
ZNF221	7638	hgsc.bcm.edu	37	19	44471209	44471209	+	Missense_Mutation	SNP	T	T	A	rs365745	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	44	44	66	0	1	0	T|0.243;A|0.757	0.757	strong	.	ZNF221	59	.	NM_013359	exon6	c.T1555A	p.S519T	CAGAGTTCACAAC	.	PASS	Atlas-SNP
TLR1	7096	hgsc.bcm.edu	37	4	38798817	38798817	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	249	3	280	1	0.0120482	0.00357143	.	.	none	TLR1,right_upper_lobe,carcinoma,0,1	TLR1	70	1	NM_003263	exon4	c.G1636A	p.V546M	CTAACACTTCACT	.	scavenged	Atlas-SNP
PRKCG	5582	hgsc.bcm.edu	37	19	54403925	54403925	+	Silent	SNP	T	T	C	rs2242244	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	95	46	131	0	0.484211	0	T|0.949;C|0.051	0.051	strong	.	PRKCG	246	.	NM_002739	exon14	c.T1497C	p.F499F	TGACTTTGGCATG	.	PASS	Atlas-SNP
HIST1H2AA	221613	hgsc.bcm.edu	37	6	25726621	25726621	+	Silent	SNP	C	C	T	rs9467583	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	83	44	108	0	0.53012	0	C|0.749;T|0.251	0.251	strong	HIST1H2AA,NS,malignant_melanoma,0,3	HIST1H2AA	34	3	NM_170745	exon1	c.G135A	p.G45G	GCCTGCCCCTATC	.	PASS	Atlas-SNP
ZFAND4	93550	hgsc.bcm.edu	37	10	46143958	46143958	+	Missense_Mutation	SNP	T	T	G	rs17854567	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	74	34	114	0	0.459459	0	T|0.909;G|0.091	0.091	strong	.	.	.	.	NM_001128324	exon5	c.A353C	p.K118T	GCCATCTTCCTAA	.	PASS	Atlas-SNP
CCDC158	339965	hgsc.bcm.edu	37	4	77272155	77272155	+	Silent	SNP	C	C	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	89	18	81	0	0.202247	0	.	.	none	.	CCDC158	114	.	NM_001042784	exon17	c.G2658T	p.L886L	ATGAGACAGGAAG	.	PASS	Atlas-SNP
MRGPRX1	259249	hgsc.bcm.edu	37	11	18956194	18956194	+	Silent	SNP	T	T	C	rs2014931	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	98	81	59	0	0.826531	0	T|0.636;C|0.364	0.364	strong	MRGPRX1,caecum,carcinoma,-2,3	MRGPRX1	84	3	NM_147199	exon1	c.A138G	p.A46A	CACAACTGCGTTT	.	PASS	Atlas-SNP
CNTNAP3	79937	hgsc.bcm.edu	37	9	39103743	39103743	+	Missense_Mutation	SNP	C	C	T	rs7852039	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	336	335	377	2	0.997024	0.00530504	C|0.824;T|0.176	0.176	strong	.	CNTNAP3	82	.	NM_033655	exon16	c.G2534A	p.R845H	TTACCACGCAGCT	.	PASS	Atlas-SNP
PHRF1	57661	hgsc.bcm.edu	37	11	607175	607175	+	Silent	SNP	G	G	A	rs936468	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	67	54	51	0	0.80597	0	G|0.828;A|0.172	0.172	strong	PHRF1_ENST00000264555,NS,carcinoma,0,2	PHRF1	188	2	NM_020901	exon14	c.G1716A	p.P572P	AGGCCCGTCAGGA	.	PASS	Atlas-SNP
PARP4	143	hgsc.bcm.edu	37	13	25029218	25029218	+	Missense_Mutation	SNP	C	C	T	rs2275660	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	90	89	95	0	0.988889	0	C|0.326;T|0.674	0.674	strong	.	PARP4	142	.	NM_006437	exon22	c.G2695A	p.A899T	GCAAGGCGATTTG	.	PASS	Atlas-SNP
FAM211A	388341	hgsc.bcm.edu	37	17	16347325	16347325	+	Missense_Mutation	SNP	T	T	C	rs61745139	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	61	30	81	0	0.491803	0	T|0.918;C|0.082	0.082	strong	FAM211A_ENST00000470794,NS,carcinoma,0,3	FAM211A	21	3	NM_207387	exon3	c.A496G	p.R166G	GCTGTCTACCTGC	.	PASS	Atlas-SNP
ZNF624	57547	hgsc.bcm.edu	37	17	16525824	16525824	+	Silent	SNP	T	T	C	rs62072858	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	65	30	90	0	0.461538	0	T|0.947;C|0.053	0.053	strong	.	ZNF624	91	.	NM_020787	exon6	c.A2376G	p.L792L	CTGTGATAGAGTA	.	PASS	Atlas-SNP
CCDC176	80127	hgsc.bcm.edu	37	14	74516497	74516497	+	Silent	SNP	G	G	A	rs34076068	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	155	77	158	0	0.496774	0	G|0.885;A|0.115	0.115	strong	.	.	.	.	NM_025057	exon8	c.G885A	p.L295L	AAACTTGGAGACT	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	77	77	81	0	1	0	T|0.664;C|0.336	0.336	strong	.	SEZ6	61	.	NM_001098635	exon8	c.A1636G	p.T546A	TGGGTGTGCTGCT	.	PASS	Atlas-SNP
HEG1	57493	hgsc.bcm.edu	37	3	124746049	124746049	+	Missense_Mutation	SNP	A	A	G	rs2981546	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	63	30	80	0	0.47619	0	A|0.534;G|0.466	0.466	strong	.	HEG1	109	.	NM_020733	exon3	c.T913C	p.S305P	ACTCACATGAGGA	.	PASS	Atlas-SNP
HS6ST3	266722	hgsc.bcm.edu	37	13	96743584	96743584	+	Silent	SNP	G	G	T	rs144263527	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	41	18	50	0	0.439024	0	G|0.998;T|0.002	0.002	strong	HS6ST3,NS,carcinoma,0,1	HS6ST3	54	1	NM_153456	exon1	c.G468T	p.T156T	GAAGACGGGGGGC	.	PASS	Atlas-SNP
WDR67	93594	hgsc.bcm.edu	37	8	124142489	124142489	+	Silent	SNP	T	T	C	rs2272724	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	156	156	221	0	1	0	T|0.650;C|0.350	0.350	strong	.	WDR67	97	.	NM_001145088	exon16	c.T2322C	p.D774D	ACAAGATGCTGCA	.	PASS	Atlas-SNP
EXO5	64789	hgsc.bcm.edu	37	1	40980559	40980559	+	Missense_Mutation	SNP	G	G	A	rs1134586	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	55	29	77	0	0.527273	0	G|0.866;A|0.134	0.134	strong	.	.	.	.	NM_022774	exon3	c.G343A	p.D115N	GTGTTGGACACTG	.	PASS	Atlas-SNP
TSHZ2	128553	hgsc.bcm.edu	37	20	51870336	51870336	+	Missense_Mutation	SNP	G	G	C	rs739869	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	38	100	0	0.535211	0	G|0.921;C|0.079	0.079	strong	.	TSHZ2	209	.	NM_173485	exon2	c.G339C	p.R113S	CGTCAGGCTTCCA	.	PASS	Atlas-SNP
CYFIP2	26999	hgsc.bcm.edu	37	5	156747669	156747669	+	Silent	SNP	A	A	G	rs1823035	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	77	42	75	0	0.545455	0	A|0.672;G|0.328	0.328	strong	.	CYFIP2	354	.	NM_001037332	exon15	c.A1530G	p.L510L	CGTCCTACAGGCA	.	PASS	Atlas-SNP
IQUB	154865	hgsc.bcm.edu	37	7	123097468	123097468	+	Silent	SNP	T	T	C	rs10234745	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	99	48	110	0	0.484848	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
TMEFF1	8577	hgsc.bcm.edu	37	9	103235853	103235853	+	Silent	SNP	G	G	T	rs77849433	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	16	9	4	0	0.5625	0	G|0.915;T|0.085	0.085	strong	.	TMEFF1	42	.	NM_003692	exon1	c.G27T	p.P9P	GGCGCCGCTCCGG	.	PASS	Atlas-SNP
KCND1	3750	hgsc.bcm.edu	37	X	48826490	48826490	+	Silent	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	166	53	254	0	0.319277	0	.	.	none	.	KCND1	63	.	NM_004979	exon1	c.C189T	p.D63D	CAAGGTGTCTGGG	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	150	149	190	1	0.993333	0.00526316	0|0.018;C|0.306	0.306	strong	.	SLC7A3	76	.	NM_032803	exon10	c.C1522G	p.L508V	TCCACAGCAGGTC	.	PASS	Atlas-SNP
AP5Z1	9907	hgsc.bcm.edu	37	7	4825314	4825314	+	Silent	SNP	C	C	T	rs11768079	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	27	16	20	0	0.592593	0	C|0.954;T|0.046	0.046	strong	.	.	.	.	NM_014855	exon9	c.C1131T	p.H377H	GAGCCACGGTGAG	.	PASS	Atlas-SNP
CCL25	6370	hgsc.bcm.edu	37	19	8121096	8121096	+	Missense_Mutation	SNP	G	G	A	rs74959615	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	123	60	160	0	0.487805	0	G|0.950;A|0.050	0.050	strong	.	CCL25	12	.	NM_001201359	exon3	c.G134A	p.R45H	TCCGGCGCGCCTG	.	PASS	Atlas-SNP
SYNE1	23345	hgsc.bcm.edu	37	6	152779933	152779933	+	Missense_Mutation	SNP	G	G	A	rs34610829	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	113	37	196	0	0.327434	0	G|0.981;A|0.019	0.019	strong	.	SYNE1	3227	.	NM_033071	exon22	c.C2548T	p.R850C	CCTCACGCTCAAG	.	PASS	Atlas-SNP
AGAP6	414189	hgsc.bcm.edu	37	10	51748584	51748584	+	Missense_Mutation	SNP	A	A	G	rs75102885		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	3	3	6	0	1	0	G|1.000;|0.000	1.000	weak	AGAP6,NS,carcinoma,0,2	AGAP6	53	2	NM_001077665	exon1	c.A109G	p.R37G	GGAGCTAGGGACA	.	scavenged	Atlas-SNP
HLA-DPB1	3115	hgsc.bcm.edu	37	6	33048542	33048542	+	Missense_Mutation	SNP	C	C	T	rs1042121	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	43	41	69	0	0.953488	0	C|0.477;T|0.523	0.523	strong	.	HLA-DPB1	28	.	NM_002121	exon2	c.C194T	p.A65V	AGTTCGCGCGCTT	.	PASS	Atlas-SNP
TUBG2	27175	hgsc.bcm.edu	37	17	40818353	40818353	+	Silent	SNP	C	C	T	rs523338	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	238	15	249	0	0.0630252	0	C|0.801;T|0.199	0.199	strong	TUBG2,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	TUBG2	43	1	NM_016437	exon10	c.C1009T	p.L337L	AAGAGCCTGCAGA	.	scavenged	Atlas-SNP
ZBBX	79740	hgsc.bcm.edu	37	3	167045779	167045779	+	Silent	SNP	G	G	A	rs375095384		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	123	26	170	0	0.211382	0	.	.	weak	ZBBX_ENST00000455345,NS,carcinoma,0,2	ZBBX	299	2	NM_024687	exon11	c.C813T	p.T271T	ATTTCCGGTTCTC	.	PASS	Atlas-SNP
TTC16	158248	hgsc.bcm.edu	37	9	130489558	130489558	+	Silent	SNP	A	A	G	rs472144	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	100	54	142	0	0.54	0	A|0.377;G|0.623	0.623	strong	TTC16,NS,carcinoma,0,1	TTC16	55	1	NM_144965	exon12	c.A1578G	p.K526K	GCTTAAACGGCAC	.	PASS	Atlas-SNP
IQSEC3	440073	hgsc.bcm.edu	37	12	274647	274647	+	Silent	SNP	T	T	C	rs4980859	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	138	64	159	0	0.463768	0	T|0.740;C|0.260	0.260	strong	.	IQSEC3	154	.	NM_001170738	exon10	c.T2757C	p.F919F	CACCTTTTGCAAG	.	PASS	Atlas-SNP
DCUN1D1	54165	hgsc.bcm.edu	37	3	182681740	182681740	+	Silent	SNP	C	C	T	rs4859146	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	150	148	201	0	0.986667	0	C|0.308;T|0.692	0.692	strong	.	DCUN1D1	27	.	NM_020640	exon3	c.G318A	p.A106A	CTTCCACGCAATA	.	PASS	Atlas-SNP
C20orf118	140711	hgsc.bcm.edu	37	20	35507542	35507542	+	Silent	SNP	G	G	A	rs3748459	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	59	35	61	0	0.59322	0	G|0.723;A|0.277	0.277	strong	.	C20orf118	21	.	NM_080628	exon3	c.G288A	p.R96R	CCGGCGGATGGAG	.	PASS	Atlas-SNP
MFI2	4241	hgsc.bcm.edu	37	3	196742290	196742290	+	Silent	SNP	T	T	C	rs9855410	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	112	58	122	0	0.517857	0	T|0.712;C|0.288	0.288	strong	.	MFI2	88	.	NM_005929	exon9	c.A1179G	p.P393P	GATCTCTGGCTTG	.	PASS	Atlas-SNP
RAB3IL1	5866	hgsc.bcm.edu	37	11	61675644	61675644	+	Missense_Mutation	SNP	T	T	C	rs174477	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	18	51	1	0.209302	0.0196078	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	.	scavenged	Atlas-SNP
PSG1	5669	hgsc.bcm.edu	37	19	43372941	43372941	+	Missense_Mutation	SNP	T	T	C	rs28374299	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	42	19	37	0	0.452381	0	T|0.830;C|0.170	0.170	strong	.	PSG1	196	.	NM_001184826	exon4	c.A955G	p.I319V	TGCGGATGCCACC	.	PASS	Atlas-SNP
COL9A2	1298	hgsc.bcm.edu	37	1	40766923	40766923	+	Silent	SNP	G	G	A	rs2229826	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	142	77	158	0	0.542253	0	G|0.984;A|0.016	0.016	strong	.	COL9A2	63	.	NM_001852	exon32	c.C2001T	p.A667A	GCAGGCGGCAGGT	.	PASS	Atlas-SNP
MS4A14	84689	hgsc.bcm.edu	37	11	60183483	60183483	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	214	162	230	0	0.757009	0	.	.	none	.	MS4A14	120	.	NM_001261828	exon6	c.T1141C	p.S381P	CAGTCTTCTAATC	.	PASS	Atlas-SNP
APOL6	80830	hgsc.bcm.edu	37	22	36055130	36055130	+	Missense_Mutation	SNP	T	T	A	rs5999923	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	54	23	61	0	0.425926	0	T|0.973;A|0.027	0.027	strong	.	APOL6	26	.	NM_030641	exon3	c.T519A	p.N173K	CTATAATCTTAGA	.	PASS	Atlas-SNP
OR51F1	256892	hgsc.bcm.edu	37	11	4790857	4790857	+	Silent	SNP	A	A	G	rs11033797	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	119	24	100	0	0.201681	0	A|0.713;G|0.287	0.287	strong	.	OR51F1	60	.	NM_001004752	exon1	c.T291C	p.Y97Y	GCAGCTATATAGA	.	PASS	Atlas-SNP
RHBDD3	25807	hgsc.bcm.edu	37	22	29659960	29659960	+	Silent	SNP	C	C	T	rs879580	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	25	60	0	0.362319	0	C|0.814;T|0.186	0.186	strong	.	RHBDD3	17	.	NM_012265	exon4	c.G396A	p.E132E	GTGTCCCTCCCCA	.	PASS	Atlas-SNP
TUBA3E	112714	hgsc.bcm.edu	37	2	130951638	130951638	+	Silent	SNP	G	G	T	rs141240951	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	145	18	171	0	0.124138	0	G|0.989;T|0.011	0.011	strong	TUBA3E,colon,carcinoma,0,1	TUBA3E	73	1	NM_207312	exon4	c.C777A	p.L259L	CGGCACGAGGTTG	.	scavenged	Atlas-SNP
FAM120B	84498	hgsc.bcm.edu	37	6	170626943	170626943	+	Silent	SNP	T	T	C	rs3800266	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	93	29	158	0	0.311828	0	T|0.857;C|0.143	0.143	strong	.	FAM120B	108	.	NM_032448	exon2	c.T465C	p.S155S	GTGTTCTTTGCAG	.	PASS	Atlas-SNP
OR4M1	441670	hgsc.bcm.edu	37	14	20249176	20249176	+	Missense_Mutation	SNP	G	G	A	rs2815960	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	426	125	345	0	0.293427	0	G|0.739;A|0.261	0.261	strong	.	OR4M1	104	.	NM_001005500	exon1	c.G695A	p.G232D	GCTCAGGTGAGAA	.	PASS	Atlas-SNP
LMBRD1	55788	hgsc.bcm.edu	37	6	70407465	70407465	+	Missense_Mutation	SNP	A	A	T	rs12648	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	38	24	37	0	0.631579	0	A|0.653;T|0.347	0.347	strong	.	LMBRD1	61	.	NM_018368	exon14	c.T1407A	p.D469E	AGGAGCATCTGCA	.	PASS	Atlas-SNP
CACTIN	58509	hgsc.bcm.edu	37	19	3612035	3612035	+	Silent	SNP	G	G	A	rs61738769	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	156	74	148	0	0.474359	0	G|0.999;A|0.001	0.001	strong	C19orf29_ENST00000429344,NS,neuroblastoma,0,2	.	.	2	NM_021231	exon10	c.C2163T	p.F721F	GATCTTGAAAGCG	.	PASS	Atlas-SNP
PLEKHG5	57449	hgsc.bcm.edu	37	1	6533393	6533393	+	Missense_Mutation	SNP	G	G	C	rs61741379	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	120	58	132	0	0.483333	0	G|0.755;C|0.245	0.245	strong	.	PLEKHG5	66	.	NM_001265592	exon9	c.C950G	p.T317S	TCGCCAGTGTTGG	.	PASS	Atlas-SNP
OR5D16	390144	hgsc.bcm.edu	37	11	55606302	55606302	+	Silent	SNP	G	G	T	rs6591699	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	291	51	339	3	0.175258	0.00884956	G|0.350;T|0.650	0.650	strong	OR5D16,NS,carcinoma,+1,1	OR5D16	94	1	NM_001005496	exon1	c.G75T	p.L25L	GGAACTGCAAATT	.	scavenged	Atlas-SNP
TSSK2	23617	hgsc.bcm.edu	37	22	19119751	19119751	+	Missense_Mutation	SNP	C	C	T	rs1052763	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	57	27	53	0	0.473684	0	C|0.762;T|0.238	0.238	strong	TSSK2,NS,carcinoma,-1,1	TSSK2	29	1	NM_053006	exon1	c.C839T	p.T280M	AAGCCACGTCTTC	.	PASS	Atlas-SNP
KRT84	3890	hgsc.bcm.edu	37	12	52779159	52779159	+	Missense_Mutation	SNP	G	G	A	rs145217788	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	118	52	165	0	0.440678	0	G|0.998;A|0.002	0.002	strong	.	KRT84	61	.	NM_033045	exon1	c.C211T	p.R71W	TGGGCCGAGAGCC	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179421609	179421609	+	Silent	SNP	C	C	T	rs9808036	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	88	50	84	0	0.568182	0	C|0.955;T|0.045	0.045	strong	.	TTN	18412	.	NM_001267550	exon330	c.G88272A	p.E29424E	TACAACCTCAGAT	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	81	80	84	0	0.987654	0	A|0.006;C|0.194	0.194	strong	.	TMPRSS3	40	.	NM_001256317	exon8	c.A757G	p.I253V	CAGTGATGATCCA	.	PASS	Atlas-SNP
MARVELD3	91862	hgsc.bcm.edu	37	16	71660404	71660404	+	Missense_Mutation	SNP	G	G	A	rs61753635	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	35	15	21	0	0.428571	0	G|0.784;A|0.216	0.216	strong	.	MARVELD3	63	.	NM_001017967	exon1	c.G272A	p.R91Q	CCCGCCGGGACAC	.	PASS	Atlas-SNP
RIN3	79890	hgsc.bcm.edu	37	14	93118198	93118198	+	Silent	SNP	C	C	T	rs3814830	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	57	27	103	0	0.473684	0	C|0.764;T|0.236	0.236	strong	.	RIN3	81	.	NM_024832	exon6	c.C804T	p.A268A	TGATGCCACCTCA	.	PASS	Atlas-SNP
NSD1	64324	hgsc.bcm.edu	37	5	176721119	176721119	+	Missense_Mutation	SNP	G	G	A	rs35848863	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	60	21	69	0	0.35	0	G|0.952;A|0.048	0.048	strong	.	NSD1	416	.	NM_022455	exon23	c.G6750A	p.M2250I	CAAAATGTCAGAT	.	PASS	Atlas-SNP
C1orf85	112770	hgsc.bcm.edu	37	1	156263940	156263940	+	Missense_Mutation	SNP	T	T	C	rs10908495	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	65	33	76	0	0.507692	0	T|0.785;C|0.215	0.215	strong	.	C1orf85	41	.	NM_001256608	exon4	c.A667G	p.I223V	CTCCAATCAGGGC	.	PASS	Atlas-SNP
AGAP1	116987	hgsc.bcm.edu	37	2	236403462	236403462	+	Silent	SNP	C	C	T	rs8178993	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	126	59	141	0	0.468254	0	C|0.978;T|0.022	0.022	strong	.	AGAP1	95	.	NM_014914	exon1	c.C132T	p.N44N	GCAGAACCAGATC	.	PASS	Atlas-SNP
DISP1	84976	hgsc.bcm.edu	37	1	223176275	223176275	+	Silent	SNP	G	G	A	rs61738819	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	148	49	175	0	0.331081	0	G|0.899;A|0.101	0.101	strong	.	DISP1	145	.	NM_032890	exon10	c.G1536A	p.V512V	CATTGTGATTGTC	.	PASS	Atlas-SNP
VIPR2	7434	hgsc.bcm.edu	37	7	158902567	158902567	+	Silent	SNP	G	G	A	rs3750071	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	61	22	56	0	0.360656	0	G|0.898;A|0.102	0.102	strong	VIPR2,NS,carcinoma,0,1	VIPR2	53	1	NM_003382	exon3	c.C195T	p.A65A	CACATTGGCAGGC	.	PASS	Atlas-SNP
PDDC1	347862	hgsc.bcm.edu	37	11	772490	772490	+	Silent	SNP	G	G	A	rs12224894	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	11	87	0	0.127907	0	G|0.633;A|0.367	0.367	strong	.	PDDC1	16	.	NM_182612	exon5	c.C387T	p.A129A	CAGGGCGGCGACA	.	PASS	Atlas-SNP
COG1	9382	hgsc.bcm.edu	37	17	71193525	71193525	+	Missense_Mutation	SNP	G	G	C	rs117208167	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	49	24	75	0	0.489796	0	G|0.994;C|0.006	0.006	strong	.	COG1	46	.	NM_018714	exon4	c.G903C	p.Q301H	AGGCCAGCATCCT	.	PASS	Atlas-SNP
RIN2	54453	hgsc.bcm.edu	37	20	19955713	19955713	+	Silent	SNP	G	G	C	rs149398614	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	34	19	36	0	0.558824	0	G|0.983;C|0.017	0.017	strong	.	RIN2	126	.	NM_001242581	exon8	c.G1191C	p.L397L	AGCTCTGCCTGGA	.	PASS	Atlas-SNP
DIP2C	22982	hgsc.bcm.edu	37	10	323283	323283	+	Silent	SNP	A	A	G	rs3740304	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	45	13	74	0	0.288889	0	A|0.732;G|0.268	0.268	strong	.	DIP2C	195	.	NM_014974	exon37	c.T4653C	p.Y1551Y	GGCCACATAGATG	.	PASS	Atlas-SNP
CARD11	84433	hgsc.bcm.edu	37	7	2946461	2946461	+	Silent	SNP	T	T	C	rs1124581	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	138	137	166	1	0.992754	0.0060241	T|0.439;C|0.561	0.561	strong	.	CARD11	339	.	NM_032415	exon25	c.A3276G	p.R1092R	CTCAGGTCGGGGC	.	PASS	Atlas-SNP
SUV39H2	79723	hgsc.bcm.edu	37	10	14943176	14943176	+	Silent	SNP	C	C	G	rs61730323	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	164	81	213	0	0.493902	0	C|0.954;G|0.045	0.045	strong	SUV39H2_ENST00000354919,NS,carcinoma,0,2	SUV39H2	72	2	NM_001193424	exon5	c.C1041G	p.L347L	TAACCTCGATACT	.	PASS	Atlas-SNP
PYURF	100996939	hgsc.bcm.edu	37	4	89443162	89443162	+	Silent	SNP	G	G	A	rs3177413	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	151	80	183	0	0.529801	0	G|0.849;A|0.151	0.151	strong	.	.	.	.	NM_032906	exon2	c.C222T	p.N74N	CAATTCGTTTGTT	.	PASS	Atlas-SNP
FNDC9	408263	hgsc.bcm.edu	37	5	156770133	156770133	+	Missense_Mutation	SNP	C	C	T	rs10037485	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	36	91	0	0.48	0	C|0.765;T|0.235	0.235	strong	.	FNDC9	22	.	NM_001001343	exon2	c.G412A	p.V138I	AACGGACACACCA	.	PASS	Atlas-SNP
HOXC4	3221	hgsc.bcm.edu	37	12	54448106	54448106	+	Missense_Mutation	SNP	A	A	G	rs75256744	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	106	48	116	0	0.45283	0	A|0.880;G|0.120	0.120	strong	.	HOXC4	29	.	NM_014620	exon3	c.A400G	p.I134V	CAACCCATAGTCT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195513345	195513345	+	Silent	SNP	A	A	C	rs71321841	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	185	83	237	0	0.448649	0	A|0.500;C|0.500	0.500	strong	.	MUC4	1505	.	NM_018406	exon2	c.T5106G	p.V1702V	CGAGGAAACGTCG	.	PASS	Atlas-SNP
DNAH5	1767	hgsc.bcm.edu	37	5	13716797	13716797	+	Silent	SNP	A	A	G	rs61744054	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	42	88	1	0.415842	0.0113636	A|0.971;G|0.029	0.029	strong	DNAH5,NS,carcinoma,-1,1	DNAH5	868	1	NM_001369	exon74	c.T12708C	p.G4236G	GGAGACACCCTGG	.	scavenged	Atlas-SNP
RPTN	126638	hgsc.bcm.edu	37	1	152129101	152129101	+	Silent	SNP	A	A	G	rs117596468	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	172	32	274	1	0.186047	0.00364964	A|0.953;G|0.047	0.047	strong	RPTN,NS,carcinoma,0,1	RPTN	123	1	NM_001122965	exon3	c.T474C	p.H158H	CTGACCATGGTGG	.	scavenged	Atlas-SNP
CTSE	1510	hgsc.bcm.edu	37	1	206327510	206327510	+	Silent	SNP	T	T	C	rs61742539	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	138	62	156	0	0.449275	0	T|0.778;C|0.222	0.222	strong	.	CTSE	72	.	NM_001910	exon6	c.T699C	p.F233F	GATTTTTGGAGGC	.	PASS	Atlas-SNP
DDX53	168400	hgsc.bcm.edu	37	X	23019317	23019317	+	Missense_Mutation	SNP	G	G	T	rs5925720	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	45	45	102	0	1	0	G|0.902;T|0.098	0.098	strong	.	DDX53	76	.	NM_182699	exon1	c.G1143T	p.M381I	TAAAATGCTGGAT	.	PASS	Atlas-SNP
U2SURP	23350	hgsc.bcm.edu	37	3	142747227	142747227	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	182	43	210	0	0.236264	0	.	.	none	.	U2SURP	66	.	NM_001080415	exon15	c.G1425A	p.W475X	TAGGTGGAAGCTT	.	PASS	Atlas-SNP
ADAMTS7	11173	hgsc.bcm.edu	37	15	79089111	79089111	+	Missense_Mutation	SNP	A	A	G	rs3825807	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	64	39	49	0	0.609375	0	A|0.704;G|0.296	0.296	strong	.	ADAMTS7	142	.	NM_014272	exon4	c.T640C	p.S214P	GTCGAGACTCCAG	.	PASS	Atlas-SNP
POLR3F	10621	hgsc.bcm.edu	37	20	18449662	18449662	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	267	67	238	0	0.250936	0	.	.	none	.	POLR3F	14	.	NM_006466	exon2	c.A137C	p.E46A	ATATAGAAGCCCA	.	PASS	Atlas-SNP
SLC37A1	54020	hgsc.bcm.edu	37	21	43974226	43974226	+	Silent	SNP	T	T	C	rs2839550	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	31	16	38	0	0.516129	0	T|0.848;C|0.152	0.152	strong	.	SLC37A1	48	.	NM_018964	exon11	c.T823C	p.L275L	CAAATCTTGAAGA	.	PASS	Atlas-SNP
TLR5	7100	hgsc.bcm.edu	37	1	223284528	223284528	+	Missense_Mutation	SNP	A	A	G	rs5744174	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	140	76	170	0	0.542857	0	A|0.691;G|0.309	0.309	strong	.	TLR5	86	.	NM_003268	exon6	c.T1846C	p.F616L	CAGAGAACGAGTC	.	PASS	Atlas-SNP
NODAL	4838	hgsc.bcm.edu	37	10	72195439	72195439	+	Missense_Mutation	SNP	T	T	C	rs1904589	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	53	112	0	0.546392	0	T|0.424;C|0.576	0.576	strong	.	NODAL	32	.	NM_018055	exon2	c.A494G	p.H165R	CCAGGGTGCTTCA	.	PASS	Atlas-SNP
ACAN	176	hgsc.bcm.edu	37	15	89386652	89386652	+	Missense_Mutation	SNP	G	G	A	rs34949187	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	124	47	102	0	0.379032	0	G|0.889;A|0.111	0.111	strong	.	ACAN	220	.	NM_001135	exon6	c.G824A	p.R275Q	GCCGGCGGCTGGG	.	PASS	Atlas-SNP
HIST1H4G	8369	hgsc.bcm.edu	37	6	26247198	26247198	+	Missense_Mutation	SNP	A	A	G	rs41266821	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	63	28	71	0	0.444444	0	A|0.903;G|0.097	0.097	strong	.	HIST1H4G	18	.	NM_003547	exon1	c.T8C	p.V3A	CCCCGAACAGACA	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	193	82	219	0	0.42487	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
CAMK2B	816	hgsc.bcm.edu	37	7	44282877	44282877	+	Silent	SNP	A	A	G	rs11542227	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	115	80	127	0	0.695652	0	A|0.735;G|0.265	0.265	strong	.	CAMK2B	56	.	NM_172081	exon8	c.T573C	p.Y191Y	CTTGCCATACGCC	.	PASS	Atlas-SNP
PAPPA	5069	hgsc.bcm.edu	37	9	118949998	118949998	+	Silent	SNP	C	C	T	rs12375498	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	31	94	0	0.378049	0	C|0.836;T|0.164	0.164	strong	.	PAPPA	243	.	NM_002581	exon2	c.C981T	p.C327C	TCTGTGCGGACAG	.	PASS	Atlas-SNP
FAT2	2196	hgsc.bcm.edu	37	5	150908813	150908813	+	Missense_Mutation	SNP	G	G	A	rs2304024	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	103	56	120	0	0.543689	0	G|0.858;N|0.001	.	strong	.	FAT2	465	.	NM_001447	exon14	c.C9952T	p.R3318W	GGGGCCGGTGTTC	.	PASS	Atlas-SNP
PLXNA2	5362	hgsc.bcm.edu	37	1	208390469	208390469	+	Missense_Mutation	SNP	C	C	T	rs3748735	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	84	79	78	0	0.940476	0	C|0.850;T|0.150	0.150	strong	.	PLXNA2	178	.	NM_025179	exon2	c.G799A	p.A267T	TGATGGCCACACC	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	37	73	0	0.637931	0	T|0.407;C|0.593	0.593	strong	.	ZNF708	66	.	NM_021269	exon4	c.A337G	p.K113E	CACTTTTACAGCC	.	PASS	Atlas-SNP
KLHL4	56062	hgsc.bcm.edu	37	X	86877348	86877348	+	Silent	SNP	G	G	T	rs2273050	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	243	243	396	1	1	0.00252525	G|0.807;T|0.193	0.193	strong	.	KLHL4	263	.	NM_019117	exon5	c.G1062T	p.G354G	GGTGGGGCATGAT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195513180	195513180	+	Missense_Mutation	SNP	C	C	G	rs77724343	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	143	47	106	1	0.328671	0.00943396	C|0.971;G|0.029	0.029	strong	MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	NM_018406	exon2	c.G5271C	p.Q1757H	GGTGGCCTGACCT	.	scavenged	Atlas-SNP
RNF17	56163	hgsc.bcm.edu	37	13	25367282	25367282	+	Missense_Mutation	SNP	A	A	C	rs1451568	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	57	27	72	0	0.473684	0	A|0.801;C|0.199	0.199	strong	.	RNF17	259	.	NM_001184993	exon10	c.A1038C	p.K346N	AAAGAAAAAGGTT	.	PASS	Atlas-SNP
OR1E1	8387	hgsc.bcm.edu	37	17	3301549	3301549	+	Silent	SNP	G	G	A	rs150988	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	225	103	268	0	0.457778	0	G|0.602;A|0.398	0.398	strong	.	OR1E1	37	.	NM_003553	exon1	c.C156T	p.D52D	ATGGGAGTCCAGT	.	PASS	Atlas-SNP
ANKEF1	63926	hgsc.bcm.edu	37	20	10032413	10032413	+	Silent	SNP	T	T	G	rs683145	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	67	36	98	0	0.537313	0	T|0.752;G|0.248	0.248	strong	.	.	.	.	NM_198798	exon7	c.T1746G	p.A582A	TGGAGCTTTAATA	.	PASS	Atlas-SNP
INPP4B	8821	hgsc.bcm.edu	37	4	143043397	143043397	+	Silent	SNP	G	G	A	rs34561493	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	59	23	66	0	0.38983	0	G|0.932;A|0.068	0.068	strong	.	INPP4B	132	.	NM_003866	exon22	c.C2019T	p.S673S	TTCATCGCCTAAA	.	PASS	Atlas-SNP
FRG1	2483	hgsc.bcm.edu	37	4	190862182	190862182	+	Silent	SNP	C	C	T	rs2411530	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	123	43	118	0	0.349593	0	C|0.506;T|0.494	0.494	strong	.	FRG1	76	.	NM_004477	exon1	c.C18T	p.Y6Y	CTCCTACGTGAAG	.	PASS	Atlas-SNP
ALS2	57679	hgsc.bcm.edu	37	2	202626437	202626437	+	Missense_Mutation	SNP	T	T	C	rs3219154	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	227	117	254	0	0.515419	0	T|0.977;C|0.023	0.023	strong	.	ALS2	172	.	NM_001135745	exon4	c.A280G	p.I94V	CAGTAATAACATA	.	PASS	Atlas-SNP
METTL2B	55798	hgsc.bcm.edu	37	7	128119514	128119514	+	Missense_Mutation	SNP	G	G	A	rs1065267	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	358	107	432	1	0.298883	0.00231481	G|0.906;A|0.094	0.094	strong	.	METTL2B	34	.	NM_018396	exon3	c.G505A	p.E169K	GACCTGGAAATTT	.	PASS	Atlas-SNP
DMWD	1762	hgsc.bcm.edu	37	19	46289503	46289503	+	Silent	SNP	C	C	T	rs8109951	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	84	39	61	0	0.464286	0	C|0.701;T|0.299	0.299	strong	DMWD,rectum,carcinoma,0,1	DMWD	46	1	NM_004943	exon3	c.G1251A	p.P417P	AGAGAGCGGGGCG	.	PASS	Atlas-SNP
GIT2	9815	hgsc.bcm.edu	37	12	110385079	110385079	+	Silent	SNP	G	G	T	rs2063388	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	201	100	208	0	0.497512	0	G|0.922;T|0.078	0.078	strong	.	GIT2	81	.	NM_001135214	exon15	c.C1623A	p.L541L	GGGCTGGAGTCTC	.	PASS	Atlas-SNP
CDHR1	92211	hgsc.bcm.edu	37	10	85972043	85972043	+	Silent	SNP	A	A	G	rs10749482	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	126	58	146	0	0.460317	0	A|0.585;G|0.415	0.415	strong	.	CDHR1	122	.	NM_001171971	exon15	c.A1662G	p.E554E	CATGGAAGGCAAG	.	PASS	Atlas-SNP
MDN1	23195	hgsc.bcm.edu	37	6	90397132	90397132	+	Missense_Mutation	SNP	G	G	C	rs34766278	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	67	28	74	0	0.41791	0	G|0.889;C|0.111	0.111	strong	.	MDN1	478	.	NM_014611	exon68	c.C11381G	p.A3794G	GACAAAGCTCGAC	.	PASS	Atlas-SNP
S1PR3	1903	hgsc.bcm.edu	37	9	91616843	91616843	+	Missense_Mutation	SNP	G	G	A	rs34075341	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	146	69	156	0	0.472603	0	G|0.964;A|0.036	0.036	strong	.	S1PR3	49	.	NM_005226	exon2	c.G728A	p.R243Q	TGCTGCGGACCGT	.	PASS	Atlas-SNP
RRP12	23223	hgsc.bcm.edu	37	10	99116903	99116903	+	Missense_Mutation	SNP	C	C	T	rs1048445	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	94	44	95	0	0.468085	0	C|0.753;T|0.247	0.247	strong	.	RRP12	97	.	NM_015179	exon34	c.G3842A	p.R1281Q	CCTCGCCGGGCAG	.	PASS	Atlas-SNP
GALNTL5	168391	hgsc.bcm.edu	37	7	151684256	151684256	+	Missense_Mutation	SNP	A	A	G	rs61729490	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	42	20	56	0	0.47619	0	A|0.814;G|0.186	0.186	strong	.	GALNTL5	87	.	NM_145292	exon5	c.A548G	p.E183G	TGAAAGAAAAACT	.	PASS	Atlas-SNP
MYO18B	84700	hgsc.bcm.edu	37	22	26219605	26219605	+	Silent	SNP	G	G	A	rs4820658	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	105	45	93	0	0.428571	0	G|0.815;A|0.185	0.185	strong	.	MYO18B	322	.	NM_032608	exon13	c.G2655A	p.G885G	GTTTGGGCCAAGC	.	PASS	Atlas-SNP
VWA3A	146177	hgsc.bcm.edu	37	16	22144378	22144378	+	Missense_Mutation	SNP	G	G	A	rs200086497	by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	27	91	0	0.375	0	G|1.000;A|0.000	0.000	strong	.	VWA3A	115	.	NM_173615	exon20	c.G2030A	p.R677Q	TCACCCGGGCTGC	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	83	45	107	0	0.542169	0	A|0.764;G|0.236	0.236	strong	.	.	.	.	NM_018229	exon2	c.A663G	p.Q221Q	CATGCAATATGAT	.	PASS	Atlas-SNP
MR1	3140	hgsc.bcm.edu	37	1	181018236	181018236	+	Missense_Mutation	SNP	A	A	G	rs2236410	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	238	132	238	0	0.554622	0	A|0.833;G|0.167	0.167	strong	MR1,NS,carcinoma,0,1	MR1	46	1	NM_001195035	exon3	c.A116G	p.H39R	CCATCCATGGGGT	.	PASS	Atlas-SNP
ERMAP	114625	hgsc.bcm.edu	37	1	43296195	43296195	+	Missense_Mutation	SNP	C	C	T	rs33953680	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	83	83	96	0	1	0	C|0.807;T|0.193	0.193	strong	.	ERMAP	30	.	NM_001017922	exon3	c.C76T	p.H26Y	TCTGTGCATGTGT	.	PASS	Atlas-SNP
TP53I11	9537	hgsc.bcm.edu	37	11	44956459	44956459	+	Silent	SNP	G	G	A	rs61752934	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	65	50	68	0	0.769231	0	G|0.970;A|0.030	0.030	strong	.	TP53I11	17	.	NM_001258324	exon7	c.C546T	p.V182V	TCGGCCGACTTGG	.	PASS	Atlas-SNP
FAM217A	222826	hgsc.bcm.edu	37	6	4069166	4069166	+	Missense_Mutation	SNP	C	C	T	rs595413	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	142	67	165	0	0.471831	0	C|0.413;T|0.587	0.587	strong	.	.	.	.	NM_173563	exon7	c.G1291A	p.V431I	TGGAGACCATTTT	.	PASS	Atlas-SNP
SLC9C1	285335	hgsc.bcm.edu	37	3	111981878	111981878	+	Missense_Mutation	SNP	T	T	C	rs9809384	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	255	254	336	1	0.996078	0.00297619	T|0.395;C|0.605	0.605	strong	.	.	.	.	NM_183061	exon10	c.A1090G	p.I364V	TGAATATCCAGCG	.	PASS	Atlas-SNP
B3GNT3	10331	hgsc.bcm.edu	37	19	17919024	17919024	+	Silent	SNP	A	A	T	rs2240813	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	60	25	57	0	0.416667	0	A|0.903;T|0.097	0.097	strong	.	B3GNT3	40	.	NM_014256	exon2	c.A408T	p.V136V	CAAGGTACGGGGT	.	PASS	Atlas-SNP
ZNF493	284443	hgsc.bcm.edu	37	19	21606429	21606429	+	Missense_Mutation	SNP	G	G	T	rs4621113	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	19	8	30	0	0.421053	0	G|0.458;T|0.542	0.542	strong	.	ZNF493	178	.	NM_001076678	exon4	c.G968T	p.C323F	ATAAATGTGAAGA	.	PASS	Atlas-SNP
PKHD1L1	93035	hgsc.bcm.edu	37	8	110412519	110412519	+	Silent	SNP	G	G	A	rs1379369	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	108	81	124	0	0.75	0	G|0.448;A|0.552	0.552	strong	.	PKHD1L1	522	.	NM_177531	exon13	c.G1227A	p.K409K	CATCAAGGGTGAT	.	PASS	Atlas-SNP
C19orf53	28974	hgsc.bcm.edu	37	19	13885309	13885309	+	Silent	SNP	C	C	T	rs1128749	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	76	37	86	0	0.486842	0	A|0.000;C|0.661;G|0.000;T|0.338	0.338	strong	C19orf53,NS,carcinoma,0,1	C19orf53	14	1	NM_014047	exon1	c.C18T	p.R6R	GCAGCGCAAGTTT	.	PASS	Atlas-SNP
SSC5D	284297	hgsc.bcm.edu	37	19	56029489	56029489	+	Silent	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	128	12	146	0	0.09375	0	.	.	none	SSC5D,NS,carcinoma,+2,1	SSC5D	65	1	NM_001144950	exon14	c.C3846T	p.H1282H	CCCTCACCCCACC	.	scavenged	Atlas-SNP
MEFV	4210	hgsc.bcm.edu	37	16	3297073	3297073	+	Silent	SNP	A	A	G	rs224206	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	121	20	132	0	0.165289	0	A|0.391;G|0.609	0.609	strong	.	MEFV	170	.	NM_000243	exon5	c.T1530C	p.D510D	CAGCGCATCGAGC	.	PASS	Atlas-SNP
OR4C13	283092	hgsc.bcm.edu	37	11	49974626	49974626	+	Missense_Mutation	SNP	G	G	A	rs150606357	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	157	111	219	0	0.707006	0	G|0.999;A|0.001	0.001	strong	.	OR4C13	96	.	NM_001001955	exon1	c.G652A	p.V218I	TGCGTGGTCATAC	.	PASS	Atlas-SNP
FMO2	2327	hgsc.bcm.edu	37	1	171168585	171168585	+	Silent	SNP	A	A	G	rs2020861	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	167	87	199	2	0.520958	0.0100503	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	.	scavenged	Atlas-SNP
ECD	11319	hgsc.bcm.edu	37	10	74899209	74899209	+	Silent	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	77	18	101	0	0.233766	0	.	.	none	.	ECD	50	.	NM_001135752	exon12	c.C1378T	p.L460L	CCTGCAGCAGCTG	.	PASS	Atlas-SNP
CLEC18C	283971	hgsc.bcm.edu	37	16	70211380	70211380	+	Silent	SNP	G	G	A	rs3869429		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	437	77	463	0	0.176201	0	.	.	weak	CLEC18C,NS,carcinoma,+1,1	CLEC18C	15	1	NM_173619	exon3	c.G453A	p.T151T	CTACACGCAGGTG	.	scavenged	Atlas-SNP
GPR123	84435	hgsc.bcm.edu	37	10	134942166	134942166	+	Silent	SNP	A	A	G	rs2806452	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	94	34	79	0	0.361702	0	A|0.559;G|0.441	0.441	strong	.	GPR123	118	.	NM_001083909	exon7	c.A834G	p.S278S	GGTGTCACAGGGC	.	PASS	Atlas-SNP
FASTKD2	22868	hgsc.bcm.edu	37	2	207631446	207631446	+	Missense_Mutation	SNP	G	G	C	rs147727753	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	148	79	174	0	0.533784	0	G|0.996;C|0.004	0.004	strong	.	FASTKD2	49	.	NM_001136193	exon2	c.G29C	p.S10T	TTGGAAGTGTTTC	.	PASS	Atlas-SNP
OR5L1	219437	hgsc.bcm.edu	37	11	55579182	55579182	+	Silent	SNP	A	A	G	rs139708815	byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	155	23	144	0	0.148387	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
PIGG	54872	hgsc.bcm.edu	37	4	515489	515489	+	Missense_Mutation	SNP	G	G	A	rs13115344	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	228	119	237	0	0.52193	0	G|0.794;A|0.206	0.206	strong	.	PIGG	86	.	NM_001127178	exon8	c.G1373A	p.R458H	CACTGCGCAGAAA	.	PASS	Atlas-SNP
ZNF555	148254	hgsc.bcm.edu	37	19	2852744	2852744	+	Silent	SNP	C	C	T	rs35627030	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	42	21	50	0	0.5	0	C|0.893;T|0.107	0.107	strong	.	ZNF555	61	.	NM_152791	exon4	c.C681T	p.T227T	GAAAACCTACGAA	.	PASS	Atlas-SNP
SCAP	22937	hgsc.bcm.edu	37	3	47467597	47467597	+	Missense_Mutation	SNP	C	C	T	rs149082564	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	63	32	64	0	0.507937	0	C|0.997;T|0.003	0.003	strong	.	SCAP	88	.	NM_012235	exon7	c.G800A	p.R267Q	TCCGCCCGAAGGC	.	PASS	Atlas-SNP
STK39	27347	hgsc.bcm.edu	37	2	169020276	169020276	+	Missense_Mutation	SNP	T	T	C	rs201338418		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	217	3	219	0	0.0138249	0	.	.	weak	STK39_ENST00000355999,bladder,carcinoma,0,8	STK39	95	8	NM_013233	exon4	c.A545G	p.Y182C	TGTAGATAGTCTA	.	scavenged	Atlas-SNP
SPTBN4	57731	hgsc.bcm.edu	37	19	41008049	41008049	+	Silent	SNP	A	A	G	rs814526	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	53	53	69	0	1	0	A|0.581;G|0.419	0.419	strong	.	SPTBN4	213	.	NM_020971	exon9	c.A912G	p.V304V	CCAGGTATTGGAG	.	PASS	Atlas-SNP
CBR3	874	hgsc.bcm.edu	37	21	37507501	37507501	+	Missense_Mutation	SNP	G	G	A	rs8133052	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	30	20	11	0	0.666667	0	G|0.602;A|0.398	0.398	strong	CBR3,NS,carcinoma,0,1	CBR3	11	1	NM_001236	exon1	c.G11A	p.C4Y	CGTCCTGCAGCCG	.	PASS	Atlas-SNP
TNS1	7145	hgsc.bcm.edu	37	2	218682474	218682474	+	Silent	SNP	A	A	G	rs12694422	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	60	28	69	0	0.466667	0	A|0.613;G|0.387	0.387	strong	.	TNS1	251	.	NM_022648	exon24	c.T4269C	p.S1423S	GCCCCCACTGGGA	.	PASS	Atlas-SNP
TACC3	10460	hgsc.bcm.edu	37	4	1737502	1737502	+	Silent	SNP	C	C	T	rs11248073	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	48	36	51	0	0.75	0	C|0.661;T|0.339	0.339	strong	.	TACC3	69	.	NM_006342	exon8	c.C1689T	p.F563F	CAAGTTCGACCCC	.	PASS	Atlas-SNP
ACACA	31	hgsc.bcm.edu	37	17	35609866	35609866	+	Silent	SNP	C	C	T	rs2229416	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	129	64	164	0	0.496124	0	T|0.139;C|0.861	0.139	strong	ACACA_ENST00000353139,right_upper_lobe,carcinoma,-2,2	ACACA	395	2	NM_198834	exon15	c.G1923A	p.Q641Q	GTTCATCTGAAAG	.	PASS	Atlas-SNP
TMEM132A	54972	hgsc.bcm.edu	37	11	60701136	60701136	+	Silent	SNP	C	C	G	rs9513	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	21	21	25	0	1	0	C|0.581;G|0.419	0.419	strong	.	TMEM132A	135	.	NM_017870	exon8	c.C1482G	p.P494P	GGCCCCCCTGCTA	.	PASS	Atlas-SNP
TRPA1	8989	hgsc.bcm.edu	37	8	72981327	72981327	+	Silent	SNP	A	A	G	rs1811457	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	123	93	154	0	0.756098	0	A|0.277;G|0.723	0.723	strong	.	TRPA1	256	.	NM_007332	exon3	c.T375C	p.N125N	TCGGAGATTTGGG	.	PASS	Atlas-SNP
APOBEC2	10930	hgsc.bcm.edu	37	6	41029109	41029109	+	Silent	SNP	T	T	C	rs2073014	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	32	113	0	0.444444	0	T|0.840;C|0.160	0.160	strong	.	APOBEC2	30	.	NM_006789	exon2	c.T174C	p.N58N	CCGGAATGTGGAG	.	PASS	Atlas-SNP
CRTAM	56253	hgsc.bcm.edu	37	11	122738261	122738261	+	Missense_Mutation	SNP	A	A	G	rs2272094	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	151	151	163	0	1	0	A|0.413;G|0.587	0.587	strong	.	CRTAM	50	.	NM_019604	exon8	c.A962G	p.K321R	GGAAGAAAGGTCA	.	PASS	Atlas-SNP
NAT8	9027	hgsc.bcm.edu	37	2	73868328	73868328	+	Missense_Mutation	SNP	A	A	G	rs13538	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	88	88	112	0	1	0	A|0.708;G|0.292	0.292	strong	.	NAT8	26	.	NM_003960	exon2	c.T428C	p.F143S	TCCACAAAGAGAT	.	PASS	Atlas-SNP
C4orf45	152940	hgsc.bcm.edu	37	4	159881479	159881479	+	Silent	SNP	T	T	C	rs9784569	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	161	64	205	0	0.397516	0	T|0.781;C|0.219	0.219	strong	.	C4orf45	8	.	NM_152543	exon3	c.A315G	p.Q105Q	AGAAGCTTGACTT	.	PASS	Atlas-SNP
GRHL3	57822	hgsc.bcm.edu	37	1	24690764	24690764	+	Missense_Mutation	SNP	T	T	A	rs545809	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	107	54	112	0	0.504673	0	A|0.304;N|0.003	0.304	strong	.	GRHL3	69	.	NM_198174	exon16	c.T1784A	p.M595K	GGAACATGGGTTT	.	PASS	Atlas-SNP
BAZ2B	29994	hgsc.bcm.edu	37	2	160241785	160241785	+	Silent	SNP	T	T	C	rs372315034		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	135	60	96	0	0.444444	0	.	.	weak	.	BAZ2B	196	.	NM_013450	exon23	c.A3567G	p.G1189G	AGTTTGTCCACAG	.	PASS	Atlas-SNP
TNFRSF6B	8771	hgsc.bcm.edu	37	20	62328742	62328742	+	Silent	SNP	C	C	T	rs909341	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	149	79	173	1	0.530201	0.00578035	C|0.799;T|0.201	0.201	strong	TNFRSF6B,caecum,carcinoma,0,2	TNFRSF6B	22	2	NM_003823	exon2	c.C486T	p.S162S	CAGCAGCTCCAGC	.	scavenged	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179642589	179642589	+	Missense_Mutation	SNP	C	C	G	rs72647876	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	126	49	127	0	0.388889	0	C|0.993;G|0.007	0.007	strong	.	TTN	18412	.	NM_001267550	exon25	c.G4322C	p.R1441P	AGCCTACGTCCAG	.	PASS	Atlas-SNP
ACCS	84680	hgsc.bcm.edu	37	11	44101118	44101118	+	Silent	SNP	C	C	T	rs7950395	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	174	124	207	0	0.712644	0	C|0.877;T|0.123	0.123	strong	.	ACCS	64	.	NM_032592	exon10	c.C871T	p.L291L	TACATGCTGTCCG	.	PASS	Atlas-SNP
ZNF749	388567	hgsc.bcm.edu	37	19	57955719	57955719	+	Silent	SNP	G	G	A	rs2240037	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	118	46	111	0	0.38983	0	G|0.959;A|0.041	0.041	strong	.	ZNF749	75	.	NM_001023561	exon3	c.G1203A	p.Q401Q	GCACCAGAGAGTT	.	PASS	Atlas-SNP
USH2A	7399	hgsc.bcm.edu	37	1	215848914	215848914	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	138	29	128	0	0.210145	0	.	.	none	.	USH2A	1168	.	NM_206933	exon63	c.G12339T	p.L4113F	ACGATTCAAACCA	.	PASS	Atlas-SNP
PCDHB14	56122	hgsc.bcm.edu	37	5	140604621	140604621	+	Missense_Mutation	SNP	C	C	T	rs144421802	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	169	92	159	0	0.544379	0	C|0.994;T|0.006	0.006	strong	.	PCDHB14	132	.	NM_018934	exon1	c.C1544T	p.A515V	TGTTTGCCCTCAG	.	PASS	Atlas-SNP
SELPLG	6404	hgsc.bcm.edu	37	12	109017672	109017672	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	91	36	116	3	0.395604	0.0258621	.	.	none	SELPLG_ENST00000550948,NS,carcinoma,0,14	SELPLG	138	14	NM_001206609	exon2	c.C460G	p.P154A	CCGTGGGCACTGG	.	scavenged	Atlas-SNP
ONECUT2	9480	hgsc.bcm.edu	37	18	55103512	55103512	+	Silent	SNP	C	C	T	rs79019704	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	38	21	41	0	0.552632	0	C|0.906;T|0.094	0.094	strong	ONECUT2,brain,glioma,0,1	ONECUT2	42	1	NM_004852	exon1	c.C564T	p.S188S	CCTGTCCGGCAAC	.	PASS	Atlas-SNP
RRP12	23223	hgsc.bcm.edu	37	10	99126249	99126249	+	Silent	SNP	G	G	A	rs2275581	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	25	86	0	0.342466	0	G|0.762;A|0.238	0.238	strong	.	RRP12	97	.	NM_015179	exon28	c.C3345T	p.D1115D	GGGCTCGTCCCCA	.	PASS	Atlas-SNP
KIF21A	55605	hgsc.bcm.edu	37	12	39716675	39716675	+	Nonsense_Mutation	SNP	T	T	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	117	28	107	0	0.239316	0	.	.	none	.	KIF21A	238	.	NM_001173464	exon27	c.A3466T	p.R1156X	TGGTTCTCCTTCG	.	PASS	Atlas-SNP
HS3ST6	64711	hgsc.bcm.edu	37	16	1962047	1962047	+	Silent	SNP	G	G	A	rs1657140	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	48	38	58	0	0.791667	0	G|0.664;A|0.336	0.336	strong	.	HS3ST6	26	.	NM_001009606	exon2	c.C480T	p.Y160Y	CTGGGCGTAGTCG	.	PASS	Atlas-SNP
TRIM26	7726	hgsc.bcm.edu	37	6	30166266	30166266	+	Silent	SNP	C	C	T	rs2523721	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	45	77	0	0.463918	0	C|0.765;T|0.235	0.235	strong	.	TRIM26	74	.	NM_001242783	exon4	c.G474A	p.R158R	TCTGTCCCTCCTT	.	PASS	Atlas-SNP
CNBD2	140894	hgsc.bcm.edu	37	20	34596371	34596371	+	Missense_Mutation	SNP	C	C	T	rs6060750	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	60	60	71	0	1	0	C|0.746;T|0.254	0.254	strong	.	.	.	.	NM_080834	exon9	c.C1123T	p.P375S	ACTCTCCCCAAGA	.	PASS	Atlas-SNP
UBQLN1	29979	hgsc.bcm.edu	37	9	86284178	86284178	+	Silent	SNP	C	C	A	rs1044175	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	114	58	128	0	0.508772	0	C|0.276;A|0.724	0.724	strong	UBQLN1,colon,carcinoma,0,1	UBQLN1	49	1	NM_053067	exon7	c.G1170T	p.L390L	TTGCATCAGTTGT	.	PASS	Atlas-SNP
VWA5B1	127731	hgsc.bcm.edu	37	1	20645086	20645086	+	Missense_Mutation	SNP	T	T	A	rs35480773	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	43	24	61	0	0.55814	0	T|0.963;A|0.037	0.037	strong	.	VWA5B1	44	.	NM_001039500	exon6	c.T713A	p.V238E	CAGGGGTGGAGAG	.	PASS	Atlas-SNP
CCSER1	401145	hgsc.bcm.edu	37	4	92519814	92519814	+	Missense_Mutation	SNP	C	C	T	rs370719096		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	74	21	107	0	0.283784	0	.	.	weak	.	.	.	.	NM_001145065	exon11	c.C2309T	p.S770L	GGTATTCGGCAGC	.	PASS	Atlas-SNP
SFI1	9814	hgsc.bcm.edu	37	22	31998612	31998612	+	Missense_Mutation	SNP	G	G	A	rs2006771	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	128	64	154	0	0.5	0	G|0.614;A|0.386	0.386	strong	.	SFI1	78	.	NM_001007467	exon17	c.G1646A	p.R549Q	CAGAGCGACAGCT	.	PASS	Atlas-SNP
MEIOB	254528	hgsc.bcm.edu	37	16	1894912	1894912	+	Silent	SNP	C	C	T	rs9806826	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	190	131	284	1	0.689474	0.00352113	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
ANO2	57101	hgsc.bcm.edu	37	12	5841733	5841733	+	Missense_Mutation	SNP	A	A	C	rs1860961	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	152	67	152	0	0.440789	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
KRTAP10-6	386674	hgsc.bcm.edu	37	21	46011718	46011718	+	Silent	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	246	17	227	2	0.0691057	0.00881057	.	.	none	KRTAP10-6,caecum,carcinoma,-2,1	KRTAP10-6	57	1	NM_198688	exon1	c.A648G	p.P216P	GCAAGTTGGCTGG	.	scavenged	Atlas-SNP
FMNL2	114793	hgsc.bcm.edu	37	2	153468107	153468107	+	Silent	SNP	C	C	T	rs35776654	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	62	29	87	0	0.467742	0	C|0.918;T|0.082	0.082	strong	FMNL2,NS,carcinoma,0,1	FMNL2	75	1	NM_052905	exon11	c.C1050T	p.D350D	CCTGGACGAATAC	.	PASS	Atlas-SNP
ZNF608	57507	hgsc.bcm.edu	37	5	123984763	123984763	+	Silent	SNP	C	C	T	rs7708070	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	95	94	91	0	0.989474	0	C|0.228;T|0.772	0.772	strong	.	ZNF608	117	.	NM_020747	exon4	c.G1314A	p.A438A	AGACCTCGCTCTC	.	PASS	Atlas-SNP
DHX38	9785	hgsc.bcm.edu	37	16	72137561	72137561	+	Silent	SNP	G	G	A	rs2240243	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	156	62	111	0	0.397436	0	G|0.533;A|0.467	0.467	strong	.	DHX38	91	.	NM_014003	exon13	c.G1698A	p.T566T	GCTGACGCAGTAC	.	PASS	Atlas-SNP
KRAS	3845	hgsc.bcm.edu	37	12	25362777	25362777	+	Silent	SNP	A	A	G	rs1137282	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	127	126	166	0	0.992126	0	T|0.136;G|0.154;C|0.028;A|0.682	0.154	strong	.	KRAS	30930	.	NM_004985	exon5	c.T519C	p.D173D	TTTACCATCTTTG	.	PASS	Atlas-SNP
CLUAP1	23059	hgsc.bcm.edu	37	16	3558381	3558381	+	Silent	SNP	T	T	C	rs11554091	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	83	66	94	0	0.795181	0	T|0.974;C|0.026	0.026	strong	.	CLUAP1	32	.	NM_015041	exon4	c.T312C	p.L104L	TGTCCTTTATAAT	.	PASS	Atlas-SNP
TROAP	10024	hgsc.bcm.edu	37	12	49721015	49721015	+	Missense_Mutation	SNP	C	C	T	rs78961476	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	122	70	135	0	0.57377	0	C|0.981;T|0.019	0.019	strong	.	TROAP	80	.	NM_005480	exon8	c.C793T	p.R265C	GGAGAACGCGAGG	.	PASS	Atlas-SNP
TSSK2	23617	hgsc.bcm.edu	37	22	19119938	19119938	+	Silent	SNP	G	G	A	rs1052773	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	33	20	39	0	0.606061	0	A|0.201;C|0.006	0.201	strong	.	TSSK2	29	.	NM_053006	exon1	c.G1026A	p.R342R	CTCCAGGGCCAAA	.	PASS	Atlas-SNP
PBRM1	55193	hgsc.bcm.edu	37	3	52661351	52661351	+	Silent	SNP	G	G	A	rs147488144	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	59	27	79	0	0.457627	0	G|0.995;A|0.005	0.005	strong	PBRM1_ENST00000356770,NS,carcinoma,0,3	PBRM1	1252	3	NM_018313	exon14	c.C1479T	p.I493I	GTCCTCGATATCG	.	PASS	Atlas-SNP
MAGEB3	4114	hgsc.bcm.edu	37	X	30254361	30254361	+	Missense_Mutation	SNP	G	G	A	rs2071308	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	86	149	1	1	0.00671141	G|0.569;A|0.431	0.431	strong	.	MAGEB3	54	.	NM_002365	exon5	c.G320A	p.R107H	AGTCTCGCACAGA	.	PASS	Atlas-SNP
AIFM2	84883	hgsc.bcm.edu	37	10	71874683	71874683	+	Silent	SNP	G	G	A	rs2271696	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	42	22	48	0	0.52381	0	G|0.882;A|0.118	0.118	strong	.	AIFM2	33	.	NM_001198696	exon8	c.C963T	p.Y321Y	CGGCTTGTAGGCC	.	PASS	Atlas-SNP
JAK1	3716	hgsc.bcm.edu	37	1	65321250	65321250	+	Silent	SNP	G	G	A	rs2230586	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	174	69	210	0	0.396552	0	G|0.957;A|0.043	0.043	strong	.	JAK1	209	.	NM_002227	exon11	c.C1590T	p.I530I	GCGCAGGATCTGC	.	PASS	Atlas-SNP
DPYD	1806	hgsc.bcm.edu	37	1	98039419	98039419	+	Silent	SNP	C	C	T	rs56038477	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	346	162	437	0	0.468208	0	C|0.986;T|0.014	0.014	strong	.	DPYD	219	.	NM_000110	exon11	c.G1236A	p.E412E	ATCTTGCTCTGTC	.	PASS	Atlas-SNP
ZNF133	7692	hgsc.bcm.edu	37	20	18296076	18296076	+	Missense_Mutation	SNP	G	G	A	rs2228273	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	59	38	53	0	0.644068	0	A|0.112;C|0.006	0.112	strong	.	ZNF133	63	.	NM_001083330	exon4	c.G578A	p.G193E	AGTCAGGGAACCC	.	PASS	Atlas-SNP
SKA3	221150	hgsc.bcm.edu	37	13	21729252	21729252	+	Missense_Mutation	SNP	T	T	C	rs11147976	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	15	96	0	0.174419	0	T|0.889;C|0.111	0.111	strong	.	SKA3	76	.	NM_001166017	exon8	c.A1157G	p.K386R	CTCATTTTGTTCA	.	PASS	Atlas-SNP
IL3RA	3563	hgsc.bcm.edu	37	X	1497644	1497644	+	Missense_Mutation	SNP	G	G	C	rs17883366	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	232	174	261	0	0.75	0	G|0.868;C|0.132	0.132	strong	.	IL3RA	49	.	NM_002183	exon10	c.G967C	p.V323L	GTCTTCGTGATCT	.	PASS	Atlas-SNP
CELA1	1990	hgsc.bcm.edu	37	12	51737562	51737562	+	Missense_Mutation	SNP	T	T	C	rs17860300	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	111	43	138	1	0.387387	0.00724638	T|0.788;C|0.212	0.212	strong	CELA1,NS,carcinoma,+2,1	CELA1	39	1	NM_001971	exon3	c.A175G	p.M59V	CTGTCATCACCCA	.	scavenged	Atlas-SNP
ZNF567	163081	hgsc.bcm.edu	37	19	37209866	37209866	+	Silent	SNP	T	T	C	rs34642314	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	96	53	112	0	0.552083	0	T|0.917;C|0.083	0.083	strong	.	ZNF567	61	.	NM_152603	exon4	c.T147C	p.A49A	GAAAGCTGAAGAC	.	PASS	Atlas-SNP
DCAF6	55827	hgsc.bcm.edu	37	1	167973976	167973976	+	Silent	SNP	C	C	T	rs1060041	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	133	58	167	0	0.43609	0	C|0.821;T|0.179	0.179	strong	.	DCAF6	99	.	NM_001198956	exon10	c.C1323T	p.D441D	TCCAGACAGTGAA	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29911239	29911239	+	Silent	SNP	T	T	C	rs9260155	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	131	61	257	1	0.465649	0.00389105	C|0.290;T|0.710	0.290	strong	HLA-A,mouth,carcinoma,-1,1	HLA-A	89	1	NM_001242758	exon3	c.T538C	p.L180L	GAGCAGTTGAGAG	.	PASS	Atlas-SNP
DLGAP1	9229	hgsc.bcm.edu	37	18	3534224	3534224	+	Missense_Mutation	SNP	C	C	T	rs35822832	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	160	70	160	0	0.4375	0	C|0.984;T|0.016	0.016	strong	.	DLGAP1	201	.	NM_001242761	exon10	c.G2447A	p.R816Q	TCTTCCCGCTCCA	.	PASS	Atlas-SNP
PSTPIP2	9050	hgsc.bcm.edu	37	18	43568717	43568717	+	Missense_Mutation	SNP	T	T	C	rs2276199	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	177	87	164	0	0.491525	0	T|0.703;C|0.297	0.297	strong	PSTPIP2,NS,carcinoma,0,1	PSTPIP2	65	1	NM_024430	exon14	c.A964G	p.N322D	AGTAATTGGGATC	.	PASS	Atlas-SNP
CHGB	1114	hgsc.bcm.edu	37	20	5903848	5903848	+	Missense_Mutation	SNP	C	C	G	rs236152	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	33	19	53	0	0.575758	0	C|0.545;G|0.455	0.455	strong	.	CHGB	112	.	NM_001819	exon4	c.C1058G	p.A353G	TCCAGGCCCCTGA	.	PASS	Atlas-SNP
SMG1	23049	hgsc.bcm.edu	37	16	18853744	18853744	+	Silent	SNP	T	T	C	rs12926959	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	110	66	125	0	0.6	0	T|0.942;C|0.058	0.058	strong	.	SMG1	401	.	NM_015092	exon40	c.A6252G	p.K2084K	TGCACGTTTCTGT	.	PASS	Atlas-SNP
PRODH	5625	hgsc.bcm.edu	37	22	18905964	18905964	+	Missense_Mutation	SNP	C	C	T	rs2904552	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	80	34	80	0	0.425	0	C|0.930;T|0.070	0.070	strong	.	PRODH	42	.	NM_016335	exon12	c.G1292A	p.R431H	TCACGGCGAGCCA	.	PASS	Atlas-SNP
C3orf30	152405	hgsc.bcm.edu	37	3	118865801	118865801	+	Silent	SNP	C	C	T	rs4077931	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	51	27	49	1	0.529412	0.0204082	C|0.750;T|0.250	0.250	strong	C3orf30,NS,malignant_melanoma,+1,1	C3orf30	64	1	NM_152539	exon1	c.C765T	p.S255S	ACCTTCCGTACAG	.	scavenged	Atlas-SNP
PEAR1	375033	hgsc.bcm.edu	37	1	156883546	156883546	+	Missense_Mutation	SNP	A	A	G	rs12137505	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	119	119	127	0	1	0	A|0.621;G|0.379	0.379	strong	.	PEAR1	118	.	NM_001080471	exon21	c.A2707G	p.N903D	TTCTACAATAAAG	.	PASS	Atlas-SNP
SALL4	57167	hgsc.bcm.edu	37	20	50406630	50406630	+	Missense_Mutation	SNP	T	T	G	rs6091375	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	301	154	285	1	0.511628	0.00350877	T|0.917;G|0.083	0.083	strong	.	SALL4	168	.	NM_020436	exon2	c.A2392C	p.I798L	ACTTGATGCTTTC	.	PASS	Atlas-SNP
ABCG4	64137	hgsc.bcm.edu	37	11	119020719	119020719	+	Missense_Mutation	SNP	C	C	T	rs113286118	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	93	66	74	0	0.709677	0	C|0.994;T|0.006	0.006	strong	.	ABCG4	77	.	NM_022169	exon2	c.C44T	p.P15L	TAGGGCCGGGGGC	.	PASS	Atlas-SNP
SCAF1	58506	hgsc.bcm.edu	37	19	50161091	50161091	+	Missense_Mutation	SNP	A	A	G	rs61743199	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	107	44	122	0	0.411215	0	A|0.956;G|0.043;T|0.000	0.043	strong	.	SCAF1	78	.	NM_021228	exon10	c.A3692G	p.K1231R	ATCAGAAGAAGGA	.	PASS	Atlas-SNP
RYR3	6263	hgsc.bcm.edu	37	15	33873751	33873751	+	Missense_Mutation	SNP	G	G	A	rs2077268	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	31	136	0	0.306931	0	G|0.846;A|0.154	0.154	strong	RYR3,NS,carcinoma,-1,1	RYR3	760	1	NM_001243996	exon14	c.G1480A	p.V494I	TTAAATGTCTACA	.	PASS	Atlas-SNP
EXOSC7	23016	hgsc.bcm.edu	37	3	45052775	45052775	+	Missense_Mutation	SNP	G	G	C	rs6794	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	140	70	146	0	0.5	0	G|0.396;C|0.604	0.604	strong	.	EXOSC7	19	.	NM_015004	exon8	c.G820C	p.V274L	AGTGTTGTGCACA	.	PASS	Atlas-SNP
PPIL1	51645	hgsc.bcm.edu	37	6	36824399	36824399	+	Silent	SNP	C	C	T	rs2071823	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	159	82	183	0	0.515723	0	C|0.796;G|0.000;T|0.204	0.204	strong	.	PPIL1	6	.	NM_016059	exon3	c.G243A	p.Q81Q	TTCAAACTGTTTG	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	65	34	82	0	0.523077	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
AHNAK2	113146	hgsc.bcm.edu	37	14	105419557	105419557	+	Missense_Mutation	SNP	G	G	A	rs78204285	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	124	57	132	0	0.459677	0	G|0.968;A|0.032	0.032	strong	.	AHNAK2	719	.	NM_138420	exon7	c.C2231T	p.P744L	CCCTCCGGAAGTT	.	PASS	Atlas-SNP
DNAH2	146754	hgsc.bcm.edu	37	17	7680159	7680159	+	Silent	SNP	G	G	A	rs62059684	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	38	89	0	0.535211	0	G|0.764;A|0.236	0.236	strong	.	DNAH2	498	.	NM_020877	exon31	c.G5010A	p.A1670A	GACAGCGAAGGAG	.	PASS	Atlas-SNP
TXNL1	9352	hgsc.bcm.edu	37	18	54281790	54281790	+	Silent	SNP	T	T	C	rs655539	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	75	104	0	0.961538	0	T|0.962;C|0.038	0.038	strong	.	TXNL1	30	.	NM_004786	exon6	c.A600G	p.L200L	TCGGGGTAGGTTG	.	PASS	Atlas-SNP
CX3CR1	1524	hgsc.bcm.edu	37	3	39307162	39307162	+	Missense_Mutation	SNP	G	G	A	rs3732378	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	110	49	153	0	0.445455	0	A|0.101;C|0.011	0.101	strong	CX3CR1_ENST00000358309,NS,adenocarcinoma,+1,4	CX3CR1	91	4	NM_001171174	exon2	c.C935T	p.T312M	GCAACCGTCTCAG	.	PASS	Atlas-SNP
HIST1H1D	3007	hgsc.bcm.edu	37	6	26234735	26234735	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	99	27	125	0	0.272727	0	.	.	none	.	HIST1H1D	40	.	NM_005320	exon1	c.G427A	p.A143T	CGCCAGCCACCTT	.	PASS	Atlas-SNP
RGPD3	653489	hgsc.bcm.edu	37	2	107041612	107041612	+	Missense_Mutation	SNP	A	A	C	rs3974037		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	859	231	734	2	0.268917	0.0027248	.	.	weak	RGPD3_ENST00000304514,NS,carcinoma,0,2	RGPD3	316	2	NM_001144013	exon20	c.T2811G	p.S937R	CTTTTCACTTTTC	.	scavenged	Atlas-SNP
BTN3A2	11118	hgsc.bcm.edu	37	6	26368279	26368279	+	Splice_Site	SNP	G	G	A	rs72841509	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	64	64	77	0	1	0	G|0.927;A|0.073	0.073	strong	.	BTN3A2	44	.	.	.	.	.	GCAGAGGTAAGAT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195508500	195508500	+	Missense_Mutation	SNP	G	G	C	rs374619108		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	34	8	116	0	0.235294	0	.	.	weak	MUC4_ENST00000463781,NS,carcinoma,0,6	MUC4	1505	6	NM_018406	exon2	c.C9951G	p.D3317E	GGAAGCGTCGGTG	.	PASS	Atlas-SNP
WWP2	11060	hgsc.bcm.edu	37	16	69970329	69970329	+	Silent	SNP	A	A	G	rs1983016	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	106	106	72	0	1	0	A|0.193;G|0.807	0.807	strong	WWP2,NS,carcinoma,0,2	WWP2	88	2	NM_001270454	exon19	c.A2091G	p.T697T	GGTCACAGAGGAG	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	89	12	91	0	0.134831	0	G|0.849;A|0.151	0.151	strong	.	PDIA2	51	.	NM_006849	exon4	c.G553A	p.E185K	CAGGACGAGGACG	.	PASS	Atlas-SNP
SMG1	23049	hgsc.bcm.edu	37	16	18847416	18847416	+	Silent	SNP	G	G	A	rs3816919	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	130	76	105	0	0.584615	0	G|0.899;A|0.101	0.101	strong	.	SMG1	401	.	NM_015092	exon48	c.C7896T	p.S2632S	GAGCACGGAGCGC	.	PASS	Atlas-SNP
ARMC2	84071	hgsc.bcm.edu	37	6	109274418	109274418	+	Silent	SNP	G	G	A	rs41287540	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	57	32	55	0	0.561404	0	G|0.986;A|0.014	0.014	strong	.	ARMC2	56	.	NM_032131	exon13	c.G1779A	p.A593A	CAGGGCGCAGAGG	.	PASS	Atlas-SNP
TMEM72	643236	hgsc.bcm.edu	37	10	45430257	45430257	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	37	83	0	0.430233	0	.	.	none	.	TMEM72	25	.	NM_001123376	exon5	c.C503T	p.T168I	AGCAAACCTACAC	.	PASS	Atlas-SNP
WWP2	11060	hgsc.bcm.edu	37	16	69973825	69973825	+	Silent	SNP	G	G	A	rs3748389	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	94	30	83	0	0.319149	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
FAM13B	51306	hgsc.bcm.edu	37	5	137275968	137275968	+	Missense_Mutation	SNP	C	C	G	rs201094212	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	163	83	197	0	0.509202	0	C|0.999;G|0.001	0.001	strong	FAM13B,NS,carcinoma,0,2	FAM13B	46	2	NM_016603	exon23	c.G2694C	p.K898N	CCTAAGCTTGGCT	.	PASS	Atlas-SNP
ARSD	414	hgsc.bcm.edu	37	X	2833631	2833631	+	Silent	SNP	A	A	G	rs377542415		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	105	11	140	0	0.104762	0	.	.	weak	.	ARSD	47	.	NM_001669	exon6	c.T966C	p.Y322Y	ATCACCATATAAG	.	PASS	Atlas-SNP
CCDC74A	90557	hgsc.bcm.edu	37	2	132288362	132288362	+	Missense_Mutation	SNP	T	T	C	rs2599971	bycluster;byfrequency;by2hit2allele;byhapmap	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	527	31	477	0	0.0588235	0	T|0.250;C|0.750	0.750	strong	CCDC74A,parotid,carcinoma,0,1	CCDC74A	44	1	NM_001258304	exon3	c.T632C	p.M211T	TCTCCATGTCAAG	.	scavenged	Atlas-SNP
TMEM8A	58986	hgsc.bcm.edu	37	16	427820	427820	+	Silent	SNP	C	C	T	rs12922073	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	133	130	173	0	0.977444	0	A|0.000;C|0.470;G|0.000;T|0.530	0.530	strong	.	TMEM8A	49	.	NM_021259	exon2	c.G150A	p.S50S	GGCCTGCGAGAAG	.	PASS	Atlas-SNP
ZNF286B	729288	hgsc.bcm.edu	37	17	18565350	18565350	+	Missense_Mutation	SNP	G	G	C	rs9912644	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	253	178	186	0	0.703557	0	G|0.648;C|0.352	0.352	strong	ZNF286B,NS,carcinoma,0,1	ZNF286B	75	1	NM_001145045	exon5	c.C1469G	p.T490S	TCTCCGGTATGAG	.	PASS	Atlas-SNP
NEURL4	84461	hgsc.bcm.edu	37	17	7221385	7221385	+	Silent	SNP	G	G	A	rs1127440	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	93	93	117	0	1	0	T|0.254;G|0.226;C|0.110;A|0.411	0.411	strong	NEURL4_ENST00000315614,NS,carcinoma,0,4	NEURL4	192	4	NM_032442	exon25	c.C4059T	p.P1353P	CTCACCGGGAAGC	.	PASS	Atlas-SNP
BIRC7	79444	hgsc.bcm.edu	37	20	61867454	61867454	+	Silent	SNP	A	A	G	rs6011691	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	137	77	160	0	0.562044	0	A|0.879;G|0.121	0.121	strong	.	BIRC7	25	.	NM_139317	exon1	c.A6G	p.G2G	CATGGGACCTAAA	.	PASS	Atlas-SNP
SLC35G5	83650	hgsc.bcm.edu	37	8	11188752	11188752	+	Missense_Mutation	SNP	G	G	A	rs77960126		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	84	20	106	0	0.238095	0	.	.	weak	.	.	.	.	NM_054028	exon1	c.G137A	p.G46D	TGCTGGGTGGGGG	.	PASS	Atlas-SNP
FRMD4B	23150	hgsc.bcm.edu	37	3	69271032	69271032	+	Silent	SNP	G	G	A	rs62254461	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	109	49	142	0	0.449541	0	G|0.928;A|0.072	0.072	strong	.	FRMD4B	90	.	NM_015123	exon9	c.C708T	p.L236L	TCGAGTGAGACCT	.	PASS	Atlas-SNP
AIRE	326	hgsc.bcm.edu	37	21	45712977	45712977	+	Silent	SNP	T	T	C	rs1800521	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	67	67	44	0	1	0	T|0.622;C|0.378	0.378	strong	AIRE_ENST00000397994,NS,carcinoma,0,2	AIRE	61	2	NM_000383	exon10	c.T1197C	p.A399A	GCCGGCTCCGCCT	.	PASS	Atlas-SNP
GRIN3A	116443	hgsc.bcm.edu	37	9	104432873	104432873	+	Silent	SNP	T	T	G	rs942142	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	89	45	108	0	0.505618	0	T|0.683;G|0.317	0.317	strong	.	GRIN3A	186	.	NM_133445	exon3	c.A1821C	p.A607A	TTTCCATGCTCCA	.	PASS	Atlas-SNP
ZSCAN5A	79149	hgsc.bcm.edu	37	19	56736094	56736094	+	Missense_Mutation	SNP	C	C	T	rs143462624	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	684	175	577	0	0.255848	0	C|0.988;T|0.012	0.012	strong	ZSCAN5A,NS,carcinoma,0,1	ZSCAN5A	118	1	NM_024303	exon2	c.G322A	p.G108S	GCACACCGTTCAT	.	scavenged	Atlas-SNP
MYO1C	4641	hgsc.bcm.edu	37	17	1377943	1377943	+	Silent	SNP	A	A	G	rs2286873	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	116	55	127	0	0.474138	0	A|0.554;G|0.446	0.446	strong	.	MYO1C	57	.	NM_001080779	exon17	c.T1758C	p.F586F	CCGGTCAAAGCAC	.	PASS	Atlas-SNP
CHMP7	91782	hgsc.bcm.edu	37	8	23118091	23118091	+	Silent	SNP	A	A	G	rs76771816	bycluster;alternate_allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	178	7	197	0	0.0393258	0	.	.	alt	CHMP7,NS,carcinoma,+1,1	CHMP7	34	1	NM_152272	exon11	c.A1341G	p.E447E	ATTGGAACCGACT	.	scavenged	Atlas-SNP
ACSM5	54988	hgsc.bcm.edu	37	16	20441020	20441020	+	Missense_Mutation	SNP	G	G	A	rs12932087	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	54	24	63	0	0.444444	0	G|0.913;A|0.087	0.087	strong	.	ACSM5	101	.	NM_017888	exon8	c.G1022A	p.R341K	GCCTGAGGCACTG	.	PASS	Atlas-SNP
ASPM	259266	hgsc.bcm.edu	37	1	197069640	197069640	+	Missense_Mutation	SNP	A	A	G	rs200856894	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	48	17	88	0	0.354167	0	A|0.999;G|0.001	0.001	weak	ASPM,NS,carcinoma,+1,1	ASPM	444	1	NM_018136	exon18	c.T8741C	p.I2914T	ATAATGATAACAC	.	PASS	Atlas-SNP
SLC9A9	285195	hgsc.bcm.edu	37	3	142985717	142985717	+	Missense_Mutation	SNP	T	T	C	rs2289491	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	139	52	166	0	0.374101	0	T|0.977;C|0.023	0.023	strong	SLC9A9,caecum,carcinoma,0,3	SLC9A9	117	3	NM_173653	exon16	c.A1765G	p.I589V	AATTTATGGCTAG	.	PASS	Atlas-SNP
ISX	91464	hgsc.bcm.edu	37	22	35463249	35463249	+	Missense_Mutation	SNP	C	C	T	rs362090	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	69	78	0	0.985714	0	C|0.453;T|0.547	0.547	strong	.	ISX	62	.	NM_001008494	exon1	c.C169T	p.P57S	GAGGGCCCCGGAG	.	PASS	Atlas-SNP
IL17RC	84818	hgsc.bcm.edu	37	3	9959713	9959713	+	Silent	SNP	C	C	T	rs4686383	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	89	41	101	0	0.460674	0	C|0.889;T|0.111	0.111	strong	.	IL17RC	55	.	NM_153461	exon3	c.C447T	p.T149T	GGAGACCGACTGT	.	PASS	Atlas-SNP
PER3	8863	hgsc.bcm.edu	37	1	7890055	7890055	+	Silent	SNP	T	T	A	rs11121034	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	56	9	148	1	0.160714	0.00675676	T|0.954;A|0.046	0.046	strong	PER3,NS,carcinoma,+2,1	PER3	95	1	NM_016831	exon18	c.T3021A	p.A1007A	CAGCGCTCTGTCC	.	scavenged	Atlas-SNP
PLB1	151056	hgsc.bcm.edu	37	2	28814033	28814033	+	Missense_Mutation	SNP	A	A	G	rs11681826	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	54	78	0	0.534653	0	A|0.739;G|0.261	0.261	strong	PLB1,NS,carcinoma,0,1	PLB1	255	1	NM_153021	exon30	c.A2122G	p.M708V	AACAGCATGCAGG	.	PASS	Atlas-SNP
EFCAB4B	84766	hgsc.bcm.edu	37	12	3788222	3788222	+	Missense_Mutation	SNP	G	G	A	rs242017	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	100	41	114	0	0.41	0	G|0.756;N|0.000	.	strong	.	EFCAB4B	100	.	NM_001144958	exon6	c.C383T	p.A128V	TCACCTGCATCTT	.	PASS	Atlas-SNP
C7orf71	285941	hgsc.bcm.edu	37	7	26685934	26685934	+	Silent	SNP	T	T	C	rs12671270	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	66	44	81	0	0.666667	0	C|0.305;N|0.000	0.305	strong	.	C7orf71	6	.	NM_001145531	exon4	c.T285C	p.C95C	CGCATGTGGGACT	.	PASS	Atlas-SNP
NFKBIZ	64332	hgsc.bcm.edu	37	3	101571753	101571753	+	Missense_Mutation	SNP	A	A	G	rs61730026	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	155	78	180	0	0.503226	0	A|0.998;G|0.002	0.002	strong	.	NFKBIZ	55	.	NM_031419	exon4	c.A484G	p.S162G	TCATACAGTGGGA	.	PASS	Atlas-SNP
GLI1	2735	hgsc.bcm.edu	37	12	57859431	57859431	+	Silent	SNP	G	G	A	rs2228225	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	114	54	99	0	0.473684	0	A|0.449;C|0.000;G|0.551	0.449	strong	.	GLI1	141	.	NM_005269	exon6	c.G576A	p.E192E	CCGGGAGGAACCC	.	PASS	Atlas-SNP
FAM83B	222584	hgsc.bcm.edu	37	6	54735301	54735301	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	128	27	131	0	0.210938	0	.	.	none	.	FAM83B	186	.	NM_001010872	exon2	c.C257G	p.T86S	ATGATACCTTATC	.	PASS	Atlas-SNP
CES1	1066	hgsc.bcm.edu	37	16	55862791	55862791	+	Missense_Mutation	SNP	T	T	C	rs3826193	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	99	14	161	0	0.141414	0	.	.	weak	.	CES1	78	.	NM_001025195	exon2	c.A148G	p.I50V	GGAAAATGGCCAC	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29912348	29912348	+	Missense_Mutation	SNP	A	A	G	rs1137078	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	157	58	211	0	0.369427	0	A|0.761;G|0.239	0.239	strong	.	HLA-A	89	.	NM_001242758	exon5	c.A967G	p.T323A	GTGATCACTGGAG	.	PASS	Atlas-SNP
FAM46C	54855	hgsc.bcm.edu	37	1	118165973	118165973	+	Silent	SNP	C	C	T	rs1627787	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	177	177	238	0	1	0	C|0.740;T|0.260	0.260	strong	.	FAM46C	25	.	NM_017709	exon2	c.C483T	p.N161N	CAAGAACGGGAAG	.	PASS	Atlas-SNP
PTBP1	5725	hgsc.bcm.edu	37	19	808742	808742	+	Silent	SNP	G	G	T	rs1135908	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	176	174	200	1	0.988636	0.005	G|0.864;T|0.136	0.136	strong	.	PTBP1	43	.	NM_002819	exon13	c.G1443T	p.T481T	GGCCACGCTGCAC	.	PASS	Atlas-SNP
KRTAP10-6	386674	hgsc.bcm.edu	37	21	46011298	46011298	+	Silent	SNP	G	G	A	rs74695406		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	193	9	145	0	0.0466321	0	A|1.000;|0.000	1.000	weak	KRTAP10-6,NS,carcinoma,0,1	KRTAP10-6	57	1	NM_198688	exon1	c.C1068T	p.S356S	GCAGAGGCTGTAG	.	scavenged	Atlas-SNP
C10orf90	118611	hgsc.bcm.edu	37	10	128202435	128202435	+	Silent	SNP	T	T	C	rs1436803	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	77	76	82	0	0.987013	0	T|0.131;C|0.869	0.869	strong	.	C10orf90	121	.	NM_001004298	exon2	c.A96G	p.A32A	AGATTTTGCCTCT	.	PASS	Atlas-SNP
CYP20A1	57404	hgsc.bcm.edu	37	2	204154552	204154552	+	Missense_Mutation	SNP	C	C	T	rs1048013	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	262	144	292	0	0.549618	0	C|0.598;T|0.402	0.402	strong	.	CYP20A1	40	.	NM_177538	exon10	c.C1036T	p.L346F	GCCCAGCTTCAAG	.	PASS	Atlas-SNP
NUP88	4927	hgsc.bcm.edu	37	17	5294976	5294976	+	Silent	SNP	T	T	A	rs14231	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	47	25	69	0	0.531915	0	T|0.571;A|0.429	0.429	strong	.	NUP88	47	.	NM_002532	exon10	c.A1389T	p.P463P	TGGAGCTGGCTGC	.	PASS	Atlas-SNP
SLC35G6	643664	hgsc.bcm.edu	37	17	7385454	7385454	+	Missense_Mutation	SNP	G	G	A	rs3760422	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	105	48	128	0	0.457143	0	G|0.841;A|0.159	0.159	strong	.	.	.	.	NM_001102614	exon2	c.G151A	p.A51T	CTGCCTGCTGGCT	.	PASS	Atlas-SNP
KIAA1751	85452	hgsc.bcm.edu	37	1	1900225	1900225	+	Missense_Mutation	SNP	C	C	T	rs72636304	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	59	17	118	0	0.288136	0	C|0.994;T|0.006	0.006	strong	.	KIAA1751	92	.	NM_001080484	exon11	c.G1094A	p.R365Q	AGAATCCGACTGA	.	PASS	Atlas-SNP
OSCP1	127700	hgsc.bcm.edu	37	1	36898067	36898067	+	Missense_Mutation	SNP	T	T	C	rs34409118	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	157	65	163	0	0.414013	0	T|0.800;C|0.200	0.200	strong	OSCP1_ENST00000354267,colon,carcinoma,0,4	OSCP1	48	4	NM_145047	exon3	c.A391G	p.T131A	GGATGGTTGGGGA	.	PASS	Atlas-SNP
STON1	11037	hgsc.bcm.edu	37	2	48808152	48808152	+	Missense_Mutation	SNP	G	G	C	rs940389	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	271	43	176	0	0.158672	0	G|0.659;C|0.341	0.341	strong	.	STON1	100	.	NM_001198595	exon3	c.G380C	p.R127T	CTACCAGACCAAC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195513173	195513173	+	Missense_Mutation	SNP	G	G	A	rs77448757	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	157	44	107	0	0.280255	0	G|0.967;A|0.033	0.033	strong	MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	NM_018406	exon2	c.C5278T	p.P1760S	GAAGAGGGGTGGC	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29910721	29910721	+	Missense_Mutation	SNP	G	G	C	rs199474424	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	183	65	267	0	0.355191	0	C|0.156;G|0.844	0.156	strong	.	HLA-A	89	.	NM_001242758	exon2	c.G261C	p.E87D	CCAGGAGACACGG	.	PASS	Atlas-SNP
ATRIP	84126	hgsc.bcm.edu	37	3	48506279	48506279	+	Missense_Mutation	SNP	G	G	A	rs76493396	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	183	77	219	0	0.420765	0	G|0.993;A|0.007	0.007	strong	.	ATRIP	41	.	NM_130384	exon12	c.G2105A	p.R702Q	CAGTGCGGAGGGC	.	PASS	Atlas-SNP
PRDM9	56979	hgsc.bcm.edu	37	5	23527324	23527324	+	Silent	SNP	T	T	A	rs200723191	byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	142	17	86	0	0.119718	0	T|0.988;A|0.012	0.012	strong	PRDM9,NS,carcinoma,+1,1	PRDM9	344	1	NM_020227	exon11	c.T2127A	p.T709T	CCTCACTCACCAG	.	PASS	Atlas-SNP
BOC	91653	hgsc.bcm.edu	37	3	112998265	112998265	+	Silent	SNP	A	A	G	rs2649878	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	57	57	60	0	1	0	A|0.504;G|0.496	0.496	strong	.	BOC	139	.	NM_033254	exon12	c.A1983G	p.P661P	CCCCCCATCGCGG	.	PASS	Atlas-SNP
SV2C	22987	hgsc.bcm.edu	37	5	75591710	75591710	+	Missense_Mutation	SNP	C	C	G	rs2270927	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	115	50	124	0	0.434783	0	C|0.830;G|0.170	0.170	strong	.	SV2C	97	.	NM_014979	exon9	c.C1445G	p.T482S	ATTTCACTATTAA	.	PASS	Atlas-SNP
C9orf89	84270	hgsc.bcm.edu	37	9	95872885	95872885	+	Silent	SNP	C	C	T	rs17593496	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	50	85	0	0.515464	0	C|0.908;T|0.092	0.092	strong	C9orf89,NS,adenoma,0,1	C9orf89	12	1	NM_032310	exon3	c.C186T	p.L62L	GCGGCTCTGTGAC	.	PASS	Atlas-SNP
TANC1	85461	hgsc.bcm.edu	37	2	160086653	160086653	+	Silent	SNP	C	C	T	rs4664277	bycluster;by2hit2allele;byhapmap;alternate_allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	102	41	108	0	0.401961	0	.	.	alt	.	TANC1	157	.	NM_033394	exon27	c.C4716T	p.A1572A	CGCTGCCACTCCT	.	PASS	Atlas-SNP
NPY5R	4889	hgsc.bcm.edu	37	4	164272703	164272703	+	Silent	SNP	G	G	A	rs11946004	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	114	56	152	0	0.491228	0	G|0.899;A|0.101	0.101	strong	.	NPY5R	101	.	NM_006174	exon4	c.G1278A	p.G426G	ATATGGGTTTCTT	.	PASS	Atlas-SNP
PRKCA	5578	hgsc.bcm.edu	37	17	64685078	64685078	+	Silent	SNP	G	G	A	rs2227857	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	48	48	84	0	1	0	G|0.741;A|0.259	0.259	strong	.	PRKCA	82	.	NM_002737	exon8	c.G831A	p.L277L	CAAGTTGCTTAAC	.	PASS	Atlas-SNP
SPECC1	92521	hgsc.bcm.edu	37	17	20013802	20013802	+	Silent	SNP	G	G	A	rs3764436	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	194	93	277	0	0.479381	0	G|0.892;A|0.108	0.108	strong	.	SPECC1	100	.	NM_001033553	exon3	c.G210A	p.V70V	GGGGGTGGTTCGC	.	PASS	Atlas-SNP
ZNF529	57711	hgsc.bcm.edu	37	19	37039069	37039069	+	Missense_Mutation	SNP	A	A	C	rs2912444	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	156	156	165	1	1	0.00606061	A|0.340;C|0.660	0.660	strong	.	ZNF529	82	.	NM_001145649	exon6	c.T391G	p.L131V	CTTGTAAGTCAAT	.	PASS	Atlas-SNP
PRICKLE4	29964	hgsc.bcm.edu	37	6	41753084	41753084	+	Silent	SNP	C	C	T	rs9394831	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	34	78	0	0.492754	0	C|0.821;T|0.179	0.179	strong	.	PRICKLE4	29	.	NM_013397	exon6	c.C388T	p.L130L	AGGGAGCTGCTGA	.	PASS	Atlas-SNP
SLC6A5	9152	hgsc.bcm.edu	37	11	20622975	20622975	+	Missense_Mutation	SNP	G	G	A	rs1443547	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	12	12	23	0	1	0	G|0.607;A|0.393	0.393	strong	.	SLC6A5	151	.	NM_004211	exon2	c.G304A	p.G102S	GCGCAAGGCGCGC	.	PASS	Atlas-SNP
RRP12	23223	hgsc.bcm.edu	37	10	99160152	99160152	+	Silent	SNP	A	A	G	rs1048442	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	36	80	0	0.48	0	A|0.622;G|0.378	0.378	strong	.	RRP12	97	.	NM_001145114	exon2	c.T279C	p.G93G	GAAGGTACCCGAG	.	PASS	Atlas-SNP
ADAM21	8747	hgsc.bcm.edu	37	14	70924955	70924955	+	Missense_Mutation	SNP	A	A	C	rs3829456		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	51	20	86	0	0.392157	0	.	.	weak	ADAM21_ENST00000267499,NS,carcinoma,0,1	ADAM21	181	1	NM_003813	exon2	c.A739C	p.K247Q	ATGTATAAGCAGT	.	PASS	Atlas-SNP
OR51L1	119682	hgsc.bcm.edu	37	11	5020832	5020832	+	Missense_Mutation	SNP	C	C	T	rs10768450	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	386	383	385	0	0.992228	0	C|0.721;T|0.279	0.279	strong	.	OR51L1	60	.	NM_001004755	exon1	c.C620T	p.A207V	TCATTGCCACACT	.	PASS	Atlas-SNP
ZNF253	56242	hgsc.bcm.edu	37	19	20003109	20003109	+	Silent	SNP	A	A	G	rs8106559	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	24	24	27	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
PTPRN2	5799	hgsc.bcm.edu	37	7	157985149	157985149	+	Missense_Mutation	SNP	C	C	G	rs3800855	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	41	84	0	0.585714	0	C|0.780;G|0.220	0.220	strong	.	PTPRN2	243	.	NM_130843	exon5	c.G419C	p.S140T	TCCCGACTGTACC	.	PASS	Atlas-SNP
FRG2B	441581	hgsc.bcm.edu	37	10	135440123	135440123	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	265	6	289	1	0.0226415	0.00346021	.	.	none	FRG2B,NS,carcinoma,0,1	FRG2B	47	1	NM_001080998	exon1	c.G124A	p.E42K	CTTTTTCTTTGAA	.	scavenged	Atlas-SNP
ZC3H7B	23264	hgsc.bcm.edu	37	22	41726053	41726053	+	Silent	SNP	G	G	A	rs4822021	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	51	28	67	0	0.54902	0	G|0.760;A|0.240	0.240	strong	.	ZC3H7B	82	.	NM_017590	exon6	c.G471A	p.Q157Q	TGGTCAGGAGCTG	.	PASS	Atlas-SNP
CDH17	1015	hgsc.bcm.edu	37	8	95143138	95143138	+	Silent	SNP	A	A	G	rs2513797	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	48	13	41	0	0.270833	0	A|0.892;G|0.108	0.108	strong	.	CDH17	119	.	NM_004063	exon16	c.T2250C	p.G750G	TGGCCGACCCCCA	.	PASS	Atlas-SNP
KRTAP10-9	386676	hgsc.bcm.edu	37	21	46047710	46047710	+	Silent	SNP	T	T	C	rs8131142	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	123	119	111	0	0.96748	0	T|0.339;C|0.661	0.661	strong	.	KRTAP10-9	24	.	NM_198690	exon1	c.T622C	p.L208L	TCCTCTTTGTGCT	.	PASS	Atlas-SNP
NOP58	51602	hgsc.bcm.edu	37	2	203155936	203155936	+	Silent	SNP	A	A	C	rs3731700	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	127	52	125	0	0.409449	0	A|0.904;C|0.096	0.096	strong	.	NOP58	41	.	NM_015934	exon8	c.A723C	p.S241S	GATATCAATGGGA	.	PASS	Atlas-SNP
GPR116	221395	hgsc.bcm.edu	37	6	46826979	46826979	+	Silent	SNP	A	A	G	rs9381487	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	137	79	132	0	0.576642	0	A|0.733;G|0.267	0.267	strong	.	GPR116	133	.	NM_015234	exon17	c.T2661C	p.Y887Y	TTCTAGATAGCTC	.	PASS	Atlas-SNP
OR51F1	256892	hgsc.bcm.edu	37	11	4790671	4790671	+	Silent	SNP	C	C	T	rs11033795	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	140	35	143	0	0.25	0	C|0.706;T|0.294	0.294	strong	.	OR51F1	60	.	NM_001004752	exon1	c.G477A	p.L159L	TAGTGGCAATATT	.	PASS	Atlas-SNP
SGK1	6446	hgsc.bcm.edu	37	6	134495725	134495725	+	Splice_Site	SNP	C	C	T	rs186450029	by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	36	11	84	0	0.305556	0	C|1.000;T|0.000	0.000	strong	SGK1_ENST00000528577,NS,lymphoid_neoplasm,0,4	SGK1	387	4	NM_005627	exon3	c.77-1G>A	.	TGAAAGCTGTGGA	.	PASS	Atlas-SNP
OR5W2	390148	hgsc.bcm.edu	37	11	55681130	55681130	+	Missense_Mutation	SNP	A	A	T	rs34573569	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	27	14	44	0	0.518519	0	A|0.877;T|0.123	0.123	strong	.	OR5W2	112	.	NM_001001960	exon1	c.T929A	p.F310Y	CCTTAAAATAAAA	.	PASS	Atlas-SNP
TPBG	7162	hgsc.bcm.edu	37	6	83075914	83075914	+	Silent	SNP	G	G	A	rs700494	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	77	39	120	0	0.506494	0	G|0.316;A|0.684	0.684	strong	.	TPBG	37	.	NM_001166392	exon2	c.G1236A	p.T412T	ATTAACGAACCTC	.	PASS	Atlas-SNP
TMPRSS5	80975	hgsc.bcm.edu	37	11	113561054	113561054	+	Missense_Mutation	SNP	A	A	G	rs7110736	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	137	35	142	0	0.255474	0	A|0.250;G|0.750	0.750	strong	.	TMPRSS5	69	.	NM_030770	exon11	c.T1105C	p.F369L	TGCTGAACAAGGG	.	PASS	Atlas-SNP
SLC5A8	160728	hgsc.bcm.edu	37	12	101587518	101587518	+	Missense_Mutation	SNP	C	C	T	rs1709189	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	151	71	165	0	0.470199	0	C|0.745;T|0.255	0.255	strong	.	SLC5A8	102	.	NM_145913	exon5	c.G577A	p.V193I	TCCCAACTTGAAA	.	PASS	Atlas-SNP
THBS1	7057	hgsc.bcm.edu	37	15	39880818	39880818	+	Silent	SNP	C	C	T	rs41338344	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	34	76	0	0.485714	0	C|0.975;T|0.025	0.025	strong	.	THBS1	106	.	NM_003246	exon10	c.C1563T	p.N521N	CAACAACCCCACA	.	PASS	Atlas-SNP
MARC2	54996	hgsc.bcm.edu	37	1	220935081	220935081	+	Silent	SNP	G	G	A	rs2275575	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	89	45	116	0	0.505618	0	G|0.831;A|0.169	0.169	strong	.	.	.	.	NM_017898	exon3	c.G528A	p.A176A	TGAAGCGTATAGA	.	PASS	Atlas-SNP
OVCH1	341350	hgsc.bcm.edu	37	12	29598292	29598292	+	Missense_Mutation	SNP	G	G	A	rs7967676	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	64	31	97	0	0.484375	0	G|0.978;A|0.022	0.022	strong	.	OVCH1	195	.	NM_183378	exon23	c.C2800T	p.P934S	GTCCAGGACTCAT	.	PASS	Atlas-SNP
TMEM173	340061	hgsc.bcm.edu	37	5	138856982	138856982	+	Missense_Mutation	SNP	C	C	T	rs7380824	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	122	56	148	0	0.459016	0	C|0.780;T|0.220	0.220	strong	.	TMEM173	19	.	NM_198282	exon7	c.G878A	p.R293Q	AGTGTCCGGCAGA	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	94	42	124	0	0.446809	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
CNTN6	27255	hgsc.bcm.edu	37	3	1424718	1424718	+	Silent	SNP	G	G	A	rs2291101	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	166	55	218	0	0.331325	0	G|0.557;A|0.443	0.443	strong	.	CNTN6	245	.	NM_014461	exon18	c.G2259A	p.V753V	GAAAGTGTCATCT	.	PASS	Atlas-SNP
RAB11FIP5	26056	hgsc.bcm.edu	37	2	73339708	73339708	+	Silent	SNP	G	G	A	rs1864488	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	144	144	114	0	1	0	G|0.462;A|0.538	0.538	strong	.	RAB11FIP5	66	.	NM_015470	exon1	c.C198T	p.C66C	CTCGGGGCAGCCG	.	PASS	Atlas-SNP
PPP1R32	220004	hgsc.bcm.edu	37	11	61254455	61254455	+	Silent	SNP	T	T	C	rs77676987	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	148	120	200	1	0.810811	0.005	T|0.960;C|0.040	0.040	strong	.	.	.	.	NM_145017	exon10	c.T870C	p.S290S	CGTGAGTCACCAG	.	PASS	Atlas-SNP
ZNF83	55769	hgsc.bcm.edu	37	19	53117809	53117809	+	Silent	SNP	C	C	A	rs10406458	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	58	80	0	1	0	C|0.304;A|0.696	0.696	strong	.	ZNF83	73	.	NM_018300	exon3	c.G9T	p.G3G	CTTTCTCCCATGC	.	PASS	Atlas-SNP
GLP2R	9340	hgsc.bcm.edu	37	17	9792872	9792872	+	Silent	SNP	T	T	C	rs17681708	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	57	31	90	0	0.54386	0	T|0.817;C|0.183	0.183	strong	GLP2R,NS,carcinoma,0,1	GLP2R	90	1	NM_004246	exon13	c.T1512C	p.H504H	CCTACATCTAGCC	.	PASS	Atlas-SNP
ADAMTSL3	57188	hgsc.bcm.edu	37	15	84581904	84581904	+	Silent	SNP	T	T	C	rs4842923	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	117	117	111	0	1	0	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
APOBEC3B	9582	hgsc.bcm.edu	37	22	39381936	39381936	+	Silent	SNP	G	G	A	rs138362043		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	168	117	244	0	0.696429	0	G|1.000;A|0.000	0.000	weak	APOBEC3B,colon,carcinoma,+1,1	APOBEC3B	32	1	NM_004900	exon3	c.G294A	p.P98P	CTGCCCGGACTGT	.	PASS	Atlas-SNP
NOL8	55035	hgsc.bcm.edu	37	9	95069242	95069242	+	Silent	SNP	A	A	G	rs375530094		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	141	56	170	0	0.397163	0	.	.	weak	.	NOL8	118	.	NM_017948	exon11	c.T2751C	p.N917N	TACAACATTCAGG	.	PASS	Atlas-SNP
RYR3	6263	hgsc.bcm.edu	37	15	33858935	33858935	+	Silent	SNP	G	G	A	rs11853872	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	173	89	237	0	0.514451	0	G|0.897;A|0.103	0.103	strong	.	RYR3	760	.	NM_001243996	exon12	c.G1203A	p.Q401Q	ATGCCAGCGTGAG	.	PASS	Atlas-SNP
MFRP	83552	hgsc.bcm.edu	37	11	119215046	119215046	+	Silent	SNP	C	C	T	rs35885438	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	10	96	0	0.108696	0	C|0.962;T|0.038	0.038	strong	.	MFRP	63	.	NM_031433	exon8	c.G954A	p.L318L	CTGCTGCAGGTAG	.	PASS	Atlas-SNP
PHRF1	57661	hgsc.bcm.edu	37	11	587425	587425	+	Silent	SNP	C	C	A	rs12800061	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	147	126	104	0	0.857143	0	A|0.194;C|0.805;G|0.000	0.194	strong	PHRF1_ENST00000264555,NS,NS,+2,1	PHRF1	188	1	NM_020901	exon4	c.C381A	p.A127A	CTGTGCCCATTAC	.	PASS	Atlas-SNP
ZBTB4	57659	hgsc.bcm.edu	37	17	7366651	7366651	+	Missense_Mutation	SNP	C	C	G	rs871990	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	74	35	94	0	0.472973	0	C|0.861;G|0.139	0.139	strong	.	ZBTB4	163	.	NM_001128833	exon4	c.G1650C	p.M550I	GGTGGCCATGGCT	.	PASS	Atlas-SNP
SLC26A7	115111	hgsc.bcm.edu	37	8	92364100	92364100	+	Silent	SNP	T	T	C	rs10109254	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	95	14	104	0	0.147368	0	T|0.739;C|0.261	0.261	strong	.	SLC26A7	207	.	NM_134266	exon10	c.T1203C	p.L401L	TTTGCTTTACTGG	.	PASS	Atlas-SNP
SH3TC1	54436	hgsc.bcm.edu	37	4	8207083	8207083	+	Silent	SNP	A	A	G	rs2677605	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	169	80	188	0	0.473373	0	A|0.516;G|0.484	0.484	strong	SH3TC1,NS,carcinoma,0,1	SH3TC1	105	1	NM_018986	exon2	c.A162G	p.P54P	GGCGCCAGTGAGA	.	PASS	Atlas-SNP
PTCHD4	442213	hgsc.bcm.edu	37	6	47847401	47847401	+	Silent	SNP	A	A	G	rs2068006	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	59	58	60	0	0.983051	0	A|0.358;G|0.642	0.642	strong	.	.	.	.	NM_001013732	exon3	c.T1179C	p.A393A	TTGGCCAGCAAAG	.	PASS	Atlas-SNP
EMR1	2015	hgsc.bcm.edu	37	19	6926378	6926378	+	Missense_Mutation	SNP	T	T	C	rs2228539	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	89	39	90	0	0.438202	0	T|0.650;C|0.350	0.350	strong	.	EMR1	153	.	NM_001974	exon16	c.T1988C	p.M663T	TCCAGATGGGCTG	.	PASS	Atlas-SNP
GFPT2	9945	hgsc.bcm.edu	37	5	179729519	179729519	+	Silent	SNP	A	A	G	rs1035411	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	31	89	0	0.442857	0	A|0.292;G|0.708	0.708	strong	.	GFPT2	74	.	NM_005110	exon18	c.T1908C	p.I636I	CAGCTCAATTGTC	.	PASS	Atlas-SNP
CYP4F12	66002	hgsc.bcm.edu	37	19	15789098	15789098	+	Missense_Mutation	SNP	A	A	G	rs609636	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	118	118	139	0	1	0	A|0.063;G|0.937	0.937	strong	.	CYP4F12	89	.	NM_023944	exon3	c.A226G	p.N76D	TTGAAGAACTCGA	.	PASS	Atlas-SNP
PEMT	10400	hgsc.bcm.edu	37	17	17415893	17415893	+	Silent	SNP	C	C	T	rs35277795	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	119	52	127	0	0.436975	0	C|0.953;T|0.047	0.047	strong	.	PEMT	12	.	NM_001267552	exon4	c.G396A	p.A132A	CAGGAGCGCGAGG	.	PASS	Atlas-SNP
AAK1	22848	hgsc.bcm.edu	37	2	69741801	69741801	+	Silent	SNP	C	C	T	rs6757825	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	79	42	104	0	0.531646	0	C|0.864;T|0.136	0.136	strong	.	AAK1	121	.	NM_014911	exon13	c.G1578A	p.Q526Q	CATTAGCTGCTGT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195507365	195507365	+	Missense_Mutation	SNP	G	G	A	rs75737861	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	60	44	68	0	0.733333	0	G|0.537;A|0.463	0.463	strong	.	MUC4	1505	.	NM_018406	exon2	c.C11086T	p.P3696S	GAAGAGGGGTGGC	.	PASS	Atlas-SNP
MDN1	23195	hgsc.bcm.edu	37	6	90408589	90408589	+	Silent	SNP	A	A	G	rs3736984	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	32	68	0	0.463768	0	A|0.865;G|0.135	0.135	strong	.	MDN1	478	.	NM_014611	exon59	c.T9163C	p.L3055L	CCTTCAATGTGGA	.	PASS	Atlas-SNP
PER3	8863	hgsc.bcm.edu	37	1	7890053	7890053	+	Missense_Mutation	SNP	G	G	A	rs1776342	bycluster;byfrequency;by2hit2allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	60	12	145	0	0.2	0	G|0.990;A|0.010	0.010	strong	PER3,NS,carcinoma,0,1	PER3	95	1	NM_016831	exon18	c.G3019A	p.A1007T	GCCAGCGCTCTGT	.	scavenged	Atlas-SNP
NCAPH	23397	hgsc.bcm.edu	37	2	97030247	97030247	+	Missense_Mutation	SNP	T	T	C	rs2305935	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	183	100	242	0	0.546448	0	T|0.688;C|0.312	0.312	strong	NCAPH,NS,carcinoma,0,1	NCAPH	67	1	NM_015341	exon13	c.T1616C	p.V539A	ATAGGGTAGAGAC	.	PASS	Atlas-SNP
FAM86C1	55199	hgsc.bcm.edu	37	11	71507157	71507157	+	Missense_Mutation	SNP	C	C	T	rs150702586	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	185	37	177	0	0.2	0	C|0.996;T|0.005	0.005	strong	.	FAM86C1	27	.	NM_018172	exon4	c.C356T	p.T119I	ATTCTACATGGCC	.	PASS	Atlas-SNP
AGXT2	64902	hgsc.bcm.edu	37	5	34998877	34998877	+	Missense_Mutation	SNP	C	C	A	rs16899974	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	110	42	106	0	0.381818	0	C|0.795;A|0.205	0.205	strong	.	AGXT2	89	.	NM_031900	exon14	c.G1492T	p.V498L	CTTCTACTGCAAA	.	PASS	Atlas-SNP
SERPINB9	5272	hgsc.bcm.edu	37	6	2892130	2892130	+	Silent	SNP	G	G	A	rs61748573	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	51	18	33	0	0.352941	0	G|0.976;A|0.024	0.024	strong	.	SERPINB9	37	.	NM_004155	exon6	c.C660T	p.P220P	GGCGTAGGGCAGC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195513413	195513413	+	Missense_Mutation	SNP	G	G	A	rs7374593	by2hit2allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	174	16	220	0	0.091954	0	.	.	weak	MUC4_ENST00000463781,trunk,malignant_melanoma,0,4	MUC4	1505	4	NM_018406	exon2	c.C5038T	p.P1680S	GAAGAGGGGTGGC	.	PASS	Atlas-SNP
DDX55	57696	hgsc.bcm.edu	37	12	124104686	124104686	+	Silent	SNP	G	G	A	rs3204541	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	114	113	152	0	0.991228	0	G|0.707;A|0.293	0.293	strong	.	DDX55	51	.	NM_020936	exon14	c.G1802A	p.X601X	ACTGCTGATTCCA	.	PASS	Atlas-SNP
RABL6	55684	hgsc.bcm.edu	37	9	139732331	139732331	+	Missense_Mutation	SNP	G	G	C	rs2811741	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	293	162	288	2	0.552901	0.00694444	G|0.193;C|0.807	0.807	strong	C9orf86_ENST00000371663,NS,carcinoma,0,2	.	.	2	NM_001173988	exon10	c.G1147C	p.E383Q	GCCGCAGAGGGCC	.	scavenged	Atlas-SNP
OR10G9	219870	hgsc.bcm.edu	37	11	123894553	123894553	+	Silent	SNP	G	G	A	rs61908612	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	156	115	166	1	0.737179	0.0060241	G|0.941;A|0.059	0.059	strong	.	OR10G9	80	.	NM_001001953	exon1	c.G834A	p.L278L	TGTGCTGACACCC	.	PASS	Atlas-SNP
OR8U1	219417	hgsc.bcm.edu	37	11	56143592	56143592	+	Missense_Mutation	SNP	C	C	T	rs17150411	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	170	19	239	2	0.111765	0.0083682	C|0.653;N|0.000	.	strong	OR8U1,colon,carcinoma,0,1	OR8U1	59	1	NM_001005204	exon1	c.C493T	p.R165C	ACCTTCCGCCTCT	.	scavenged	Atlas-SNP
DIS3L	115752	hgsc.bcm.edu	37	15	66625470	66625470	+	Silent	SNP	G	G	A	rs3759785	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	51	28	33	0	0.54902	0	G|0.973;A|0.027	0.027	strong	.	DIS3L	175	.	NM_001143688	exon17	c.G2985A	p.E995E	GAGTGAGTTAGTG	.	PASS	Atlas-SNP
CLCN7	1186	hgsc.bcm.edu	37	16	1500567	1500567	+	Silent	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	136	106	90	0	0.779412	0	.	.	none	.	CLCN7	53	.	NM_001287	exon17	c.G1548A	p.P516P	CAGGGACGGGATG	.	PASS	Atlas-SNP
DENND2C	163259	hgsc.bcm.edu	37	1	115168600	115168600	+	Missense_Mutation	SNP	A	A	T	rs7541738	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	47	18	82	0	0.382979	0	A|0.824;T|0.176	0.176	strong	.	DENND2C	105	.	NM_001256404	exon4	c.T6A	p.D2E	ACCAACATCCATG	.	PASS	Atlas-SNP
ADAMTS7	11173	hgsc.bcm.edu	37	15	79067055	79067055	+	Missense_Mutation	SNP	C	C	T	rs2277549	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	115	18	96	0	0.156522	0	C|0.727;T|0.273	0.273	strong	ADAMTS7,NS,carcinoma,-1,1	ADAMTS7	142	1	NM_014272	exon12	c.G1787A	p.R596H	GAGGGGCGGCCAG	.	PASS	Atlas-SNP
NES	10763	hgsc.bcm.edu	37	1	156639753	156639753	+	Silent	SNP	G	G	A	rs11582300	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	200	101	235	0	0.505	0	G|0.413;A|0.587	0.587	strong	.	NES	196	.	NM_006617	exon4	c.C4227T	p.S1409S	CCCATCGGACTCC	.	PASS	Atlas-SNP
OR51A4	401666	hgsc.bcm.edu	37	11	4967834	4967834	+	Missense_Mutation	SNP	C	C	G	rs201205025		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	155	11	980	0	0.0709677	0	.	.	weak	OR51A4,colon,carcinoma,-1,1	OR51A4	73	1	NM_001005329	exon1	c.G497C	p.R166T	AAGTTTCTTAAAG	.	scavenged	Atlas-SNP
PRX	57716	hgsc.bcm.edu	37	19	40904602	40904602	+	Silent	SNP	G	G	A	rs744389	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	113	64	109	0	0.566372	0	G|0.889;A|0.111	0.111	strong	.	PRX	151	.	NM_181882	exon6	c.C306T	p.T102T	GTCCCCGGTGGGC	.	PASS	Atlas-SNP
OR1A2	26189	hgsc.bcm.edu	37	17	3101578	3101578	+	Missense_Mutation	SNP	G	G	T	rs2241091	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	151	148	175	1	0.980132	0.00571429	G|0.704;T|0.295	0.295	strong	.	OR1A2	52	.	NM_012352	exon1	c.G766T	p.G256C	ACGATGGGCATGT	.	PASS	Atlas-SNP
CD3G	917	hgsc.bcm.edu	37	11	118219742	118219742	+	Missense_Mutation	SNP	G	G	A	rs146393315	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	192	43	186	0	0.223958	0	G|0.999;A|0.001	0.001	strong	.	CD3G	31	.	NM_000073	exon2	c.G56A	p.G19D	TTACAGGTACTTT	.	PASS	Atlas-SNP
STARD8	9754	hgsc.bcm.edu	37	X	67937976	67937976	+	Missense_Mutation	SNP	G	G	A	rs55962426	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	126	126	175	0	1	0	G|0.938;A|0.062	0.062	strong	.	STARD8	282	.	NM_001142503	exon6	c.G1220A	p.R407Q	GGTCTCGGGCCAT	.	PASS	Atlas-SNP
CDH19	28513	hgsc.bcm.edu	37	18	64211251	64211251	+	Missense_Mutation	SNP	C	C	T	rs72954429	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	32	95	0	0.551724	0	C|0.896;T|0.104	0.104	strong	.	CDH19	141	.	NM_021153	exon7	c.G1171A	p.V391M	ACACCACGCCTAC	.	PASS	Atlas-SNP
TFB2M	64216	hgsc.bcm.edu	37	1	246707858	246707858	+	Silent	SNP	A	A	G	rs3129568	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	115	52	133	0	0.452174	0	A|0.783;G|0.217	0.217	strong	.	TFB2M	46	.	NM_022366	exon7	c.T984C	p.F328F	CCTCCCAAAACAG	.	PASS	Atlas-SNP
IGFL1	374918	hgsc.bcm.edu	37	19	46733409	46733409	+	Missense_Mutation	SNP	G	G	A	rs75105417	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	113	52	153	0	0.460177	0	G|0.932;A|0.068	0.068	strong	.	IGFL1	10	.	NM_198541	exon2	c.G70A	p.G24R	TCACACGGAGCCC	.	PASS	Atlas-SNP
LMO7	4008	hgsc.bcm.edu	37	13	76382100	76382100	+	Missense_Mutation	SNP	C	C	T	rs2241913	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	27	77	0	0.36	0	C|0.885;T|0.115	0.115	strong	.	LMO7	334	.	NM_015842	exon7	c.C982T	p.L328F	TGTGTACTTGAAA	.	PASS	Atlas-SNP
ZNF814	730051	hgsc.bcm.edu	37	19	58385714	58385714	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	175	6	213	0	0.0342857	0	.	.	none	ZNF814,NS,carcinoma,0,2	ZNF814	93	2	NM_001144989	exon3	c.A1044C	p.E348D	TTTTTTTTCAGTG	.	scavenged	Atlas-SNP
PATE3	100169851	hgsc.bcm.edu	37	11	125659371	125659371	+	Missense_Mutation	SNP	G	G	A	rs78883072	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	76	53	91	0	0.697368	0	G|0.923;A|0.077	0.077	strong	.	PATE3	4	.	NM_001129883	exon2	c.G140A	p.G47D	AGAAGGGCGAGGC	.	PASS	Atlas-SNP
KCNJ13	3769	hgsc.bcm.edu	37	2	233633460	233633460	+	Missense_Mutation	SNP	G	G	A	rs1801251	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	118	62	179	0	0.525424	0	G|0.684;N|0.000	.	strong	KCNJ13,NS,carcinoma,0,1	KCNJ13	18	1	NM_002242	exon3	c.C524T	p.T175I	ACTGCTGTGTCAG	.	PASS	Atlas-SNP
UTP20	27340	hgsc.bcm.edu	37	12	101693534	101693534	+	Missense_Mutation	SNP	C	C	G	rs4764643	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	46	149	0	0.5	0	C|0.865;G|0.135	0.135	strong	.	UTP20	222	.	NM_014503	exon13	c.C1505G	p.S502C	TTTTATCTATAAT	.	PASS	Atlas-SNP
SLC7A11	23657	hgsc.bcm.edu	37	4	139140494	139140494	+	Silent	SNP	G	G	C	rs6838248	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	121	52	202	0	0.429752	0	G|0.601;C|0.399	0.399	strong	.	SLC7A11	40	.	NM_014331	exon5	c.C672G	p.A224A	TGAAAAGGCGTCT	.	PASS	Atlas-SNP
USP34	9736	hgsc.bcm.edu	37	2	61647901	61647901	+	Silent	SNP	A	A	G	rs778155	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	282	281	100	0	0.996454	0	A|0.679;G|0.320	0.320	strong	USP34,colon,carcinoma,0,1	USP34	334	1	NM_014709	exon2	c.T111C	p.Y37Y	ATTGATATAAGTA	.	PASS	Atlas-SNP
CXCR2	3579	hgsc.bcm.edu	37	2	219000310	219000310	+	Silent	SNP	C	C	T	rs2230054	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	101	48	124	0	0.475248	0	C|0.465;T|0.535	0.535	strong	CXCR2,NS,carcinoma,0,1	CXCR2	54	1	NM_001168298	exon4	c.C786T	p.L262L	CCTGCTCTGCTGG	.	PASS	Atlas-SNP
COL9A3	1299	hgsc.bcm.edu	37	20	61448933	61448933	+	Silent	SNP	C	C	A	rs2273078	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	43	16	36	0	0.372093	0	C|0.816;A|0.184	0.184	strong	.	COL9A3	70	.	NM_001853	exon2	c.C93A	p.P31P	ACTCCCCGGCCCC	.	PASS	Atlas-SNP
LAMA5	3911	hgsc.bcm.edu	37	20	60926828	60926828	+	Silent	SNP	G	G	A	rs62204553	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	32	63	0	0.551724	0	G|0.924;A|0.076	0.076	strong	.	LAMA5	268	.	NM_005560	exon6	c.C888T	p.I296I	GCCTCCGATGCTG	.	PASS	Atlas-SNP
PGD	5226	hgsc.bcm.edu	37	1	10460485	10460485	+	Silent	SNP	T	T	C	rs1049887	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	124	63	179	0	0.508065	0	T|0.754;C|0.246	0.246	strong	PGD,NS,adenoma,0,2	PGD	39	2	NM_002631	exon3	c.T120C	p.D40D	AGTTGATGATTTC	.	PASS	Atlas-SNP
ANGPTL4	51129	hgsc.bcm.edu	37	19	8436289	8436289	+	Missense_Mutation	SNP	G	G	A	rs139998264	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	81	40	92	0	0.493827	0	G|0.999;A|0.001	0.001	strong	.	ANGPTL4	21	.	NM_139314	exon6	c.G922A	p.V308M	GCACCCGTGGCCG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195505930	195505930	+	Missense_Mutation	SNP	C	C	G	rs201499581	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	51	19	46	2	0.372549	0.0434783	.	.	weak	MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	NM_018406	exon2	c.G12521C	p.G4174A	GGGGTGCCGTGAC	.	scavenged	Atlas-SNP
EHD4	30844	hgsc.bcm.edu	37	15	42211486	42211486	+	Silent	SNP	A	A	G	rs1704396	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	62	37	45	0	0.596774	0	A|0.517;G|0.483	0.483	strong	.	EHD4	46	.	NM_139265	exon4	c.T846C	p.F282F	GTCTCTAAAGAGG	.	PASS	Atlas-SNP
ADAM28	10863	hgsc.bcm.edu	37	8	24177788	24177788	+	Missense_Mutation	SNP	A	A	G	rs200839167	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	91	19	96	0	0.208791	0	A|0.999;G|0.001	0.001	weak	.	ADAM28	100	.	NM_014265	exon7	c.A616G	p.I206V	AAATACATAGAAT	.	PASS	Atlas-SNP
AKR1B10	57016	hgsc.bcm.edu	37	7	134215403	134215403	+	Silent	SNP	T	T	C	rs1722883	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	119	116	104	0	0.97479	0	T|0.460;C|0.540	0.540	strong	.	AKR1B10	42	.	NM_020299	exon2	c.T75C	p.L25L	TCCTCTTGGCAAA	.	PASS	Atlas-SNP
OR6M1	390261	hgsc.bcm.edu	37	11	123676413	123676413	+	Silent	SNP	G	G	A	rs7952150	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	55	37	73	0	0.672727	0	G|0.788;A|0.212	0.212	strong	.	OR6M1	60	.	NM_001005325	exon1	c.C645T	p.Y215Y	GTACACGTAGGAC	.	PASS	Atlas-SNP
TRIM31	11074	hgsc.bcm.edu	37	6	30080496	30080496	+	Silent	SNP	G	G	A	rs2844793	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	96	53	134	0	0.552083	0	G|0.893;A|0.107	0.107	strong	.	TRIM31	40	.	NM_007028	exon2	c.C87T	p.I29I	ACAGTCGATGGTG	.	PASS	Atlas-SNP
OR6S1	341799	hgsc.bcm.edu	37	14	21109671	21109671	+	Silent	SNP	A	A	G	rs11627574	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	106	53	96	0	0.5	0	A|0.484;G|0.516	0.516	strong	.	OR6S1	49	.	NM_001001968	exon1	c.T180C	p.P60P	GTACATAGGGGTC	.	PASS	Atlas-SNP
ANKRD13A	88455	hgsc.bcm.edu	37	12	110456175	110456175	+	Silent	SNP	A	A	G	rs2302689	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	226	125	256	0	0.553097	0	A|0.706;G|0.294	0.294	strong	.	ANKRD13A	39	.	NM_033121	exon5	c.A426G	p.P142P	ATGCCCAAATGAT	.	PASS	Atlas-SNP
C1orf141	400757	hgsc.bcm.edu	37	1	67558739	67558739	+	Silent	SNP	C	C	T	rs6588237	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	75	116	0	1	0	C|0.118;T|0.882	0.882	strong	.	C1orf141	58	.	NM_001276351	exon8	c.G1152A	p.T384T	CAGTGGCGTTACA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195507836	195507836	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	231	19	176	2	0.0822511	0.0113636	.	.	none	MUC4_ENST00000463781,trunk,malignant_melanoma,0,2	MUC4	1505	2	NM_018406	exon2	c.G10615C	p.V3539L	TGGTGACAGGAAG	.	scavenged	Atlas-SNP
ZNF782	158431	hgsc.bcm.edu	37	9	99581568	99581568	+	Missense_Mutation	SNP	T	T	C	rs34763627	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	28	88	0	0.373333	0	T|0.930;C|0.070	0.070	strong	.	ZNF782	64	.	NM_001001662	exon6	c.A737G	p.N246S	AATTTATTGAAAT	.	PASS	Atlas-SNP
H2AFV	94239	hgsc.bcm.edu	37	7	44875203	44875203	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	56	15	87	0	0.267857	0	.	.	none	.	H2AFV	14	.	NM_012412	exon4	c.C250G	p.P84A	GACGCGGAGTGAT	.	PASS	Atlas-SNP
PDE4DIP	9659	hgsc.bcm.edu	37	1	144916676	144916676	+	Nonsense_Mutation	SNP	C	C	T	rs1698683	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	283	68	318	0	0.240283	0	T|0.001;G|0.732	0.001	strong	.	PDE4DIP	817	.	NM_001002811	exon9	c.G2168A	p.W723X	TTCAGCCACTGGA	.	PASS	Atlas-SNP
CALCOCO2	10241	hgsc.bcm.edu	37	17	46939658	46939658	+	Missense_Mutation	SNP	C	C	G	rs10278	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	158	74	171	0	0.468354	0	C|0.673;G|0.327	0.327	strong	.	CALCOCO2	29	.	NM_001261390	exon13	c.C1237G	p.P413A	TCTTCCCCCAGCC	.	PASS	Atlas-SNP
GOLGB1	2804	hgsc.bcm.edu	37	3	121410844	121410844	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	483	236	491	0	0.488613	0	.	.	none	.	GOLGB1	319	.	NM_001256486	exon14	c.A7367C	p.E2456A	ATGTTTTCCTTTT	.	PASS	Atlas-SNP
TDRD9	122402	hgsc.bcm.edu	37	14	104497543	104497543	+	Silent	SNP	C	C	T	rs10135507	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	128	65	149	0	0.507812	0	C|0.684;T|0.316	0.316	strong	TDRD9_ENST00000409874,NS,carcinoma,0,2	TDRD9	175	2	NM_153046	exon29	c.C3381T	p.L1127L	ATATCTCATCCGG	.	PASS	Atlas-SNP
CLDN20	49861	hgsc.bcm.edu	37	6	155597147	155597147	+	Silent	SNP	C	C	T	rs1555774	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	111	76	152	0	0.684685	0	C|0.681;T|0.319	0.319	strong	.	CLDN20	10	.	NM_001001346	exon2	c.C294T	p.S98S	CACTTCCACAGTA	.	PASS	Atlas-SNP
MYOC	4653	hgsc.bcm.edu	37	1	171621525	171621525	+	Missense_Mutation	SNP	C	C	T	rs2234926	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	264	122	300	0	0.462121	0	C|0.909;T|0.091	0.091	strong	.	MYOC	69	.	NM_000261	exon1	c.G227A	p.R76K	CTGTCTCTCTGTA	.	PASS	Atlas-SNP
UBR2	23304	hgsc.bcm.edu	37	6	42627434	42627434	+	Missense_Mutation	SNP	G	G	A	rs6917033	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	38	82	0	0.487179	0	A|0.421;G|0.579	0.421	strong	.	UBR2	134	.	NM_015255	exon30	c.G3283A	p.A1095T	GGCCCCGCACAAA	.	PASS	Atlas-SNP
C17orf104	284071	hgsc.bcm.edu	37	17	42745180	42745180	+	Missense_Mutation	SNP	A	A	G	rs77416189	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	40	82	0	0.555556	0	A|0.990;G|0.010	0.010	strong	.	C17orf104	75	.	NM_001145080	exon5	c.A1901G	p.Y634C	ATACATACCAAGA	.	PASS	Atlas-SNP
MTFR1	9650	hgsc.bcm.edu	37	8	66620359	66620359	+	Silent	SNP	G	G	A	rs13274205	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	19	19	17	0	1	0	G|0.693;A|0.307	0.307	strong	.	MTFR1	26	.	NM_001145839	exon7	c.G1046A	p.X349X	GGAGGTGATACAG	.	PASS	Atlas-SNP
MYH2	4620	hgsc.bcm.edu	37	17	10447057	10447057	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	307	6	344	2	0.019544	0.00581395	.	.	none	MYH2,NS,carcinoma,+2,1	MYH2	390	1	NM_017534	exon8	c.A712G	p.T238A	TCACGGTCTTGGC	.	scavenged	Atlas-SNP
CHRNA3	1136	hgsc.bcm.edu	37	15	78894339	78894339	+	Silent	SNP	G	G	A	rs1051730	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	338	338	288	0	1	0	G|0.754;A|0.246	0.246	strong	.	CHRNA3	56	.	NM_000743	exon5	c.C645T	p.Y215Y	GTGTTTGTAGCCT	.	PASS	Atlas-SNP
KIAA1549	57670	hgsc.bcm.edu	37	7	138601826	138601826	+	Missense_Mutation	SNP	G	G	A	rs2251220	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	41	21	45	0	0.512195	0	G|0.579;A|0.421	0.421	strong	.	KIAA1549	314	.	NM_020910	exon2	c.C2546T	p.S849L	ACAAACGAGGATC	.	PASS	Atlas-SNP
C4orf17	84103	hgsc.bcm.edu	37	4	100443784	100443784	+	Silent	SNP	C	C	G	rs61732380	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	91	41	111	0	0.450549	0	C|0.769;G|0.231	0.231	strong	.	C4orf17	42	.	NM_032149	exon3	c.C255G	p.S85S	CCCCTCCAGCACT	.	PASS	Atlas-SNP
RP1L1	94137	hgsc.bcm.edu	37	8	10467124	10467124	+	Missense_Mutation	SNP	G	G	C	rs4841399	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	45	37	45	0	0.822222	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
GATA2	2624	hgsc.bcm.edu	37	3	128204951	128204951	+	Missense_Mutation	SNP	C	C	T	rs2335052	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	104	60	118	1	0.576923	0.00847458	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	.	scavenged	Atlas-SNP
OR4K14	122740	hgsc.bcm.edu	37	14	20482919	20482919	+	Missense_Mutation	SNP	A	A	C	rs17308108	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	63	32	96	0	0.507937	0	A|0.922;C|0.078	0.078	strong	.	OR4K14	86	.	NM_001004712	exon1	c.T434G	p.L145R	AGCACCAGCCTGA	.	PASS	Atlas-SNP
TMEM140	55281	hgsc.bcm.edu	37	7	134849577	134849577	+	Silent	SNP	A	A	C	rs2288237	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	123	123	129	0	1	0	A|0.538;C|0.462	0.462	strong	TMEM140,NS,carcinoma,+1,1	TMEM140	18	1	NM_018295	exon2	c.A384C	p.A128A	GCTGGCAGGCGGC	.	PASS	Atlas-SNP
C10orf71	118461	hgsc.bcm.edu	37	10	50531606	50531606	+	Missense_Mutation	SNP	C	C	A	rs55780106	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	42	16	45	0	0.380952	0	C|0.803;A|0.197	0.197	strong	.	C10orf71	179	.	NM_001135196	exon3	c.C1016A	p.A339E	GACTTGCAGCAGG	.	PASS	Atlas-SNP
C17orf102	400591	hgsc.bcm.edu	37	17	32906038	32906038	+	Missense_Mutation	SNP	G	G	C	rs117721431	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	45	27	54	0	0.6	0	G|0.965;C|0.035	0.035	strong	C17orf102,NS,carcinoma,0,2	C17orf102	24	2	NM_207454	exon1	c.C262G	p.R88G	AGCAGCGAGGCTG	.	PASS	Atlas-SNP
ALDH1A3	220	hgsc.bcm.edu	37	15	101445815	101445815	+	Missense_Mutation	SNP	A	A	G	rs3803430	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	71	52	57	0	0.732394	0	A|0.882;G|0.118	0.118	strong	.	ALDH1A3	61	.	NM_000693	exon10	c.A1156G	p.M386V	TCAGCCATGGAAG	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29911086	29911086	+	Missense_Mutation	SNP	T	T	C	rs1136700	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	136	134	216	3	0.985294	0.0138889	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	.	scavenged	Atlas-SNP
IZUMO1	284359	hgsc.bcm.edu	37	19	49244220	49244220	+	Missense_Mutation	SNP	G	G	A	rs66877153	alternate_allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	104	51	126	0	0.490385	0	AA|0.500;CG|0.500	.	alt	.	IZUMO1	30	.	NM_182575	exon10	c.C998T	p.A333V	TCGGCCGCTCCAC	.	PASS	Atlas-SNP
SLC12A5	57468	hgsc.bcm.edu	37	20	44664493	44664493	+	Silent	SNP	G	G	T	rs77659338	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	167	90	130	0	0.538922	0	G|0.935;T|0.065	0.065	strong	.	SLC12A5	181	.	NM_001134771	exon4	c.G426T	p.R142R	CCTGCGGCTCACC	.	PASS	Atlas-SNP
CEP164	22897	hgsc.bcm.edu	37	11	117214881	117214881	+	Splice_Site	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	157	28	183	0	0.178344	0	.	.	none	CEP164,colon,carcinoma,-2,1	CEP164	121	1	NM_001271933	exon3	c.83-1G>A	.	CTTGCAGAAATTC	.	PASS	Atlas-SNP
KDM3B	51780	hgsc.bcm.edu	37	5	137717213	137717213	+	Silent	SNP	G	G	A	rs10073922	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	75	100	1	1	0.01	G|0.716;A|0.284	0.284	strong	KDM3B,NS,carcinoma,+2,2	KDM3B	177	2	NM_016604	exon6	c.G714A	p.E238E	TGGTGAGATCAAG	.	PASS	Atlas-SNP
WDR93	56964	hgsc.bcm.edu	37	15	90245174	90245174	+	Missense_Mutation	SNP	T	T	A	rs4287542	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	159	61	159	0	0.383648	0	T|0.574;A|0.426	0.426	strong	.	WDR93	63	.	NM_020212	exon2	c.T197A	p.L66H	TGAACCTTCTGTT	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	36	36	41	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
EXOC3L2	90332	hgsc.bcm.edu	37	19	45728123	45728123	+	Silent	SNP	C	C	T	rs10410003	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	290	137	292	0	0.472414	0	C|0.898;T|0.102	0.102	strong	.	EXOC3L2	30	.	NM_138568	exon6	c.G453A	p.P151P	CCGGGCCGGCTCG	.	PASS	Atlas-SNP
GTPBP10	85865	hgsc.bcm.edu	37	7	90014408	90014408	+	Missense_Mutation	SNP	G	G	A	rs17863999	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	38	20	76	0	0.526316	0	G|0.805;A|0.195	0.195	strong	.	GTPBP10	31	.	NM_033107	exon10	c.G1104A	p.M368I	TACAATGTCTTCT	.	PASS	Atlas-SNP
MAGEA4	4103	hgsc.bcm.edu	37	X	151092653	151092653	+	Missense_Mutation	SNP	G	G	A	rs1047251	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	188	182	278	0	0.968085	0	0|0.004;A|0.556	0.556	strong	.	MAGEA4	68	.	NM_001011548	exon3	c.G517A	p.A173T	GACCCCGCCAGCA	.	PASS	Atlas-SNP
ZFYVE16	9765	hgsc.bcm.edu	37	5	79735832	79735832	+	Silent	SNP	C	C	T	rs114761271	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	67	23	79	0	0.343284	0	C|0.986;T|0.014	0.014	strong	.	ZFYVE16	100	.	NM_001105251	exon5	c.C2400T	p.C800C	AGTCTGCTATGAA	.	PASS	Atlas-SNP
KIAA1107	23285	hgsc.bcm.edu	37	1	92649498	92649498	+	Missense_Mutation	SNP	T	T	A	rs75212872	byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	206	84	251	0	0.407767	0	T|0.999;A|0.001	0.001	strong	.	KIAA1107	60	.	NM_015237	exon9	c.T3676A	p.Y1226N	CCAATATATGAGA	.	PASS	Atlas-SNP
PALLD	23022	hgsc.bcm.edu	37	4	169432841	169432841	+	Silent	SNP	G	G	A	rs1806729	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	100	98	140	0	0.98	0	G|0.728;A|0.272	0.272	strong	.	PALLD	179	.	NM_001166108	exon2	c.G186A	p.K62K	GGAAAAGGAGATC	.	PASS	Atlas-SNP
TAF4B	6875	hgsc.bcm.edu	37	18	23865851	23865851	+	Silent	SNP	C	C	T	rs12456749	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	81	46	107	0	0.567901	0	C|0.797;T|0.203	0.203	strong	.	TAF4B	71	.	NM_005640	exon7	c.C978T	p.S326S	GAAAAGCGTGGTT	.	PASS	Atlas-SNP
ITGB6	3694	hgsc.bcm.edu	37	2	160968628	160968628	+	Silent	SNP	A	A	G	rs16844790	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	213	118	232	0	0.553991	0	A|0.805;G|0.195	0.195	strong	.	ITGB6	68	.	NM_000888	exon13	c.T2064C	p.N688N	CCCCTCATTATCT	.	PASS	Atlas-SNP
FAM160A1	729830	hgsc.bcm.edu	37	4	152498625	152498625	+	Silent	SNP	C	C	T	rs17275536	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	125	62	142	0	0.496	0	C|0.718;T|0.282	0.282	strong	.	FAM160A1	60	.	NM_001109977	exon5	c.C129T	p.H43H	GAAGCACGACCCC	.	PASS	Atlas-SNP
EPS8L2	64787	hgsc.bcm.edu	37	11	721931	721931	+	Silent	SNP	C	C	T	rs7949926	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	121	103	97	0	0.85124	0	C|0.874;T|0.126	0.126	strong	EPS8L2,NS,carcinoma,0,1	EPS8L2	42	1	NM_022772	exon11	c.C924T	p.P308P	ACGGCCCCCCTCT	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29912108	29912108	+	Missense_Mutation	SNP	G	G	C	rs75766454		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	118	47	147	0	0.398305	0	.	.	weak	.	HLA-A	89	.	NM_001242758	exon4	c.G829C	p.E277Q	TCTGGAGAGGAGC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195505835	195505835	+	Missense_Mutation	SNP	C	C	T	rs58500707	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	113	11	70	3	0.0973451	0.0428571	.	.	weak	MUC4_ENST00000463781,NS,carcinoma,0,6	MUC4	1505	6	NM_018406	exon2	c.G12616A	p.A4206T	GGGTGGCGTGACC	.	scavenged	Atlas-SNP
ITGA4	3676	hgsc.bcm.edu	37	2	182392096	182392096	+	Silent	SNP	A	A	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	32	84	0	0.551724	0	.	.	none	.	ITGA4	142	.	NM_000885	exon22	c.A2412G	p.K804K	GGAGAAAATGAAC	.	PASS	Atlas-SNP
ZNF578	147660	hgsc.bcm.edu	37	19	53014346	53014346	+	Missense_Mutation	SNP	G	G	A	rs56234253		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	76	38	72	0	0.5	0	.	.	weak	.	.	.	.	NM_001099694	exon6	c.G712A	p.E238K	ACTGGCGAAGCCT	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	249	115	258	0	0.461847	0	T|0.790;C|0.210	0.210	strong	.	PIGG	86	.	NM_001127178	exon13	c.T2795C	p.F932S	CAGTTTTCACGTA	.	PASS	Atlas-SNP
TCP10L	140290	hgsc.bcm.edu	37	21	33951068	33951068	+	Missense_Mutation	SNP	T	T	C	rs9622	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	374	138	364	1	0.368984	0.00274725	T|0.791;C|0.209	0.209	strong	.	TCP10L	24	.	NM_144659	exon4	c.A434G	p.H145R	TTCTTGTGGCCAG	.	PASS	Atlas-SNP
KLF17	128209	hgsc.bcm.edu	37	1	44595113	44595113	+	Missense_Mutation	SNP	G	G	C	rs2429051	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	106	41	88	0	0.386792	0	G|0.456;C|0.544	0.544	strong	.	KLF17	92	.	NM_173484	exon2	c.G170C	p.S57T	TACCAAGCATTCA	.	PASS	Atlas-SNP
IL4R	3566	hgsc.bcm.edu	37	16	27374696	27374696	+	Missense_Mutation	SNP	C	C	T	rs3024678	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	72	34	51	0	0.472222	0	C|0.989;T|0.011	0.011	strong	.	IL4R	70	.	NM_000418	exon11	c.C2023T	p.P675S	AGCTCCCCAGAGC	.	PASS	Atlas-SNP
GATA5	140628	hgsc.bcm.edu	37	20	61048549	61048549	+	Silent	SNP	G	G	A	rs41305803	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	128	49	167	0	0.382812	0	G|0.568;A|0.432	0.432	strong	.	GATA5	22	.	NM_080473	exon3	c.C609T	p.D203D	GGTGCCGTCTCGG	.	PASS	Atlas-SNP
MAGEA4	4103	hgsc.bcm.edu	37	X	151092220	151092220	+	Silent	SNP	A	A	G	rs1047248	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	149	147	231	1	0.986577	0.004329	A|0.460;G|0.540	0.540	strong	.	MAGEA4	68	.	NM_001011548	exon3	c.A84G	p.A28A	GGGTGCACAGGCT	.	PASS	Atlas-SNP
GABRA2	2555	hgsc.bcm.edu	37	4	46314593	46314593	+	Silent	SNP	T	T	C	rs279858	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	173	100	194	0	0.578035	0	T|0.616;C|0.384	0.384	strong	GABRA2,NS,carcinoma,0,2	GABRA2	134	2	NM_000807	exon5	c.A396G	p.K132K	TGATTTTTTCCCA	.	PASS	Atlas-SNP
TECPR1	25851	hgsc.bcm.edu	37	7	97861156	97861156	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	61	14	57	0	0.229508	0	.	.	none	.	TECPR1	77	.	NM_015395	exon13	c.G1934T	p.S645I	AGGATGCTGTCCC	.	PASS	Atlas-SNP
ARMC8	25852	hgsc.bcm.edu	37	3	137928677	137928677	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	160	4	191	0	0.025	0	.	.	none	ARMC8_ENST00000481646,colon,carcinoma,-1,4	ARMC8	79	4	NM_001267041	exon2	c.C64T	p.R22C	AGCAGTCGCCACT	.	scavenged	Atlas-SNP
PLCG1	5335	hgsc.bcm.edu	37	20	39802374	39802374	+	Silent	SNP	C	C	T	rs150104210		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	226	135	239	0	0.597345	0	C|1.000;T|0.000	0.000	weak	.	PLCG1	111	.	NM_182811	exon29	c.C3477T	p.F1159F	GCGCTTCGTGGTG	.	PASS	Atlas-SNP
CCDC111	201973	hgsc.bcm.edu	37	4	185615764	185615764	+	Missense_Mutation	SNP	C	C	A	rs14969	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	240	114	285	0	0.475	0	C|0.824;A|0.176	0.176	strong	.	CCDC111	43	.	NM_152683	exon14	c.C1514A	p.T505K	TGTCAACAGGTGC	.	PASS	Atlas-SNP
FAM19A4	151647	hgsc.bcm.edu	37	3	68782299	68782299	+	Silent	SNP	C	C	T	rs146641270	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	62	29	81	0	0.467742	0	C|0.999;T|0.001	0.001	strong	.	FAM19A4	23	.	NM_182522	exon6	c.G417A	p.T139T	CTACCGCGTTACC	.	PASS	Atlas-SNP
GPR162	27239	hgsc.bcm.edu	37	12	6935977	6935977	+	Missense_Mutation	SNP	A	A	G	rs11612427	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	70	38	74	0	0.542857	0	A|0.801;G|0.199	0.199	strong	.	GPR162	55	.	NM_019858	exon5	c.A1375G	p.R459G	GGACAAAGACACA	.	PASS	Atlas-SNP
KIAA0368	23392	hgsc.bcm.edu	37	9	114174415	114174415	+	Missense_Mutation	SNP	T	T	C	rs2418163	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	52	50	75	0	0.961538	0	C|0.419;N|0.002	0.419	strong	.	KIAA0368	144	.	NM_001080398	exon22	c.A2627G	p.N876S	TTACTGTTATTCA	.	PASS	Atlas-SNP
VRK1	7443	hgsc.bcm.edu	37	14	97321689	97321689	+	Silent	SNP	C	C	T	rs2230532	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	36	98	0	0.418605	0	C|0.650;T|0.350	0.350	strong	.	VRK1	34	.	NM_003384	exon8	c.C705T	p.G235G	CAATGGCGTGGGT	.	PASS	Atlas-SNP
IPO11	51194	hgsc.bcm.edu	37	5	61772535	61772535	+	Silent	SNP	G	G	T	rs26635	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	422	145	371	0	0.343602	0	G|0.567;T|0.433	0.433	strong	IPO11,NS,carcinoma,0,1	IPO11	76	1	NM_001134779	exon9	c.G903T	p.V301V	TAATGTGTGTAGA	.	PASS	Atlas-SNP
MFGE8	4240	hgsc.bcm.edu	37	15	89450546	89450546	+	Silent	SNP	C	C	T	rs1878327	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	201	200	174	0	0.995025	0	C|0.333;T|0.667	0.667	strong	MFGE8,NS,carcinoma,0,1	MFGE8	60	1	NM_001114614	exon3	c.G267A	p.S89S	CACAGACGAGGCG	.	PASS	Atlas-SNP
GXYLT1	283464	hgsc.bcm.edu	37	12	42503467	42503467	+	Silent	SNP	T	T	C	rs7312933	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	90	47	75	0	0.522222	0	T|0.670;C|0.330	0.330	strong	.	GXYLT1	47	.	NM_173601	exon4	c.A513G	p.T171T	ATTAAATGTTTGT	.	PASS	Atlas-SNP
AMPD3	272	hgsc.bcm.edu	37	11	10503736	10503736	+	Missense_Mutation	SNP	C	C	T	rs11042836	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	72	51	0	0.837209	0	C|0.954;T|0.046	0.046	strong	.	AMPD3	68	.	NM_000480	exon4	c.C580T	p.R194W	CATCCGCGGGCGG	.	PASS	Atlas-SNP
ZNF880	400713	hgsc.bcm.edu	37	19	52888210	52888210	+	Silent	SNP	T	T	C	rs56151179	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	25	25	47	0	1	0	T|0.633;C|0.367	0.367	strong	.	ZNF880	45	.	NM_001145434	exon4	c.T1377C	p.T459T	TCATACTGGAGAG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195506037	195506037	+	Silent	SNP	G	G	T	rs2432527	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	95	53	89	0	0.557895	0	G|0.534;T|0.466	0.466	strong	MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	NM_018406	exon2	c.C12414A	p.S4138S	ACCTGTGGATACT	.	PASS	Atlas-SNP
ATOH7	220202	hgsc.bcm.edu	37	10	69991266	69991266	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	55	32	42	0	0.581818	0	.	.	none	.	ATOH7	4	.	NM_145178	exon1	c.A169G	p.N57D	CAGTGTTGAGCCC	.	PASS	Atlas-SNP
TDRD6	221400	hgsc.bcm.edu	37	6	46657057	46657057	+	Missense_Mutation	SNP	A	A	G	rs3799277	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	97	126	0	1	0	A|0.137;G|0.863	0.863	strong	.	TDRD6	205	.	NM_001168359	exon1	c.A1192G	p.T398A	CTGAAGACACTGA	.	PASS	Atlas-SNP
MEGF6	1953	hgsc.bcm.edu	37	1	3428160	3428160	+	Silent	SNP	T	T	G	rs2820999	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	68	48	118	0	0.705882	0	T|0.574;G|0.426	0.426	strong	.	MEGF6	91	.	NM_001409	exon9	c.A1068C	p.T356T	GGGACATGTGCAC	.	PASS	Atlas-SNP
CCDC27	148870	hgsc.bcm.edu	37	1	3669201	3669201	+	Silent	SNP	A	A	G	rs10797410	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	94	68	177	0	0.723404	0	A|0.502;G|0.498	0.498	strong	.	CCDC27	79	.	NM_152492	exon1	c.A156G	p.P52P	CAGCCCATCTCAG	.	PASS	Atlas-SNP
CCDC64B	146439	hgsc.bcm.edu	37	16	3078165	3078165	+	Missense_Mutation	SNP	A	A	G	rs12448103	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	8	4	8	0	0.5	0	A|0.823;G|0.177	0.177	strong	CCDC64B,NS,carcinoma,0,1	CCDC64B	19	1	NM_001103175	exon9	c.T1469C	p.L490P	AGGCGCAGCGAGA	.	scavenged	Atlas-SNP
AAK1	22848	hgsc.bcm.edu	37	2	69746296	69746296	+	Silent	SNP	C	C	T	rs7603932	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	118	58	138	0	0.491525	0	C|0.894;T|0.106	0.106	strong	.	AAK1	121	.	NM_014911	exon12	c.G1287A	p.P429P	AGTTTGCGGCAGA	.	PASS	Atlas-SNP
KCNN1	3780	hgsc.bcm.edu	37	19	18100552	18100552	+	Silent	SNP	A	A	C	rs41278194	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	47	23	70	0	0.489362	0	A|0.997;C|0.003	0.003	strong	.	KCNN1	74	.	NM_002248	exon8	c.A1198C	p.R400R	GTTCTCAGGGAGA	.	PASS	Atlas-SNP
PCSK5	5125	hgsc.bcm.edu	37	9	78936492	78936492	+	Missense_Mutation	SNP	A	A	G	rs1110223	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	35	18	38	0	0.514286	0	A|0.687;G|0.313	0.313	strong	.	PCSK5	329	.	NM_001190482	exon30	c.A3958G	p.K1320E	GCTGTGAAGGGGG	.	PASS	Atlas-SNP
ONECUT2	9480	hgsc.bcm.edu	37	18	55104016	55104016	+	Silent	SNP	T	T	C	rs61735644	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	98	51	94	0	0.520408	0	T|0.902;C|0.098	0.098	strong	ONECUT2,brain,glioma,0,2	ONECUT2	42	2	NM_004852	exon1	c.T1068C	p.F356F	GATCTTTGCGCAG	.	PASS	Atlas-SNP
CAMK2B	816	hgsc.bcm.edu	37	7	44282868	44282868	+	Silent	SNP	A	A	G	rs11542228	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	118	82	135	0	0.694915	0	G|0.378;N|0.001	0.378	strong	.	CAMK2B	56	.	NM_172081	exon8	c.T582C	p.P194P	GTCCACAGGCTTG	.	PASS	Atlas-SNP
GALNT14	79623	hgsc.bcm.edu	37	2	31135184	31135184	+	Missense_Mutation	SNP	G	G	T	rs2288101	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	54	54	87	0	1	0	G|0.797;T|0.203	0.203	strong	.	GALNT14	103	.	NM_001253826	exon15	c.C1420A	p.Q474K	GGATCTGCTGGGT	.	PASS	Atlas-SNP
PCDHB3	56132	hgsc.bcm.edu	37	5	140481475	140481475	+	Missense_Mutation	SNP	A	A	T	rs3733699	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	115	56	176	0	0.486957	0	A|0.825;T|0.175	0.175	strong	.	PCDHB3	208	.	NM_018937	exon1	c.A1242T	p.R414S	GACCAGATCCGAG	.	PASS	Atlas-SNP
VPS37A	137492	hgsc.bcm.edu	37	8	17123477	17123477	+	Missense_Mutation	SNP	A	A	G	rs372276569		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	183	42	230	0	0.229508	0	.	.	weak	.	VPS37A	22	.	NM_152415	exon2	c.A187G	p.I63V	CTGACAATTAACA	.	PASS	Atlas-SNP
TNN	63923	hgsc.bcm.edu	37	1	175092674	175092674	+	Missense_Mutation	SNP	C	C	T	rs2285215	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	122	55	139	2	0.45082	0.0143885	C|0.379;T|0.621	0.621	strong	TNN,colon,carcinoma,0,3	TNN	297	3	NM_022093	exon12	c.C2789T	p.P930L	AGGTTCCGGTGGG	.	scavenged	Atlas-SNP
TMEM79	84283	hgsc.bcm.edu	37	1	156255456	156255456	+	Missense_Mutation	SNP	G	G	A	rs6684514	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	74	41	72	0	0.554054	0	G|0.784;A|0.216	0.216	strong	.	TMEM79	43	.	NM_032323	exon2	c.G439A	p.V147M	CTTATCGTGCGCT	.	PASS	Atlas-SNP
MRC2	9902	hgsc.bcm.edu	37	17	60769803	60769803	+	Silent	SNP	A	A	G	rs3826537	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	76	76	60	0	1	0	A|0.680;G|0.320	0.320	strong	.	MRC2	126	.	NM_006039	exon30	c.A4431G	p.Q1477Q	TGAGCAACAAGAA	.	PASS	Atlas-SNP
BTN3A2	11118	hgsc.bcm.edu	37	6	26368938	26368938	+	Silent	SNP	C	C	T	rs77887107		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	410	268	373	0	0.653659	0	C|0.500;T|0.500	0.500	weak	.	BTN3A2	44	.	NM_001197246	exon2	c.C231T	p.N77N	GGTGAACGTGTAT	.	PASS	Atlas-SNP
OR10T2	128360	hgsc.bcm.edu	37	1	158368392	158368392	+	Missense_Mutation	SNP	C	C	T	rs61818748	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	84	42	122	0	0.5	0	C|0.948;T|0.052	0.052	strong	.	OR10T2	76	.	NM_001004475	exon1	c.G865A	p.V289I	TGTAGACAAGAGG	.	PASS	Atlas-SNP
CD82	3732	hgsc.bcm.edu	37	11	44640640	44640640	+	Silent	SNP	C	C	G	rs7107335	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	15	91	0	0.192308	0	C|0.834;G|0.165	0.165	strong	.	CD82	27	.	NM_002231	exon10	c.C768G	p.V256V	GCACGTCCATTCC	.	PASS	Atlas-SNP
KIAA1549L	25758	hgsc.bcm.edu	37	11	33628193	33628193	+	Missense_Mutation	SNP	C	C	T	rs202027343		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	149	3	153	0	0.0201342	0	.	.	weak	C11orf41_ENST00000321505,NS,carcinoma,0,1	.	.	1	NM_012194	exon13	c.C3995T	p.A1332V	TGCCAGCGAGTGA	.	scavenged	Atlas-SNP
DDX55	57696	hgsc.bcm.edu	37	12	124104049	124104049	+	Silent	SNP	A	A	G	rs15587	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	69	63	0	1	0	A|0.701;G|0.299	0.299	strong	.	DDX55	51	.	NM_020936	exon13	c.A1404G	p.G468G	GAGAGGAAAGCAG	.	PASS	Atlas-SNP
KRTAP12-2	353323	hgsc.bcm.edu	37	21	46086377	46086377	+	Missense_Mutation	SNP	A	A	G	rs2838622	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	342	182	276	1	0.532164	0.00362319	A|0.429;G|0.571	0.571	strong	.	KRTAP12-2	10	.	NM_181684	exon1	c.T427C	p.S143P	AGGAAGAGATACT	.	PASS	Atlas-SNP
BTN2A1	11120	hgsc.bcm.edu	37	6	26463574	26463574	+	Missense_Mutation	SNP	G	G	T	rs34505465	alternate_allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	65	32	65	0	0.492308	0	.	.	alt	.	BTN2A1	118	.	NM_001197234	exon4	c.G533T	p.W178L	CAGTGTGGAGGGA	.	PASS	Atlas-SNP
CD8A	925	hgsc.bcm.edu	37	2	87016506	87016506	+	Silent	SNP	A	A	G	rs3020726	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	134	70	115	0	0.522388	0	A|0.873;G|0.127	0.127	strong	.	CD8A	28	.	NM_001145873	exon7	c.T565C	p.L189L	CGGCCAAGGGCGC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195511403	195511403	+	Missense_Mutation	SNP	C	C	T	rs78846267	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	51	24	97	0	0.470588	0	C|0.995;T|0.005	0.005	weak	MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	NM_018406	exon2	c.G7048A	p.A2350T	GGGTGGCGTGACC	.	scavenged	Atlas-SNP
AZU1	566	hgsc.bcm.edu	37	19	830854	830854	+	Silent	SNP	T	T	C	rs595844	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	44	44	32	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
HDAC4	9759	hgsc.bcm.edu	37	2	240003870	240003870	+	Silent	SNP	G	G	A	rs1063639	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	262	118	261	0	0.450382	0	G|0.456;A|0.544	0.544	strong	.	HDAC4	127	.	NM_006037	exon21	c.C2565T	p.P855P	GACGCTGGGGTCG	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29911190	29911190	+	Silent	SNP	G	G	A	rs1059514	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	137	59	285	0	0.430657	0	G|0.519;A|0.481	0.481	strong	.	HLA-A	89	.	NM_001242758	exon3	c.G489A	p.A163A	CATGGCGGCTCAG	.	PASS	Atlas-SNP
OR10V1	390201	hgsc.bcm.edu	37	11	59481214	59481214	+	Silent	SNP	A	A	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	76	24	90	0	0.315789	0	.	.	none	.	OR10V1	40	.	NM_001005324	exon1	c.T105C	p.Y35Y	GGTCAGATACATC	.	PASS	Atlas-SNP
OR51G1	79324	hgsc.bcm.edu	37	11	4945199	4945199	+	Missense_Mutation	SNP	C	C	T	rs34742470	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	18	55	0	0.26087	0	C|0.911;T|0.089	0.089	strong	.	OR51G1	74	.	NM_001005237	exon1	c.G371A	p.R124H	ACGTAGCGGTCAA	.	PASS	Atlas-SNP
NSD1	64324	hgsc.bcm.edu	37	5	176636882	176636882	+	Silent	SNP	C	C	T	rs1363405	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	160	68	190	0	0.425	0	C|0.607;T|0.393	0.393	strong	.	NSD1	416	.	NM_022455	exon5	c.C1482T	p.C494C	GCCTTGCGCTAAA	.	PASS	Atlas-SNP
PDIA2	64714	hgsc.bcm.edu	37	16	336916	336916	+	Missense_Mutation	SNP	C	C	T	rs1048786	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	77	56	88	0	0.727273	0	C|0.891;T|0.109	0.109	strong	PDIA2,NS,carcinoma,0,1	PDIA2	51	1	NM_006849	exon10	c.C1504T	p.P502S	GAGGAGCCCCCGG	.	PASS	Atlas-SNP
SLC6A2	6530	hgsc.bcm.edu	37	16	55731835	55731835	+	Silent	SNP	G	G	A	rs5569	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	89	89	71	0	1	0	G|0.744;N|0.001	.	strong	.	SLC6A2	189	.	NM_001172501	exon10	c.G1287A	p.T429T	CATCACGGGCCTG	.	PASS	Atlas-SNP
TRIM65	201292	hgsc.bcm.edu	37	17	73888354	73888354	+	Silent	SNP	G	G	A	rs34974290	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	32	18	55	0	0.5625	0	G|0.787;A|0.213	0.213	strong	.	TRIM65	23	.	NM_001256124	exon3	c.C738T	p.F246F	CTGCAGGAAGGTC	.	PASS	Atlas-SNP
APBA3	9546	hgsc.bcm.edu	37	19	3753769	3753769	+	Silent	SNP	C	C	T	rs3746120	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	16	16	15	0	1	0	C|0.654;T|0.346	0.346	strong	APBA3,NS,carcinoma,0,1	APBA3	28	1	NM_004886	exon6	c.G1005A	p.A335A	GTCCTCCGCGTAG	.	PASS	Atlas-SNP
GEMIN5	25929	hgsc.bcm.edu	37	5	154282235	154282235	+	Silent	SNP	T	T	C	rs1421813	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	104	53	110	0	0.509615	0	T|0.893;C|0.107	0.107	strong	.	GEMIN5	120	.	NM_015465	exon20	c.A2730G	p.G910G	ACCTTTTCCTGTT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195508986	195508986	+	Silent	SNP	G	G	A	rs71291870	alternate_allele	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	49	23	35	0	0.469388	0	AACAG|0.500;GACAT|0.500	.	alt	MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	NM_018406	exon2	c.C9465T	p.V3155V	GTCGGTGACAGGA	.	PASS	Atlas-SNP
B4GALNT1	2583	hgsc.bcm.edu	37	12	58023981	58023981	+	Missense_Mutation	SNP	C	C	A	rs715930	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	227	101	235	0	0.444934	0	C|0.771;A|0.229	0.229	strong	B4GALNT1,NS,carcinoma,0,1	B4GALNT1	53	1	NM_001478	exon6	c.G666T	p.Q222H	AGTGACCAGTTGT	.	PASS	Atlas-SNP
KIAA1324	57535	hgsc.bcm.edu	37	1	109656946	109656946	+	Silent	SNP	T	T	C	rs667524	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	180	83	199	0	0.461111	0	T|0.512;C|0.488	0.488	strong	.	KIAA1324	77	.	NM_020775	exon1	c.T141C	p.H47H	GCTTCATGCCTGC	.	PASS	Atlas-SNP
ESYT2	57488	hgsc.bcm.edu	37	7	158528269	158528269	+	Silent	SNP	C	C	G	rs35914882	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	62	24	79	1	0.387097	0.0126582	C|0.876;G|0.124	0.124	strong	ESYT2,medulla,primitive_neuroectodermal_tumour-medulloblastoma,0,1	ESYT2	70	1	NM_020728	exon20	c.G2511C	p.V837V	CCTCTGCACTTCT	.	scavenged	Atlas-SNP
LBP	3929	hgsc.bcm.edu	37	20	36997655	36997655	+	Missense_Mutation	SNP	C	C	T	rs2232613	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	86	49	86	0	0.569767	0	C|0.926;T|0.074	0.074	strong	.	LBP	60	.	NM_004139	exon10	c.C998T	p.P333L	TCTACCCCAACAT	.	PASS	Atlas-SNP
PLEKHG5	57449	hgsc.bcm.edu	37	1	6531589	6531589	+	Missense_Mutation	SNP	C	C	T	rs74809741	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	76	34	51	0	0.447368	0	C|0.938;T|0.062	0.062	strong	.	PLEKHG5	66	.	NM_001265592	exon13	c.G1477A	p.A493T	GCAGCGCTCGCGT	.	PASS	Atlas-SNP
GNS	2799	hgsc.bcm.edu	37	12	65141588	65141588	+	Silent	SNP	C	C	T	rs2230291	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	254	121	266	0	0.476378	0	T|0.080;G|0.000;C|0.920	0.080	strong	.	GNS	41	.	NM_002076	exon3	c.G363A	p.K121K	CCAGGACTTACTA	.	PASS	Atlas-SNP
C12orf65	91574	hgsc.bcm.edu	37	12	123738265	123738265	+	Missense_Mutation	SNP	G	G	A	rs78651634	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	167	90	184	0	0.538922	0	G|0.984;A|0.016	0.016	strong	.	C12orf65	15	.	NM_001194995	exon2	c.G44A	p.R15Q	TGACCCGAATATG	.	PASS	Atlas-SNP
ABCC11	85320	hgsc.bcm.edu	37	16	48258198	48258198	+	Missense_Mutation	SNP	C	C	T	rs17822931	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	96	28	80	0	0.291667	0	C|0.792;T|0.208	0.208	strong	.	ABCC11	177	.	NM_033151	exon4	c.G538A	p.G180R	CTGGCCCGAGTAC	.	PASS	Atlas-SNP
RBBP6	5930	hgsc.bcm.edu	37	16	24582299	24582299	+	Silent	SNP	C	C	G	rs7196736	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	195	64	165	0	0.328205	0	C|0.848;G|0.152	0.152	strong	RBBP6,NS,adenocarcinoma,+2,1	RBBP6	158	1	NM_006910	exon18	c.C3912G	p.T1304T	CAATACCGCGCCA	.	PASS	Atlas-SNP
OGDH	4967	hgsc.bcm.edu	37	7	44747514	44747514	+	Silent	SNP	C	C	T	rs61756583	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	93	62	75	0	0.666667	0	C|0.956;T|0.044	0.044	strong	.	OGDH	145	.	NM_002541	exon23	c.C2988T	p.T996T	AGCCACCGGCAAC	.	PASS	Atlas-SNP
LRRIQ1	84125	hgsc.bcm.edu	37	12	85459100	85459100	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	82	16	105	0	0.195122	0	.	.	none	.	LRRIQ1	512	.	NM_001079910	exon9	c.A2452C	p.T818P	GAGTGTACAAATC	.	PASS	Atlas-SNP
NRAP	4892	hgsc.bcm.edu	37	10	115389356	115389356	+	Silent	SNP	G	G	A	rs2286736	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	92	45	94	0	0.48913	0	G|0.727;A|0.273	0.273	strong	.	NRAP	208	.	NM_001261463	exon19	c.C2031T	p.L677L	GCTCTGGAGCCCA	.	PASS	Atlas-SNP
ALPK2	115701	hgsc.bcm.edu	37	18	56202683	56202683	+	Missense_Mutation	SNP	T	T	C	rs33910491	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	185	85	176	0	0.459459	0	T|0.911;C|0.089	0.089	strong	.	ALPK2	487	.	NM_052947	exon5	c.A4736G	p.Q1579R	ACATACTGACGCT	.	PASS	Atlas-SNP
PKHD1L1	93035	hgsc.bcm.edu	37	8	110455321	110455321	+	Missense_Mutation	SNP	C	C	A	rs1673408	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	98	76	104	0	0.77551	0	C|0.475;A|0.525	0.525	strong	.	PKHD1L1	522	.	NM_177531	exon36	c.C4540A	p.R1514S	GTGGGTCGCTCTG	.	PASS	Atlas-SNP
FHL5	9457	hgsc.bcm.edu	37	6	97052754	97052754	+	Silent	SNP	C	C	T	rs2064947	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	58	26	74	0	0.448276	0	C|0.849;T|0.151	0.151	strong	.	FHL5	73	.	NM_020482	exon4	c.C288T	p.N96N	TTCTAACGAGTGC	.	PASS	Atlas-SNP
PKD1L2	114780	hgsc.bcm.edu	37	16	81249927	81249927	+	Missense_Mutation	SNP	C	C	T	rs7185774	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	87	85	75	0	0.977012	0	C|0.772;T|0.228	0.228	strong	.	PKD1L2	361	.	NM_001076780	exon2	c.G386A	p.G129D	ATGTGGCCGCAGG	.	PASS	Atlas-SNP
PRDM9	56979	hgsc.bcm.edu	37	5	23527273	23527273	+	Silent	SNP	T	T	C	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	98	26	74	0	0.265306	0	.	.	none	PRDM9,NS,carcinoma,+1,1	PRDM9	344	1	NM_020227	exon11	c.T2076C	p.Y692Y	GCCCTATGTCTGC	.	PASS	Atlas-SNP
CDH6	1004	hgsc.bcm.edu	37	5	31317529	31317529	+	Silent	SNP	A	A	G	rs2302903	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	127	127	180	1	1	0.00555556	A|0.482;G|0.518	0.518	strong	.	CDH6	175	.	NM_004932	exon10	c.A1560G	p.G520G	TAGTGGACACCAA	.	PASS	Atlas-SNP
ALDH16A1	126133	hgsc.bcm.edu	37	19	49965173	49965173	+	Silent	SNP	A	A	T	rs7259560	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	39	19	20	0	0.487179	0	A|0.718;T|0.282	0.282	strong	.	ALDH16A1	54	.	NM_153329	exon7	c.A792T	p.G264G	GGCGGGAGAGTGT	.	PASS	Atlas-SNP
ACER3	55331	hgsc.bcm.edu	37	11	76637651	76637651	+	Missense_Mutation	SNP	G	G	A	rs4379869	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	106	15	110	0	0.141509	0	G|0.314;A|0.686	0.686	strong	ACER3,NS,carcinoma,0,1	ACER3	19	1	NM_018367	exon2	c.G154A	p.V52I	GGTGCAGTTCAGA	.	PASS	Atlas-SNP
DPP6	1804	hgsc.bcm.edu	37	7	154667628	154667628	+	Silent	SNP	A	A	G	rs2293353	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	73	28	78	0	0.383562	0	G|0.584;N|0.001	0.584	strong	.	DPP6	383	.	NM_130797	exon20	c.A1896G	p.P632P	CACCCCAGGCAGC	.	PASS	Atlas-SNP
EIF4G1	1981	hgsc.bcm.edu	37	3	184049143	184049143	+	Silent	SNP	C	C	T	rs76779558	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	52	87	0	0.536082	0	C|0.983;T|0.017	0.017	strong	.	EIF4G1	151	.	NM_001194946	exon30	c.C4272T	p.V1424V	ATTCGTCGCTGAA	.	PASS	Atlas-SNP
TM6SF2	53345	hgsc.bcm.edu	37	19	19379549	19379549	+	Missense_Mutation	SNP	C	C	T	rs58542926	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	76	29	62	0	0.381579	0	C|0.939;T|0.061	0.061	strong	.	TM6SF2	39	.	NM_001001524	exon6	c.G499A	p.E167K	TGATCTCGGAGCT	.	PASS	Atlas-SNP
IQCA1	79781	hgsc.bcm.edu	37	2	237374309	237374309	+	Silent	SNP	C	C	T	rs35432941	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	141	65	200	0	0.460993	0	C|0.896;T|0.104	0.104	strong	.	IQCA1	170	.	NM_001270585	exon6	c.G786A	p.Q262Q	TTCAGCCTGGATT	.	PASS	Atlas-SNP
CERK	64781	hgsc.bcm.edu	37	22	47087670	47087670	+	Silent	SNP	G	G	A	rs36211083	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	106	45	119	0	0.424528	0	G|0.888;A|0.112	0.112	strong	.	CERK	40	.	NM_022766	exon11	c.C1131T	p.D377D	CTCCACGTCCTCT	.	PASS	Atlas-SNP
VIT	5212	hgsc.bcm.edu	37	2	36970364	36970364	+	Silent	SNP	A	A	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	98	45	129	0	0.459184	0	.	.	none	.	VIT	138	.	NM_001177969	exon4	c.A240G	p.A80A	GTATGCATCCTAC	.	PASS	Atlas-SNP
USP31	57478	hgsc.bcm.edu	37	16	23080634	23080634	+	Missense_Mutation	SNP	C	C	A	rs10083789	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	83	29	70	0	0.349398	0	C|0.785;A|0.215	0.215	strong	.	USP31	122	.	NM_020718	exon16	c.G2792T	p.R931L	TCACGGCGACTAT	.	PASS	Atlas-SNP
TMC4	147798	hgsc.bcm.edu	37	19	54665970	54665970	+	Silent	SNP	C	C	T	rs36655	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	28	14	44	0	0.5	0	C|0.743;T|0.257	0.257	strong	.	TMC4	89	.	NM_001145303	exon11	c.G1572A	p.Q524Q	GAACTCCTGGGTC	.	PASS	Atlas-SNP
BCL11A	53335	hgsc.bcm.edu	37	2	60689522	60689522	+	Silent	SNP	G	G	A	rs61748090	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	208	165	103	0	0.793269	0	G|0.982;A|0.018	0.018	strong	.	BCL11A	298	.	NM_018014	exon4	c.C525T	p.C175C	CTGTTTGCAAGTT	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	208	208	309	1	1	0.00323625	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
ADAMTS7	11173	hgsc.bcm.edu	37	15	79057989	79057989	+	Missense_Mutation	SNP	C	C	T	rs200769684	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	173	14	167	0	0.0809249	0	C|0.999;T|0.001	0.001	weak	ADAMTS7,face,carcinoma,0,3	ADAMTS7	142	3	NM_014272	exon19	c.G4264A	p.E1422K	TTGCCTCGCTCCA	.	scavenged	Atlas-SNP
SCAI	286205	hgsc.bcm.edu	37	9	127818276	127818276	+	Missense_Mutation	SNP	C	C	T	rs589292	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	79	36	107	0	0.455696	0	C|0.748;T|0.252	0.252	strong	.	SCAI	84	.	NM_173690	exon4	c.G178A	p.A60T	TAAGAGCAAATTC	.	PASS	Atlas-SNP
ALMS1	7840	hgsc.bcm.edu	37	2	73679866	73679866	+	Missense_Mutation	SNP	T	T	C	rs10496192	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	108	108	114	0	1	0	T|0.882;C|0.118	0.118	strong	.	ALMS1	384	.	NM_015120	exon8	c.T6209C	p.I2070T	AAGGTATTCTAAA	.	PASS	Atlas-SNP
WDR88	126248	hgsc.bcm.edu	37	19	33655144	33655144	+	Silent	SNP	C	C	T	rs1981827	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	122	51	151	0	0.418033	0	C|0.874;T|0.126	0.126	strong	.	WDR88	50	.	NM_173479	exon9	c.C1122T	p.N374N	CAACAACAAGAAA	.	PASS	Atlas-SNP
PRDM9	56979	hgsc.bcm.edu	37	5	23527472	23527472	+	Missense_Mutation	SNP	G	G	A	rs112666693		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	69	11	86	1	0.15942	0.0116279	G|0.500;A|0.500	0.500	weak	PRDM9,NS,carcinoma,0,2	PRDM9	344	2	NM_020227	exon11	c.G2275A	p.D759N	TTTCGCGATAAGT	.	scavenged	Atlas-SNP
NAT2	10	hgsc.bcm.edu	37	8	18258316	18258316	+	Missense_Mutation	SNP	G	G	A	rs1208	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	43	9	50	0	0.209302	0	G|0.370;A|0.630	0.630	strong	.	NAT2	34	.	NM_000015	exon2	c.G803A	p.R268K	TGCTGAGAAATAT	.	PASS	Atlas-SNP
MYO3B	140469	hgsc.bcm.edu	37	2	171225841	171225841	+	Missense_Mutation	SNP	A	A	G	rs4668246	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	194	75	219	0	0.386598	0	A|0.686;G|0.314	0.314	strong	.	MYO3B	320	.	NM_001083615	exon9	c.A925G	p.K309E	CTGGCCAAGGTTC	.	PASS	Atlas-SNP
TH	7054	hgsc.bcm.edu	37	11	2190982	2190982	+	Silent	SNP	A	A	G	rs7950050	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	143	116	110	0	0.811189	0	A|0.952;G|0.048	0.048	strong	.	TH	43	.	NM_199292	exon3	c.T303C	p.A101A	GGCCACAGCCTCC	.	PASS	Atlas-SNP
TRPA1	8989	hgsc.bcm.edu	37	8	72966002	72966002	+	Silent	SNP	G	G	A	rs3735943	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	96	70	109	0	0.729167	0	G|0.483;A|0.517	0.517	strong	.	TRPA1	256	.	NM_007332	exon13	c.C1630T	p.L544L	CATCCAGGCGATC	.	PASS	Atlas-SNP
OR10H3	26532	hgsc.bcm.edu	37	19	15852363	15852363	+	Missense_Mutation	SNP	G	G	A	rs11670007	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	156	67	208	1	0.429487	0.00480769	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	.	scavenged	Atlas-SNP
ITGAM	3684	hgsc.bcm.edu	37	16	31276811	31276811	+	Missense_Mutation	SNP	G	G	A	rs1143679	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	178	99	152	0	0.55618	0	G|0.914;A|0.086	0.086	strong	.	ITGAM	137	.	NM_000632	exon3	c.G230A	p.R77H	CCATCCGCCTGCA	.	PASS	Atlas-SNP
CD163L1	283316	hgsc.bcm.edu	37	12	7528471	7528471	+	Silent	SNP	G	G	A	rs7306824	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	37	97	0	0.493333	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
MUC5B	727897	hgsc.bcm.edu	37	11	1266599	1266599	+	Missense_Mutation	SNP	C	C	T	rs139960671	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	353	342	305	1	0.968839	0.00327869	C|0.895;T|0.105	0.105	strong	.	MUC5B	473	.	NM_002458	exon31	c.C8489T	p.P2830L	CCACCCCGGGCCA	.	PASS	Atlas-SNP
CCHCR1	54535	hgsc.bcm.edu	37	6	31116245	31116245	+	Missense_Mutation	SNP	C	C	T	rs130069	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	121	52	106	0	0.429752	0	C|0.955;T|0.045	0.045	strong	.	CCHCR1	68	.	NM_001105564	exon10	c.G1517A	p.R506Q	TGCCACCGACGCC	.	PASS	Atlas-SNP
FRG2B	441581	hgsc.bcm.edu	37	10	135438933	135438933	+	Silent	SNP	C	C	T	rs200793608		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	314	4	316	2	0.0127389	0.00632911	C|0.996;T|0.004	0.004	weak	FRG2B,colon,carcinoma,-1,1	FRG2B	47	1	NM_001080998	exon4	c.G507A	p.P169P	AATTGACGGTGTT	.	scavenged	Atlas-SNP
CCDC146	57639	hgsc.bcm.edu	37	7	76922490	76922490	+	Silent	SNP	C	C	T	rs17151219	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	52	51	100	0	0.980769	0	C|0.779;T|0.221	0.221	strong	.	CCDC146	87	.	NM_020879	exon18	c.C2637T	p.H879H	AATGCACGCCTTG	.	PASS	Atlas-SNP
HLA-DPB1	3115	hgsc.bcm.edu	37	6	33048538	33048538	+	Missense_Mutation	SNP	T	T	C	rs9277348	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	42	19	69	0	0.452381	0	T|0.945;C|0.055	0.055	strong	HLA-DPB1,rectum,carcinoma,-2,1	HLA-DPB1	28	1	NM_002121	exon2	c.T190C	p.F64L	GAGGAGTTCGCGC	.	PASS	Atlas-SNP
PTPRH	5794	hgsc.bcm.edu	37	19	55716800	55716800	+	Silent	SNP	A	A	G	rs2288516	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	238	104	232	1	0.436975	0.00431034	A|0.556;G|0.444	0.444	strong	.	PTPRH	139	.	NM_002842	exon4	c.T513C	p.T171T	GATGTTAGTGTGT	.	PASS	Atlas-SNP
KIAA1804	0	hgsc.bcm.edu	37	1	233515413	233515413	+	Silent	SNP	G	G	A	rs1402815	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	66	29	74	0	0.439394	0	G|0.748;A|0.252	0.252	strong	.	KIAA1804	129	.	NM_032435	exon9	c.G2661A	p.P887P	TAGACCGTCACAT	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	107	54	131	0	0.504673	0	A|0.313;G|0.687	0.687	strong	.	MYLIP	44	.	NM_013262	exon6	c.A1025G	p.N342S	CAAGAAACAACCA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195512302	195512302	+	Missense_Mutation	SNP	G	G	A	rs201164821	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	80	18	62	0	0.225	0	A|0.008;G|0.989;T|0.002	0.008	strong	MUC4_ENST00000463781,NS,lymphoid_neoplasm,0,1	MUC4	1505	1	NM_018406	exon2	c.C6149T	p.P2050L	GTGACAGGAAGAG	.	PASS	Atlas-SNP
NEK4	6787	hgsc.bcm.edu	37	3	52802402	52802402	+	Silent	SNP	A	A	C	rs2230534	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	122	120	133	0	0.983607	0	A|0.653;C|0.347	0.347	strong	.	NEK4	51	.	NM_003157	exon2	c.T312G	p.P104P	ATTCTCAGGCAGA	.	PASS	Atlas-SNP
SLFN12	55106	hgsc.bcm.edu	37	17	33749546	33749546	+	Missense_Mutation	SNP	A	A	G	rs2586514	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	88	86	133	0	0.977273	0	A|0.416;G|0.584	0.584	strong	.	SLFN12	56	.	NM_018042	exon2	c.T502C	p.C168R	CAACACAGGGCCT	.	PASS	Atlas-SNP
ANXA11	311	hgsc.bcm.edu	37	10	81926718	81926718	+	Silent	SNP	A	A	G	rs2228427	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	44	26	35	0	0.590909	0	T|0.009;G|0.096	0.096	strong	.	ANXA11	32	.	NM_145868	exon7	c.T672C	p.I224I	GCAGTCAATGATG	.	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	253	129	299	0	0.509881	0	A|0.560;C|0.440	0.440	strong	.	OR13D1	42	.	NM_001004484	exon1	c.A573C	p.Q191H	ATTGCAAACAGTT	.	PASS	Atlas-SNP
DRD5	1816	hgsc.bcm.edu	37	4	9784550	9784550	+	Silent	SNP	G	G	A	rs2227844	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	33	2	35	2	0.0606061	0.0571429	G|0.885;A|0.115	0.115	strong	DRD5,colon,carcinoma,0,2	DRD5	119	2	NM_000798	exon1	c.G897A	p.S299S	CCTGTCGGTGATC	.	scavenged	Atlas-SNP
ADAMTS14	140766	hgsc.bcm.edu	37	10	72513635	72513635	+	Missense_Mutation	SNP	C	C	A	rs12774070	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	39	26	53	0	0.666667	0	A|0.174;C|0.826;G|0.000	0.174	strong	ADAMTS14,NS,carcinoma,0,2	ADAMTS14	148	2	NM_139155	exon19	c.C2818A	p.L940M	TGCCTGCTGCCCC	.	PASS	Atlas-SNP
FAM53A	152877	hgsc.bcm.edu	37	4	1657281	1657281	+	Silent	SNP	G	G	A	rs79735962	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	124	65	111	0	0.524194	0	G|0.787;A|0.213	0.213	strong	.	FAM53A	25	.	NM_001013622	exon4	c.C306T	p.T102T	GTCCACGGTGCTG	.	PASS	Atlas-SNP
GFM2	84340	hgsc.bcm.edu	37	5	74017499	74017499	+	Missense_Mutation	SNP	C	C	T	rs1048167	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	115	54	75	0	0.469565	0	C|0.856;T|0.144	0.144	strong	.	GFM2	38	.	NM_032380	exon21	c.G2321A	p.R774Q	CTTCTCCGGTTGA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195513285	195513285	+	Silent	SNP	G	G	T	rs200293322	byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	122	4	132	0	0.0327869	0	G|0.988;T|0.013	0.013	strong	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.C5166A	p.S1722S	ACCTGTGGATACT	.	scavenged	Atlas-SNP
DNAH14	127602	hgsc.bcm.edu	37	1	225555602	225555602	+	Missense_Mutation	SNP	T	T	G	rs12737248	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	41	27	74	0	0.658537	0	T|0.631;G|0.369	0.369	strong	.	DNAH14	300	.	NM_001373	exon75	c.T11907G	p.N3969K	TGAAAATCCTGAC	.	PASS	Atlas-SNP
ARHGEF10	9639	hgsc.bcm.edu	37	8	1905132	1905132	+	Silent	SNP	G	G	A	rs3735876	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	104	84	90	0	0.807692	0	G|0.648;A|0.352	0.352	strong	.	ARHGEF10	255	.	NM_014629	exon29	c.G3738A	p.S1246S	AGATTCGCTGGGA	.	PASS	Atlas-SNP
ATAD5	79915	hgsc.bcm.edu	37	17	29161503	29161503	+	Missense_Mutation	SNP	A	A	G	rs11080134	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	25	15	35	0	0.6	0	A|0.786;G|0.214	0.214	strong	.	ATAD5	150	.	NM_024857	exon2	c.A404G	p.E135G	CAATTGAAATTAG	.	PASS	Atlas-SNP
PPP2R5A	5525	hgsc.bcm.edu	37	1	212515613	212515613	+	Silent	SNP	C	C	T	rs1774249	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	38	111	0	0.391753	0	C|0.701;T|0.299	0.299	strong	.	PPP2R5A	48	.	NM_006243	exon4	c.C564T	p.F188F	GAAATTCGTACAA	.	PASS	Atlas-SNP
CAPRIN1	4076	hgsc.bcm.edu	37	11	34093289	34093289	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	106	2	122	0	0.0188679	0	.	.	none	CAPRIN1_ENST00000389645,NS,carcinoma,0,2	CAPRIN1	110	2	NM_203364	exon3	c.A233G	p.Y78C	ATGATTACCAGGA	.	scavenged	Atlas-SNP
KANSL1	284058	hgsc.bcm.edu	37	17	44248848	44248848	+	Missense_Mutation	SNP	G	G	A	rs17662853	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	209	98	374	0	0.4689	0	G|0.900;A|0.100	0.100	strong	.	.	.	.	NM_001193466	exon2	c.C662T	p.T221I	TACAAAGTTGTGT	.	PASS	Atlas-SNP
TTC28	23331	hgsc.bcm.edu	37	22	28504258	28504258	+	Silent	SNP	A	A	G	rs9625409	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	97	54	92	0	0.556701	0	A|0.942;G|0.058	0.058	strong	.	TTC28	84	.	NM_001145418	exon7	c.T1575C	p.N525N	CAGGGCATTGTAG	.	PASS	Atlas-SNP
SREBF2	6721	hgsc.bcm.edu	37	22	42300948	42300948	+	Silent	SNP	C	C	A	rs17848337	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	59	21	45	0	0.355932	0	C|0.945;A|0.055	0.055	strong	.	SREBF2	99	.	NM_004599	exon18	c.C3175A	p.R1059R	AGCCTGCGGCGGC	.	PASS	Atlas-SNP
PHIP	55023	hgsc.bcm.edu	37	6	79675701	79675701	+	Missense_Mutation	SNP	A	A	G	rs9350797	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	119	119	147	0	1	0	A|0.746;G|0.254	0.254	strong	.	PHIP	177	.	NM_017934	exon28	c.T3278C	p.L1093P	TACTCAAGTTGAA	.	PASS	Atlas-SNP
OR8S1	341568	hgsc.bcm.edu	37	12	48919793	48919793	+	Missense_Mutation	SNP	T	T	C	rs2705143	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	128	65	178	0	0.507812	0	T|0.781;C|0.219	0.219	strong	.	OR8S1	47	.	NM_001005203	exon1	c.T379C	p.C127R	GCCATCTGCCGCC	.	PASS	Atlas-SNP
SLC26A2	1836	hgsc.bcm.edu	37	5	149361221	149361221	+	Missense_Mutation	SNP	A	A	T	rs3776070	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	41	15	65	0	0.365854	0	A|0.811;T|0.190	0.190	strong	.	SLC26A2	48	.	NM_000112	exon3	c.A2065T	p.T689S	AATCCCACTGTGA	.	PASS	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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	183	93	181	0	0.508197	0	A|0.848;G|0.152	0.152	strong	.	DST	1427	.	NM_001723	exon1	c.T98C	p.L33S	TGAACCAAGAGAA	.	PASS	Atlas-SNP
CANX	821	hgsc.bcm.edu	37	5	179135309	179135309	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	246	78	202	0	0.317073	0	.	.	none	.	CANX	47	.	NM_001746	exon5	c.G374A	p.R125Q	TGTCTCGGGCCAA	.	PASS	Atlas-SNP
DHRS13	147015	hgsc.bcm.edu	37	17	27228198	27228198	+	Silent	SNP	G	G	A	rs4795474	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	177	176	232	1	0.99435	0.00431034	G|0.885;A|0.115	0.115	strong	DHRS13,NS,carcinoma,-1,1	DHRS13	22	1	NM_144683	exon4	c.C492T	p.R164R	CACCACGCGGCTA	.	PASS	Atlas-SNP
RNF26	79102	hgsc.bcm.edu	37	11	119206427	119206427	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	179	46	197	0	0.256983	0	.	.	none	RNF26,NS,carcinoma,-1,1	RNF26	23	1	NM_032015	exon1	c.G595A	p.A199T	GCCATGGCCATCC	.	PASS	Atlas-SNP
ELTD1	64123	hgsc.bcm.edu	37	1	79357360	79357360	+	Missense_Mutation	SNP	G	G	C	rs2275902	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	38	18	46	0	0.473684	0	G|0.733;C|0.266	0.266	strong	.	ELTD1	143	.	NM_022159	exon14	c.C1859G	p.A620G	GCGAGGGCTCCTC	.	PASS	Atlas-SNP
TCF19	6941	hgsc.bcm.edu	37	6	31129310	31129310	+	Missense_Mutation	SNP	C	C	T	rs7750641	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	116	49	160	0	0.422414	0	C|0.947;T|0.053	0.053	strong	TCF19,colon,carcinoma,0,1	TCF19	16	1	NM_001077511	exon3	c.C325T	p.P109S	GAAGGGCCCCCAG	.	PASS	Atlas-SNP
PCDHB8	56128	hgsc.bcm.edu	37	5	140558628	140558628	+	Missense_Mutation	SNP	T	T	C	rs62378901	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	402	215	317	0	0.534826	0	T|0.976;C|0.024	0.024	strong	.	PCDHB8	199	.	NM_019120	exon1	c.T1013C	p.V338A	TTCAAGTGATAGA	.	PASS	Atlas-SNP
OVCH1	341350	hgsc.bcm.edu	37	12	29642573	29642573	+	Missense_Mutation	SNP	A	A	C	rs967181	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	74	37	91	0	0.5	0	A|0.579;C|0.421	0.421	strong	OVCH1,colon,carcinoma,0,1	OVCH1	195	1	NM_183378	exon6	c.T682G	p.W228G	TTCCCCAATCAGG	.	PASS	Atlas-SNP
TAAR6	319100	hgsc.bcm.edu	37	6	132891538	132891538	+	Silent	SNP	C	C	T	rs8192622	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	88	87	136	0	0.988636	0	C|0.966;T|0.034	0.034	strong	.	TAAR6	68	.	NM_175067	exon1	c.C78T	p.P26P	AATCCCCTTCTCG	.	PASS	Atlas-SNP
C5	727	hgsc.bcm.edu	37	9	123782299	123782299	+	Silent	SNP	G	G	A	rs2230214	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	143	66	154	0	0.461538	0	G|0.895;A|0.105	0.105	strong	.	C5	124	.	NM_001735	exon12	c.C1461T	p.T487T	TTTGGGGGTAACA	.	PASS	Atlas-SNP
LRP2	4036	hgsc.bcm.edu	37	2	170115588	170115588	+	Silent	SNP	T	T	C	rs2241190	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	133	70	179	0	0.526316	0	T|0.449;C|0.551	0.551	strong	.	LRP2	751	.	NM_004525	exon17	c.A2460G	p.T820T	AACTACTGTGCGT	.	PASS	Atlas-SNP
CEP290	80184	hgsc.bcm.edu	37	12	88520192	88520192	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	197	56	234	0	0.284264	0	.	.	none	.	CEP290	195	.	NM_025114	exon12	c.T966A	p.D322E	AATTTCATCATCT	.	PASS	Atlas-SNP
FAM170A	340069	hgsc.bcm.edu	37	5	118969960	118969960	+	Missense_Mutation	SNP	C	C	T	rs328694	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	103	44	128	0	0.427184	0	C|0.562;T|0.438	0.438	strong	FAM170A,NS,carcinoma,0,1	FAM170A	47	1	NM_182761	exon3	c.C517T	p.P173S	ACTCCCCCCTCTG	.	PASS	Atlas-SNP
SACS	26278	hgsc.bcm.edu	37	13	23910850	23910850	+	Missense_Mutation	SNP	C	C	T	rs142869943	bycluster;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	81	44	85	0	0.54321	0	C|1.000;T|0.000	0.000	strong	.	SACS	871	.	NM_014363	exon10	c.G7165A	p.V2389M	CACCCACGGTTTC	.	PASS	Atlas-SNP
TTLL4	9654	hgsc.bcm.edu	37	2	219610433	219610433	+	Silent	SNP	A	A	G	rs586194	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	106	106	101	0	1	0	A|0.446;G|0.554	0.554	strong	.	TTLL4	96	.	NM_014640	exon7	c.A1806G	p.E602E	CTGGGAACAGAGG	.	PASS	Atlas-SNP
SRGAP1	57522	hgsc.bcm.edu	37	12	64519806	64519806	+	Silent	SNP	T	T	C	rs789722	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	217	92	233	0	0.423963	0	T|0.405;C|0.595	0.595	strong	.	SRGAP1	146	.	NM_020762	exon19	c.T2274C	p.S758S	GCGGTCTGCCAGA	.	PASS	Atlas-SNP
LZTS2	84445	hgsc.bcm.edu	37	10	102766574	102766574	+	Silent	SNP	A	A	G	rs807024	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	62	32	61	0	0.516129	0	A|0.651;G|0.349	0.349	strong	LZTS2,colon,carcinoma,+1,1	LZTS2	57	1	NM_032429	exon5	c.A1659G	p.A553A	CCTGGCAGAGAGT	.	PASS	Atlas-SNP
OR5T1	390155	hgsc.bcm.edu	37	11	56043604	56043604	+	Missense_Mutation	SNP	A	A	G	rs12360890	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	258	56	330	0	0.217054	0	A|0.653;G|0.347	0.347	strong	.	OR5T1	95	.	NM_001004745	exon1	c.A490G	p.S164G	GTTGCTAGCATTT	.	PASS	Atlas-SNP
AR	367	hgsc.bcm.edu	37	X	66765158	66765158	+	Missense_Mutation	SNP	T	T	A	rs78686797	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	47	6	78	0	0.12766	0	.	.	weak	.	AR	249	.	NM_000044	exon1	c.T170A	p.L57Q	TGCTGCTGCAGCA	.	PASS	Atlas-SNP
CDHR2	54825	hgsc.bcm.edu	37	5	176017455	176017455	+	Missense_Mutation	SNP	C	C	T	rs2291442	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	156	95	127	0	0.608974	0	C|0.719;T|0.281	0.281	strong	CDHR2,colon,carcinoma,0,1	CDHR2	152	1	NM_017675	exon27	c.C3383T	p.T1128M	CGCTGACGCAGCT	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29910558	29910558	+	Missense_Mutation	SNP	T	T	A	rs2075684	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	38	15	26	1	0.394737	0.0384615	T|0.574;C|0.414;A|0.012	0.012	strong	HLA-A,NS,lymphoid_neoplasm,0,1	HLA-A	89	1	NM_001242758	exon2	c.T98A	p.F33Y	ATTTCTTCACATC	.	scavenged	Atlas-SNP
LRP3	4037	hgsc.bcm.edu	37	19	33698448	33698448	+	Silent	SNP	G	G	A	rs3745973	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	48	28	62	0	0.583333	0	G|0.910;C|0.000;A|0.090	0.090	strong	.	LRP3	46	.	NM_002333	exon7	c.G2280A	p.E760E	GCTGGAGGCCAGC	.	PASS	Atlas-SNP
NFE2L3	9603	hgsc.bcm.edu	37	7	26224323	26224323	+	Silent	SNP	T	T	C	rs113074870		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	465	71	382	0	0.152688	0	T|0.500;C|0.500	0.500	weak	.	NFE2L3	77	.	NM_004289	exon4	c.T1005C	p.T335T	AAGGACTTCACAG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195508969	195508969	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	52	9	33	0	0.173077	0	.	.	none	MUC4_ENST00000463781,NS,carcinoma,-1,1	MUC4	1505	1	NM_018406	exon2	c.C9482T	p.A3161V	GTGGATGCTGAGG	.	scavenged	Atlas-SNP
NRP1	8829	hgsc.bcm.edu	37	10	33510663	33510663	+	Silent	SNP	G	G	A	rs2229935	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	126	50	131	0	0.396825	0	G|0.708;A|0.292	0.292	strong	.	NRP1	126	.	NM_001244973	exon8	c.C1266T	p.Y422Y	GCAACCGTATACT	.	PASS	Atlas-SNP
KIAA1549	57670	hgsc.bcm.edu	37	7	138602523	138602523	+	Missense_Mutation	SNP	T	T	C	rs2774962	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	78	39	89	0	0.5	0	T|0.509;C|0.491	0.491	strong	KIAA1549_ENST00000422774,colon,carcinoma,0,3	KIAA1549	314	3	NM_020910	exon2	c.A1849G	p.R617G	CACCTCTGGGTTT	.	PASS	Atlas-SNP
TMCO3	55002	hgsc.bcm.edu	37	13	114157846	114157846	+	Silent	SNP	G	G	A	rs9805588	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	192	96	245	0	0.5	0	G|0.905;A|0.095	0.095	strong	.	TMCO3	77	.	NM_017905	exon6	c.G981A	p.G327G	ATTTGGGGTGTTT	.	PASS	Atlas-SNP
PLEKHH2	130271	hgsc.bcm.edu	37	2	43926943	43926943	+	Silent	SNP	T	T	A	rs7606783	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	300	298	231	0	0.993333	0	T|0.440;A|0.560	0.560	strong	.	PLEKHH2	156	.	NM_172069	exon8	c.T846A	p.P282P	GGCTCCTGTGAGT	.	PASS	Atlas-SNP
CLEC4M	10332	hgsc.bcm.edu	37	19	7831047	7831047	+	Silent	SNP	G	G	A	rs868878	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	47	17	57	0	0.361702	0	A|0.087;C|0.000;G|0.913	0.087	strong	.	CLEC4M	58	.	NM_014257	exon4	c.G738A	p.K246K	GTCCAAGCAGCAG	.	PASS	Atlas-SNP
SEMA4B	10509	hgsc.bcm.edu	37	15	90768271	90768271	+	Silent	SNP	C	C	T	rs11547966	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	187	111	158	0	0.593583	0	C|0.835;T|0.165	0.165	strong	.	SEMA4B	51	.	NM_020210	exon11	c.C1266T	p.F422F	GAACTTCCTCAAG	.	PASS	Atlas-SNP
FURIN	5045	hgsc.bcm.edu	37	15	91424574	91424574	+	Silent	SNP	G	G	C	rs6226	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	118	36	108	0	0.305085	0	C|0.737;G|0.263	0.737	strong	FURIN,NS,carcinoma,+2,1	FURIN	85	1	NM_002569	exon16	c.G1851C	p.G617G	TCCAGGGTTCGCC	.	PASS	Atlas-SNP
NOS1	4842	hgsc.bcm.edu	37	12	117693817	117693817	+	Missense_Mutation	SNP	G	G	A	rs11068428	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	56	32	49	0	0.571429	0	G|0.651;A|0.349	0.349	strong	.	NOS1	240	.	NM_001204218	exon17	c.C2557T	p.P853S	TACGGGGAAAGAA	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1092890	1092890	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	75	9	45	2	0.12	0.0444444	.	.	none	MUC2_ENST00000441003,NS,carcinoma,-1,2	MUC2	614	2	NM_002457	exon30	c.C4709T	p.T1570I	CGGTGACCCCAAC	.	scavenged	Atlas-SNP
KCNJ18	100134444	hgsc.bcm.edu	37	17	21318770	21318770	+	Missense_Mutation	SNP	G	G	A	rs3752033	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	118	29	111	0	0.245763	0	G|0.743;A|0.257	0.257	strong	.	.	.	.	NM_001194958	exon3	c.G116A	p.R39Q	ACACGCGGCGCAG	.	PASS	Atlas-SNP
ZNF592	9640	hgsc.bcm.edu	37	15	85326939	85326939	+	Missense_Mutation	SNP	C	C	A	rs138966830	bycluster	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	121	42	117	0	0.347107	0	A|0.001;C|0.999	0.001	weak	ZNF592,arm,malignant_melanoma,0,1	ZNF592	95	1	NM_014630	exon4	c.C1033A	p.P345T	ATCAAGCCATCGG	.	PASS	Atlas-SNP
KRTAP4-6	81871	hgsc.bcm.edu	37	17	39296254	39296254	+	Silent	SNP	C	C	T	rs72483263		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	90	26	71	0	0.288889	0	C|0.500;T|0.500	0.500	weak	.	KRTAP4-6	46	.	NM_030976	exon1	c.G486A	p.P162P	GCAGCACGGGCGG	.	PASS	Atlas-SNP
DYNC2H1	79659	hgsc.bcm.edu	37	11	103058126	103058126	+	Silent	SNP	C	C	T	rs586592	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	119	118	152	1	0.991597	0.00657895	C|0.378;T|0.622	0.622	strong	.	DYNC2H1	246	.	NM_001377	exon43	c.C6951T	p.H2317H	AGTTCACTGTAGT	.	PASS	Atlas-SNP
GPR98	84059	hgsc.bcm.edu	37	5	90086955	90086955	+	Missense_Mutation	SNP	G	G	A	rs41304892	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	269	115	255	1	0.427509	0.00392157	G|0.997;A|0.003	0.003	strong	.	GPR98	605	.	NM_032119	exon70	c.G14309A	p.R4770H	CGGATCGCCAGTC	.	PASS	Atlas-SNP
ZNF423	23090	hgsc.bcm.edu	37	16	49671177	49671177	+	Missense_Mutation	SNP	T	T	C	rs34214571	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	183	75	156	0	0.409836	0	T|0.972;C|0.028	0.028	strong	.	ZNF423	463	.	NM_015069	exon4	c.A1886G	p.N629S	TCCCCATTGGAGA	.	PASS	Atlas-SNP
RERG	85004	hgsc.bcm.edu	37	12	15262179	15262179	+	Silent	SNP	G	G	A	rs1055151	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	158	70	170	0	0.443038	0	G|0.741;A|0.259	0.259	strong	.	RERG	30	.	NM_032918	exon5	c.C465T	p.N155N	TGTGATGTTCCCT	.	PASS	Atlas-SNP
PTH1R	5745	hgsc.bcm.edu	37	3	46944274	46944274	+	Silent	SNP	T	T	C	rs1138518	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	93	35	130	0	0.376344	0	T|0.343;C|0.657	0.657	strong	PTH1R,NS,carcinoma,0,1	PTH1R	49	1	NM_001184744	exon14	c.T1389C	p.N463N	CTGCAATGGCGAG	.	PASS	Atlas-SNP
CDHR5	53841	hgsc.bcm.edu	37	11	618013	618013	+	Missense_Mutation	SNP	C	C	T	rs7108757	bycluster;byfrequency;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	161	132	171	0	0.819876	0	C|0.770;T|0.230	0.230	strong	.	CDHR5	77	.	NM_021924	exon14	c.G2059A	p.A687T	GGACGGCGAGGCC	.	PASS	Atlas-SNP
CDRT1	374286	hgsc.bcm.edu	37	17	15510988	15510988	+	Missense_Mutation	SNP	T	T	C	rs62070402	bycluster;byfrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	179	170	176	0	0.949721	0	T|0.810;C|0.190	0.190	strong	.	CDRT1	83	.	NM_006382	exon6	c.A1132G	p.N378D	ACAGGTTGTACTC	.	PASS	Atlas-SNP
DHRS7C	201140	hgsc.bcm.edu	37	17	9676148	9676148	+	Silent	SNP	C	C	T	rs2280489	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	40	16	32	0	0.4	0	T|0.103;C|0.897	0.103	strong	.	DHRS7C	34	.	NM_001220493	exon5	c.G666A	p.P222P	GAAAGTCGGGCTC	.	PASS	Atlas-SNP
BAGE3	85318	hgsc.bcm.edu	37	21	11058316	11058316	+	Missense_Mutation	SNP	G	G	T	rs3877860		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	238	13	198	0	0.0546218	0	.	.	weak	.	.	.	.	NM_182481	exon3	c.C124A	p.H42N	CAAAATGCACATC	.	PASS	Atlas-SNP
