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
CDC42EP1	11135	hgsc.bcm.edu	37	22	37964409	37964429	+	In_Frame_Del	DEL	CAGCGCCTGCTGCAAACCCCT	CAGCGCCTGCTGCAAACCCCT	-	rs200195385	by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CAGCGCCTGCTGCAAACCCCT	CAGCGCCTGCTGCAAACCCCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	102	37	153	0	0.362745	0	CAGCGCCTGCTGCAAACCCCT|0.610;-|0.390	0.390	strong	.	CDC42EP1	53	.	NM_152243	exon3	c.757_777del	p.253_259del	.	.	PASS	Atlas-Indel
ABCF1	23	hgsc.bcm.edu	37	6	30558477	30558478	+	Frame_Shift_Ins	INS	-	-	A	rs72545970	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	184	72	160	.	0.391	.	A|1.000;|0.000	1.000	strong	.	ABCF1	61	.	NM_001025091	exon25	c.2537_2538insA	p.X846delinsX	.	.	PASS	Pindel,Atlas-Indel
NUDT17	200035	hgsc.bcm.edu	37	1	145586672	145586676	+	Frame_Shift_Del	DEL	TTTTA	TTTTA	-	rs201063949	by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TTTTA	TTTTA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	18	116	0	0.222222	0	TTTTA|0.983;-|0.017	0.017	strong	.	NUDT17	25	.	NM_001012758	exon8	c.901_905del	p.301_302del	.	.	PASS	Atlas-Indel
SYNPO2	171024	hgsc.bcm.edu	37	4	119947962	119947964	+	In_Frame_Del	DEL	AAG	AAG	-	rs70944826	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	70	20	78	.	0.286	.	AAG|0.631;-|0.369	0.369	strong	.	SYNPO2	353	.	NM_001128934	exon3	c.437_439del	p.146_147del	.	.	PASS	Pindel,Atlas-Indel
C11orf40	143501	hgsc.bcm.edu	37	11	4592706	4592707	+	Frame_Shift_Ins	INS	-	-	AC	rs141600462	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	115	29	121	.	0.252	.	-|0.377;AC|0.623	0.623	strong	.	C11orf40	37	.	NM_144663	exon4	c.601_602insGT	p.M201fs	.	.	PASS	Pindel,Atlas-Indel
HYDIN	54768	hgsc.bcm.edu	37	16	70934989	70934989	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110	16	45	0	0.145455	0	.	.	none	.	HYDIN	788	.	NM_001270974	exon53	c.8967delC	p.I2989fs	.	.	PASS	Atlas-Indel
OR6A2	8590	hgsc.bcm.edu	37	11	6816750	6816751	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	157	33	149	0	0.210191	0	.	.	none	.	OR6A2	68	.	NM_003696	exon1	c.190_191insT	p.L64fs	.	.	PASS	Atlas-Indel
P2RX5	5026	hgsc.bcm.edu	37	17	3594277	3594277	+	Frame_Shift_Del	DEL	G	G	-	rs3215407	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	34	18	53	.	0.529	.	G|0.374;-|0.626	0.626	strong	.	P2RX5	36	.	NM_001204519	exon3	c.334delA	p.N112fs	.	.	PASS	Pindel,Atlas-Indel
FAM115C	285966	hgsc.bcm.edu	37	7	143417404	143417405	+	Frame_Shift_Del	DEL	CT	CT	-	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	16	106	0	0.183908	0	.	.	none	.	FAM115C	29	.	NM_173678	exon3	c.1251_1252del	p.417_418del	.	.	PASS	Atlas-Indel
HRCT1	646962	hgsc.bcm.edu	37	9	35906584	35906586	+	In_Frame_Del	DEL	CCA	CCA	-	rs143611048	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CCA	CCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	36	12	27	0	0.333333	0	.	.	strong	HRCT1,NS,malignant_melanoma,0,1	HRCT1	14	1	NM_001039792	exon1	c.299_301del	p.100_101del	.	.	PASS	Atlas-Indel
HOMEZ	57594	hgsc.bcm.edu	37	14	23744827	23744829	+	In_Frame_Del	DEL	TCC	TCC	-	rs67447855	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TCC	TCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69	21	77	.	0.304	.	TCC|0.500;-|0.500	0.500	weak	.	HOMEZ	80	.	NM_020834	exon2	c.1609_1611del	p.537_537del	.	.	PASS	Pindel,Atlas-Indel
MIR600HG	81571	hgsc.bcm.edu	37	9	125876697	125876697	+	RNA	DEL	G	G	-	rs149751997	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	16	73	.	0.340	.	.	.	strong	.	.	.	.	.	.	.	.	.	.	PASS	Pindel,Atlas-Indel
ACIN1	22985	hgsc.bcm.edu	37	14	23548787	23548788	+	In_Frame_Ins	INS	-	-	GTGAAT	rs34870944	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	154	34	177	.	0.221	.	-|0.604;GTGAAT|0.396	0.396	strong	.	ACIN1	147	.	NM_014977	exon6	c.1931_1932insATTCAC	p.R644delinsHSR	.	.	PASS	Pindel,Atlas-Indel
GNLY	10578	hgsc.bcm.edu	37	2	85922121	85922122	+	Splice_Site	INS	-	-	A	rs113717357	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	16	10	25	.	0.625	.	-|0.808;A|0.192	0.192	strong	.	GNLY	29	.	NM_012483	exon2	c.7+2->A	.	.	.	PASS	Pindel,Atlas-Indel
OR13C2	392376	hgsc.bcm.edu	37	9	107367665	107367666	+	Frame_Shift_Del	DEL	GC	GC	-	rs143760725	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	372	113	399	0	0.303763	0	.	.	strong	.	OR13C2	46	.	NM_001004481	exon1	c.244_245del	p.82_82del	.	.	PASS	Atlas-Indel
WDR81	124997	hgsc.bcm.edu	37	17	1631341	1631343	+	In_Frame_Del	DEL	GAG	GAG	-	rs35048651	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	GAG	GAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	43	12	60	.	0.279	.	-|0.172;GAG|0.828	0.172	strong	.	WDR81	180	.	NM_001163809	exon1	c.3087_3089del	p.1029_1030del	.	.	PASS	Pindel,Atlas-Indel
RTKN2	219790	hgsc.bcm.edu	37	10	63976913	63976918	+	In_Frame_Del	DEL	AGCTTC	AGCTTC	-	rs149331212	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	AGCTTC	AGCTTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	21	18	59	.	0.857	.	AGCTTC|0.861;-|0.139	0.139	strong	.	RTKN2	68	.	NM_145307	exon9	c.980_985del	p.327_329del	.	.	PASS	Pindel,Atlas-Indel
TSPAN10	83882	hgsc.bcm.edu	37	17	79614933	79614936	+	Splice_Site	DEL	TAAC	TAAC	-	rs34872037	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TAAC	TAAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	23	10	36	.	0.435	.	TAAC|0.198;-|0.802	0.802	strong	.	TSPAN10	21	.	.	.	.	.	.	.	PASS	Pindel,Atlas-Indel
FASTKD1	79675	hgsc.bcm.edu	37	2	170387132	170387133	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	222	69	190	.	0.311	.	.	.	none	.	FASTKD1	86	.	NM_024622	exon14	c.2407_2408insA	p.R803fs	.	.	PASS	Pindel,Atlas-Indel
CAPN11	11131	hgsc.bcm.edu	37	6	44140054	44140055	+	Frame_Shift_Ins	INS	-	-	GGCTGCC	rs57288791	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48	11	59	.	0.229	.	-|0.944;GGCTGCC|0.056	0.056	strong	CAPN11,colon,carcinoma,0,1	CAPN11	66	1	NM_007058	exon5	c.425_426insGGCTGCC	p.L142fs	.	.	PASS	Pindel,Atlas-Indel
CLDN16	10686	hgsc.bcm.edu	37	3	190106072	190106072	+	Frame_Shift_Del	DEL	G	G	-	rs56086318	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	148	78	176	0	0.527027	0	.	.	strong	.	CLDN16	59	.	NM_006580	exon1	c.163delA	p.R55fs	.	.	PASS	Atlas-Indel
PTPRZ1	5803	hgsc.bcm.edu	37	7	121653375	121653377	+	In_Frame_Del	DEL	TGA	TGA	-	rs35947407	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TGA	TGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94	26	123	.	0.277	.	TGA|0.585;-|0.415	0.415	strong	PTPRZ1,leg,malignant_melanoma,-1,1	PTPRZ1	605	1	NM_002851	exon12	c.4274_4276del	p.1425_1426del	.	.	PASS	Pindel,Atlas-Indel
RIC8A	60626	hgsc.bcm.edu	37	11	209895	209897	+	In_Frame_Del	DEL	CCC	CCC	-	rs3832797	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CCC	CCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	24	11	16	0	0.458333	0	CCC|0.579;-|0.421	0.421	strong	.	RIC8A	45	.	NM_021932	exon3	c.620_622del	p.207_208del	.	.	PASS	Atlas-Indel
FARP2	9855	hgsc.bcm.edu	37	2	242407679	242407680	+	Frame_Shift_Del	DEL	CT	CT	-	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	17	82	.	0.274	.	.	.	none	.	FARP2	92	.	NM_014808	exon18	c.2017_2018del	p.673_673del	.	.	PASS	Pindel,Atlas-Indel
NCL	4691	hgsc.bcm.edu	37	2	232325406	232325408	+	In_Frame_Del	DEL	TCA	TCA	-	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TCA	TCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	153	34	154	.	0.222	.	.	.	none	.	NCL	80	.	NM_005381	exon4	c.784_786del	p.262_262del	.	.	PASS	Pindel,Atlas-Indel
TET2	54790	hgsc.bcm.edu	37	4	106158509	106158510	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	272	55	250	.	0.202	.	.	.	none	TET2,NS,haematopoietic_neoplasm,0,1	TET2	1762	1	NM_017628	exon3	c.3410_3411insT	p.G1137fs	.	.	PASS	Pindel,Atlas-Indel
ZNF250	58500	hgsc.bcm.edu	37	8	146112247	146112249	+	In_Frame_Del	DEL	TTG	TTG	-	rs138214845	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TTG	TTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	173	57	155	.	0.329	.	TTG|0.994;-|0.006	0.006	strong	.	ZNF250	37	.	NM_021061	exon5	c.338_340del	p.113_114del	.	.	PASS	Pindel,Atlas-Indel
OXA1L	5018	hgsc.bcm.edu	37	14	23240713	23240714	+	In_Frame_Ins	INS	-	-	AGC	rs148216086	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110	31	103	.	0.282	.	-|0.809;AGC|0.191	0.191	strong	.	OXA1L	49	.	NM_005015	exon10	c.1434_1435insAGC	p.P478delinsPS	.	.	PASS	Pindel,Atlas-Indel
CYP2D6	1565	hgsc.bcm.edu	37	22	42524176	42524178	+	Frame_Shift_Del	DEL	CTT	CTT	-	rs5030656	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	163	40	153	.	0.245	.	CTT|0.989;-|0.011	0.011	strong	.	CYP2D6	104	.	NM_000106	exon5	c.842_843del	p.281_281del	.	.	PASS	Pindel,Atlas-Indel
PRSS16	10279	hgsc.bcm.edu	37	6	27223065	27223079	+	In_Frame_Del	DEL	AAGGAGAGCCAGATT	AAGGAGAGCCAGATT	-	rs141138864	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	AAGGAGAGCCAGATT	AAGGAGAGCCAGATT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	30	119	.	0.577	.	AAGGAGAGCCAGATT|0.883;-|0.117	0.117	strong	.	PRSS16	66	.	NM_005865	exon12	c.1515_1529del	p.505_510del	.	.	PASS	Pindel,Atlas-Indel
ITGB5	3693	hgsc.bcm.edu	37	3	124482495	124482503	+	In_Frame_Del	DEL	TTGTTGAAC	TTGTTGAAC	-	rs150512726	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TTGTTGAAC	TTGTTGAAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	101	62	159	.	0.614	.	TTGTTGAAC|0.922;-|0.078	0.078	strong	.	ITGB5	66	.	NM_002213	exon15	c.2368_2376del	p.790_792del	.	.	PASS	Pindel,Atlas-Indel
PTPRQ	374462	hgsc.bcm.edu	37	12	80943506	80943523	+	In_Frame_Del	DEL	TGAAACAGGTAACTAACG	TGAAACAGGTAACTAACG	-	rs141686707	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TGAAACAGGTAACTAACG	TGAAACAGGTAACTAACG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85	28	81	.	0.329	.	.	.	strong	.	PTPRQ	119	.	NM_001145026	exon22	c.3761_3769del	p.1254_1257del	.	.	PASS	Pindel,Atlas-Indel
METTL21A	151194	hgsc.bcm.edu	37	2	208477923	208477924	+	Frame_Shift_Del	DEL	CA	CA	-	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CA	CA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	103	22	128	.	0.214	.	.	.	none	.	METTL21A	24	.	NM_001127395	exon4	c.504_505del	p.168_169del	.	.	PASS	Pindel,Atlas-Indel
DMKN	93099	hgsc.bcm.edu	37	19	36002419	36002421	+	In_Frame_Del	DEL	CCA	CCA	-	rs72334573	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CCA	CCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	50	16	56	0	0.32	0	CCA|0.786;-|0.214	0.214	strong	DMKN,colon,carcinoma,-2,1	DMKN	116	1	NM_033317	exon5	c.811_813del	p.271_271del	.	.	PASS	Atlas-Indel
GLIPR1L2	144321	hgsc.bcm.edu	37	12	75816814	75816815	+	In_Frame_Ins	INS	-	-	ACA	rs144850646	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48	20	58	.	0.417	.	.	.	strong	.	GLIPR1L2	54	.	NM_152436	exon4	c.715_716insACA	p.D239delinsDN	.	.	PASS	Pindel,Atlas-Indel
MUC4	4585	hgsc.bcm.edu	37	3	195505765	195505766	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68	10	91	0	0.147059	0	.	.	none	.	MUC4	1505	.	NM_018406	exon2	c.12686_12687insT	p.S4229fs	.	.	PASS	Atlas-Indel
CPNE2	221184	hgsc.bcm.edu	37	16	57153565	57153565	+	Splice_Site	DEL	G	G	-	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	28	94	0	0.325581	0	.	.	none	.	CPNE2	48	.	NM_152727	exon7	c.681+2G>-	.	.	.	PASS	Atlas-Indel
GATAD2A	54815	hgsc.bcm.edu	37	19	19612012	19612014	+	In_Frame_Del	DEL	GGA	GGA	-	rs372055939		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	GGA	GGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	120	30	146	.	0.250	.	.	.	weak	.	GATAD2A	81	.	NM_017660	exon9	c.1286_1288del	p.429_430del	.	.	PASS	Pindel,Atlas-Indel
SRA1	10011	hgsc.bcm.edu	37	5	139931628	139931629	+	Frame_Shift_Ins	INS	-	-	GT	rs3085220	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	109	31	152	0	0.284404	0	.	.	strong	SRA1,NS,carcinoma,0,2	SRA1	24	2	NM_001035235	exon3	c.329_330insAC	p.V110fs	.	.	PASS	Atlas-Indel
TSPYL1	7259	hgsc.bcm.edu	37	6	116600465	116600466	+	In_Frame_Ins	INS	-	-	CAC	rs78371471	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	29	16	31	.	0.552	.	.	.	strong	.	TSPYL1	28	.	NM_003309	exon1	c.529_530insGTG	p.K177delinsVK	.	.	PASS	Pindel,Atlas-Indel
DHDH	27294	hgsc.bcm.edu	37	19	49442849	49442850	+	Frame_Shift_Ins	INS	-	-	G	rs3830420	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	56	19	45	.	0.339	.	-|0.754;G|0.246	0.246	strong	.	DHDH	35	.	NM_014475	exon4	c.510_511insG	p.A170fs	.	.	PASS	Pindel,Atlas-Indel
AAK1	22848	hgsc.bcm.edu	37	2	69741754	69741756	+	In_Frame_Del	DEL	TGT	TGT	-	rs3832159	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TGT	TGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57	12	86	0	0.210526	0	TGT|0.607;-|0.393	0.393	strong	.	AAK1	121	.	NM_014911	exon13	c.1624_1626del	p.542_542del	.	.	PASS	Atlas-Indel
OR52B4	143496	hgsc.bcm.edu	37	11	4389405	4389405	+	Frame_Shift_Del	DEL	G	G	-	rs11310407	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	95	24	94	.	0.253	.	G|0.671;-|0.329	0.329	strong	.	OR52B4	56	.	NM_001005161	exon1	c.122delT	p.L41fs	.	.	PASS	Pindel,Atlas-Indel
C14orf23	387978	hgsc.bcm.edu	37	14	29261305	29261305	+	RNA	DEL	A	A	-	rs202195469	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	15	85	0	0.227273	0	A|0.648;-|0.352	0.352	strong	.	C14orf23	5	.	.	.	.	.	.	.	PASS	Atlas-Indel
TBCK	93627	hgsc.bcm.edu	37	4	107171638	107171642	+	Splice_Site	DEL	AAATA	AAATA	-	rs139991421	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	AAATA	AAATA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60	22	68	.	0.367	.	AAATA|0.864;-|0.136	0.136	strong	.	TBCK	89	.	.	.	.	.	.	.	PASS	Pindel,Atlas-Indel
ZNF660	285349	hgsc.bcm.edu	37	3	44636279	44636280	+	Frame_Shift_Del	DEL	AT	AT	-	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	AT	AT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	38	13	41	.	0.342	.	.	.	none	.	ZNF660	28	.	NM_173658	exon3	c.593_594del	p.198_198del	.	.	PASS	Pindel,Atlas-Indel
GPSM1	26086	hgsc.bcm.edu	37	9	139235482	139235482	+	Frame_Shift_Del	DEL	C	C	-	rs145729152	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	43	70	.	0.642	.	C|0.857;-|0.143	0.143	strong	.	GPSM1	50	.	NM_015597	exon9	c.1238delT	p.L413fs	.	.	PASS	Pindel,Atlas-Indel
CHEK1	1111	hgsc.bcm.edu	37	11	125505377	125505378	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	10	108	0	0.114943	0	.	.	none	CHEK1,colon,carcinoma,-1,1	CHEK1	44	1	NM_001114122	exon7	c.667_668insA	p.E223fs	.	.	PASS	Atlas-Indel
LDHAL6A	160287	hgsc.bcm.edu	37	11	18487252	18487253	+	Frame_Shift_Del	DEL	AC	AC	-	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	179	56	152	.	0.313	.	.	.	none	.	LDHAL6A	35	.	NM_144972	exon3	c.312_313del	p.104_105del	.	.	PASS	Pindel,Atlas-Indel
PGPEP1L	145814	hgsc.bcm.edu	37	15	99511804	99511805	+	Frame_Shift_Ins	INS	-	-	C	rs5814919	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	120	37	117	.	0.308	.	-|0.556;C|0.444	0.444	strong	.	PGPEP1L	26	.	NM_001102612	exon5	c.494_495insG	p.V165fs	.	.	PASS	Pindel,Atlas-Indel
CTU2	348180	hgsc.bcm.edu	37	16	88780635	88780636	+	Frame_Shift_Ins	INS	-	-	GTGT	rs149847195		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	59	14	59	.	0.237	.	.	.	weak	.	CTU2	66	.	NM_001012759	exon10	c.1097_1098insGTGT	p.R366fs	.	.	PASS	Pindel,Atlas-Indel
NINL	22981	hgsc.bcm.edu	37	20	25457050	25457055	+	In_Frame_Del	DEL	CTCCCA	CTCCCA	-	rs68078266	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CTCCCA	CTCCCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	15	68	0	0.277778	0	CTCCCA|0.450;-|0.550	0.550	strong	.	NINL	148	.	NM_025176	exon17	c.2873_2878del	p.958_960del	.	.	PASS	Atlas-Indel
BDNF	627	hgsc.bcm.edu	37	11	27681176	27681177	+	RNA	INS	-	-	TG	rs149254890	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	147	68	132	0	0.462585	0	.	.	strong	.	BDNF	63	.	.	.	.	.	.	.	PASS	Atlas-Indel
CNDP1	84735	hgsc.bcm.edu	37	18	72223591	72223592	+	In_Frame_Ins	INS	-	-	TGC	rs10663835	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69	16	64	.	0.232	.	-|0.500;TGC|0.500	0.500	strong	.	CNDP1	98	.	NM_032649	exon2	c.43_44insTGC	p.V15delinsVL	.	.	PASS	Pindel,Atlas-Indel
A2M	2	hgsc.bcm.edu	37	12	9246177	9246181	+	Splice_Site	DEL	TATGG	TATGG	-	rs3832852	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TATGG	TATGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	59	16	75	.	0.271	.	TATGG|0.860;-|0.140	0.140	strong	.	A2M	180	.	.	.	.	.	.	.	PASS	Pindel,Atlas-Indel
EPSTI1	94240	hgsc.bcm.edu	37	13	43462434	43462435	+	Frame_Shift_Ins	INS	-	-	TCAGG	rs61389340	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	223	81	179	.	0.363	.	-|0.890;TCAGG|0.110	0.110	strong	EPSTI1,NS,carcinoma,0,1	EPSTI1	47	1	NM_001002264	exon13	c.1185_1186insCCTGA	p.E395fs	.	.	PASS	Pindel,Atlas-Indel
SUPT20HL2	170067	hgsc.bcm.edu	37	X	24329897	24329908	+	In_Frame_Del	DEL	AGCAGGAGCAGG	AGCAGGAGCAGG	-	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	AGCAGGAGCAGG	AGCAGGAGCAGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	153	38	101	0	0.248366	0	.	.	none	.	.	.	.	NM_001136233	exon1	c.1526_1537del	p.509_513del	.	.	PASS	Atlas-Indel
KRTAP4-5	85289	hgsc.bcm.edu	37	17	39305774	39305775	+	In_Frame_Ins	INS	-	-	TGGCAGCAGCTGGGG	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	31	17	22	0	0.548387	0	.	.	none	KRTAP4-5,NS,carcinoma,0,1	KRTAP4-5	34	1	NM_033188	exon1	c.246_247insCCCCAGCTGCTGCCA	p.Q82delinsHPSCCQ	.	.	PASS	Atlas-Indel
HAVCR1	26762	hgsc.bcm.edu	37	5	156479568	156479569	+	In_Frame_Ins	INS	-	-	GTT	rs139041445	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	257	54	233	.	0.210	.	.	.	strong	.	HAVCR1	84	.	NM_001099414	exon4	c.477_478insAAC	p.T159delinsTT	.	.	PASS	Pindel,Atlas-Indel
SLC3A1	6519	hgsc.bcm.edu	37	2	44528268	44528268	+	Splice_Site	DEL	T	T	-	rs61179824	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94	24	97	.	0.255	.	T|0.888;-|0.112	0.112	strong	.	SLC3A1	62	.	NM_000341	exon6	c.1136+1T>-	.	.	.	PASS	Pindel,Atlas-Indel
HYDIN	54768	hgsc.bcm.edu	37	16	70934990	70934991	+	In_Frame_Ins	INS	-	-	CCC	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	108	16	47	0	0.148148	0	.	.	none	.	HYDIN	788	.	NM_001270974	exon53	c.8965_8966insGGG	p.I2989delinsGI	.	.	PASS	Atlas-Indel
CTAGE5	4253	hgsc.bcm.edu	37	14	39784005	39784008	+	Splice_Site	DEL	TATA	TATA	-	rs75318507	bycluster;by1000genomes;alternate_allele	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TATA	TATA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	131	79	116	0	0.603053	0	.	.	alt	.	CTAGE5	75	.	.	.	.	.	.	.	PASS	Atlas-Indel
LCE4A	199834	hgsc.bcm.edu	37	1	152681680	152681681	+	In_Frame_Ins	INS	-	-	AGCTCTGGGGGCTGCTGT	rs6143428	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	147	31	143	.	0.211	.	.	.	strong	LCE4A,rectum,carcinoma,+1,3	LCE4A	37	3	NM_178356	exon1	c.129_130insAGCTCTGGGGGCTGCTGT	p.S43delinsSSSGGCC	.	.	PASS	Pindel,Atlas-Indel
PCDH9	5101	hgsc.bcm.edu	37	13	67802190	67802190	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	154	12	103	0	0.0779221	0	.	.	none	.	PCDH9	252	.	NM_020403	exon2	c.384delA	p.I128fs	.	.	PASS	Atlas-Indel
IL33	90865	hgsc.bcm.edu	37	9	6254555	6254556	+	Splice_Site	INS	-	-	A	rs113609242		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	27	10	18	0	0.37037	0	A|1.000;|0.000	1.000	weak	.	IL33	27	.	NM_033439	exon7	c.612+2->A	.	.	.	PASS	Atlas-Indel
SUPT20HL1	100130302	hgsc.bcm.edu	37	X	24382374	24382388	+	In_Frame_Del	DEL	TGCTGCTGCTGCTGC	TGCTGCTGCTGCTGC	-	rs371342199	alternate_allele	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TGCTGCTGCTGCTGC	TGCTGCTGCTGCTGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	195	52	131	0	0.266667	0	.	.	alt	.	.	.	.	NM_001136234	exon1	c.1496_1510del	p.499_504del	.	.	PASS	Atlas-Indel
PBOV1	59351	hgsc.bcm.edu	37	6	138539183	138539184	+	Frame_Shift_Ins	INS	-	-	G	rs3841283	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	213	58	208	.	0.272	.	-|0.811;G|0.189	0.189	strong	PBOV1_ENST00000527246,bladder,carcinoma,-1,2	PBOV1	12	2	NM_021635	exon1	c.350_351insC	p.L117fs	.	.	PASS	Pindel,Atlas-Indel
GJB4	127534	hgsc.bcm.edu	37	1	35227008	35227011	+	Frame_Shift_Del	DEL	TGTC	TGTC	-	rs146812843	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TGTC	TGTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	118	44	125	.	0.373	.	TGTC|0.987;-|0.013	0.013	strong	.	GJB4	51	.	NM_153212	exon2	c.152_155del	p.51_52del	.	.	PASS	Pindel,Atlas-Indel
PVRL1	5818	hgsc.bcm.edu	37	11	119535677	119535678	+	In_Frame_Ins	INS	-	-	CCT	rs137909701	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	88	11	88	0	0.125	0	-|0.937;CCT|0.063	0.063	strong	PVRL1,colon,carcinoma,+1,1	PVRL1	133	1	NM_002855	exon6	c.1334_1335insAGG	p.G445delinsEG	.	.	PASS	Atlas-Indel
SYNJ1	8867	hgsc.bcm.edu	37	21	34003928	34003929	+	In_Frame_Ins	INS	-	-	AGTATT	rs71640263	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93	57	129	.	0.613	.	-|0.489;AGTATT|0.511	0.511	strong	.	SYNJ1	253	.	NM_003895	exon32	c.4216_4217insAATACT	p.L1406delinsNTL	.	.	PASS	Pindel,Atlas-Indel
CYP2F1	1572	hgsc.bcm.edu	37	19	41622107	41622108	+	Frame_Shift_Ins	INS	-	-	C	rs3833221	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	25	66	.	0.379	.	-|0.741;C|0.259	0.259	strong	.	CYP2F1	60	.	NM_000774	exon2	c.14_15insC	p.S5fs	.	.	PASS	Pindel,Atlas-Indel
MROH2B	133558	hgsc.bcm.edu	37	5	41064591	41064598	+	Frame_Shift_Del	DEL	TTCATCCT	TTCATCCT	-	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TTCATCCT	TTCATCCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	36	13	46	.	0.361	.	.	.	none	.	.	.	.	NM_173489	exon5	c.437_444del	p.146_148del	.	.	PASS	Pindel,Atlas-Indel
HAVCR1	26762	hgsc.bcm.edu	37	5	156479444	156479446	+	In_Frame_Del	DEL	TTG	TTG	-	rs45439103	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TTG	TTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	250	64	236	.	0.256	.	TTG|0.766;-|0.234	0.234	strong	HAVCR1,NS,carcinoma,-1,1	HAVCR1	84	1	NM_001099414	exon4	c.600_602del	p.200_201del	.	.	PASS	Pindel,Atlas-Indel
CNKSR1	10256	hgsc.bcm.edu	37	1	26510311	26510311	+	Frame_Shift_Del	DEL	C	C	-	rs201305445	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	21	63	.	0.259	.	C|0.980;-|0.020	0.020	strong	.	CNKSR1	66	.	NM_006314	exon9	c.844delA	p.T282fs	.	.	PASS	Pindel,Atlas-Indel
A2ML1	144568	hgsc.bcm.edu	37	12	9016563	9016564	+	Frame_Shift_Del	DEL	GC	GC	-	rs144686314	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	70	14	89	.	0.200	.	GC|0.979;-|0.021	0.021	strong	.	A2ML1	199	.	NM_144670	exon29	c.3675_3676del	p.1225_1226del	.	.	PASS	Pindel,Atlas-Indel
GRWD1	83743	hgsc.bcm.edu	37	19	48950002	48950004	+	In_Frame_Del	DEL	GAA	GAA	-	rs141552216	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	65	16	85	.	0.246	.	GAA|0.945;-|0.055	0.055	strong	.	GRWD1	41	.	NM_031485	exon3	c.369_371del	p.123_124del	.	.	PASS	Pindel,Atlas-Indel
UHRF2	115426	hgsc.bcm.edu	37	9	6413513	6413513	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	14	87	0	0.186667	0	.	.	none	.	UHRF2	50	.	NM_152896	exon1	c.22delA	p.I8fs	.	.	PASS	Atlas-Indel
CTDP1	9150	hgsc.bcm.edu	37	18	77475187	77475188	+	In_Frame_Ins	INS	-	-	GGA	rs35893234	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100	23	102	.	0.230	.	-|0.926;GGA|0.074	0.074	strong	.	CTDP1	67	.	NM_004715	exon8	c.1727_1728insGGA	p.M576delinsME	.	.	PASS	Pindel,Atlas-Indel
FOXD4L2	100036519	hgsc.bcm.edu	37	9	70427650	70427652	+	In_Frame_Del	DEL	CAG	CAG	-	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CAG	CAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	111	22	215	.	0.198	.	.	.	none	.	FOXD4L2	4	.	NM_001099279	exon1	c.1249_1251del	p.417_417del	.	.	PASS	Pindel,Atlas-Indel
WT1-AS	51352	hgsc.bcm.edu	37	11	32461025	32461026	+	RNA	INS	-	-	AG	rs144116821	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	37	15	44	0	0.405405	0	.	.	strong	.	WT1-AS	7	.	.	.	.	.	.	.	PASS	Atlas-Indel
NKAP	79576	hgsc.bcm.edu	37	X	119070328	119070330	+	In_Frame_Del	DEL	GAT	GAT	-	rs10577974	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	GAT	GAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	238	76	202	.	0.319	.	.	.	weak	.	NKAP	53	.	NM_024528	exon4	c.604_606del	p.202_202del	.	.	PASS	Pindel,Atlas-Indel
TSR1	55720	hgsc.bcm.edu	37	17	2237939	2237941	+	In_Frame_Del	DEL	CCA	CCA	-	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CCA	CCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	29	110	.	0.333	.	.	.	none	.	TSR1	57	.	NM_018128	exon5	c.807_809del	p.269_270del	.	.	PASS	Pindel,Atlas-Indel
CDSN	1041	hgsc.bcm.edu	37	6	31084943	31084945	+	In_Frame_Del	DEL	CTT	CTT	-	rs34182778	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	50	13	49	.	0.260	.	CTT|0.500;-|0.500	0.500	strong	.	CDSN	48	.	NM_001264	exon2	c.448_450del	p.150_150del	.	.	PASS	Pindel,Atlas-Indel
OR4L1	122742	hgsc.bcm.edu	37	14	20528449	20528467	+	Frame_Shift_Del	DEL	CATAGATTTGCTCACTGAC	CATAGATTTGCTCACTGAC	-	rs112192573	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CATAGATTTGCTCACTGAC	CATAGATTTGCTCACTGAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	141	32	184	.	0.227	.	CATAGATTTGCTCACTGAC|0.504;-|0.496	0.496	strong	.	OR4L1	98	.	NM_001004717	exon1	c.245_263del	p.82_88del	.	.	PASS	Pindel,Atlas-Indel
C11orf40	143501	hgsc.bcm.edu	37	11	4592708	4592709	+	Frame_Shift_Ins	INS	-	-	AG	rs71280817	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	118	33	120	.	0.280	.	-|0.378;AC|0.622	.	strong	.	C11orf40	37	.	NM_144663	exon4	c.599_600insCT	p.C200fs	.	.	PASS	Pindel,Atlas-Indel
MUC20	200958	hgsc.bcm.edu	37	3	195453018	195453018	+	Frame_Shift_Del	DEL	C	C	-	rs144288174	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	417	93	307	0	0.223022	0	C|0.915;-|0.085	0.085	strong	.	MUC20	84	.	NM_152673	exon3	c.1030delG	p.A344fs	.	.	PASS	Atlas-Indel
NPVF	64111	hgsc.bcm.edu	37	7	25266570	25266572	+	In_Frame_Del	DEL	TAA	TAA	-	rs3216928	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TAA	TAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	124	27	179	.	0.218	.	TAA|0.862;-|0.138	0.138	strong	.	NPVF	36	.	NM_022150	exon2	c.213_215del	p.71_72del	.	.	PASS	Pindel,Atlas-Indel
GCC2	9648	hgsc.bcm.edu	37	2	109087929	109087931	+	In_Frame_Del	DEL	AAG	AAG	-	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83	24	109	.	0.289	.	.	.	none	.	GCC2	129	.	NM_181453	exon6	c.2143_2145del	p.715_715del	.	.	PASS	Pindel,Atlas-Indel
KRT36	8689	hgsc.bcm.edu	37	17	39642658	39642660	+	In_Frame_Del	DEL	GGA	GGA	-	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	GGA	GGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	25	95	.	0.352	.	.	.	none	.	KRT36	52	.	NM_003771	exon7	c.1373_1375del	p.458_459del	.	.	PASS	Pindel,Atlas-Indel
GPSM2	29899	hgsc.bcm.edu	37	1	109465166	109465168	+	In_Frame_Del	DEL	CTT	CTT	-	rs35029887	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	140	41	156	.	0.293	.	CTT|0.700;-|0.300	0.300	strong	.	GPSM2	56	.	NM_013296	exon13	c.1567_1569del	p.523_523del	.	.	PASS	Pindel,Atlas-Indel
GTF2I	2969	hgsc.bcm.edu	37	7	74149837	74149840	+	Frame_Shift_Del	DEL	AAGA	AAGA	-	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	AAGA	AAGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	122	12	91	0	0.0983607	0	.	.	none	.	GTF2I	40	.	NM_032999	exon17	c.1397_1400del	p.466_467del	.	.	PASS	Atlas-Indel
GLT6D1	360203	hgsc.bcm.edu	37	9	138516347	138516347	+	Frame_Shift_Del	DEL	A	A	-	rs34217442	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68	20	66	.	0.294	.	A|0.829;-|0.171	0.171	strong	.	GLT6D1	56	.	NM_182974	exon5	c.428delG	p.W143fs	.	.	PASS	Pindel,Atlas-Indel
TET2	54790	hgsc.bcm.edu	37	4	106196525	106196525	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	13	96	.	0.171	.	.	.	none	.	TET2	1762	.	NM_001127208	exon11	c.4857delT	p.P1619fs	.	.	PASS	Pindel,Atlas-Indel
GDPD4	220032	hgsc.bcm.edu	37	11	76954788	76954789	+	Frame_Shift_Ins	INS	-	-	A	rs34784710	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	115	19	88	0	0.165217	0	-|0.773;A|0.227	0.227	strong	.	GDPD4	49	.	NM_182833	exon12	c.1192_1193insT	p.I398fs	.	.	PASS	Atlas-Indel
USP40	55230	hgsc.bcm.edu	37	2	234429739	234429740	+	In_Frame_Ins	INS	-	-	TTC	rs141501074	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	29	62	.	0.617	.	-|0.837;TTC|0.163	0.163	strong	.	USP40	174	.	NM_018218	exon16	c.2256_2257insGAA	p.K752delinsKK	.	.	PASS	Pindel,Atlas-Indel
APOBEC3H	164668	hgsc.bcm.edu	37	22	39496323	39496325	+	In_Frame_Del	DEL	AAC	AAC	-	rs140936762	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	AAC	AAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	123	42	131	.	0.341	.	AAC|0.696;-|0.304	0.304	strong	.	APOBEC3H	28	.	NM_181773	exon2	c.39_41del	p.13_14del	.	.	PASS	Pindel,Atlas-Indel
KIAA0586	9786	hgsc.bcm.edu	37	14	58899157	58899157	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	152	56	170	.	0.368	.	.	.	none	.	KIAA0586	180	.	NM_001244189	exon5	c.427delA	p.R143fs	.	.	PASS	Pindel,Atlas-Indel
FOXD4L2	100036519	hgsc.bcm.edu	37	9	42719309	42719311	+	In_Frame_Del	DEL	GCT	GCT	-	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	GCT	GCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	127	18	227	0	0.141732	0	.	.	none	.	FOXD4L2	4	.	NM_001099279	exon1	c.1243_1245del	p.415_415del	.	.	PASS	Atlas-Indel
ZNF880	400713	hgsc.bcm.edu	37	19	52887146	52887146	+	Frame_Shift_Del	DEL	A	A	-	rs34470614	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	52	87	.	0.598	.	A|0.672;-|0.328	0.328	strong	.	ZNF880	45	.	NM_001145434	exon4	c.312delT	p.L104fs	.	.	PASS	Pindel,Atlas-Indel
RETNLB	84666	hgsc.bcm.edu	37	3	108475993	108475994	+	Frame_Shift_Ins	INS	-	-	GGGGATTA	rs5851607	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	50	17	45	.	0.340	.	-|0.879;GGGGATTA|0.121	0.121	strong	.	RETNLB	38	.	NM_032579	exon1	c.40_41insTAATCCCC	p.L14_L15delinsX	.	.	PASS	Pindel,Atlas-Indel
IGLL5	100423062	hgsc.bcm.edu	37	22	23230370	23230370	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	45	10	144	.	0.222	.	.	.	none	.	IGLL5	26	.	NM_001178126	exon1	c.136delC	p.Q46fs	.	.	PASS	Pindel,Atlas-Indel
CREB3L2	64764	hgsc.bcm.edu	37	7	137612914	137612916	+	In_Frame_Del	DEL	TGG	TGG	-	rs66593747	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TGG	TGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	168	83	246	.	0.494	.	TGG|0.250;-|0.750	0.750	strong	.	CREB3L2	62	.	NM_001253775	exon2	c.300_302del	p.100_101del	.	.	PASS	Pindel,Atlas-Indel
MUC4	4585	hgsc.bcm.edu	37	3	195505762	195505763	+	Frame_Shift_Del	DEL	AG	AG	-	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68	10	88	0	0.147059	0	.	.	none	MUC4_ENST00000463781,NS,carcinoma,-2,4	MUC4	1505	4	NM_018406	exon2	c.12689_12690del	p.4230_4230del	.	.	PASS	Atlas-Indel
OR13C5	138799	hgsc.bcm.edu	37	9	107360769	107360769	+	Frame_Shift_Del	DEL	T	T	-	rs11314210	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94	33	97	.	0.351	.	T|0.620;-|0.380	0.380	strong	.	OR13C5	60	.	NM_001004482	exon1	c.927delC	p.H309fs	.	.	PASS	Pindel,Atlas-Indel
MYO5B	4645	hgsc.bcm.edu	37	18	47405425	47405426	+	In_Frame_Ins	INS	-	-	GAG	rs3841750	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	144	42	131	.	0.292	.	-|0.623;GAG|0.377	0.377	strong	MYO5B,NS,carcinoma,0,1	MYO5B	178	1	NM_001080467	exon24	c.3166_3167insCTC	p.M1056delinsLM	.	.	PASS	Pindel,Atlas-Indel
OR10AD1	121275	hgsc.bcm.edu	37	12	48596875	48596876	+	Frame_Shift_Ins	INS	-	-	A	rs144247841	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	166	48	176	.	0.289	.	-|0.791;A|0.209	0.209	strong	.	OR10AD1	24	.	NM_001004134	exon1	c.201_202insT	p.L67fs	.	.	PASS	Pindel,Atlas-Indel
LMOD3	56203	hgsc.bcm.edu	37	3	69171497	69171499	+	In_Frame_Del	DEL	AGA	AGA	-	rs139192915	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	92	27	105	.	0.293	.	AGA|0.988;-|0.012	0.012	strong	.	LMOD3	92	.	NM_198271	exon1	c.40_42del	p.14_14del	.	.	PASS	Pindel,Atlas-Indel
C14orf23	387978	hgsc.bcm.edu	37	14	29261307	29261308	+	RNA	INS	-	-	C	rs56363493	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	11	85	0	0.164179	0	-|0.736;C|0.264	0.264	strong	.	C14orf23	5	.	.	.	.	.	.	.	PASS	Atlas-Indel
RP1L1	94137	hgsc.bcm.edu	37	8	10466004	10466024	+	In_Frame_Del	DEL	CTGGGCCTCCCCTTCAGCCTC	CTGGGCCTCCCCTTCAGCCTC	-	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CTGGGCCTCCCCTTCAGCCTC	CTGGGCCTCCCCTTCAGCCTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	29	26	44	0	0.896552	0	.	.	none	RP1L1,lower_third,carcinoma,+2,1	RP1L1	453	1	NM_178857	exon4	c.5585_5605del	p.1862_1869del	.	.	PASS	Atlas-Indel
SERINC2	347735	hgsc.bcm.edu	37	1	31905889	31905890	+	In_Frame_Ins	INS	-	-	CAG	rs3050461	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	45	93	.	0.536	.	.	.	strong	.	SERINC2	44	.	NM_001199038	exon10	c.1116_1117insCAG	p.T372delinsTQ	.	.	PASS	Pindel,Atlas-Indel
ZNF543	125919	hgsc.bcm.edu	37	19	57839629	57839630	+	In_Frame_Ins	INS	-	-	GCG	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	20	55	.	0.426	.	.	.	none	.	ZNF543	61	.	NM_213598	exon4	c.799_800insGCG	p.R267delinsSG	.	.	PASS	Pindel,Atlas-Indel
NUDT17	200035	hgsc.bcm.edu	37	1	145586679	145586679	+	Frame_Shift_Del	DEL	C	C	-	rs199513201	by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80	18	113	0	0.225	0	C|0.983;-|0.017	0.017	strong	.	NUDT17	25	.	NM_001012758	exon8	c.898delT	p.C300fs	.	.	PASS	Atlas-Indel
DDN	23109	hgsc.bcm.edu	37	12	49391394	49391395	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	11	41	.	0.212	.	.	.	none	.	DDN	54	.	NM_015086	exon2	c.1265_1266insG	p.A422fs	.	.	PASS	Pindel,Atlas-Indel
CHRFAM7A	89832	hgsc.bcm.edu	37	15	30665281	30665282	+	Frame_Shift_Del	DEL	CA	CA	-	rs201490160	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CA	CA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	1183	697	1086	0	0.58918	0	.	.	strong	.	CHRFAM7A	15	.	NM_139320	exon6	c.228_229del	p.76_77del	.	.	PASS	Atlas-Indel
KIAA0040	9674	hgsc.bcm.edu	37	1	175129924	175129925	+	In_Frame_Ins	INS	-	-	CTT	rs150137790	bycluster;by1000genomes;alternate_allele	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93	15	78	.	0.161	.	.	.	alt	.	KIAA0040	2	.	NM_001162893	exon5	c.226_227insAAG	p.D76delinsKD	.	.	PASS	Pindel,Atlas-Indel
ZNF623	9831	hgsc.bcm.edu	37	8	144733650	144733654	+	Frame_Shift_Del	DEL	ATAAA	ATAAA	-	rs202122969	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	ATAAA	ATAAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	143	57	145	.	0.399	.	ATAAA|0.993;-|0.007	0.007	strong	.	ZNF623	63	.	NM_014789	exon1	c.1607_1611del	p.536_537del	.	.	PASS	Pindel,Atlas-Indel
OR2W3	343171	hgsc.bcm.edu	37	1	248059353	248059355	+	In_Frame_Del	DEL	CTC	CTC	-	rs147816311	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CTC	CTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	170	45	171	.	0.265	.	CTC|0.980;-|0.020	0.020	strong	.	OR2W3	113	.	NM_001001957	exon1	c.464_466del	p.155_156del	.	.	PASS	Pindel,Atlas-Indel
LRRC17	10234	hgsc.bcm.edu	37	7	102575000	102575002	+	In_Frame_Del	DEL	GAA	GAA	-	rs3832497	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	38	41	.	0.603	.	GAA|0.331;-|0.669	0.669	strong	.	LRRC17	45	.	NM_005824	exon2	c.639_641del	p.213_214del	.	.	PASS	Pindel,Atlas-Indel
TOP3A	7156	hgsc.bcm.edu	37	17	18205751	18205760	+	Splice_Site	DEL	GGAGAGTGAA	GGAGAGTGAA	-	rs66697088	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	GGAGAGTGAA	GGAGAGTGAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	19	66	.	0.297	.	GGAGAGTGAA|0.758;-|0.242	0.242	strong	.	TOP3A	85	.	.	.	.	.	.	.	PASS	Pindel,Atlas-Indel
CCDC37	348807	hgsc.bcm.edu	37	3	126142434	126142436	+	In_Frame_Del	DEL	GGA	GGA	-	rs140223152	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	GGA	GGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	108	29	111	.	0.269	.	GGA|0.949;-|0.051	0.051	strong	.	CCDC37	69	.	NM_182628	exon13	c.1232_1234del	p.411_412del	.	.	PASS	Pindel,Atlas-Indel
OR13C2	392376	hgsc.bcm.edu	37	9	107367393	107367396	+	Frame_Shift_Del	DEL	GTTA	GTTA	-	rs143198170	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	GTTA	GTTA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	267	93	357	0	0.348315	0	.	.	strong	.	OR13C2	46	.	NM_001004481	exon1	c.514_517del	p.172_173del	.	.	PASS	Atlas-Indel
MCCC1	56922	hgsc.bcm.edu	37	3	182755074	182755074	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	131	39	122	.	0.298	.	.	.	none	.	MCCC1	87	.	NM_020166	exon13	c.1527delC	p.C509fs	.	.	PASS	Pindel,Atlas-Indel
SRA1	10011	hgsc.bcm.edu	37	5	139931629	139931630	+	Frame_Shift_Ins	INS	-	-	G	rs5871740	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	106	31	153	0	0.292453	0	.	.	weak	SRA1,NS,carcinoma,+1,2	SRA1	24	2	NM_001035235	exon3	c.328_329insC	p.V110fs	.	.	PASS	Atlas-Indel
DSPP	1834	hgsc.bcm.edu	37	4	88536543	88536551	+	In_Frame_Del	DEL	ACAGCAGTG	ACAGCAGTG	-	rs111456637	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	ACAGCAGTG	ACAGCAGTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82	13	115	0	0.158537	0	ACAGCAGTG|0.500;-|0.500	0.500	weak	.	DSPP	174	.	NM_014208	exon5	c.2728_2736del	p.910_912del	.	.	PASS	Atlas-Indel
QRICH2	84074	hgsc.bcm.edu	37	17	74288565	74288567	+	In_Frame_Del	DEL	TGA	TGA	-	rs35035566	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TGA	TGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79	33	92	0	0.417722	0	TGA|0.548;-|0.452	0.452	strong	QRICH2,NS,carcinoma,-1,1	QRICH2	143	1	NM_032134	exon4	c.1744_1746del	p.582_582del	.	.	PASS	Atlas-Indel
DMTF1	9988	hgsc.bcm.edu	37	7	86795881	86795883	+	In_Frame_Del	DEL	TGA	TGA	-	rs148453627	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TGA	TGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91	23	120	.	0.253	.	TGA|0.983;-|0.017	0.017	strong	.	DMTF1	48	.	NM_001142327	exon4	c.191_193del	p.64_65del	.	.	PASS	Pindel,Atlas-Indel
FOXD4L5	653427	hgsc.bcm.edu	37	9	70176734	70176736	+	In_Frame_Del	DEL	CAG	CAG	-	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CAG	CAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	125	17	231	0	0.136	0	.	.	none	.	FOXD4L5	27	.	NM_001126334	exon1	c.1249_1251del	p.417_417del	.	.	PASS	Atlas-Indel
SLC23A1	9963	hgsc.bcm.edu	37	5	138715033	138715034	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	99	16	85	.	0.162	.	.	.	none	.	SLC23A1	51	.	NM_152685	exon9	c.948_949insG	p.G316fs	.	.	PASS	Pindel,Atlas-Indel
ZNF880	400713	hgsc.bcm.edu	37	19	52887246	52887247	+	In_Frame_Ins	INS	-	-	CAA	rs34678014	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	137	78	118	.	0.569	.	-|0.657;CAA|0.343	0.343	strong	.	ZNF880	45	.	NM_001145434	exon4	c.413_414insCAA	p.I138delinsIN	.	.	PASS	Pindel,Atlas-Indel
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057613	46057627	+	In_Frame_Del	DEL	CTGCTGTGTGCCTGT	CTGCTGTGTGCCTGT	-	rs66931310	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CTGCTGTGTGCCTGT	CTGCTGTGTGCCTGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	145	43	121	0	0.296552	0	CTGCTGTGTGCCTGT|0.469;-|0.531	0.531	strong	.	KRTAP10-10	37	.	NM_181688	exon1	c.278_292del	p.93_98del	.	.	PASS	Atlas-Indel
ASMTL	8623	hgsc.bcm.edu	37	X	1522164	1522164	+	In_Frame_Del	DEL	A	A	-	rs113329185	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	15	112	.	0.246	.	A|0.500;-|0.500	0.500	weak	.	ASMTL	56	.	NM_004192	exon13	c.1865delG	p.X622X	.	.	PASS	Pindel,Atlas-Indel
RFC4	5984	hgsc.bcm.edu	37	3	186508121	186508122	+	Frame_Shift_Del	DEL	CA	CA	-	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CA	CA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	112	24	134	.	0.214	.	.	.	none	RFC4,NS,carcinoma,+2,2	RFC4	54	2	NM_002916	exon9	c.876_877del	p.292_293del	.	.	PASS	Pindel,Atlas-Indel
C16orf88	400506	hgsc.bcm.edu	37	16	19725766	19725767	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	36	18	45	.	0.500	.	.	.	none	.	C16orf88	41	.	NM_001012991	exon2	c.592_593insG	p.Q198fs	.	.	PASS	Pindel,Atlas-Indel
TSPYL6	388951	hgsc.bcm.edu	37	2	54482704	54482709	+	In_Frame_Del	DEL	GGGCCC	GGGCCC	-	rs76397255	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	GGGCCC	GGGCCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	20	63	.	0.312	.	GGGCCC|0.831;-|0.169	0.169	strong	.	TSPYL6	54	.	NM_001003937	exon1	c.581_586del	p.194_196del	.	.	PASS	Pindel,Atlas-Indel
OR13C5	138799	hgsc.bcm.edu	37	9	107361451	107361452	+	Frame_Shift_Del	DEL	GC	GC	-	rs35762823	byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	325	50	382	0	0.153846	0	GC|0.500;-|0.500	0.500	strong	.	OR13C5	60	.	NM_001004482	exon1	c.244_245del	p.82_82del	.	.	PASS	Atlas-Indel
WDR73	84942	hgsc.bcm.edu	37	15	85186877	85186894	+	In_Frame_Del	DEL	CTTGGCTCCGTGTTCCAT	CTTGGCTCCGTGTTCCAT	-	rs11267906	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CTTGGCTCCGTGTTCCAT	CTTGGCTCCGTGTTCCAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	88	26	120	.	0.295	.	.	.	strong	.	WDR73	15	.	NM_032856	exon8	c.945_962del	p.315_321del	.	.	PASS	Pindel,Atlas-Indel
IL32	9235	hgsc.bcm.edu	37	16	3119297	3119298	+	Frame_Shift_Ins	INS	-	-	G	rs71818662	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	172	27	81	.	0.157	.	.	.	strong	IL32,NS,carcinoma,0,1	IL32	32	1	NM_004221	exon7	c.508_509insG	p.R170fs	.	.	PASS	Pindel,Atlas-Indel
OR52A1	23538	hgsc.bcm.edu	37	11	5172795	5172796	+	Frame_Shift_Ins	INS	-	-	C	rs112098990	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	28	76	.	0.346	.	-|0.838;C|0.162	0.162	strong	OR52A1,NS,carcinoma,+1,1	OR52A1	58	1	NM_012375	exon1	c.805_806insG	p.S269fs	.	.	PASS	Pindel,Atlas-Indel
TRIM52	84851	hgsc.bcm.edu	37	5	180687429	180687431	+	In_Frame_Del	DEL	TCT	TCT	-	rs33972170	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TCT	TCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	114	54	131	.	0.474	.	TCT|0.580;-|0.420	0.420	strong	.	TRIM52	20	.	NM_032765	exon1	c.385_387del	p.129_129del	.	.	PASS	Pindel
KLF17	128209	hgsc.bcm.edu	37	1	44596380	44596382	+	In_Frame_Del	DEL	CAA	CAA	-	rs34057178	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CAA	CAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	65	18	81	.	0.277	.	CAA|0.811;-|0.189	0.189	strong	.	KLF17	92	.	NM_173484	exon3	c.1121_1123del	p.374_375del	.	.	PASS	Pindel
B2M	567	hgsc.bcm.edu	37	15	45007888	45007891	+	Frame_Shift_Del	DEL	TAGT	TAGT	-	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TAGT	TAGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51	17	71	.	0.333	.	.	.	none	.	B2M	99	.	NM_004048	exon2	c.334_337del	p.112_113del	.	.	PASS	Pindel
LINC00238	440184	hgsc.bcm.edu	37	14	66953309	66953310	+	RNA	DEL	TC	TC	-	rs10569333	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TC	TC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	14	37	.	0.269	.	TC|0.500;-|0.500	0.500	strong	.	.	.	.	.	.	.	.	.	.	PASS	Pindel
OR5P2	120065	hgsc.bcm.edu	37	11	7818383	7818384	+	In_Frame_Ins	INS	-	-	ATATGGTTACCAGGTAGATGC	rs138967151	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	27	13	51	.	0.481	.	.	.	strong	.	OR5P2	68	.	NM_153444	exon1	c.107_108insGCATCTACCTGGTAACCATAT	p.S36delinsCIYLVTIS	.	.	PASS	Pindel
TNRC6B	23112	hgsc.bcm.edu	37	22	40697177	40697179	+	In_Frame_Del	DEL	GCA	GCA	-	rs10617561	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	GCA	GCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	40	21	27	.	0.525	.	GCA|0.779;-|0.221	0.221	strong	.	TNRC6B	195	.	NM_001162501	exon15	c.3959_3961del	p.1320_1321del	.	.	PASS	Pindel
PI4KAP2	375133	hgsc.bcm.edu	37	22	21829514	21829517	+	RNA	DEL	TGTC	TGTC	-	rs113567369	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TGTC	TGTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	97	29	155	.	0.299	.	TGTC|0.500;-|0.500	0.500	strong	.	PI4KAP2	11	.	.	.	.	.	.	.	PASS	Pindel
EVA1A	84141	hgsc.bcm.edu	37	2	75720569	75720577	+	In_Frame_Del	DEL	GCTGTCGCT	GCTGTCGCT	-	rs148155576	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	GCTGTCGCT	GCTGTCGCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55	11	62	.	0.200	.	GCTGTCGCT|0.959;-|0.041	0.041	strong	.	.	.	.	NM_001135032	exon4	c.245_253del	p.82_85del	.	.	PASS	Pindel
GPRIN1	114787	hgsc.bcm.edu	37	5	176026115	176026138	+	In_Frame_Del	DEL	CCTTTCTCAAAGACCCAGGATCCT	CCTTTCTCAAAGACCCAGGATCCT	-	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CCTTTCTCAAAGACCCAGGATCCT	CCTTTCTCAAAGACCCAGGATCCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	104	26	141	.	0.250	.	.	.	none	.	GPRIN1	77	.	NM_052899	exon2	c.699_722del	p.233_241del	.	.	PASS	Pindel
RBM27	54439	hgsc.bcm.edu	37	5	145647319	145647320	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	266	41	220	.	0.154	.	.	.	none	.	RBM27	119	.	NM_018989	exon15	c.2439_2440insA	p.L813fs	.	.	PASS	Pindel
SRA1	10011	hgsc.bcm.edu	37	5	139931629	139931629	+	Frame_Shift_Del	DEL	C	C	-	rs3085220	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	108	17	153	.	0.157	.	.	.	strong	SRA1,NS,carcinoma,0,2	SRA1	24	2	NM_001035235	exon3	c.329delT	p.V110fs	.	.	PASS	Pindel
NUDT17	200035	hgsc.bcm.edu	37	1	145586672	145586679	+	Frame_Shift_Del	DEL	TTTTACAC	TTTTACAC	-	rs201063949	by1000genomes;alternate_allele	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TTTTACAC	TTTTACAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	21	116	.	0.250	.	-|0.017;TTTTA|0.983	0.017	alt	.	NUDT17	25	.	NM_001012758	exon8	c.898_905del	p.300_302del	.	.	PASS	Pindel
C14orf23	387978	hgsc.bcm.edu	37	14	29261305	29261306	+	RNA	INS	-	-	AACAAAC	rs200251419	by1000genomes;alternate_allele	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	12	86	.	0.179	.	-|0.668;AAC|0.332	.	alt	.	C14orf23	5	.	.	.	.	.	.	.	PASS	Pindel
MAB21L1	4081	hgsc.bcm.edu	37	13	36050434	36050451	+	RNA	DEL	CTGCTGCTGCTGCTGCTG	CTGCTGCTGCTGCTGCTG	-	rs11275995	alternate_allele	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CTGCTGCTGCTGCTGCTG	CTGCTGCTGCTGCTGCTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	59	11	73	.	0.186	.	.	.	alt	.	MAB21L1	52	.	.	.	.	.	.	.	PASS	Pindel
CACNA1B	774	hgsc.bcm.edu	37	9	140918171	140918185	+	In_Frame_Del	DEL	GGAGAAGGAGACCAC	GGAGAAGGAGACCAC	-	rs145816559	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	GGAGAAGGAGACCAC	GGAGAAGGAGACCAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72	17	87	.	0.236	.	GGAGAAGGAGACCAC|0.621;-|0.379	0.379	strong	.	CACNA1B	266	.	NM_001243812	exon19	c.2975_2989del	p.992_997del	.	.	PASS	Pindel
NRD1	4898	hgsc.bcm.edu	37	1	52306064	52306066	+	In_Frame_Del	DEL	TCT	TCT	-	rs35723519	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TCT	TCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	242	76	229	.	0.314	.	TCT|0.388;-|0.612	0.612	strong	NRD1,caecum,carcinoma,0,1	NRD1	89	1	NM_002525	exon2	c.463_465del	p.155_155del	.	.	PASS	Pindel
PLD1	5337	hgsc.bcm.edu	37	3	171455452	171455452	+	Splice_Site	DEL	A	A	-	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	56	14	39	.	0.250	.	.	.	none	.	PLD1	134	.	NM_001130081	exon4	c.161-2T>-	.	.	.	PASS	Pindel
LRRC37A3	374819	hgsc.bcm.edu	37	17	62882286	62882287	+	Splice_Site	INS	-	-	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100	21	93	.	0.210	.	.	.	none	.	LRRC37A3	75	.	NM_199340	exon8	c.2826-2->T	.	.	.	PASS	Pindel
HLA-B	3106	hgsc.bcm.edu	37	6	31324525	31324531	+	Frame_Shift_Del	DEL	CCTGGGC	CCTGGGC	-	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CCTGGGC	CCTGGGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98	39	37	.	0.398	.	.	.	none	.	HLA-B	54	.	NM_005514	exon2	c.278_284del	p.93_95del	.	.	PASS	Pindel
RTN1	6252	hgsc.bcm.edu	37	14	60063508	60063508	+	Splice_Site	DEL	A	A	-	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	109	34	104	.	0.312	.	.	.	none	.	RTN1	139	.	NM_021136	exon10	c.2289-2T>-	.	.	.	PASS	Pindel
DMKN	93099	hgsc.bcm.edu	37	19	36002362	36002412	+	In_Frame_Del	DEL	CTGCTGCCACCACTGCTGCCGCCACTGCTGCCGCCACTGCTGCTGCCACTG	CTGCTGCCACCACTGCTGCCGCCACTGCTGCCGCCACTGCTGCTGCCACTG	-	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CTGCTGCCACCACTGCTGCCGCCACTGCTGCCGCCACTGCTGCTGCCACTG	CTGCTGCCACCACTGCTGCCGCCACTGCTGCCGCCACTGCTGCTGCCACTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49	14	50	.	0.286	.	.	.	none	.	DMKN	116	.	NM_033317	exon5	c.820_870del	p.274_290del	.	.	PASS	Pindel
STK17B	9262	hgsc.bcm.edu	37	2	197004468	197004575	+	In_Frame_Del	DEL	CTCCCACAAATGGTGATGTGTGAGTTAACAACATATATGCTATTATACCAATATTCCTGAAAAACAAGGGAGGGGAACTTAAAATGTATGTTAATTTTTAAACATTTA	CTCCCACAAATGGTGATGTGTGAGTTAACAACATATATGCTATTATACCAATATTCCTGAAAAACAAGGGAGGGGAACTTAAAATGTATGTTAATTTTTAAACATTTA	-	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CTCCCACAAATGGTGATGTGTGAGTTAACAACATATATGCTATTATACCAATATTCCTGAAAAACAAGGGAGGGGAACTTAAAATGTATGTTAATTTTTAAACATTTA	CTCCCACAAATGGTGATGTGTGAGTTAACAACATATATGCTATTATACCAATATTCCTGAAAAACAAGGGAGGGGAACTTAAAATGTATGTTAATTTTTAAACATTTA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68	15	84	.	0.221	.	.	.	none	.	STK17B	28	.	NM_004226	exon7	c.657_713del	p.219_238del	.	.	PASS	Pindel
CHIT1	1118	hgsc.bcm.edu	37	1	203186950	203186951	+	In_Frame_Ins	INS	-	-	AGACCATGGCCCCGCCCAGTCCCT	rs150192398	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	35	19	62	.	0.543	.	.	.	strong	CHIT1,colon,carcinoma,0,2	CHIT1	61	2	NM_003465	exon10	c.1073_1074insAGGGACTGGGCGGGGCCATGGTCT	p.W358delinsX	.	.	PASS	Pindel
CLDN16	10686	hgsc.bcm.edu	37	3	190106073	190106074	+	Frame_Shift_Del	DEL	GG	GG	-	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	GG	GG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	155	25	180	.	0.161	.	.	.	none	.	CLDN16	59	.	NM_006580	exon1	c.164_165del	p.55_55del	.	.	PASS	Pindel
SLC12A9	56996	hgsc.bcm.edu	37	7	100464136	100464136	+	Missense_Mutation	SNP	G	G	A	rs374047787		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	20	26	0	0.384615	0	.	.	weak	.	SLC12A9	81	.	NM_020246	exon14	c.G2654A	p.R885H	ACCCCCGCTACCT	.	PASS	Atlas-SNP
MN1	4330	hgsc.bcm.edu	37	22	28192809	28192809	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	96	30	81	0	0.3125	0	.	.	none	.	MN1	122	.	NM_002430	exon1	c.C3723T	p.D1241D	CTTGTCGTCGTCC	.	PASS	Atlas-SNP
SEC14L3	266629	hgsc.bcm.edu	37	22	30860830	30860830	+	Missense_Mutation	SNP	C	C	T	rs2269961	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	103	48	114	0	0.466019	0	C|0.774;N|0.001	.	strong	.	SEC14L3	46	.	NM_174975	exon8	c.G641A	p.R214H	TTCCTGCGAGTGT	.	PASS	Atlas-SNP
FKBP10	60681	hgsc.bcm.edu	37	17	39974642	39974642	+	Missense_Mutation	SNP	A	A	G	rs34764749	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	152	85	164	0	0.559211	0	A|0.935;G|0.065	0.065	strong	.	FKBP10	57	.	NM_021939	exon4	c.A590G	p.K197R	ACAGTAAGGGCGG	.	PASS	Atlas-SNP
SLC2A9	56606	hgsc.bcm.edu	37	4	10027542	10027542	+	Missense_Mutation	SNP	C	C	T	rs6820230	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	51	82	0	0.586207	0	C|0.682;T|0.318	0.318	strong	SLC2A9,NS,carcinoma,+2,1	SLC2A9	158	1	NM_001001290	exon2	c.G49A	p.A17T	TTTTCGCTGAATC	.	PASS	Atlas-SNP
CLCA2	9635	hgsc.bcm.edu	37	1	86913384	86913384	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	89	20	76	0	0.224719	0	.	.	none	.	CLCA2	102	.	NM_006536	exon11	c.T1907A	p.L636H	CCATTCTTAATGC	.	PASS	Atlas-SNP
ZNF239	8187	hgsc.bcm.edu	37	10	44053013	44053013	+	Missense_Mutation	SNP	G	G	C	rs2230660	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	40	77	0	0.56338	0	G|0.474;C|0.525	0.525	strong	.	ZNF239	45	.	NM_001099283	exon2	c.C515G	p.A172G	GTATGAGCTCTCT	.	PASS	Atlas-SNP
VWA7	80737	hgsc.bcm.edu	37	6	31734345	31734345	+	Silent	SNP	G	G	T	rs3115671	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	30	28	27	0	0.933333	0	G|0.932;T|0.068	0.068	strong	.	.	.	.	NM_025258	exon14	c.C2079A	p.S693S	AGGGGTGGACAGC	.	PASS	Atlas-SNP
KRT23	25984	hgsc.bcm.edu	37	17	39092735	39092735	+	Missense_Mutation	SNP	C	C	A	rs34861030	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	40	26	61	0	0.65	0	C|0.987;A|0.013	0.013	strong	.	KRT23	59	.	NM_015515	exon2	c.G121T	p.A41S	TGCGGGCTCCCCC	.	PASS	Atlas-SNP
KIF23	9493	hgsc.bcm.edu	37	15	69709792	69709792	+	Missense_Mutation	SNP	C	C	T	rs61751119	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83	38	44	0	0.457831	0	C|0.956;T|0.044	0.044	strong	.	KIF23	57	.	NM_138555	exon3	c.C152T	p.T51I	ATACAACTGTTCA	.	PASS	Atlas-SNP
CCDC93	54520	hgsc.bcm.edu	37	2	118771566	118771566	+	Silent	SNP	C	C	A	rs11545372	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	62	94	0	0.96875	0	C|0.673;A|0.327	0.327	strong	CCDC93,NS,carcinoma,0,1	CCDC93	70	1	NM_019044	exon1	c.G6T	p.G2G	GGGCAACCCCATG	.	PASS	Atlas-SNP
RRP8	23378	hgsc.bcm.edu	37	11	6622218	6622218	+	Missense_Mutation	SNP	G	G	A	rs17834692	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91	39	60	0	0.428571	0	G|0.986;A|0.014	0.014	strong	.	RRP8	40	.	NM_015324	exon4	c.C985T	p.P329S	GCACAGGGTTCCG	.	PASS	Atlas-SNP
RTTN	25914	hgsc.bcm.edu	37	18	67687860	67687860	+	Silent	SNP	T	T	C	rs2304378	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	112	52	123	0	0.464286	0	T|0.826;C|0.174	0.174	strong	.	RTTN	184	.	NM_173630	exon45	c.A6144G	p.V2048V	CTGAATTACTCCT	.	PASS	Atlas-SNP
MAP7D2	256714	hgsc.bcm.edu	37	X	20134902	20134902	+	Silent	SNP	C	C	G	rs142065916	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72	49	66	0	0.680556	0	C|0.990;G|0.010	0.010	strong	.	MAP7D2	165	.	NM_001168466	exon1	c.G96C	p.A32A	CCGCACCGCGCCC	.	PASS	Atlas-SNP
ZNF79	7633	hgsc.bcm.edu	37	9	130206762	130206762	+	Silent	SNP	C	C	T	rs2248025	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	50	21	38	0	0.42	0	C|0.612;T|0.388	0.388	strong	ZNF79,NS,carcinoma,0,1	ZNF79	47	1	NM_007135	exon5	c.C783T	p.N261N	CCAGAACGCCAAC	.	PASS	Atlas-SNP
ATP13A2	23400	hgsc.bcm.edu	37	1	17312743	17312743	+	Missense_Mutation	SNP	C	C	T	rs3170740	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	24	54	0	0.45283	0	C|0.645;T|0.355	0.355	strong	.	ATP13A2	85	.	NM_001141974	exon27	c.G3214A	p.A1072T	CAGCGGCGGCCAG	.	PASS	Atlas-SNP
NIPBL	25836	hgsc.bcm.edu	37	5	36985303	36985303	+	Missense_Mutation	SNP	A	A	G	rs3822471	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	109	50	118	0	0.458716	0	A|0.879;G|0.121	0.121	strong	NIPBL_ENST00000448238,NS,carcinoma,-1,2	NIPBL	513	2	NM_015384	exon10	c.A2021G	p.N674S	AACAAAATGAAAA	.	PASS	Atlas-SNP
KANSL1	284058	hgsc.bcm.edu	37	17	44111613	44111613	+	Silent	SNP	A	A	G	rs17574604	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	119	119	114	0	1	0	A|0.853;G|0.147	0.147	strong	KIAA1267,NS,carcinoma,0,1	.	.	1	NM_001193466	exon11	c.T2580C	p.F860F	AATATCAAATGAG	.	PASS	Atlas-SNP
DEFB136	613210	hgsc.bcm.edu	37	8	11832079	11832079	+	Silent	SNP	A	A	G	rs10108075	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	23	50	0	0.425926	0	A|0.331;G|0.669	0.669	strong	.	DEFB136	16	.	NM_001033018	exon1	c.T30C	p.F10F	CAGGAAAAAGAGT	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	50	25	48	0	0.5	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
OR4L1	122742	hgsc.bcm.edu	37	14	20528505	20528505	+	Missense_Mutation	SNP	T	T	A	rs2775253	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	102	45	135	0	0.441176	0	T|0.639;A|0.361	0.361	strong	.	OR4L1	98	.	NM_001004717	exon1	c.T302A	p.M101K	CCCAGATGTTCTT	.	PASS	Atlas-SNP
CALCOCO2	10241	hgsc.bcm.edu	37	17	46929908	46929908	+	Missense_Mutation	SNP	T	T	C	rs2303015	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	223	106	247	0	0.475336	0	T|0.868;G|0.001	.	strong	.	CALCOCO2	29	.	NM_001261390	exon9	c.T815C	p.V272A	AGCTTGTTCAGGG	.	PASS	Atlas-SNP
MMP27	64066	hgsc.bcm.edu	37	11	102576358	102576358	+	Missense_Mutation	SNP	T	T	C	rs2846707	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	231	23	166	0	0.0995671	0	T|0.229;C|0.771	0.771	strong	.	MMP27	84	.	NM_022122	exon1	c.A88G	p.M30V	GTTGCATATTTTC	.	PASS	Atlas-SNP
OR10H2	26538	hgsc.bcm.edu	37	19	15838967	15838967	+	Silent	SNP	G	G	A	rs45442392	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	189	78	133	0	0.412698	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
FAM71D	161142	hgsc.bcm.edu	37	14	67671293	67671293	+	Silent	SNP	T	T	C	rs17836680	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	229	117	245	0	0.510917	0	T|0.957;C|0.043	0.043	strong	.	FAM71D	33	.	NM_173526	exon5	c.T399C	p.D133D	GCATGATGCGGAG	.	PASS	Atlas-SNP
CCDC176	80127	hgsc.bcm.edu	37	14	74523869	74523869	+	Missense_Mutation	SNP	A	A	G	rs3742809	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49	27	76	0	0.55102	0	G|0.185;N|0.001	0.185	strong	.	.	.	.	NM_025057	exon11	c.A1486G	p.K496E	CAAGATAAAATCT	.	PASS	Atlas-SNP
CCDC53	51019	hgsc.bcm.edu	37	12	102455729	102455729	+	Silent	SNP	G	G	A	rs3751129	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	31	31	45	0	1	0	G|0.694;A|0.306	0.306	strong	.	CCDC53	14	.	NM_016053	exon1	c.C12T	p.D4D	AAGCCCGTCCTCA	.	PASS	Atlas-SNP
EXOC1	55763	hgsc.bcm.edu	37	4	56756531	56756531	+	Silent	SNP	T	T	C	rs2290016	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69	36	76	0	0.521739	0	T|0.688;C|0.312	0.312	strong	.	EXOC1	103	.	NM_018261	exon12	c.T1518C	p.A506A	TGTTGCTGACAGG	.	PASS	Atlas-SNP
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46058060	46058060	+	Silent	SNP	C	C	T	rs74695406		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	177	58	166	0	0.327684	0	T|1.000;|0.000	1.000	weak	.	KRTAP10-10	37	.	NM_181688	exon1	c.C726T	p.S242S	CTACAGCCTCTGC	.	PASS	Atlas-SNP
CCDC168	643677	hgsc.bcm.edu	37	13	103394239	103394239	+	Silent	SNP	C	C	T	rs16960471	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	26	141	0	0.351351	0	C|0.924;T|0.076	0.076	strong	.	.	.	.	NM_001146197	exon4	c.G8808A	p.P2936P	CCTTAACGGTCCA	.	PASS	Atlas-SNP
CNDP2	55748	hgsc.bcm.edu	37	18	72176083	72176083	+	Missense_Mutation	SNP	T	T	C	rs2278161	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93	48	84	1	0.516129	0.0119048	T|0.801;C|0.198	0.198	strong	CNDP2,NS,carcinoma,0,1	CNDP2	55	1	NM_018235	exon5	c.T376C	p.Y126H	AAGCTGTATGGGA	.	scavenged	Atlas-SNP
ALDH3A2	224	hgsc.bcm.edu	37	17	19575096	19575096	+	Missense_Mutation	SNP	C	C	T	rs61737992	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	104	50	102	0	0.480769	0	C|0.996;T|0.004	0.004	strong	.	ALDH3A2	41	.	NM_001031806	exon9	c.C1270T	p.P424S	CAGCGTCCCTGTT	.	PASS	Atlas-SNP
SPRR1B	6699	hgsc.bcm.edu	37	1	153004983	153004983	+	Silent	SNP	C	C	T	rs12195	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93	49	127	0	0.526882	0	C|0.493;T|0.507	0.507	strong	.	SPRR1B	18	.	NM_003125	exon2	c.C162T	p.P54P	AGTGCCCGAGCCC	.	PASS	Atlas-SNP
AFF3	3899	hgsc.bcm.edu	37	2	100210074	100210074	+	Silent	SNP	G	G	C	rs1047281	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	34	72	0	0.515152	0	G|0.832;C|0.168	0.168	strong	AFF3,NS,carcinoma,0,1	AFF3	164	1	NM_001025108	exon14	c.C2124G	p.S708S	CTGCTCGGACTCC	.	PASS	Atlas-SNP
METTL13	51603	hgsc.bcm.edu	37	1	171763549	171763549	+	Silent	SNP	C	C	T	rs2232825	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93	42	110	0	0.451613	0	C|0.859;T|0.141	0.141	strong	METTL13,NS,carcinoma,0,1	METTL13	67	1	NM_015935	exon7	c.C1707T	p.Y569Y	TTGCTACGATGTC	.	PASS	Atlas-SNP
APOBEC3H	164668	hgsc.bcm.edu	37	22	39498038	39498038	+	Missense_Mutation	SNP	G	G	C	rs139302	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	31	30	31	0	0.967742	0	G|0.460;C|0.540	0.540	strong	.	APOBEC3H	28	.	NM_001166003	exon4	c.G534C	p.E178D	GCTTGAGAGGATA	.	PASS	Atlas-SNP
ZNF630	57232	hgsc.bcm.edu	37	X	47918160	47918160	+	Silent	SNP	A	A	G	rs61736415	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	31	8	26	0	0.258065	0	A|0.987;G|0.013	0.013	strong	.	ZNF630	71	.	NM_001037735	exon5	c.T1671C	p.H557H	AATGAGATGTGAC	.	PASS	Atlas-SNP
ZNF880	400713	hgsc.bcm.edu	37	19	52887904	52887904	+	Silent	SNP	T	T	C	rs2042913	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	33	28	49	0	0.848485	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
RASGRF1	5923	hgsc.bcm.edu	37	15	79277391	79277391	+	Silent	SNP	T	T	G	rs117481060	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	154	63	137	0	0.409091	0	T|0.986;G|0.014	0.014	strong	.	RASGRF1	168	.	NM_002891	exon24	c.A3420C	p.A1140A	GAAGATTGCACTG	.	PASS	Atlas-SNP
SERPINB10	5273	hgsc.bcm.edu	37	18	61582751	61582751	+	Missense_Mutation	SNP	T	T	G	rs17072097	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	147	91	156	0	0.619048	0	T|0.744;G|0.256	0.256	strong	SERPINB10,colon,carcinoma,0,2	SERPINB10	53	2	NM_005024	exon1	c.T7G	p.S3A	ATGGACTCTCTAG	.	PASS	Atlas-SNP
ZBTB22	9278	hgsc.bcm.edu	37	6	33283766	33283766	+	Missense_Mutation	SNP	T	T	C	rs3130100	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80	54	88	0	0.675	0	T|0.467;C|0.533	0.533	strong	.	ZBTB22	48	.	NM_001145338	exon2	c.A928G	p.T310A	GGGGTGTTGGCGC	.	PASS	Atlas-SNP
MYOCD	93649	hgsc.bcm.edu	37	17	12656417	12656417	+	Silent	SNP	T	T	C	rs28730824	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	70	36	63	0	0.514286	0	T|0.963;C|0.037	0.037	strong	.	MYOCD	291	.	NM_001146312	exon10	c.T1812C	p.A604A	AGCTGCTCAACTC	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1088815	1088815	+	Silent	SNP	A	A	G	rs7103978	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	78	36	68	0	0.461538	0	A|0.939;G|0.061	0.061	strong	.	MUC2	614	.	NM_002457	exon26	c.A3600G	p.A1200A	TGGAGCATCGGTT	.	PASS	Atlas-SNP
N4BP2	55728	hgsc.bcm.edu	37	4	40103817	40103817	+	Missense_Mutation	SNP	G	G	A	rs61748746	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91	32	82	0	0.351648	0	G|0.938;A|0.062	0.062	strong	.	N4BP2	166	.	NM_018177	exon4	c.G352A	p.E118K	ATAATGGAAAAAC	.	PASS	Atlas-SNP
TAX1BP1	8887	hgsc.bcm.edu	37	7	27827103	27827103	+	Missense_Mutation	SNP	T	T	A	rs11540483	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72	51	125	1	0.708333	0.008	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	.	scavenged	Atlas-SNP
PPL	5493	hgsc.bcm.edu	37	16	4947748	4947748	+	Silent	SNP	T	T	C	rs61734748	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	127	54	123	0	0.425197	0	T|0.988;C|0.012	0.012	strong	PPL,NS,carcinoma,-2,1	PPL	168	1	NM_002705	exon9	c.A900G	p.A300A	CCAGTCTGCGTGC	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9049910	9049910	+	Missense_Mutation	SNP	C	C	T	rs56307190	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	255	141	252	0	0.552941	0	C|0.794;T|0.206	0.206	strong	.	MUC16	4315	.	NM_024690	exon5	c.G31721A	p.R10574H	CCAGAACGAGAGA	.	PASS	Atlas-SNP
GOLGA6L6	727832	hgsc.bcm.edu	37	15	20739922	20739922	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	47	61	0	0.54023	0	.	.	none	.	GOLGA6L6	37	.	NM_001145004	exon8	c.C1828T	p.Q610X	CCTCCTGCTTCCA	.	PASS	Atlas-SNP
SEL1L2	80343	hgsc.bcm.edu	37	20	13830137	13830137	+	Missense_Mutation	SNP	A	A	C	rs2073290	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	125	54	124	0	0.432	0	A|0.837;C|0.163	0.163	strong	.	SEL1L2	103	.	NM_001271539	exon18	c.T1722G	p.H574Q	CTACCCATGGTGA	.	PASS	Atlas-SNP
ALOX15	246	hgsc.bcm.edu	37	17	4536241	4536241	+	Silent	SNP	T	T	C	rs743646	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	120	58	117	0	0.483333	0	T|0.920;C|0.080	0.080	strong	.	ALOX15	70	.	NM_001140	exon11	c.A1455G	p.T485T	CACGTCTGTCTTA	.	PASS	Atlas-SNP
IFITM2	10581	hgsc.bcm.edu	37	11	308314	308314	+	Missense_Mutation	SNP	T	T	C	rs55900504		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	112	46	121	0	0.410714	0	.	.	weak	IFITM2,rectum,carcinoma,0,1	IFITM2	21	1	NM_006435	exon1	c.T122C	p.M41T	CCCCGATGTCCAC	.	PASS	Atlas-SNP
FAM196A	642938	hgsc.bcm.edu	37	10	128974220	128974220	+	Missense_Mutation	SNP	G	G	A	rs11594560	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	114	58	111	0	0.508772	0	G|0.829;A|0.171	0.171	strong	.	FAM196A	55	.	NM_001039762	exon4	c.C440T	p.A147V	TCTTTCGCATCTG	.	PASS	Atlas-SNP
RPL7L1	285855	hgsc.bcm.edu	37	6	42852357	42852357	+	Silent	SNP	C	C	T	rs16896142	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	49	98	0	0.604938	0	C|0.975;T|0.025	0.025	strong	.	RPL7L1	20	.	NM_198486	exon4	c.C291T	p.D97D	GATTGACGGCGTG	.	PASS	Atlas-SNP
PLCB3	5331	hgsc.bcm.edu	37	11	64034911	64034911	+	Silent	SNP	G	G	A	rs28395877	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	19	14	28	0	0.736842	0	G|0.845;A|0.155	0.155	strong	PLCB3,colon,carcinoma,0,1	PLCB3	103	1	NM_000932	exon31	c.G3588A	p.P1196P	GATGCCGGAGGGG	.	PASS	Atlas-SNP
APOH	350	hgsc.bcm.edu	37	17	64210580	64210580	+	Missense_Mutation	SNP	A	A	C	rs1801689	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	146	79	134	0	0.541096	0	A|0.976;C|0.024	0.024	strong	.	APOH	45	.	NM_000042	exon7	c.T973G	p.C325G	TGAAGCATTTGGG	.	PASS	Atlas-SNP
ND6	0	hgsc.bcm.edu	37	MT	14149	14149	+	Silent	SNP	C	C	T	rs28357668	bycluster;byfrequency;alternate_allele	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	19	19	12	0	1	0	A|0.995;G|0.005	.	alt	.	.	.	.	ENST00000361681	exon1	c.G525A	p.X175X	ACATAACCTATTC	.	PASS	Atlas-SNP
SYCE1	93426	hgsc.bcm.edu	37	10	135370639	135370639	+	Missense_Mutation	SNP	C	C	A	rs8181357	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	114	50	125	0	0.438596	0	C|0.892;A|0.108	0.108	strong	SYCE1_ENST00000343131,NS,carcinoma,0,2	SYCE1	81	2	NM_001143763	exon7	c.G396T	p.E132D	CTTGCACTCCTGC	.	PASS	Atlas-SNP
SFMBT2	57713	hgsc.bcm.edu	37	10	7412243	7412243	+	Silent	SNP	G	G	A	rs142871492	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73	32	119	0	0.438356	0	G|0.997;A|0.003	0.003	strong	.	SFMBT2	209	.	NM_001029880	exon3	c.C195T	p.H65H	ACATACGTGTTTG	.	PASS	Atlas-SNP
ACP6	51205	hgsc.bcm.edu	37	1	147131611	147131611	+	Missense_Mutation	SNP	C	C	T	rs144959805	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	124	61	69	0	0.491935	0	C|0.999;T|0.001	0.001	strong	.	ACP6	36	.	NM_016361	exon3	c.G379A	p.V127M	TGCCCACCTTGGT	.	PASS	Atlas-SNP
IL16	3603	hgsc.bcm.edu	37	15	81582868	81582868	+	Silent	SNP	G	G	A	rs8031107	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	163	76	162	0	0.466258	0	G|0.455;A|0.545	0.545	strong	IL16_ENST00000302987,right_upper_lobe,carcinoma,+1,2	IL16	254	2	NM_001172128	exon11	c.G1407A	p.Q469Q	GCATCAGTGGAGT	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228412308	228412308	+	Silent	SNP	G	G	A	rs1757152	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	165	76	186	0	0.460606	0	G|0.567;A|0.433	0.433	strong	.	OBSCN	2142	.	NM_001271223	exon10	c.G3078A	p.S1026S	CAGCTCGAAAGTG	.	PASS	Atlas-SNP
BTNL8	79908	hgsc.bcm.edu	37	5	180376972	180376972	+	Missense_Mutation	SNP	C	C	G	rs77534051		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48	38	110	0	0.791667	0	C|1.000;|0.000	.	weak	.	BTNL8	114	.	NM_001040462	exon8	c.C931G	p.H311D	GTAACCCATAGAA	.	PASS	Atlas-SNP
TLR10	81793	hgsc.bcm.edu	37	4	38775040	38775040	+	Silent	SNP	A	A	G	rs10776483	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57	32	88	0	0.561404	0	A|0.738;G|0.262	0.262	strong	.	TLR10	87	.	NM_001017388	exon2	c.T2172C	p.H724H	AATTATATGATCA	.	PASS	Atlas-SNP
MAPK6	5597	hgsc.bcm.edu	37	15	52353498	52353498	+	Missense_Mutation	SNP	C	C	G	rs35697691	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	196	103	162	0	0.52551	0	C|0.939;G|0.061	0.061	strong	MAPK6,face,carcinoma,0,5	MAPK6	70	5	NM_002748	exon5	c.C868G	p.L290V	GCAGCACTGGATT	.	PASS	Atlas-SNP
B3GALTL	145173	hgsc.bcm.edu	37	13	31848657	31848657	+	Silent	SNP	C	C	T	rs35019745	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	43	16	62	0	0.372093	0	C|0.985;T|0.015	0.015	strong	.	B3GALTL	48	.	NM_194318	exon9	c.C672T	p.Y224Y	CCTCTACATCTGG	.	PASS	Atlas-SNP
CEACAM5	1048	hgsc.bcm.edu	37	19	42213782	42213782	+	Missense_Mutation	SNP	T	T	C	rs28683503	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	162	100	184	0	0.617284	0	T|0.810;C|0.190	0.190	strong	.	CEACAM5	84	.	NM_004363	exon2	c.T248C	p.V83A	GATATGTAATAGG	.	PASS	Atlas-SNP
SPAG17	200162	hgsc.bcm.edu	37	1	118565953	118565953	+	Missense_Mutation	SNP	G	G	A	rs10923472	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	26	75	0	0.366197	0	G|0.682;A|0.318	0.318	strong	.	SPAG17	263	.	NM_206996	exon28	c.C4043T	p.P1348L	TCAGATGGTATCG	.	PASS	Atlas-SNP
LRRK2	120892	hgsc.bcm.edu	37	12	40716260	40716260	+	Silent	SNP	T	T	C	rs10878371	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	96	45	98	0	0.46875	0	T|0.448;C|0.552	0.552	strong	.	LRRK2	763	.	NM_198578	exon37	c.T5457C	p.G1819G	TGATGGTGAAGAA	.	PASS	Atlas-SNP
CASP8AP2	9994	hgsc.bcm.edu	37	6	90577602	90577602	+	Silent	SNP	C	C	T	rs60966143	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	113	50	116	0	0.442478	0	C|0.879;T|0.121	0.121	strong	.	CASP8AP2	108	.	NM_001137667	exon8	c.C4593T	p.A1531A	GCATGCCGTCATA	.	PASS	Atlas-SNP
ATP13A4	84239	hgsc.bcm.edu	37	3	193209178	193209178	+	Missense_Mutation	SNP	T	T	C	rs6788448	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	31	61	0	0.469697	0	T|0.559;C|0.441	0.441	strong	.	ATP13A4	154	.	NM_032279	exon6	c.A543G	p.I181M	CCCACATATTAAC	.	PASS	Atlas-SNP
ELMOD3	84173	hgsc.bcm.edu	37	2	85617327	85617327	+	Silent	SNP	C	C	T	rs17850708	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	116	87	165	0	0.75	0	C|0.951;T|0.049	0.049	strong	.	ELMOD3	53	.	NM_001135022	exon13	c.C882T	p.H294H	CCTCCACCTCGCA	.	PASS	Atlas-SNP
PDK2	5164	hgsc.bcm.edu	37	17	48174908	48174908	+	Silent	SNP	C	C	T	rs9839	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	26	16	35	0	0.615385	0	C|0.639;T|0.361	0.361	strong	PDK2,NS,carcinoma,0,1	PDK2	41	1	NM_002611	exon2	c.C240T	p.S80S	ACCCTCCGTGCAG	.	PASS	Atlas-SNP
DUSP13	51207	hgsc.bcm.edu	37	10	76867899	76867899	+	Missense_Mutation	SNP	T	T	C	rs7912300	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	103	50	111	0	0.485437	0	T|0.574;C|0.426	0.426	strong	.	DUSP13	82	.	NM_001007271	exon2	c.A218G	p.K73R	AGGCCCTTGTGGG	.	PASS	Atlas-SNP
DNAH5	1767	hgsc.bcm.edu	37	5	13865980	13865980	+	Silent	SNP	T	T	C	rs7703349	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	22	63	0	0.407407	0	T|0.533;C|0.467	0.467	strong	DNAH5,NS,carcinoma,0,1	DNAH5	868	1	NM_001369	exon27	c.A4152G	p.T1384T	AGTATATGTGATG	.	PASS	Atlas-SNP
CEACAM1	634	hgsc.bcm.edu	37	19	43031318	43031318	+	Missense_Mutation	SNP	G	G	A	rs199627333		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	313	13	275	0	0.0415335	0	.	.	weak	.	CEACAM1	43	.	NM_001184816	exon2	c.C299T	p.T100I	TATATTGTCTCTC	.	PASS	Atlas-SNP
PCSK5	5125	hgsc.bcm.edu	37	9	78925765	78925765	+	Silent	SNP	G	G	A	rs61744750	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	58	38	59	0	0.655172	0	G|0.966;A|0.034	0.034	strong	.	PCSK5	329	.	NM_001190482	exon29	c.G3801A	p.P1267P	GTGCCCGGAGTAA	.	PASS	Atlas-SNP
FOLR4	390243	hgsc.bcm.edu	37	11	94040783	94040783	+	Silent	SNP	C	C	T	rs367878279		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	125	28	107	1	0.224	0.00934579	.	.	weak	FOLR4,NS,carcinoma,0,2	FOLR4	31	2	NM_001199206	exon4	c.C678T	p.F226F	CCTCTTCGCCAGC	.	scavenged	Atlas-SNP
TSC22D2	9819	hgsc.bcm.edu	37	3	150128484	150128484	+	Silent	SNP	C	C	A	rs3749400	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	22	16	6	0	0.727273	0	C|0.879;A|0.121	0.121	strong	.	TSC22D2	42	.	NM_014779	exon1	c.C1347A	p.V449V	GCAGGTCGCGCCT	.	PASS	Atlas-SNP
SCYL2	55681	hgsc.bcm.edu	37	12	100732327	100732327	+	Silent	SNP	C	C	T	rs10860580	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	24	66	0	0.380952	0	C|0.721;T|0.279	0.279	strong	.	SCYL2	99	.	NM_017988	exon18	c.C2167T	p.L723L	GACACACTGATGG	.	PASS	Atlas-SNP
SYNJ1	8867	hgsc.bcm.edu	37	21	34059352	34059352	+	Missense_Mutation	SNP	T	T	C	rs2254562	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	56	56	37	0	1	0	T|0.699;C|0.301	0.301	strong	.	SYNJ1	253	.	NM_203446	exon8	c.A1001G	p.K334R	ATTTGTTTACCAT	.	PASS	Atlas-SNP
OR2F1	26211	hgsc.bcm.edu	37	7	143657427	143657427	+	Missense_Mutation	SNP	C	C	T	rs2072164	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	120	58	141	0	0.483333	0	C|0.910;T|0.090	0.090	strong	.	OR2F1	71	.	NM_012369	exon1	c.C364T	p.R122C	TATGACCGCTATG	.	PASS	Atlas-SNP
ZNF717	100131827	hgsc.bcm.edu	37	3	75786685	75786685	+	Missense_Mutation	SNP	T	T	A	rs201963249		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	14	11	27	0	0.785714	0	.	.	weak	.	ZNF717	160	.	NM_001128223	exon5	c.A2089T	p.T697S	CCGGTGTGAGTTC	.	PASS	Atlas-SNP
MXRA5	25878	hgsc.bcm.edu	37	X	3241317	3241317	+	Silent	SNP	T	T	C	rs1635249	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	88	87	65	0	0.988636	0	0|0.003;C|0.737	0.737	strong	.	MXRA5	815	.	NM_015419	exon5	c.A2409G	p.P803P	AATCAATGGGGGT	.	PASS	Atlas-SNP
NAP1L3	4675	hgsc.bcm.edu	37	X	92927634	92927634	+	Missense_Mutation	SNP	G	G	C	rs1045686	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98	24	71	0	0.244898	0	G|0.390;0|0.015	.	strong	.	NAP1L3	81	.	NM_004538	exon1	c.C670G	p.P224A	CTTTAGGAACTTC	.	PASS	Atlas-SNP
CYP3A4	1576	hgsc.bcm.edu	37	7	99358598	99358598	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	252	105	276	0	0.416667	0	.	.	none	.	CYP3A4	56	.	NM_017460	exon12	c.C1260T	p.S420S	CTTCTTGCTGAAT	.	PASS	Atlas-SNP
OR2W5	441932	hgsc.bcm.edu	37	1	247654993	247654993	+	Silent	SNP	T	T	C	rs10925061	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	29	85	0	0.345238	0	T|0.645;C|0.355	0.355	strong	.	OR2W5	97	.	NM_001004698	exon1	c.T564C	p.S188S	CATGTCTTGTGAG	.	PASS	Atlas-SNP
SLC9C1	285335	hgsc.bcm.edu	37	3	111996554	111996554	+	Missense_Mutation	SNP	T	T	C	rs9828502	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	123	67	107	0	0.544715	0	T|0.713;C|0.287	0.287	strong	.	.	.	.	NM_183061	exon5	c.A472G	p.I158V	CTCTTATAGCAGC	.	PASS	Atlas-SNP
MOS	4342	hgsc.bcm.edu	37	8	57026229	57026229	+	Missense_Mutation	SNP	C	C	A	rs35392772	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	44	90	0	0.505747	0	C|0.888;A|0.112	0.112	strong	.	MOS	63	.	NM_005372	exon1	c.G313T	p.A105S	GCTCAGCCCAGAA	.	PASS	Atlas-SNP
GLDC	2731	hgsc.bcm.edu	37	9	6620216	6620216	+	Silent	SNP	C	C	T	rs13289273	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	138	57	128	0	0.413043	0	C|0.941;T|0.059	0.059	strong	.	GLDC	118	.	NM_000170	exon3	c.G438A	p.T146T	CAAAATCGTCTGT	.	PASS	Atlas-SNP
RGPD4	285190	hgsc.bcm.edu	37	2	108475968	108475968	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	196	4	173	0	0.0204082	0	.	.	none	RGPD4,NS,carcinoma,0,1	RGPD4	112	1	NM_182588	exon11	c.C1592T	p.S531F	AAAAATCTTGGTG	.	scavenged	Atlas-SNP
CPNE8	144402	hgsc.bcm.edu	37	12	39087609	39087609	+	Silent	SNP	G	G	A	rs3759139	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	142	142	182	0	1	0	G|0.695;A|0.305	0.305	strong	CPNE8,NS,carcinoma,0,1	CPNE8	66	1	NM_153634	exon15	c.C993T	p.Y331Y	ATTCATGTAGTGG	.	PASS	Atlas-SNP
ANKRD36	375248	hgsc.bcm.edu	37	2	97790211	97790211	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	178	9	153	1	0.0505618	0.00653595	.	.	none	ANKRD36_ENST00000420699,extremity,malignant_melanoma,0,2	ANKRD36	170	2	NM_001164315	exon5	c.A608T	p.H203L	TCATACATGCTGT	.	scavenged	Atlas-SNP
MST1	4485	hgsc.bcm.edu	37	3	49722303	49722303	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	168	10	129	1	0.0595238	0.00775194	.	.	none	MST1,NS,carcinoma,0,2	MST1	84	2	NM_020998	exon15	c.C1637T	p.T546M	TAGCCCGTGAGAG	.	scavenged	Atlas-SNP
SEMA5B	54437	hgsc.bcm.edu	37	3	122632436	122632436	+	Missense_Mutation	SNP	A	A	G	rs2276781	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	21	86	0	0.388889	0	A|0.949;G|0.051	0.051	strong	SEMA5B_ENST00000451055,NS,carcinoma,0,2	SEMA5B	303	2	NM_001256347	exon16	c.T2387C	p.M796T	GACTGCATGCCCC	.	PASS	Atlas-SNP
HDAC6	10013	hgsc.bcm.edu	37	X	48681187	48681187	+	Missense_Mutation	SNP	G	G	A	rs61735967	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98	18	53	0	0.183673	0	G|0.983;A|0.017	0.017	strong	.	HDAC6	111	.	NM_006044	exon24	c.G2495A	p.R832H	ACTGGCGCAGCTT	.	PASS	Atlas-SNP
COL2A1	1280	hgsc.bcm.edu	37	12	48391416	48391416	+	Silent	SNP	G	G	T	rs3737548	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	59	27	72	0	0.457627	0	G|0.784;T|0.216	0.216	strong	.	COL2A1	368	.	NM_001844	exon7	c.C504A	p.G168G	AGGGGGGCCGGGA	.	PASS	Atlas-SNP
SBF1	6305	hgsc.bcm.edu	37	22	50901009	50901009	+	Silent	SNP	C	C	T	rs5771037	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68	34	59	0	0.5	0	C|0.857;T|0.143	0.143	strong	SBF1_ENST00000380817,NS,carcinoma,0,2	SBF1	211	2	NM_002972	exon18	c.G2106A	p.T702T	GTCCTCCGTGGGC	.	PASS	Atlas-SNP
CDH8	1006	hgsc.bcm.edu	37	16	61935317	61935317	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98	20	87	0	0.204082	0	.	.	none	CDH8,NS,carcinoma,0,1	CDH8	273	1	NM_001796	exon3	c.G313T	p.A105S	TCCCAGCTCCATC	.	PASS	Atlas-SNP
ANAPC4	29945	hgsc.bcm.edu	37	4	25408838	25408838	+	Missense_Mutation	SNP	G	G	A	rs34811474	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	77	33	86	0	0.428571	0	G|0.858;A|0.142	0.142	strong	ANAPC4,NS,carcinoma,+1,1	ANAPC4	61	1	NM_013367	exon20	c.G1394A	p.R465Q	ATAATCGAAAAGG	.	PASS	Atlas-SNP
UMODL1	89766	hgsc.bcm.edu	37	21	43557637	43557637	+	Silent	SNP	C	C	T	rs200233807	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	205	127	131	0	0.619512	0	C|0.999;T|0.001	0.001	strong	.	UMODL1	186	.	NM_173568	exon21	c.C4248T	p.A1416A	AACAGCCACCCTT	.	PASS	Atlas-SNP
CENPB	1059	hgsc.bcm.edu	37	20	3766137	3766137	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73	35	88	0	0.479452	0	.	.	none	.	CENPB	24	.	NM_001810	exon1	c.C994A	p.Q332K	TCACCTGCTGGAC	.	PASS	Atlas-SNP
C9orf89	84270	hgsc.bcm.edu	37	9	95872885	95872885	+	Silent	SNP	C	C	T	rs17593496	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	70	34	82	0	0.485714	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
HRG	3273	hgsc.bcm.edu	37	3	186395113	186395113	+	Missense_Mutation	SNP	A	A	G	rs2228243	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	122	60	125	0	0.491803	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
RGS17	26575	hgsc.bcm.edu	37	6	153365112	153365112	+	Silent	SNP	G	G	A	rs41292882	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	33	85	0	0.37931	0	G|0.971;A|0.029	0.029	strong	.	RGS17	32	.	NM_012419	exon2	c.C42T	p.A14A	AGACACGGCAGGT	.	PASS	Atlas-SNP
PCK1	5105	hgsc.bcm.edu	37	20	56138621	56138621	+	Missense_Mutation	SNP	A	A	G	rs8192708	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	27	62	0	0.5	0	A|0.915;G|0.085	0.085	strong	.	PCK1	95	.	NM_002591	exon6	c.A799G	p.I267V	CAACAGATTCTGG	.	PASS	Atlas-SNP
PTGER3	5733	hgsc.bcm.edu	37	1	71512643	71512643	+	Silent	SNP	C	C	A	rs5671	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44	22	70	1	0.5	0.0142857	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
AIRE	326	hgsc.bcm.edu	37	21	45717550	45717550	+	Silent	SNP	T	T	C	rs1133779	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	89	57	82	0	0.640449	0	T|0.483;C|0.517	0.517	strong	AIRE,NS,lymphoid_neoplasm,0,1	AIRE	61	1	NM_000383	exon14	c.T1578C	p.D526D	CTTCGATGGCATC	.	PASS	Atlas-SNP
GPANK1	7918	hgsc.bcm.edu	37	6	31632134	31632134	+	Missense_Mutation	SNP	C	C	A	rs3130618	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80	58	91	0	0.725	0	C|0.839;A|0.161	0.161	strong	GPANK1,colon,carcinoma,0,1	GPANK1	19	1	NM_001199238	exon3	c.G122T	p.R41L	AAAGCTCGGGCTG	.	PASS	Atlas-SNP
AMER1	139285	hgsc.bcm.edu	37	X	63412987	63412987	+	Silent	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	123	51	73	0	0.414634	0	.	.	none	.	.	.	.	NM_152424	exon2	c.T180C	p.F60F	GCCACCAAAGAGT	.	PASS	Atlas-SNP
BPIFB1	92747	hgsc.bcm.edu	37	20	31897554	31897554	+	Missense_Mutation	SNP	G	G	C	rs1999663	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	99	52	91	0	0.525253	0	G|0.390;C|0.610	0.610	strong	.	.	.	.	NM_033197	exon16	c.G1436C	p.S479T	AACCCAGCTCTCC	.	PASS	Atlas-SNP
AIFM2	84883	hgsc.bcm.edu	37	10	71880858	71880858	+	Missense_Mutation	SNP	A	A	G	rs10999147	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	37	15	30	0	0.405405	0	A|0.920;G|0.080	0.080	strong	.	AIFM2	33	.	NM_001198696	exon4	c.T404C	p.M135T	CTCACCATGTCCT	.	PASS	Atlas-SNP
OR4N4	283694	hgsc.bcm.edu	37	15	22383249	22383249	+	Missense_Mutation	SNP	G	G	A	rs112081824	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	170	53	118	0	0.311765	0	G|0.983;A|0.017	0.017	strong	.	OR4N4	108	.	NM_001005241	exon1	c.G777A	p.M259I	CTACATGTGCCCT	.	PASS	Atlas-SNP
TPTE	7179	hgsc.bcm.edu	37	21	10959771	10959771	+	Missense_Mutation	SNP	A	A	T	rs111657679	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	441	121	433	0	0.274376	0	A|0.964;T|0.036	0.036	strong	.	TPTE	513	.	NM_199261	exon8	c.T203A	p.V68D	TCTTCAACTTCAA	.	PASS	Atlas-SNP
UBAC1	10422	hgsc.bcm.edu	37	9	138831567	138831567	+	Silent	SNP	T	T	C	rs1044193	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	163	75	223	0	0.460123	0	T|0.917;C|0.083	0.083	strong	.	UBAC1	40	.	NM_016172	exon8	c.A915G	p.K305K	CACCTCTTTCTCG	.	PASS	Atlas-SNP
LRIG2	9860	hgsc.bcm.edu	37	1	113657233	113657233	+	Missense_Mutation	SNP	T	T	G	rs41296184	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	115	52	121	0	0.452174	0	T|0.990;G|0.010	0.010	strong	.	LRIG2	67	.	NM_014813	exon15	c.T2265G	p.D755E	TGTAGATGCCGGG	.	PASS	Atlas-SNP
CPA6	57094	hgsc.bcm.edu	37	8	68536470	68536470	+	Missense_Mutation	SNP	A	A	G	rs10957393	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	32	43	0	0.516129	0	A|0.750;G|0.249	0.249	strong	CPA6,NS,adenoma,0,1	CPA6	69	1	NM_020361	exon2	c.T133C	p.F45L	GAATAAATCTTAT	.	PASS	Atlas-SNP
ICAM5	7087	hgsc.bcm.edu	37	19	10407169	10407169	+	Silent	SNP	G	G	C	rs710845	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	13	4	10	0	0.307692	0	G|0.499;C|0.501	0.501	strong	.	ICAM5	53	.	NM_003259	exon11	c.G2652C	p.L884L	GTGTCTGAACGGA	.	PASS	Atlas-SNP
FCF1	51077	hgsc.bcm.edu	37	14	75190002	75190002	+	Missense_Mutation	SNP	T	T	C	rs41309250	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	122	67	115	0	0.54918	0	T|0.995;C|0.005	0.005	strong	.	FCF1	15	.	NM_015962	exon5	c.T320C	p.M107T	GTGTAATGGCTGA	.	PASS	Atlas-SNP
SLC5A9	200010	hgsc.bcm.edu	37	1	48695081	48695081	+	Missense_Mutation	SNP	G	G	A	rs212989	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	182	94	197	0	0.516484	0	G|0.805;A|0.195	0.195	strong	.	SLC5A9	82	.	NM_001135181	exon5	c.G529A	p.V177M	ATCCAGGTGTACA	.	PASS	Atlas-SNP
ZNF30	90075	hgsc.bcm.edu	37	19	35434582	35434582	+	Missense_Mutation	SNP	G	G	T	rs142299823	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73	40	72	0	0.547945	0	G|0.983;T|0.017	0.017	strong	.	ZNF30	44	.	NM_001099438	exon5	c.G715T	p.G239W	GAATGTGGGAAAG	.	PASS	Atlas-SNP
ASPM	259266	hgsc.bcm.edu	37	1	197072420	197072420	+	Silent	SNP	T	T	C	rs41310925	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	179	178	148	0	0.994413	0	T|0.699;C|0.301	0.301	strong	.	ASPM	444	.	NM_018136	exon18	c.A5961G	p.Q1987Q	CTTCTTTTGTTGC	.	PASS	Atlas-SNP
CDC42EP1	11135	hgsc.bcm.edu	37	22	37964299	37964299	+	Silent	SNP	C	C	G	rs2281098	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	19	73	0	0.358491	0	C|0.541;G|0.459	0.459	strong	.	CDC42EP1	53	.	NM_152243	exon3	c.C648G	p.L216L	GAGCCTCCCAGAA	.	PASS	Atlas-SNP
PEAK1	0	hgsc.bcm.edu	37	15	77472871	77472871	+	Silent	SNP	G	G	A	rs10519162	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	180	71	178	0	0.394444	0	G|0.935;A|0.065	0.065	strong	.	.	.	.	NM_024776	exon5	c.C1398T	p.N466N	TTCCAGGTTCACA	.	PASS	Atlas-SNP
UPP2	151531	hgsc.bcm.edu	37	2	158991346	158991346	+	Missense_Mutation	SNP	C	C	T	rs144945330	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91	20	138	0	0.21978	0	C|0.999;T|0.001	0.001	strong	.	UPP2	60	.	NM_001135098	exon9	c.C1069T	p.R357W	CAGCAACGGCCTC	.	PASS	Atlas-SNP
SAMD12	401474	hgsc.bcm.edu	37	8	119452073	119452073	+	Missense_Mutation	SNP	G	G	A	rs117020479	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	111	48	111	0	0.432432	0	G|0.997;A|0.003	0.003	strong	.	SAMD12	24	.	NM_207506	exon3	c.C320T	p.T107I	TTACCAGTTATGT	.	PASS	Atlas-SNP
SUSD2	56241	hgsc.bcm.edu	37	22	24581207	24581207	+	Silent	SNP	C	C	T	rs3752497	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	36	47	0	0.571429	0	C|0.922;T|0.078	0.078	strong	.	SUSD2	68	.	NM_019601	exon6	c.C928T	p.L310L	GAGGAGCTGCCGG	.	PASS	Atlas-SNP
MUT	4594	hgsc.bcm.edu	37	6	49412433	49412433	+	Missense_Mutation	SNP	C	C	T	rs1141321	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48	27	64	0	0.5625	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
DYRK4	8798	hgsc.bcm.edu	37	12	4705317	4705317	+	Silent	SNP	C	C	T	rs3741925	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	45	17	43	0	0.377778	0	C|0.758;T|0.242	0.242	strong	.	DYRK4	75	.	NM_003845	exon5	c.C285T	p.V95V	ACAGGTCCTGCAT	.	PASS	Atlas-SNP
BOLA1	51027	hgsc.bcm.edu	37	1	149871905	149871905	+	Missense_Mutation	SNP	G	G	C	rs1044808	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57	24	42	0	0.421053	0	G|0.951;C|0.049	0.049	strong	.	BOLA1	24	.	NM_016074	exon2	c.G293C	p.G98A	AGCTGGGAGGTCC	.	PASS	Atlas-SNP
PTGIS	5740	hgsc.bcm.edu	37	20	48129706	48129706	+	Silent	SNP	G	G	T	rs5629	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	32	32	46	0	1	0	G|0.782;T|0.218	0.218	strong	PTGIS,colon,carcinoma,+1,2	PTGIS	60	2	NM_000961	exon8	c.C1117A	p.R373R	ATTCTCGCCCGTC	.	PASS	Atlas-SNP
FAM47E-STBD1	0	hgsc.bcm.edu	37	4	77192838	77192838	+	Missense_Mutation	SNP	A	A	C	rs3733251	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	88	88	93	0	1	0	A|0.845;C|0.155	0.155	strong	.	.	.	.	NM_001242939	exon5	c.A787C	p.K263Q	GAGCTAAAGCGTA	.	PASS	Atlas-SNP
GPRC5A	9052	hgsc.bcm.edu	37	12	13061294	13061294	+	Silent	SNP	C	C	T	rs2075288	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	105	58	99	0	0.552381	0	C|0.726;T|0.274	0.274	strong	.	GPRC5A	38	.	NM_003979	exon2	c.C111T	p.A37A	CACAGCCGGGGTT	.	PASS	Atlas-SNP
NDFIP2	54602	hgsc.bcm.edu	37	13	80095030	80095030	+	Missense_Mutation	SNP	C	C	T	rs11549502	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	160	82	120	0	0.5125	0	C|0.910;G|0.000;T|0.090	0.090	strong	NDFIP2,NS,carcinoma,-1,1	NDFIP2	23	1	NM_019080	exon2	c.C407T	p.A136V	AGGCTGCGTCTTC	.	PASS	Atlas-SNP
LRP1	4035	hgsc.bcm.edu	37	12	57603636	57603636	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49	18	47	0	0.367347	0	.	.	none	.	LRP1	428	.	NM_002332	exon80	c.C12424T	p.H4142Y	CATCAGCACAAGC	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	130	130	134	0	1	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
SLC14A2	8170	hgsc.bcm.edu	37	18	43262359	43262359	+	Missense_Mutation	SNP	G	G	A	rs3745009	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	161	76	156	0	0.47205	0	G|0.573;A|0.427	0.427	strong	SLC14A2,NS,carcinoma,0,2	SLC14A2	121	2	NM_001242692	exon21	c.G2638A	p.A880T	AACCCCGCCATCT	.	PASS	Atlas-SNP
MGAT5B	146664	hgsc.bcm.edu	37	17	74921129	74921129	+	Silent	SNP	C	C	T	rs34056052	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	43	83	0	0.5	0	C|0.932;T|0.068	0.068	strong	MGAT5B,NS,carcinoma,0,2	MGAT5B	98	2	NM_198955	exon8	c.C1140T	p.H380H	CTACCACGGCCTG	.	PASS	Atlas-SNP
EPPK1	83481	hgsc.bcm.edu	37	8	144941181	144941181	+	Missense_Mutation	SNP	G	G	C	rs7839934	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	109	106	115	0	0.972477	0	G|0.737;C|0.263	0.263	strong	.	EPPK1	199	.	NM_031308	exon1	c.C6241G	p.L2081V	ACAGCAGCCAGCC	.	PASS	Atlas-SNP
CCND3	896	hgsc.bcm.edu	37	6	41909273	41909273	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72	22	104	0	0.305556	0	.	.	none	.	CCND3	40	.	NM_001760	exon1	c.G115A	p.V39I	GGGGTACGTAGCG	.	PASS	Atlas-SNP
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32634313	32634313	+	Missense_Mutation	SNP	C	C	G	rs1049059	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	12	8	10	0	0.666667	0	C|0.813;G|0.187	0.187	strong	.	HLA-DQB1	15	.	NM_002123	exon1	c.G72C	p.M24I	GCTCAGCATCGCC	.	PASS	Atlas-SNP
SYNPO2L	79933	hgsc.bcm.edu	37	10	75406912	75406912	+	Missense_Mutation	SNP	G	G	T	rs34163229	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	41	63	0	0.539474	0	G|0.842;T|0.158	0.158	strong	.	SYNPO2L	118	.	NM_001114133	exon4	c.C2498A	p.S833Y	CCCTGGGATTGGG	.	PASS	Atlas-SNP
ANKRD1	27063	hgsc.bcm.edu	37	10	92679979	92679979	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	147	71	144	0	0.482993	0	.	.	none	.	ANKRD1	50	.	NM_014391	exon2	c.C154G	p.P52A	TCACAGGGTGGGC	.	PASS	Atlas-SNP
EFCAB7	84455	hgsc.bcm.edu	37	1	64021096	64021096	+	Missense_Mutation	SNP	G	G	A	rs2273367	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	119	61	122	1	0.512605	0.00819672	G|0.849;A|0.151	0.151	strong	EFCAB7,right_upper_lobe,carcinoma,-1,1	EFCAB7	45	1	NM_032437	exon9	c.G1124A	p.R375K	GCTGTAGGCTGAG	.	scavenged	Atlas-SNP
ZFAND2B	130617	hgsc.bcm.edu	37	2	220072382	220072382	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82	28	80	0	0.341463	0	.	.	none	ZFAND2B_ENST00000444522,NS,carcinoma,-1,2	ZFAND2B	28	2	NM_138802	exon3	c.C163T	p.P55S	CAGGTACCTGTGT	.	PASS	Atlas-SNP
ZNF646	9726	hgsc.bcm.edu	37	16	31090221	31090221	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91	4	83	0	0.043956	0	.	.	none	.	ZNF646	133	.	NM_014699	exon2	c.C2576T	p.S859F	TTGACTCTCTGCC	.	PASS	Atlas-SNP
EIF3F	8665	hgsc.bcm.edu	37	11	8009241	8009241	+	Silent	SNP	C	C	T	rs12421289	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83	37	97	0	0.445783	0	C|0.889;T|0.111	0.111	strong	.	EIF3F	23	.	NM_003754	exon1	c.C342T	p.A114A	TGCTGCCCGAGTT	.	PASS	Atlas-SNP
STAB1	23166	hgsc.bcm.edu	37	3	52557136	52557136	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	5	61	0	0.0925926	0	.	.	none	.	STAB1	178	.	NM_015136	exon63	c.T7006G	p.S2336A	AACTTCTCCACCT	.	PASS	Atlas-SNP
SLC34A2	10568	hgsc.bcm.edu	37	4	25669530	25669530	+	Silent	SNP	T	T	C	rs77319279	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100	100	96	0	1	0	T|0.980;C|0.020	0.020	strong	.	SLC34A2	93	.	NM_006424	exon6	c.T552C	p.I184I	CCCCATTATCATG	.	PASS	Atlas-SNP
FHIT	2272	hgsc.bcm.edu	37	3	60522657	60522657	+	Silent	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	59	13	42	0	0.220339	0	.	.	none	.	FHIT	44	.	NM_002012	exon5	c.T39G	p.S13S	CACTACAGAGGGC	.	PASS	Atlas-SNP
MTTP	4547	hgsc.bcm.edu	37	4	100516022	100516022	+	Missense_Mutation	SNP	C	C	G	rs2306985	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	160	67	156	0	0.41875	0	C|0.483;G|0.516	0.516	strong	.	MTTP	127	.	NM_000253	exon8	c.C891G	p.H297Q	GAGCCACTGTAAA	.	PASS	Atlas-SNP
UBASH3B	84959	hgsc.bcm.edu	37	11	122665437	122665437	+	Silent	SNP	A	A	G	rs872414	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	104	90	113	0	0.865385	0	A|0.478;G|0.522	0.522	strong	.	UBASH3B	73	.	NM_032873	exon7	c.A1008G	p.S336S	ATCGTCATCCAAC	.	PASS	Atlas-SNP
C5orf60	285679	hgsc.bcm.edu	37	5	179071836	179071836	+	Silent	SNP	C	C	T	rs4990391	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	113	54	129	4	0.477876	0.0310078	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	.	scavenged	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1103873	1103873	+	Silent	SNP	C	C	T	rs11245957	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68	35	75	0	0.514706	0	C|0.867;T|0.133	0.133	strong	MUC2_ENST00000441003,NS,carcinoma,0,1	MUC2	614	1	NM_002457	exon49	c.C8160T	p.Y2720Y	TTCGTACGCCGGC	.	PASS	Atlas-SNP
SYNJ2	8871	hgsc.bcm.edu	37	6	158497717	158497717	+	Silent	SNP	T	T	C	rs2296508	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	46	58	0	0.978723	0	T|0.420;C|0.580	0.580	strong	.	SYNJ2	111	.	NM_003898	exon17	c.T2352C	p.V784V	TGACGTTGGCTCA	.	PASS	Atlas-SNP
PKD1L1	168507	hgsc.bcm.edu	37	7	47854956	47854956	+	Silent	SNP	C	C	T	rs17545564	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	24	15	45	0	0.625	0	C|0.867;T|0.133	0.133	strong	.	PKD1L1	328	.	NM_138295	exon47	c.G7065A	p.P2355P	GGCTGACGGGGTG	.	PASS	Atlas-SNP
NID2	22795	hgsc.bcm.edu	37	14	52481917	52481917	+	Silent	SNP	C	C	T	rs946615	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	50	48	78	0	0.96	0	C|0.604;T|0.396	0.396	strong	NID2,NS,carcinoma,0,1	NID2	201	1	NM_007361	exon15	c.G3105A	p.R1035R	GTCATCCCGGGGG	.	PASS	Atlas-SNP
HLA-G	3135	hgsc.bcm.edu	37	6	29796327	29796327	+	Silent	SNP	C	C	T	rs1130356	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	73	102	0	0.848837	0	C|0.734;T|0.266	0.266	strong	.	HLA-G	90	.	NM_002127	exon4	c.C351T	p.H117H	TTCTCACACCCTC	.	PASS	Atlas-SNP
SLC22A2	6582	hgsc.bcm.edu	37	6	160679400	160679400	+	Silent	SNP	C	C	A	rs624249	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	38	18	37	0	0.473684	0	C|0.673;A|0.327	0.327	strong	.	SLC22A2	78	.	NM_003058	exon1	c.G390T	p.T130T	GCCAGGCGTCTCG	.	PASS	Atlas-SNP
DSC3	1825	hgsc.bcm.edu	37	18	28611061	28611061	+	Missense_Mutation	SNP	A	A	T	rs276937	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	42	86	0	0.552632	0	A|0.626;T|0.374	0.374	strong	.	DSC3	225	.	NM_024423	exon3	c.T232A	p.S78T	ACACTGACCCATC	.	PASS	Atlas-SNP
CLCC1	23155	hgsc.bcm.edu	37	1	109479978	109479978	+	Missense_Mutation	SNP	G	G	T	rs168107	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	31	94	0	0.5	0	A|0.000;C|0.006	.	strong	.	CLCC1	55	.	NM_001048210	exon10	c.C1104A	p.S368R	AGGTTCGCTCTCA	.	PASS	Atlas-SNP
ABCA5	23461	hgsc.bcm.edu	37	17	67267317	67267317	+	Missense_Mutation	SNP	T	T	C	rs557491	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	109	56	102	0	0.513761	0	T|0.519;C|0.481	0.481	strong	.	ABCA5	162	.	NM_018672	exon20	c.A2878G	p.M960V	AATGCATCACATT	.	PASS	Atlas-SNP
CSMD1	64478	hgsc.bcm.edu	37	8	3019696	3019696	+	Silent	SNP	G	G	A	rs145598896	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	45	18	40	0	0.4	0	G|0.999;A|0.001	0.001	strong	.	CSMD1	1469	.	NM_033225	exon38	c.C5829T	p.P1943P	GTACCCGGGCTCG	.	PASS	Atlas-SNP
BTBD11	121551	hgsc.bcm.edu	37	12	107713696	107713696	+	Missense_Mutation	SNP	G	G	A	rs111260184	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	26	26	15	0	1	0	G|0.595;A|0.405	0.405	strong	.	BTBD11	122	.	NM_001018072	exon1	c.G979A	p.A327T	CCGCCGGCAGCCG	.	PASS	Atlas-SNP
GJB7	375519	hgsc.bcm.edu	37	6	87994504	87994504	+	Missense_Mutation	SNP	C	C	T	rs35259282	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	199	87	149	0	0.437186	0	C|0.939;T|0.061	0.061	strong	.	GJB7	28	.	NM_198568	exon3	c.G127A	p.V43M	TCCACACGTGCTC	.	PASS	Atlas-SNP
GRIN3B	116444	hgsc.bcm.edu	37	19	1008683	1008683	+	Missense_Mutation	SNP	G	G	A	rs2285906	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	35	34	21	0	0.971429	0	G|0.875;A|0.125	0.125	strong	GRIN3B,NS,carcinoma,0,1	GRIN3B	46	1	NM_138690	exon7	c.G2533A	p.A845T	GGCAGCGCTCTGC	.	PASS	Atlas-SNP
CEACAM5	1048	hgsc.bcm.edu	37	19	42213868	42213868	+	Missense_Mutation	SNP	A	A	G	rs34155934	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	175	92	174	0	0.525714	0	A|0.834;G|0.166	0.166	strong	.	CEACAM5	84	.	NM_004363	exon2	c.A334G	p.I112V	CAGAACATCATCC	.	PASS	Atlas-SNP
BIRC6	57448	hgsc.bcm.edu	37	2	32774473	32774473	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	258	72	237	0	0.27907	0	.	.	none	.	BIRC6	838	.	NM_016252	exon65	c.C13069T	p.P4357S	GCCCTTCCTTCTG	.	PASS	Atlas-SNP
CEP120	153241	hgsc.bcm.edu	37	5	122718736	122718736	+	Missense_Mutation	SNP	G	G	C	rs6595440	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	163	78	200	0	0.478528	0	G|0.598;C|0.402	0.402	strong	.	CEP120	72	.	NM_153223	exon13	c.C1804G	p.L602V	CTTCTAGAGTCAC	.	PASS	Atlas-SNP
ABCC8	6833	hgsc.bcm.edu	37	11	17419279	17419279	+	Silent	SNP	C	C	T	rs1799859	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	52	55	0	1	0	C|0.611;T|0.389	0.389	strong	.	ABCC8	170	.	NM_000352	exon31	c.G3819A	p.R1273R	GAGCTCCCTGTGC	.	PASS	Atlas-SNP
TNFSF13	8741	hgsc.bcm.edu	37	17	7462555	7462555	+	Missense_Mutation	SNP	G	G	A	rs11552708	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	127	61	112	0	0.480315	0	G|0.857;A|0.143	0.143	strong	.	TNFSF13	12	.	NM_001198623	exon1	c.G199A	p.G67R	CTGCAGGGGACAG	.	PASS	Atlas-SNP
NECAB3	63941	hgsc.bcm.edu	37	20	32248163	32248163	+	Silent	SNP	C	C	T	rs3746460	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60	31	53	0	0.516667	0	C|0.701;T|0.299	0.299	strong	.	NECAB3	27	.	NM_031232	exon6	c.G426A	p.T142T	GAAGCGCGTCACA	.	PASS	Atlas-SNP
CCDC54	84692	hgsc.bcm.edu	37	3	107096926	107096926	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	215	50	207	0	0.232558	0	.	.	none	.	CCDC54	56	.	NM_032600	exon1	c.A492C	p.K164N	GGGTAAAGAAATC	.	PASS	Atlas-SNP
MAPK12	6300	hgsc.bcm.edu	37	22	50695370	50695370	+	Silent	SNP	G	G	A	rs2072876	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	26	12	22	0	0.461538	0	G|0.968;A|0.032	0.032	strong	.	MAPK12	43	.	NM_002969	exon5	c.C450T	p.I150I	TCTGTGGATGATG	.	PASS	Atlas-SNP
TNRC18	84629	hgsc.bcm.edu	37	7	5353344	5353344	+	Missense_Mutation	SNP	G	G	A	rs12532973	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	16	13	19	0	0.8125	0	G|0.908;A|0.092	0.092	strong	.	TNRC18	311	.	NM_001080495	exon27	c.C7178T	p.P2393L	TGCGGCGGTGCCG	.	PASS	Atlas-SNP
SMTNL1	219537	hgsc.bcm.edu	37	11	57317522	57317522	+	Silent	SNP	A	A	G	rs117673759	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	112	50	115	0	0.446429	0	A|0.999;G|0.001	0.001	strong	.	SMTNL1	68	.	NM_001105565	exon7	c.A1422G	p.T474T	CTACACATACATC	.	PASS	Atlas-SNP
MYBPH	4608	hgsc.bcm.edu	37	1	203143725	203143725	+	Missense_Mutation	SNP	G	G	C	rs2642531	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	299	157	309	0	0.525084	0	G|0.736;C|0.264	0.264	strong	.	MYBPH	41	.	NM_004997	exon3	c.C341G	p.A114G	TCCGAGGCTGAGG	.	PASS	Atlas-SNP
GRID2IP	392862	hgsc.bcm.edu	37	7	6550584	6550584	+	Missense_Mutation	SNP	G	G	A	rs61732374	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	35	57	0	0.57377	0	G|0.990;A|0.010	0.010	strong	.	GRID2IP	82	.	NM_001145118	exon9	c.C1510T	p.R504C	TGCGGCGGCACAT	.	PASS	Atlas-SNP
CTAGE5	4253	hgsc.bcm.edu	37	14	39790149	39790149	+	Missense_Mutation	SNP	C	C	G	rs36060072	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100	52	86	0	0.52	0	G|0.005;C|0.995	0.005	strong	.	CTAGE5	75	.	NM_001247989	exon19	c.C1576G	p.P526A	TATGGTCCCTCAC	.	PASS	Atlas-SNP
RHCG	51458	hgsc.bcm.edu	37	15	90023558	90023558	+	Missense_Mutation	SNP	G	G	A	rs17807723	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80	46	89	0	0.575	0	G|0.905;A|0.095	0.095	strong	.	RHCG	49	.	NM_016321	exon4	c.C604T	p.R202C	GGTTGCGTCGGTA	.	PASS	Atlas-SNP
GJB3	2707	hgsc.bcm.edu	37	1	35250457	35250457	+	Missense_Mutation	SNP	C	C	T	rs1805063	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	118	43	131	0	0.364407	0	C|0.980;T|0.020	0.020	strong	.	GJB3	40	.	NM_001005752	exon2	c.C94T	p.R32W	GTCTTCCGGGTGC	.	PASS	Atlas-SNP
SYNGR2	9144	hgsc.bcm.edu	37	17	76167047	76167047	+	Silent	SNP	C	C	T	rs1062668	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91	44	88	0	0.483516	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
PLOD1	5351	hgsc.bcm.edu	37	1	12009956	12009956	+	Missense_Mutation	SNP	G	G	A	rs7551175	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	65	30	64	0	0.461538	0	G|0.733;A|0.267	0.267	strong	.	PLOD1	75	.	NM_000302	exon3	c.G295A	p.A99T	CTCTTCGCAGACA	.	PASS	Atlas-SNP
GLT6D1	360203	hgsc.bcm.edu	37	9	138515991	138515991	+	Silent	SNP	A	A	G	rs12351198	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	158	64	128	0	0.405063	0	A|0.850;G|0.150	0.150	strong	.	GLT6D1	56	.	NM_182974	exon5	c.T783C	p.T261T	TTCATAAGTGCTA	.	PASS	Atlas-SNP
ACAN	176	hgsc.bcm.edu	37	15	89398407	89398407	+	Missense_Mutation	SNP	C	C	T	rs3743398	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	46	54	0	0.978723	0	C|0.871;T|0.129	0.129	strong	.	ACAN	220	.	NM_001135	exon12	c.C2591T	p.P864L	GGGCCCCTGATGT	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100	32	138	0	0.32	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
STK17B	9262	hgsc.bcm.edu	37	2	197021372	197021372	+	Silent	SNP	T	T	A	rs12478353	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	101	46	72	0	0.455446	0	T|0.406;A|0.594	0.594	strong	.	STK17B	28	.	NM_004226	exon3	c.A126T	p.G42G	AAATTTTCCTCTG	.	PASS	Atlas-SNP
POLR2B	5431	hgsc.bcm.edu	37	4	57881715	57881715	+	Silent	SNP	G	G	A	rs1713982	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	78	37	72	1	0.474359	0.0138889	G|0.634;A|0.366	0.366	strong	POLR2B,colon,carcinoma,0,1	POLR2B	108	1	NM_000938	exon14	c.G1848A	p.T616T	CTATACGGATGCA	.	scavenged	Atlas-SNP
ARMC4	55130	hgsc.bcm.edu	37	10	28228865	28228865	+	Silent	SNP	A	A	G	rs7893462	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	105	50	125	0	0.47619	0	A|0.488;G|0.512	0.512	strong	.	ARMC4	177	.	NM_018076	exon14	c.T2058C	p.N686N	CTGCTCATTCTCA	.	PASS	Atlas-SNP
ZBBX	79740	hgsc.bcm.edu	37	3	167023485	167023485	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	169	37	202	0	0.218935	0	.	.	none	.	ZBBX	299	.	NM_024687	exon17	c.C1671A	p.S557R	CAGATTGCTCAAT	.	PASS	Atlas-SNP
CR1	1378	hgsc.bcm.edu	37	1	207790088	207790088	+	Missense_Mutation	SNP	C	C	G	rs3811381	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	212	212	200	0	1	0	C|0.800;G|0.200	0.200	strong	.	CR1	354	.	NM_000651	exon41	c.C6830G	p.P2277R	GTGACCCTCAAGG	.	PASS	Atlas-SNP
ADAMTSL3	57188	hgsc.bcm.edu	37	15	84651185	84651185	+	Silent	SNP	C	C	A	rs8031704	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	128	126	126	0	0.984375	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
MAGEC3	139081	hgsc.bcm.edu	37	X	140967195	140967195	+	Missense_Mutation	SNP	T	T	A	rs11095910	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	163	117	122	0	0.717791	0	T|0.739;A|0.261	0.261	strong	.	MAGEC3	228	.	NM_138702	exon3	c.T493A	p.L165M	AAAAGGTTGTGGG	.	PASS	Atlas-SNP
MAML1	9794	hgsc.bcm.edu	37	5	179193598	179193598	+	Silent	SNP	C	C	T	rs3797776	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	31	91	0	0.413333	0	C|0.800;T|0.200	0.200	strong	.	MAML1	118	.	NM_014757	exon2	c.C1587T	p.S529S	AGGCAGCCCGGGG	.	PASS	Atlas-SNP
PCDHGB3	56102	hgsc.bcm.edu	37	5	140751891	140751891	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	27	9	35	0	0.333333	0	.	.	none	.	PCDHGB3	168	.	NM_018924	exon1	c.G1930A	p.V644I	CTGCTGGTCACTG	.	PASS	Atlas-SNP
FAT3	120114	hgsc.bcm.edu	37	11	92088177	92088177	+	Silent	SNP	C	C	T	rs7479732	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110	99	74	0	0.9	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
MGAT5B	146664	hgsc.bcm.edu	37	17	74936576	74936576	+	Silent	SNP	G	G	A	rs8081793	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	28	69	0	0.41791	0	G|0.734;A|0.266	0.266	strong	.	MGAT5B	98	.	NM_198955	exon12	c.G1704A	p.P568P	CAGCCCGCCCCAC	.	PASS	Atlas-SNP
MYOM2	9172	hgsc.bcm.edu	37	8	2041894	2041894	+	Missense_Mutation	SNP	G	G	A	rs35335787	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	95	41	103	0	0.431579	0	G|0.958;A|0.042	0.042	strong	.	MYOM2	251	.	NM_003970	exon17	c.G2101A	p.V701I	TCAGACGTCATAA	.	PASS	Atlas-SNP
KRI1	65095	hgsc.bcm.edu	37	19	10664661	10664661	+	Missense_Mutation	SNP	C	C	T	rs34495400	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	37	72	0	0.486842	0	C|0.991;T|0.009	0.009	strong	.	KRI1	65	.	NM_023008	exon19	c.G2096A	p.R699Q	TTCCTCCGCTGCC	.	PASS	Atlas-SNP
KDM2B	84678	hgsc.bcm.edu	37	12	121880520	121880520	+	Silent	SNP	G	G	A	rs3751131	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	43	71	1	0.581081	0.0140845	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	.	scavenged	Atlas-SNP
RALB	5899	hgsc.bcm.edu	37	2	121036333	121036333	+	Silent	SNP	G	G	A	rs11545293	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	40	27	62	0	0.675	0	G|0.926;A|0.074	0.074	strong	.	RALB	27	.	NM_002881	exon2	c.G93A	p.T31T	CCTGACGCTTCAG	.	PASS	Atlas-SNP
CAPG	822	hgsc.bcm.edu	37	2	85629256	85629256	+	Missense_Mutation	SNP	T	T	C	rs113987685	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	155	37	250	0	0.23871	0	T|0.997;C|0.003	0.003	strong	.	CAPG	32	.	NM_001256140	exon2	c.A13G	p.I5V	GGGGAATGGCTGT	.	PASS	Atlas-SNP
MKL1	57591	hgsc.bcm.edu	37	22	40814636	40814636	+	Silent	SNP	C	C	T	rs4821944	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	19	11	35	0	0.578947	0	C|0.829;T|0.171	0.171	strong	.	MKL1	69	.	NM_020831	exon12	c.G1806A	p.A602A	TGGGGCCGCCAGG	.	PASS	Atlas-SNP
CPO	130749	hgsc.bcm.edu	37	2	207820276	207820276	+	Missense_Mutation	SNP	G	G	A	rs13420911	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100	44	99	0	0.44	0	G|0.569;A|0.431	0.431	strong	.	CPO	42	.	NM_173077	exon3	c.G255A	p.M85I	CCCCATGTATTAT	.	PASS	Atlas-SNP
UCK2	7371	hgsc.bcm.edu	37	1	165865478	165865478	+	Silent	SNP	G	G	A	rs11553301	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	114	59	104	0	0.517544	0	G|0.887;A|0.113	0.113	strong	.	UCK2	31	.	NM_012474	exon4	c.G408A	p.G136G	TGAAGGGATCCTG	.	PASS	Atlas-SNP
HRNR	388697	hgsc.bcm.edu	37	1	152186837	152186837	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	516	30	221	0	0.0581395	0	.	.	none	HRNR,NS,carcinoma,0,4	HRNR	403	4	NM_001009931	exon3	c.G7268A	p.R2423Q	CCATGTCGGCCAC	.	scavenged	Atlas-SNP
C3	718	hgsc.bcm.edu	37	19	6710782	6710782	+	Silent	SNP	G	G	T	rs2230203	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	105	42	114	0	0.4	0	G|0.888;T|0.112	0.112	strong	.	C3	192	.	NM_000064	exon13	c.C1554A	p.P518P	GGACAGGGGCAGC	.	PASS	Atlas-SNP
PRR22	163154	hgsc.bcm.edu	37	19	5783840	5783840	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	36	14	19	0	0.388889	0	.	.	none	.	PRR22	25	.	NM_001134316	exon3	c.C418G	p.P140A	ACTGGGGCCCCCC	.	PASS	Atlas-SNP
SPRR2E	6704	hgsc.bcm.edu	37	1	153066067	153066067	+	Missense_Mutation	SNP	C	C	T	rs75229137	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	134	5	195	1	0.0373134	0.00512821	C|0.500;T|0.500	0.500	weak	SPRR2E,NS,malignant_melanoma,0,1	SPRR2E	21	1	NM_001024209	exon2	c.G161A	p.C54Y	GGAGGACATTTTT	.	scavenged	Atlas-SNP
ZNF880	400713	hgsc.bcm.edu	37	19	52888245	52888245	+	Missense_Mutation	SNP	A	A	G	rs55748277	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51	48	64	0	0.941176	0	A|0.631;G|0.369	0.369	strong	.	ZNF880	45	.	NM_001145434	exon4	c.A1412G	p.K471R	GTGGCAAGGACTT	.	PASS	Atlas-SNP
PWWP2B	170394	hgsc.bcm.edu	37	10	134218175	134218175	+	Silent	SNP	C	C	T	rs111647732	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	36	101	0	0.507042	0	C|0.954;T|0.046	0.046	strong	.	PWWP2B	33	.	NM_001098637	exon2	c.C171T	p.V57V	CCAGGTCGATGAG	.	PASS	Atlas-SNP
SPTBN5	51332	hgsc.bcm.edu	37	15	42149596	42149596	+	Missense_Mutation	SNP	C	C	G	rs1197675	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	45	45	72	0	1	0	C|0.770;G|0.230	0.230	strong	SPTBN5,colon,carcinoma,+1,1	SPTBN5	171	1	NM_016642	exon51	c.G8356C	p.G2786R	CCACCCCAGGCAG	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	123	66	155	0	0.536585	0	C|0.553;T|0.447	0.447	strong	.	RIMS2	1357	.	NM_001100117	exon24	c.C3981T	p.A1327A	CTTGGCCCCTCTG	.	PASS	Atlas-SNP
ILK	3611	hgsc.bcm.edu	37	11	6629665	6629665	+	Silent	SNP	C	C	T	rs1043388	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	128	57	120	0	0.445312	0	C|0.690;T|0.310	0.310	strong	.	ILK	41	.	NM_001014794	exon4	c.C297T	p.H99H	TGAACACGGGAAT	.	PASS	Atlas-SNP
NRP1	8829	hgsc.bcm.edu	37	10	33510663	33510663	+	Silent	SNP	G	G	A	rs2229935	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83	34	94	0	0.409639	0	G|0.708;A|0.292	0.292	strong	.	NRP1	126	.	NM_001244973	exon8	c.C1266T	p.Y422Y	GCAACCGTATACT	.	PASS	Atlas-SNP
FBN3	84467	hgsc.bcm.edu	37	19	8161450	8161450	+	Missense_Mutation	SNP	C	C	T	rs3829817	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44	43	37	0	0.977273	0	C|0.810;T|0.190	0.190	strong	.	FBN3	300	.	NM_032447	exon43	c.G5417A	p.R1806Q	TCATTCCGTCCTG	.	PASS	Atlas-SNP
PCDHA4	56144	hgsc.bcm.edu	37	5	140188709	140188709	+	Missense_Mutation	SNP	G	G	T	rs147674000	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	99	48	121	0	0.484848	0	G|0.993;T|0.007	0.007	strong	PCDHA4_ENST00000530339,colon,carcinoma,0,2	PCDHA4	419	2	NM_031500	exon1	c.G1937T	p.R646L	GCCACCGCCTACT	.	PASS	Atlas-SNP
CDH4	1002	hgsc.bcm.edu	37	20	60509209	60509209	+	Silent	SNP	C	C	T	rs3753045	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57	30	71	1	0.526316	0.0140845	C|0.826;T|0.174	0.174	strong	CDH4,colon,carcinoma,0,1	CDH4	172	1	NM_001794	exon15	c.C2475T	p.G825G	GGTGGGCGCTGAG	.	scavenged	Atlas-SNP
TANK	10010	hgsc.bcm.edu	37	2	162036195	162036195	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100	41	136	0	0.41	0	.	.	none	.	TANK	35	.	NM_004180	exon2	c.C22T	p.Q8X	GGCGAGCAACTCA	.	PASS	Atlas-SNP
MARK1	4139	hgsc.bcm.edu	37	1	220791729	220791729	+	Silent	SNP	G	G	T	rs36024488	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	31	80	0	0.369048	0	G|0.985;T|0.015	0.015	strong	MARK1,NS,carcinoma,0,1	MARK1	161	1	NM_018650	exon8	c.G630T	p.G210G	AGTTGGGAACAAA	.	PASS	Atlas-SNP
SP100	6672	hgsc.bcm.edu	37	2	231333763	231333763	+	Missense_Mutation	SNP	A	A	G	rs12724	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93	40	102	0	0.430108	0	A|0.778;G|0.221;N|0.000;T|0.000	0.221	strong	.	SP100	167	.	NM_001206702	exon14	c.A1297G	p.M433V	GCTCCTATGACTT	.	PASS	Atlas-SNP
FAT2	2196	hgsc.bcm.edu	37	5	150901597	150901597	+	Silent	SNP	G	G	C	rs3734047	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	30	12	47	0	0.4	0	G|0.858;C|0.142	0.142	strong	.	FAT2	465	.	NM_001447	exon18	c.C10557G	p.V3519V	GACATGGACACGG	.	PASS	Atlas-SNP
INPP5J	27124	hgsc.bcm.edu	37	22	31529463	31529463	+	Silent	SNP	C	C	A	rs35342535	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83	34	64	0	0.409639	0	C|0.726;A|0.274	0.274	strong	.	INPP5J	94	.	NM_001002837	exon11	c.C1299A	p.T433T	GAATACCTACCAG	.	PASS	Atlas-SNP
LAMA2	3908	hgsc.bcm.edu	37	6	129813567	129813567	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73	39	90	0	0.534247	0	.	.	none	.	LAMA2	481	.	NM_000426	exon58	c.T8183A	p.V2728D	AAATAGTTATCCA	.	PASS	Atlas-SNP
CDKAL1	54901	hgsc.bcm.edu	37	6	21065450	21065450	+	Silent	SNP	A	A	G	rs56087852	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	56	15	60	0	0.267857	0	A|0.809;G|0.191	0.191	strong	CDKAL1,NS,carcinoma,0,1	CDKAL1	55	1	NM_017774	exon12	c.A1227G	p.P409P	AGTTCCAGCACAA	.	PASS	Atlas-SNP
LRPPRC	10128	hgsc.bcm.edu	37	2	44201376	44201376	+	Silent	SNP	T	T	C	rs4953042	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	300	148	317	0	0.493333	0	T|0.840;C|0.160	0.160	strong	.	LRPPRC	105	.	NM_133259	exon9	c.A1068G	p.Q356Q	TAAAATTTGCAAC	.	PASS	Atlas-SNP
PRSS55	203074	hgsc.bcm.edu	37	8	10390452	10390452	+	Missense_Mutation	SNP	C	C	T	rs4406360	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	29	69	0	0.408451	0	C|0.668;T|0.332	0.332	strong	.	PRSS55	67	.	NM_001197020	exon4	c.C635T	p.A212V	TGAAAGCGCCAAT	.	PASS	Atlas-SNP
ACSM5	54988	hgsc.bcm.edu	37	16	20442608	20442608	+	Missense_Mutation	SNP	C	C	A	rs79364355	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	119	14	97	0	0.117647	0	C|0.500;A|0.500	0.500	weak	ACSM5,NS,NS,0,1	ACSM5	101	1	NM_017888	exon10	c.C1273A	p.P425T	ATCAGACCCACTC	.	PASS	Atlas-SNP
SMCR8	140775	hgsc.bcm.edu	37	17	18226177	18226177	+	Silent	SNP	G	G	T	rs4925171	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	131	70	144	0	0.534351	0	G|0.744;T|0.256	0.256	strong	SMCR8,NS,carcinoma,0,1	SMCR8	62	1	NM_144775	exon2	c.G2607T	p.L869L	GCACCTGCCTACC	.	PASS	Atlas-SNP
HIST1H2BE	8344	hgsc.bcm.edu	37	6	26184102	26184102	+	Missense_Mutation	SNP	G	G	A	rs7766641	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73	59	95	0	0.808219	0	G|0.744;A|0.256	0.256	strong	.	HIST1H2BE	10	.	NM_003523	exon1	c.G79A	p.G27S	AAGGACGGCAAGA	.	PASS	Atlas-SNP
VPS13C	54832	hgsc.bcm.edu	37	15	62243197	62243197	+	Missense_Mutation	SNP	T	T	C	rs11629598	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	212	106	179	0	0.5	0	T|0.946;C|0.054	0.054	strong	VPS13C,NS,carcinoma,0,1	VPS13C	506	1	NM_020821	exon40	c.A4483G	p.I1495V	AGTTAATAATGTG	.	PASS	Atlas-SNP
ENGASE	64772	hgsc.bcm.edu	37	17	77075631	77075631	+	Silent	SNP	C	C	T	rs3744182	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72	23	84	0	0.319444	0	C|0.878;T|0.122	0.122	strong	ENGASE,NS,carcinoma,+2,2	ENGASE	55	2	NM_001042573	exon4	c.C477T	p.D159D	CATCGACGTCTTT	.	PASS	Atlas-SNP
CCL4	6351	hgsc.bcm.edu	37	17	34432663	34432663	+	Silent	SNP	A	A	G	rs1049807	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	380	379	291	0	0.997368	0	A|0.816;G|0.184	0.184	strong	.	CCL4	14	.	NM_002984	exon3	c.A237G	p.E79E	CAGTGAATCCTGG	.	PASS	Atlas-SNP
CCL14	6358	hgsc.bcm.edu	37	17	34311387	34311387	+	Missense_Mutation	SNP	T	T	C	rs16971802	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	106	46	114	0	0.433962	0	T|0.925;C|0.075	0.075	strong	.	CCL14	22	.	NM_032962	exon3	c.A229G	p.K77E	CGGGCTTGGAGCA	.	PASS	Atlas-SNP
SIGLEC6	946	hgsc.bcm.edu	37	19	52033158	52033158	+	Missense_Mutation	SNP	C	C	T	rs35931837	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	105	49	102	0	0.466667	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
DCAF13	25879	hgsc.bcm.edu	37	8	104427541	104427541	+	Missense_Mutation	SNP	C	C	T	rs3134296	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	59	28	66	0	0.474576	0	C|0.817;T|0.183	0.183	strong	DCAF13,NS,carcinoma,-1,1	DCAF13	66	1	NM_015420	exon1	c.C323T	p.P108L	TTGAGCCAGCAGG	.	PASS	Atlas-SNP
ZNF700	90592	hgsc.bcm.edu	37	19	12059467	12059467	+	Missense_Mutation	SNP	C	C	G	rs73509026	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	31	48	0	0.584906	0	C|0.940;G|0.060	0.060	strong	ZNF700,NS,carcinoma,-1,1	ZNF700	81	1	NM_001271848	exon4	c.C637G	p.R213G	AGCATTCGAAGAC	.	PASS	Atlas-SNP
SYNRG	11276	hgsc.bcm.edu	37	17	35937637	35937637	+	Missense_Mutation	SNP	T	T	C	rs12602536	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	152	82	134	0	0.539474	0	C|0.151;T|0.849	0.151	strong	SYNRG,NS,carcinoma,0,1	SYNRG	101	1	NM_007247	exon7	c.A664G	p.T222A	CAGAAGTATTTAA	.	PASS	Atlas-SNP
PARP15	165631	hgsc.bcm.edu	37	3	122296647	122296647	+	Missense_Mutation	SNP	G	G	A	rs7632426	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	41	92	0	0.650794	0	G|0.835;A|0.165	0.165	strong	.	PARP15	115	.	NM_001113523	exon1	c.G133A	p.A45T	CTGCCGGCCGGGA	.	PASS	Atlas-SNP
GP1BA	2811	hgsc.bcm.edu	37	17	4836381	4836381	+	Missense_Mutation	SNP	C	C	T	rs6065	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	89	32	69	0	0.359551	0	C|0.878;T|0.122	0.122	strong	GP1BA,colon,carcinoma,-1,1	GP1BA	53	1	NM_000173	exon2	c.C482T	p.T161M	TCCTGACGCCCAC	.	PASS	Atlas-SNP
PPARGC1A	10891	hgsc.bcm.edu	37	4	23815522	23815522	+	Silent	SNP	C	C	T	rs3755863	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	112	47	122	0	0.419643	0	C|0.640;T|0.360	0.360	strong	PPARGC1A,colon,carcinoma,0,1	PPARGC1A	129	1	NM_013261	exon8	c.G1584A	p.T528T	GGATTGCGTGCCA	.	PASS	Atlas-SNP
COL20A1	57642	hgsc.bcm.edu	37	20	61929348	61929348	+	Missense_Mutation	SNP	C	C	A	rs144861412	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	31	51	0	0.508197	0	C|0.995;A|0.005	0.005	strong	.	COL20A1	137	.	NM_020882	exon3	c.C169A	p.L57M	GGCTACCTGGTGC	.	PASS	Atlas-SNP
NEK10	152110	hgsc.bcm.edu	37	3	27326451	27326451	+	Silent	SNP	A	A	G	rs10510594	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	42	15	50	0	0.357143	0	A|0.792;G|0.208	0.208	strong	NEK10_ENST00000429845,NS,carcinoma,0,3	NEK10	271	3	NM_199347	exon22	c.T1791C	p.N597N	CCTATCATCTATA	.	PASS	Atlas-SNP
SLC52A3	113278	hgsc.bcm.edu	37	20	741847	741847	+	Silent	SNP	A	A	G	rs910857	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	32	31	64	0	0.96875	0	A|0.391;G|0.609	0.609	strong	.	.	.	.	NM_033409	exon5	c.T1233C	p.S411S	GACGTAACTGAGG	.	PASS	Atlas-SNP
HUNK	30811	hgsc.bcm.edu	37	21	33368191	33368191	+	Missense_Mutation	SNP	G	G	C	rs138721520	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	180	106	162	0	0.588889	0	G|0.998;C|0.002	0.002	strong	.	HUNK	74	.	NM_014586	exon10	c.G1416C	p.M472I	GCTTATGACACAG	.	PASS	Atlas-SNP
HAGHL	84264	hgsc.bcm.edu	37	16	777590	777590	+	Silent	SNP	C	C	T	rs143758903	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	96	45	92	0	0.46875	0	C|0.999;T|0.001	0.001	strong	.	HAGHL	18	.	NM_032304	exon1	c.C81T	p.A27A	GGTGGCCGTGGAC	.	PASS	Atlas-SNP
CD48	962	hgsc.bcm.edu	37	1	160681535	160681535	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	265	53	275	0	0.2	0	.	.	none	.	CD48	31	.	NM_001256030	exon1	c.G19A	p.D7N	ACGAATCCCAACC	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	106	52	102	0	0.490566	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
TEP1	7011	hgsc.bcm.edu	37	14	20863677	20863677	+	Silent	SNP	C	C	A	rs2228036	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	184	79	180	0	0.429348	0	C|0.753;A|0.247	0.247	strong	.	TEP1	224	.	NM_007110	exon12	c.G1860T	p.R620R	TGCCATCCGAAGC	.	PASS	Atlas-SNP
C9orf171	389799	hgsc.bcm.edu	37	9	135413085	135413085	+	Missense_Mutation	SNP	A	A	C	rs34650498	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	43	19	43	0	0.44186	0	A|0.952;C|0.048	0.048	strong	C9orf171,colon,carcinoma,-1,1	C9orf171	53	1	NM_207417	exon5	c.A730C	p.K244Q	GAGAAGAAGCAGA	.	PASS	Atlas-SNP
LBP	3929	hgsc.bcm.edu	37	20	36979265	36979265	+	Silent	SNP	T	T	C	rs2232582	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	43	17	42	0	0.395349	0	T|0.792;C|0.208	0.208	strong	.	LBP	60	.	NM_004139	exon3	c.T291C	p.P97P	TGTCCCTGGCCAG	.	PASS	Atlas-SNP
TMEM63A	9725	hgsc.bcm.edu	37	1	226041438	226041438	+	Silent	SNP	C	C	T	rs2292556	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	137	61	119	0	0.445255	0	C|0.960;T|0.040	0.040	strong	TMEM63A,NS,carcinoma,0,1	TMEM63A	75	1	NM_014698	exon19	c.G1689A	p.S563S	GAAGGCCGAGGCG	.	PASS	Atlas-SNP
B4GALT4	8702	hgsc.bcm.edu	37	3	118948716	118948716	+	Silent	SNP	G	G	A	rs4422294	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98	47	78	0	0.479592	0	G|0.776;A|0.224	0.224	strong	B4GALT4,NS,carcinoma,0,1	B4GALT4	30	1	NM_212543	exon4	c.C231T	p.C77C	AGAAGGGCAGTTG	.	PASS	Atlas-SNP
ZNF792	126375	hgsc.bcm.edu	37	19	35449486	35449486	+	Missense_Mutation	SNP	T	T	C	rs34687332	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	28	60	0	0.41791	0	T|0.966;C|0.034	0.034	strong	.	ZNF792	46	.	NM_175872	exon4	c.A1273G	p.N425D	ATTCGTTACACTT	.	PASS	Atlas-SNP
SETD4	54093	hgsc.bcm.edu	37	21	37410477	37410477	+	Missense_Mutation	SNP	T	T	C	rs2835239	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	193	192	178	0	0.994819	0	T|0.963;C|0.037	0.037	strong	.	SETD4	37	.	NM_017438	exon10	c.A1159G	p.I387V	CTTCTATGAAATA	.	PASS	Atlas-SNP
ADAM19	8728	hgsc.bcm.edu	37	5	156917340	156917340	+	Missense_Mutation	SNP	A	A	C	rs10067096	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	88	38	119	0	0.431818	0	A|0.827;C|0.173	0.173	strong	.	ADAM19	216	.	NM_033274	exon19	c.T2218G	p.S740A	GCTTGGAAGGGAG	.	PASS	Atlas-SNP
PNN	5411	hgsc.bcm.edu	37	14	39644498	39644498	+	Silent	SNP	G	G	A	rs1061583	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	50	17	34	0	0.34	0	G|0.804;A|0.196	0.196	strong	PNN,right_upper_lobe,carcinoma,+2,1	PNN	67	1	NM_002687	exon1	c.G15A	p.V5V	CGCCGTGAGAACT	.	PASS	Atlas-SNP
INMT	11185	hgsc.bcm.edu	37	7	30795331	30795331	+	Missense_Mutation	SNP	A	A	G	rs2302340	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	59	59	78	2	1	0.025641	A|0.661;G|0.339	0.339	strong	INMT,NS,carcinoma,0,1	INMT	38	1	NM_006774	exon3	c.A656G	p.E219G	AGAAAGAGGAGGT	.	scavenged	Atlas-SNP
PAX5	5079	hgsc.bcm.edu	37	9	37033992	37033992	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	89	41	61	0	0.460674	0	.	.	none	.	PAX5	250	.	NM_016734	exon1	c.A37G	p.S13G	TCCTGCTGGTCCG	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179413110	179413110	+	Silent	SNP	G	G	A	rs3731748	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	38	97	0	0.5	0	G|0.798;A|0.202	0.202	strong	.	TTN	18412	.	NM_001267550	exon339	c.C93243T	p.A31081A	ACCTTCGGCCAGG	.	PASS	Atlas-SNP
HERC1	8925	hgsc.bcm.edu	37	15	63988400	63988400	+	Missense_Mutation	SNP	G	G	C	rs74814914	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100	48	109	0	0.48	0	G|0.985;C|0.015	0.015	strong	.	HERC1	624	.	NM_003922	exon27	c.C5044G	p.L1682V	CTGCTAGGAACTG	.	PASS	Atlas-SNP
ABCD4	5826	hgsc.bcm.edu	37	14	74759301	74759301	+	Silent	SNP	G	G	T	rs4148078	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83	49	80	0	0.590361	0	G|0.719;T|0.281	0.281	strong	.	ABCD4	54	.	NM_005050	exon10	c.C981A	p.L327L	GTCGATGAGCTGG	.	PASS	Atlas-SNP
NPLOC4	55666	hgsc.bcm.edu	37	17	79589242	79589242	+	Silent	SNP	G	G	A	rs6565604	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	33	65	0	0.464789	0	G|0.403;A|0.597	0.597	strong	.	NPLOC4	27	.	NM_017921	exon3	c.C159T	p.T53T	CTCTCCGGTCTTG	.	PASS	Atlas-SNP
ZNF441	126068	hgsc.bcm.edu	37	19	11890921	11890921	+	Silent	SNP	C	C	T	rs33949590	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	38	60	0	0.5	0	C|0.939;T|0.061	0.061	strong	.	ZNF441	123	.	NM_152355	exon4	c.C282T	p.N94N	TGTGAACGAGAAA	.	PASS	Atlas-SNP
DYNC2LI1	51626	hgsc.bcm.edu	37	2	44028013	44028013	+	Missense_Mutation	SNP	A	A	T	rs11556157	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	66	71	0	0.985075	0	A|0.758;T|0.242	0.242	strong	.	DYNC2LI1	46	.	NM_001193464	exon9	c.A691T	p.I231L	CTAAAAATACGTG	.	PASS	Atlas-SNP
AGPAT4	56895	hgsc.bcm.edu	37	6	161557662	161557662	+	Silent	SNP	G	G	A	rs3734462	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	41	17	75	1	0.414634	0.0133333	G|0.858;A|0.142	0.142	strong	AGPAT4,brain,glioma,-1,1	AGPAT4	50	1	NM_020133	exon9	c.C1047T	p.S349S	TCCCACGGAGGCT	.	scavenged	Atlas-SNP
UAP1L1	91373	hgsc.bcm.edu	37	9	139975195	139975195	+	Silent	SNP	C	C	T	rs41302685	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	24	42	0	0.510638	0	C|0.927;T|0.073	0.073	strong	UAP1L1_ENST00000409858,NS,carcinoma,0,2	UAP1L1	46	2	NM_207309	exon7	c.C1233T	p.N411N	GAAGAACGCAGAG	.	PASS	Atlas-SNP
RFTN2	130132	hgsc.bcm.edu	37	2	198498595	198498595	+	Missense_Mutation	SNP	C	C	T	rs139323535	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	170	85	173	0	0.5	0	C|0.998;T|0.002	0.002	strong	RFTN2,NS,carcinoma,0,2	RFTN2	68	2	NM_144629	exon4	c.G565A	p.G189S	CTGAACCGTGTCT	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	115	88	96	1	0.765217	0.0104167	G|0.876;N|0.000	.	strong	C11orf67,NS,carcinoma,0,1	.	.	1	NM_024684	exon4	c.G274A	p.V92M	ATTGATGTGCGGG	.	scavenged	Atlas-SNP
CACNG5	27091	hgsc.bcm.edu	37	17	64873552	64873552	+	Silent	SNP	G	G	A	rs11652480	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91	38	96	0	0.417582	0	G|0.922;A|0.078	0.078	strong	.	CACNG5	77	.	NM_145811	exon1	c.G102A	p.L34L	CTGGCTGTACCTG	.	PASS	Atlas-SNP
OR8B4	283162	hgsc.bcm.edu	37	11	124294349	124294349	+	Missense_Mutation	SNP	C	C	A	rs7116575	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	77	117	0	0.885057	0	C|0.845;A|0.155	0.155	strong	OR8B4,NS,carcinoma,-1,1	OR8B4	60	1	NM_001005196	exon1	c.G419T	p.C140F	AGAAAGCAGACCC	.	PASS	Atlas-SNP
CARD9	64170	hgsc.bcm.edu	37	9	139266496	139266496	+	Missense_Mutation	SNP	C	C	T	rs4077515	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	77	77	76	0	1	0	C|0.634;T|0.366	0.366	strong	CARD9,NS,carcinoma,0,1	CARD9	47	1	NM_052813	exon2	c.G35A	p.S12N	AGGACGCTCCAGC	.	PASS	Atlas-SNP
PLCXD1	55344	hgsc.bcm.edu	37	X	207362	207362	+	Silent	SNP	C	C	T	rs11556996	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	207	56	333	0	0.270531	0	T|0.530;G|0.000;C|0.470	0.530	strong	.	PLCXD1	18	.	NM_018390	exon4	c.C312T	p.D104D	CCTGGACCTGCGG	.	PASS	Atlas-SNP
ZNF860	344787	hgsc.bcm.edu	37	3	32032397	32032397	+	Missense_Mutation	SNP	G	G	T	rs4955216	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	64	89	0	1	0	G|0.644;T|0.356	0.356	strong	.	ZNF860	96	.	NM_001137674	exon2	c.G1826T	p.R609L	CACATCGCATTAG	.	PASS	Atlas-SNP
HDAC4	9759	hgsc.bcm.edu	37	2	240003870	240003870	+	Silent	SNP	G	G	A	rs1063639	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	212	103	178	0	0.485849	0	G|0.456;A|0.544	0.544	strong	.	HDAC4	127	.	NM_006037	exon21	c.C2565T	p.P855P	GACGCTGGGGTCG	.	PASS	Atlas-SNP
CYP11B2	1585	hgsc.bcm.edu	37	8	143994702	143994702	+	Silent	SNP	G	G	T	rs4538	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	117	43	147	0	0.367521	0	G|0.462;T|0.538	0.538	strong	CYP11B2,NS,carcinoma,0,2	CYP11B2	107	2	NM_000498	exon6	c.C1120A	p.R374R	CCCACCGCAAGGT	.	PASS	Atlas-SNP
SEC14L6	730005	hgsc.bcm.edu	37	22	30934887	30934887	+	Silent	SNP	G	G	A	rs5753191	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	77	38	76	0	0.493506	0	G|0.494;A|0.506	0.506	strong	.	SEC14L6	6	.	NM_001193336	exon2	c.C57T	p.F19F	CTCCCGGAACTGA	.	PASS	Atlas-SNP
B4GALNT4	338707	hgsc.bcm.edu	37	11	372157	372157	+	Missense_Mutation	SNP	C	C	T	rs34063493	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72	68	67	0	0.944444	0	A|0.000;C|0.629;G|0.000;T|0.371	0.371	strong	.	B4GALNT4	83	.	NM_178537	exon2	c.C200T	p.A67V	ACGCTGCGCCATC	.	PASS	Atlas-SNP
COL12A1	1303	hgsc.bcm.edu	37	6	75844458	75844458	+	Silent	SNP	C	C	T	rs77425231	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	207	98	202	0	0.47343	0	C|0.993;T|0.007	0.007	strong	.	COL12A1	385	.	NM_004370	exon32	c.G5508A	p.T1836T	TCTTCCCGTCATC	.	PASS	Atlas-SNP
THBS1	7057	hgsc.bcm.edu	37	15	39882178	39882178	+	Missense_Mutation	SNP	A	A	G	rs2228262	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	77	35	88	0	0.454545	0	A|0.930;G|0.070	0.070	strong	THBS1,NS,carcinoma,0,3	THBS1	106	3	NM_003246	exon13	c.A2099G	p.N700S	GGCCCAATGAGAA	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29910731	29910731	+	Missense_Mutation	SNP	G	G	A	rs79361534	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	145	133	192	0	0.917241	0	A|0.124;G|0.876	0.124	strong	.	HLA-A	89	.	NM_001242758	exon2	c.G271A	p.V91M	CGGAATGTGAAGG	.	PASS	Atlas-SNP
ADAMTSL3	57188	hgsc.bcm.edu	37	15	84639350	84639350	+	Missense_Mutation	SNP	C	C	T	rs2277849	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91	39	116	0	0.428571	0	C|0.712;T|0.288	0.288	strong	ADAMTSL3,NS,carcinoma,0,1	ADAMTSL3	290	1	NM_207517	exon20	c.C2605T	p.L869F	CCAGGGCTCCCTC	.	PASS	Atlas-SNP
RNF152	220441	hgsc.bcm.edu	37	18	59483508	59483508	+	Silent	SNP	G	G	T	rs116886631	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	26	66	0	0.42623	0	G|0.958;T|0.042	0.042	strong	.	RNF152	37	.	NM_173557	exon2	c.C189A	p.G63G	GGAGAAGCCGGGA	.	PASS	Atlas-SNP
COBLL1	22837	hgsc.bcm.edu	37	2	165586466	165586466	+	Silent	SNP	T	T	C	rs13392281	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	18	149	0	0.253521	0	T|0.804;C|0.196	0.196	strong	.	COBLL1	122	.	NM_014900	exon3	c.A390G	p.P130P	CATTTTTGGCTTT	.	PASS	Atlas-SNP
CIT	11113	hgsc.bcm.edu	37	12	120156141	120156141	+	Silent	SNP	G	G	A	rs278102	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	70	34	62	0	0.485714	0	G|0.760;A|0.240	0.240	strong	.	CIT	535	.	NM_001206999	exon32	c.C4077T	p.S1359S	GATGGCGGACATG	.	PASS	Atlas-SNP
FBXL5	26234	hgsc.bcm.edu	37	4	15640168	15640168	+	Silent	SNP	C	C	T	rs3182730	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69	26	94	0	0.376812	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
TGS1	96764	hgsc.bcm.edu	37	8	56708701	56708701	+	Missense_Mutation	SNP	T	T	C	rs10100659	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	58	33	69	0	0.568965	0	T|0.847;C|0.153	0.153	strong	.	TGS1	66	.	NM_024831	exon7	c.T1532C	p.I511T	GCAAAATTCTGAG	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	99	77	106	0	0.777778	0	G|0.714;A|0.286	0.286	strong	.	ANKK1	83	.	NM_178510	exon5	c.G715A	p.A239T	CGAGTGGCGGCAG	.	PASS	Atlas-SNP
OR2F1	26211	hgsc.bcm.edu	37	7	143657801	143657801	+	Silent	SNP	A	A	G	rs2072166	bycluster;byfrequency;bysubmitter;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	129	127	115	0	0.984496	0	A|0.568;G|0.432	0.432	strong	.	OR2F1	71	.	NM_012369	exon1	c.A738G	p.T246T	CCTCACAGTGGTT	.	PASS	Atlas-SNP
IGFBP1	3484	hgsc.bcm.edu	37	7	45932669	45932669	+	Missense_Mutation	SNP	A	A	G	rs4619	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	21	21	34	0	1	0	A|0.602;G|0.397	0.397	strong	.	IGFBP1	19	.	NM_000596	exon4	c.A759G	p.I253M	CCAGATATATTTT	.	PASS	Atlas-SNP
OR2L3	391192	hgsc.bcm.edu	37	1	248224216	248224216	+	Missense_Mutation	SNP	C	C	T	rs6658227	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	223	110	226	0	0.493274	0	C|0.801;T|0.199	0.199	strong	.	OR2L3	97	.	NM_001004687	exon1	c.C233T	p.P78L	TTGTTCCTAAGAT	.	PASS	Atlas-SNP
C2orf53	339779	hgsc.bcm.edu	37	2	27360773	27360773	+	Missense_Mutation	SNP	G	G	A	rs61741796	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	43	20	47	0	0.465116	0	G|0.993;A|0.007	0.007	strong	.	C2orf53	45	.	NM_178553	exon3	c.C425T	p.P142L	TGGCAAGGTGAGT	.	PASS	Atlas-SNP
MCMDC2	157777	hgsc.bcm.edu	37	8	67786817	67786817	+	Missense_Mutation	SNP	C	C	T	rs116671744	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	117	50	120	0	0.42735	0	C|0.970;T|0.030	0.030	strong	.	MCMDC2	84	.	NM_173518	exon4	c.C281T	p.T94M	CTGAAACGCAAGT	.	PASS	Atlas-SNP
PRDM11	56981	hgsc.bcm.edu	37	11	45245778	45245778	+	Missense_Mutation	SNP	G	G	T	rs35090414	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	50	28	54	0	0.56	0	G|0.940;T|0.060	0.060	strong	PRDM11,caecum,carcinoma,0,2	PRDM11	53	2	NM_001256695	exon7	c.G753T	p.R251S	GAAGAGGTTGCAG	.	PASS	Atlas-SNP
CRIPAK	285464	hgsc.bcm.edu	37	4	1388759	1388759	+	Missense_Mutation	SNP	C	C	T	rs112233131	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	21	6	2	0	0.285714	0	C|0.966;T|0.034	0.034	strong	CRIPAK,rectum,carcinoma,0,3	CRIPAK	185	3	NM_175918	exon1	c.C460T	p.R154W	CCCATGCGGAGTG	.	PASS	Atlas-SNP
PCDHB8	56128	hgsc.bcm.edu	37	5	140559029	140559029	+	Missense_Mutation	SNP	G	G	C	rs139165988	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	234	56	179	0	0.239316	0	G|0.991;C|0.009	0.009	strong	.	PCDHB8	199	.	NM_019120	exon1	c.G1414C	p.G472R	CACATCGGCAGCG	.	PASS	Atlas-SNP
CCDC168	643677	hgsc.bcm.edu	37	13	103410782	103410782	+	Missense_Mutation	SNP	T	T	C	rs1375719	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57	40	90	0	0.701754	0	A|0.014;C|0.352	0.352	strong	.	.	.	.	NM_001146197	exon3	c.A286G	p.I96V	AATTAATAACTGA	.	PASS	Atlas-SNP
CBY1	25776	hgsc.bcm.edu	37	22	39069181	39069181	+	Silent	SNP	T	T	C	rs3747174	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	66	65	0	0.985075	0	T|0.702;C|0.298	0.298	strong	.	CBY1	10	.	NM_001002880	exon6	c.T450C	p.A150A	CACTGCTGAATCC	.	PASS	Atlas-SNP
TOX3	27324	hgsc.bcm.edu	37	16	52484278	52484278	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	113	33	97	0	0.292035	0	.	.	none	.	TOX3	121	.	NM_001080430	exon4	c.C589T	p.H197Y	ATGTGTGAGGCAT	.	PASS	Atlas-SNP
JARID2	3720	hgsc.bcm.edu	37	6	15496662	15496662	+	Silent	SNP	C	C	T	rs742099	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	40	54	0	0.754717	0	C|0.798;T|0.202	0.202	strong	.	JARID2	135	.	NM_004973	exon7	c.C1206T	p.P402P	TGGGCCCGCCGTC	.	PASS	Atlas-SNP
GREB1	9687	hgsc.bcm.edu	37	2	11736305	11736305	+	Missense_Mutation	SNP	G	G	A	rs36030386	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	111	65	122	0	0.585586	0	G|0.826;A|0.174	0.174	strong	.	GREB1	308	.	NM_014668	exon13	c.G1894A	p.A632T	TCACTCGCTGCCT	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9086318	9086318	+	Missense_Mutation	SNP	G	G	A	rs4520945	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	147	73	137	0	0.496599	0	G|0.812;A|0.188	0.188	strong	.	MUC16	4315	.	NM_024690	exon1	c.C5497T	p.L1833F	GAGTGAGAGAAAT	.	PASS	Atlas-SNP
SYMPK	8189	hgsc.bcm.edu	37	19	46320218	46320218	+	Silent	SNP	G	G	A	rs140350780	byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	92	47	110	0	0.51087	0	G|0.997;A|0.003	0.003	strong	.	SYMPK	104	.	NM_004819	exon24	c.C3096T	p.P1032P	CACCTTGGGGTAC	.	PASS	Atlas-SNP
SMG6	23293	hgsc.bcm.edu	37	17	2203175	2203175	+	Missense_Mutation	SNP	C	C	G	rs1885986	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	104	54	102	0	0.519231	0	C|0.743;G|0.257	0.257	strong	.	SMG6	97	.	NM_017575	exon2	c.G872C	p.R291P	TTCAGTCGTGGCC	.	PASS	Atlas-SNP
CPZ	8532	hgsc.bcm.edu	37	4	8613867	8613867	+	Silent	SNP	G	G	A	rs2302573	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	45	17	63	0	0.377778	0	G|0.956;A|0.044	0.044	strong	CPZ,NS,carcinoma,+1,2	CPZ	95	2	NM_001014447	exon8	c.G1341A	p.A447A	CGGGGCGGACTGG	.	PASS	Atlas-SNP
KHDRBS1	10657	hgsc.bcm.edu	37	1	32479924	32479924	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	28	73	0	0.333333	0	.	.	none	.	KHDRBS1	34	.	NM_006559	exon1	c.G328A	p.E110K	ATGGCCGAGAAGG	.	PASS	Atlas-SNP
SRA1	10011	hgsc.bcm.edu	37	5	139936980	139936980	+	Missense_Mutation	SNP	A	A	G	rs250427	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	50	110	0	0.961538	0	A|0.290;G|0.710	0.710	strong	.	SRA1	24	.	NM_001253764	exon1	c.T58C	p.C20R	GGCGACAACCTAG	.	PASS	Atlas-SNP
ERCC6	2074	hgsc.bcm.edu	37	10	50681033	50681033	+	Silent	SNP	G	G	A	rs2229760	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82	43	91	0	0.52439	0	G|0.702;A|0.298	0.298	strong	ERCC6,NS,carcinoma,0,1	ERCC6	162	1	NM_000124	exon15	c.G2751T	p.R917R	TAAGCCGCCCACC	.	PASS	Atlas-SNP
TYK2	7297	hgsc.bcm.edu	37	19	10477206	10477206	+	Silent	SNP	G	G	A	rs280523	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	122	55	100	0	0.45082	0	G|0.905;A|0.095	0.095	strong	.	TYK2	126	.	NM_003331	exon6	c.C516T	p.T172T	CTCCTCGGTCGAC	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	97	34	125	0	0.350515	0	C|0.625;G|0.375	0.375	strong	.	CCDC27	79	.	NM_152492	exon1	c.C160G	p.Q54E	CCATCTCAGAGGC	.	PASS	Atlas-SNP
ATAD3B	83858	hgsc.bcm.edu	37	1	1425644	1425644	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	101	50	92	0	0.49505	0	.	.	none	.	ATAD3B	68	.	NM_031921	exon14	c.C1345G	p.L449V	TTCATGCTGGTCC	.	PASS	Atlas-SNP
USP35	57558	hgsc.bcm.edu	37	11	77911745	77911745	+	Missense_Mutation	SNP	C	C	T	rs147270370	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	119	95	95	0	0.798319	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
EVC2	132884	hgsc.bcm.edu	37	4	5690902	5690902	+	Missense_Mutation	SNP	T	T	C	rs4689278	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	36	15	44	0	0.416667	0	T|0.776;C|0.224	0.224	strong	EVC2,NS,carcinoma,0,1	EVC2	202	1	NM_147127	exon5	c.A688G	p.S230G	TCTTGCTAAAAGC	.	PASS	Atlas-SNP
OR10H1	26539	hgsc.bcm.edu	37	19	15918654	15918654	+	Missense_Mutation	SNP	G	G	A	rs74729097		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	16	169	1	0.183908	0.00591716	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
LRRC47	57470	hgsc.bcm.edu	37	1	3700618	3700618	+	Silent	SNP	G	G	A	rs74764187	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	50	22	55	0	0.44	0	G|0.987;A|0.013	0.013	strong	LRRC47,NS,haematopoietic_neoplasm,0,1	LRRC47	42	1	NM_020710	exon4	c.C1252T	p.L418L	CCTCCAGCTGCAG	.	PASS	Atlas-SNP
PARP4	143	hgsc.bcm.edu	37	13	25075859	25075859	+	Silent	SNP	C	C	T	rs1539096	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	114	54	133	0	0.473684	0	C|0.431;T|0.569	0.569	strong	.	PARP4	142	.	NM_006437	exon3	c.G246A	p.R82R	CTTTTCCCTGATA	.	PASS	Atlas-SNP
SAMD9L	219285	hgsc.bcm.edu	37	7	92761064	92761064	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	17	63	0	0.226667	0	.	.	none	.	SAMD9L	227	.	NM_152703	exon5	c.A4221C	p.K1407N	TTGTTTTTTTAGC	.	PASS	Atlas-SNP
RUFY1	80230	hgsc.bcm.edu	37	5	179025789	179025789	+	Silent	SNP	G	G	A	rs72824522	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	167	82	154	0	0.491018	0	G|0.912;A|0.088	0.088	strong	.	RUFY1	101	.	NM_025158	exon14	c.G1728A	p.R576R	ACTCAGGATGGAG	.	PASS	Atlas-SNP
C8A	731	hgsc.bcm.edu	37	1	57383358	57383358	+	Missense_Mutation	SNP	C	C	T	rs17300936	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	239	239	191	0	1	0	C|0.917;N|0.000	.	strong	.	C8A	103	.	NM_000562	exon11	c.C1724T	p.P575L	CGTGTCCAGGGCG	.	PASS	Atlas-SNP
ZNFX1	57169	hgsc.bcm.edu	37	20	47865784	47865784	+	Missense_Mutation	SNP	C	C	T	rs6512577	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	128	71	167	0	0.554688	0	C|0.824;T|0.176	0.176	strong	.	ZNFX1	194	.	NM_021035	exon14	c.G3777A	p.M1259I	CCGGAGCATGGGG	.	PASS	Atlas-SNP
SYNPO2L	79933	hgsc.bcm.edu	37	10	75407649	75407649	+	Silent	SNP	A	A	C	rs4746139	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49	24	53	0	0.489796	0	A|0.855;C|0.145	0.145	strong	.	SYNPO2L	118	.	NM_001114133	exon4	c.T1761G	p.P587P	TCGCAAAGGCGCA	.	PASS	Atlas-SNP
RP1	6101	hgsc.bcm.edu	37	8	55541450	55541450	+	Missense_Mutation	SNP	G	G	A	rs446227	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	125	122	130	1	0.976	0.00769231	G|0.766;A|0.233	0.233	strong	.	RP1	429	.	NM_006269	exon4	c.G5008A	p.A1670T	AGGAAAGCAAGTC	.	PASS	Atlas-SNP
OR10A5	144124	hgsc.bcm.edu	37	11	6867588	6867588	+	Silent	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	224	12	243	0	0.0535714	0	.	.	none	.	OR10A5	48	.	NM_178168	exon1	c.T675C	p.A225A	TGCTGCTATCCTC	.	PASS	Atlas-SNP
CAPG	822	hgsc.bcm.edu	37	2	85628745	85628745	+	Silent	SNP	C	C	T	rs2229669	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	89	71	140	0	0.797753	0	C|0.940;T|0.060	0.060	strong	CAPG,colon,carcinoma,0,1	CAPG	32	1	NM_001256140	exon4	c.G258A	p.T86T	CAGCAGCGTGTTG	.	PASS	Atlas-SNP
PAMR1	25891	hgsc.bcm.edu	37	11	35456085	35456085	+	Missense_Mutation	SNP	T	T	A	rs138978009	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	124	55	127	0	0.443548	0	T|0.997;A|0.003	0.003	strong	PAMR1,NS,malignant_melanoma,-1,1	PAMR1	85	1	NM_015430	exon11	c.A1652T	p.D551V	TTCTCATCCCGGT	.	PASS	Atlas-SNP
ECE1	1889	hgsc.bcm.edu	37	1	21564631	21564631	+	Missense_Mutation	SNP	C	C	T	rs141146885	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	42	77	0	0.636364	0	C|0.997;T|0.003	0.003	strong	.	ECE1	76	.	NM_001397	exon11	c.G1385A	p.S462N	ACTATGCTCTTGC	.	PASS	Atlas-SNP
PRSS58	136541	hgsc.bcm.edu	37	7	141952110	141952110	+	Silent	SNP	G	G	A	rs1052406	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	31	73	0	0.418919	0	G|0.709;A|0.291	0.291	strong	.	PRSS58	41	.	NM_001001317	exon6	c.C657T	p.A219A	AACATCGGCTCTC	.	PASS	Atlas-SNP
KRTAP13-2	337959	hgsc.bcm.edu	37	21	31744062	31744062	+	Missense_Mutation	SNP	C	C	A	rs150635388	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110	65	105	0	0.590909	0	C|0.999;A|0.001	0.001	strong	KRTAP13-2,NS,carcinoma,0,1	KRTAP13-2	29	1	NM_181621	exon1	c.G470T	p.C157F	GACTGGCAGCTCC	.	PASS	Atlas-SNP
ZFPM1	161882	hgsc.bcm.edu	37	16	88599659	88599659	+	Missense_Mutation	SNP	G	G	T	rs71395304	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	13	13	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
STX2	2054	hgsc.bcm.edu	37	12	131306314	131306314	+	Missense_Mutation	SNP	C	C	G	rs17564	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	106	106	138	0	1	0	C|0.443;G|0.557	0.557	strong	.	STX2	66	.	NM_194356	exon3	c.G125C	p.S42T	TCAATACTGTTTC	.	PASS	Atlas-SNP
NUAK2	81788	hgsc.bcm.edu	37	1	205273100	205273100	+	Silent	SNP	G	G	A	rs56091501	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	103	47	125	1	0.456311	0.008	G|0.962;A|0.038	0.038	strong	NUAK2_ENST00000367157,NS,carcinoma,0,2	NUAK2	107	2	NM_030952	exon7	c.C1365T	p.R455R	AGACTCGCGCTGT	.	scavenged	Atlas-SNP
IRX3	79191	hgsc.bcm.edu	37	16	54318172	54318172	+	Missense_Mutation	SNP	C	C	A	rs1126960	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82	81	58	0	0.987805	0	T|0.000;G|0.000;C|0.792;A|0.208	0.208	strong	.	IRX3	25	.	NM_024336	exon3	c.G1437T	p.Q479H	CACGGGCTGGAAA	.	PASS	Atlas-SNP
FRAS1	80144	hgsc.bcm.edu	37	4	79385632	79385632	+	Silent	SNP	C	C	T	rs13123710	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	89	42	71	0	0.47191	0	C|0.962;T|0.038	0.038	strong	.	FRAS1	779	.	NM_025074	exon49	c.C6924T	p.V2308V	CCCTGTCGATGAT	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1075747	1075747	+	Missense_Mutation	SNP	T	T	C	rs2856111	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	109	63	112	0	0.577982	0	T|0.739;C|0.261	0.261	strong	.	MUC2	614	.	NM_002457	exon2	c.T173C	p.L58P	CCGGCCTCTGCGA	.	PASS	Atlas-SNP
ZNF211	10520	hgsc.bcm.edu	37	19	58153009	58153009	+	Silent	SNP	C	C	T	rs3746217	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	36	17	22	0	0.472222	0	C|0.789;T|0.211	0.211	strong	.	ZNF211	78	.	NM_001265597	exon5	c.C1350T	p.I450I	CCTGATCTACCAC	.	PASS	Atlas-SNP
SNX30	401548	hgsc.bcm.edu	37	9	115598610	115598610	+	Missense_Mutation	SNP	A	A	G	rs76424583	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	43	93	0	0.581081	0	A|0.922;G|0.078	0.078	strong	.	SNX30	32	.	NM_001012994	exon5	c.A735G	p.I245M	TGCCATAGGTGAC	.	PASS	Atlas-SNP
HLA-C	3107	hgsc.bcm.edu	37	6	31238929	31238929	+	Silent	SNP	C	C	G	rs71552047	alternate_allele	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	155	14	111	1	0.0903226	0.00900901	CCG|0.500;GTC|0.500	.	alt	HLA-C_ENST00000383329,NS,carcinoma,-1,2	HLA-C	92	2	NM_002117	exon3	c.G540C	p.L180L	GGCTCTCAGCTGC	.	scavenged	Atlas-SNP
UNC13A	23025	hgsc.bcm.edu	37	19	17746940	17746940	+	Silent	SNP	C	C	T	rs77267738	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	152	77	142	0	0.506579	0	C|0.958;T|0.042	0.042	strong	.	UNC13A	299	.	NM_001080421	exon25	c.G3108A	p.E1036E	CTGTTCCTCTGGG	.	PASS	Atlas-SNP
NHLRC2	374354	hgsc.bcm.edu	37	10	115644040	115644040	+	Missense_Mutation	SNP	G	G	A	rs7913176	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	38	82	0	0.44186	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
KIAA0196	9897	hgsc.bcm.edu	37	8	126056088	126056088	+	Silent	SNP	C	C	T	rs369339497		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	137	70	112	0	0.510949	0	.	.	weak	KIAA0196,NS,carcinoma,0,1	KIAA0196	90	1	NM_014846	exon23	c.G2829A	p.A943A	GAGATACGCAGTC	.	PASS	Atlas-SNP
ACSM5	54988	hgsc.bcm.edu	37	16	20442562	20442562	+	Silent	SNP	C	C	T	rs78006992	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91	8	86	0	0.0879121	0	C|0.500;T|0.500	0.500	strong	ACSM5,NS,carcinoma,0,1	ACSM5	101	1	NM_017888	exon10	c.C1227T	p.N409N	GGGCAACGTCCTG	.	PASS	Atlas-SNP
POM121L2	94026	hgsc.bcm.edu	37	6	27278020	27278020	+	Missense_Mutation	SNP	C	C	A	rs16897515	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55	35	74	0	0.636364	0	C|0.850;A|0.150	0.150	strong	.	POM121L2	61	.	NM_033482	exon1	c.G1930T	p.G644C	CTACACCAAAATC	.	PASS	Atlas-SNP
VWF	7450	hgsc.bcm.edu	37	12	6153534	6153534	+	Missense_Mutation	SNP	T	T	C	rs1063856	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83	36	106	0	0.433735	0	T|0.617;C|0.383;N|0.000	0.383	strong	.	VWF	338	.	NM_000552	exon18	c.A2365G	p.T789A	TTTTGGTACACTC	.	PASS	Atlas-SNP
SPPL2C	162540	hgsc.bcm.edu	37	17	43922942	43922942	+	Missense_Mutation	SNP	T	T	C	rs62621252	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	33	32	25	0	0.969697	0	T|0.851;C|0.149	0.149	strong	.	.	.	.	NM_175882	exon1	c.T670C	p.S224P	GGGGGGTCTGGTG	.	PASS	Atlas-SNP
COL24A1	255631	hgsc.bcm.edu	37	1	86590948	86590948	+	Silent	SNP	A	A	G	rs11161746	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	184	87	219	0	0.472826	0	A|0.886;G|0.114	0.114	strong	.	COL24A1	202	.	NM_152890	exon3	c.T1071C	p.S357S	TGCCTCACTGATG	.	PASS	Atlas-SNP
KIF13A	63971	hgsc.bcm.edu	37	6	17781450	17781450	+	Silent	SNP	G	G	A	rs942376	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	31	21	51	0	0.677419	0	G|0.825;A|0.175	0.175	strong	.	KIF13A	276	.	NM_001105566	exon30	c.C3627T	p.S1209S	AAACTGGCTGCCA	.	PASS	Atlas-SNP
IQCA1	79781	hgsc.bcm.edu	37	2	237374309	237374309	+	Silent	SNP	C	C	T	rs35432941	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	130	60	134	0	0.461538	0	C|0.896;T|0.104	0.104	strong	.	IQCA1	170	.	NM_001270585	exon6	c.G786A	p.Q262Q	TTCAGCCTGGATT	.	PASS	Atlas-SNP
MXRA5	25878	hgsc.bcm.edu	37	X	3239545	3239545	+	Missense_Mutation	SNP	C	C	T	rs1726199	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68	67	55	0	0.985294	0	0|0.013;T|0.704	0.704	strong	.	MXRA5	815	.	NM_015419	exon5	c.G4181A	p.G1394D	GGTATGCCTGTCT	.	PASS	Atlas-SNP
REG1B	5968	hgsc.bcm.edu	37	2	79313990	79313990	+	Missense_Mutation	SNP	C	C	T	rs62640882	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	113	31	126	0	0.274336	0	C|0.975;T|0.025	0.025	strong	.	REG1B	83	.	NM_006507	exon3	c.G131A	p.R44H	TAGGAGCGATAGG	.	PASS	Atlas-SNP
NCOA3	8202	hgsc.bcm.edu	37	20	46268493	46268493	+	Silent	SNP	A	A	G	rs2076546	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73	37	65	0	0.506849	0	A|0.863;G|0.137	0.137	strong	.	NCOA3	156	.	NM_181659	exon15	c.A2880G	p.T960T	TCCCACATTGCCT	.	PASS	Atlas-SNP
IRF1	3659	hgsc.bcm.edu	37	5	131822055	131822055	+	Silent	SNP	T	T	C	rs9282762	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	35	22	12	0	0.628571	0	T|0.623;C|0.377	0.377	strong	.	IRF1	26	.	NM_002198	exon7	c.A555G	p.P185P	AGCACATGGCGAC	.	PASS	Atlas-SNP
HIST3H3	8290	hgsc.bcm.edu	37	1	228612892	228612892	+	Silent	SNP	G	G	A	rs56336130	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	46	24	68	0	0.521739	0	G|0.942;A|0.058	0.058	strong	.	HIST3H3	20	.	NM_003493	exon1	c.C135T	p.G45G	CACCGTGCCGGGC	.	PASS	Atlas-SNP
TLR1	7096	hgsc.bcm.edu	37	4	38798935	38798935	+	Silent	SNP	C	C	T	rs5743614	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	213	102	188	0	0.478873	0	C|0.575;T|0.425	0.425	strong	TLR1,NS,carcinoma,-1,1	TLR1	70	1	NM_003263	exon4	c.G1518A	p.S506S	ATCAGCCGATGGG	.	PASS	Atlas-SNP
TMEM45B	120224	hgsc.bcm.edu	37	11	129722553	129722553	+	Missense_Mutation	SNP	C	C	T	rs558813	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	244	206	168	0	0.844262	0	C|0.754;T|0.246	0.246	strong	TMEM45B,NS,carcinoma,0,1	TMEM45B	25	1	NM_138788	exon2	c.C176T	p.T59I	CCGTCACTGGTAA	.	PASS	Atlas-SNP
NNT	23530	hgsc.bcm.edu	37	5	43656024	43656024	+	Silent	SNP	T	T	C	rs56193661	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	92	40	82	0	0.434783	0	T|0.933;C|0.067	0.067	strong	.	NNT	92	.	NM_182977	exon15	c.T2142C	p.A714A	GGCAGCTGTACTT	.	PASS	Atlas-SNP
UNC45A	55898	hgsc.bcm.edu	37	15	91486305	91486305	+	Silent	SNP	C	C	T	rs8034551	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	32	15	48	0	0.46875	0	C|0.944;T|0.056	0.056	strong	.	UNC45A	57	.	NM_018671	exon8	c.C1020T	p.I340I	GGTCATCGACCAA	.	PASS	Atlas-SNP
C12orf71	728858	hgsc.bcm.edu	37	12	27234200	27234200	+	Silent	SNP	T	T	C	rs708165	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	42	22	42	0	0.52381	0	T|0.739;C|0.261	0.261	strong	.	C12orf71	20	.	NM_001080406	exon2	c.A717G	p.K239K	GGGACTTTTGGTG	.	PASS	Atlas-SNP
LILRB5	10990	hgsc.bcm.edu	37	19	54755923	54755923	+	Silent	SNP	A	A	G	rs12976868	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	125	48	131	0	0.384	0	A|0.786;G|0.214	0.214	strong	.	LILRB5	176	.	NM_001081442	exon12	c.T1623C	p.D541D	CCGAGCATCCATC	.	PASS	Atlas-SNP
MYOM3	127294	hgsc.bcm.edu	37	1	24421474	24421474	+	Missense_Mutation	SNP	G	G	A	rs6678540	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	44	121	0	0.511628	0	G|0.633;A|0.367	0.367	strong	.	MYOM3	131	.	NM_152372	exon9	c.C797T	p.T266M	CCAAACGTCGATC	.	PASS	Atlas-SNP
NBPF10	100132406	hgsc.bcm.edu	37	1	145323656	145323656	+	Missense_Mutation	SNP	A	A	T	rs75252120	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	24	6	17	0	0.25	0	A|0.625;T|0.375	0.375	strong	NBPF10,NS,carcinoma,0,7	NBPF10	221	7	NM_001039703	exon27	c.A3493T	p.I1165F	GCAGGAATTAAAA	.	scavenged	Atlas-SNP
ANK3	288	hgsc.bcm.edu	37	10	61868716	61868716	+	Silent	SNP	C	C	A	rs3750800	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100	46	93	0	0.46	0	C|0.791;A|0.209	0.209	strong	.	ANK3	703	.	NM_001204404	exon28	c.G3048T	p.T1016T	GGGGGCCGTACAC	.	PASS	Atlas-SNP
UBE4B	10277	hgsc.bcm.edu	37	1	10190575	10190575	+	Missense_Mutation	SNP	G	G	C	rs61760196	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	167	70	180	0	0.419162	0	G|0.961;C|0.039	0.039	strong	.	UBE4B	233	.	NM_001105562	exon13	c.G1713C	p.L571F	GCGGTTGTGGTTG	.	PASS	Atlas-SNP
GALNT14	79623	hgsc.bcm.edu	37	2	31348076	31348076	+	Missense_Mutation	SNP	G	G	A	rs41280621	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	36	15	37	0	0.416667	0	G|0.994;A|0.006	0.006	strong	.	GALNT14	103	.	NM_001253826	exon2	c.C173T	p.A58V	TGAGGCGCCCAAG	.	PASS	Atlas-SNP
CFHR3	10878	hgsc.bcm.edu	37	1	196759282	196759282	+	Missense_Mutation	SNP	C	C	T	rs379370	byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	301	9	318	2	0.0299003	0.00628931	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
TCEB3B	51224	hgsc.bcm.edu	37	18	44561630	44561630	+	Silent	SNP	C	C	T	rs61746775	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98	47	77	0	0.479592	0	C|0.933;T|0.067	0.067	strong	.	TCEB3B	141	.	NM_016427	exon1	c.G6A	p.A2A	CCCTGCCGCCATC	.	PASS	Atlas-SNP
LRRC16A	55604	hgsc.bcm.edu	37	6	25600968	25600968	+	Silent	SNP	G	G	A	rs10456324	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110	109	114	0	0.990909	0	G|0.607;A|0.393	0.393	strong	LRRC16A_ENST00000329474,NS,carcinoma,0,1	LRRC16A	168	1	NM_001173977	exon33	c.G3546A	p.A1182A	GTGTGCGCAGAAG	.	PASS	Atlas-SNP
SPSB1	80176	hgsc.bcm.edu	37	1	9416151	9416151	+	Silent	SNP	G	G	A	rs9435243	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	75	103	0	1	0	G|0.765;A|0.235	0.235	strong	.	SPSB1	22	.	NM_025106	exon2	c.G201A	p.V67V	CTTTGTGAAGGAG	.	PASS	Atlas-SNP
ZNF880	400713	hgsc.bcm.edu	37	19	52888049	52888049	+	Missense_Mutation	SNP	C	C	A	rs75346003	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	7	4	24	0	0.571429	0	C|0.872;A|0.128	0.128	strong	ZNF880,colon,carcinoma,-1,2	ZNF880	45	2	NM_001145434	exon4	c.C1216A	p.Q406K	GGAGAGCAACCTT	.	PASS	Atlas-SNP
TRAPPC12	51112	hgsc.bcm.edu	37	2	3391458	3391458	+	Missense_Mutation	SNP	G	G	A	rs200941005	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	46	34	43	0	0.73913	0	G|0.998;A|0.002	0.002	strong	.	.	.	.	NM_016030	exon2	c.G64A	p.A22T	CAGCTCGCGCCTC	.	PASS	Atlas-SNP
NRAP	4892	hgsc.bcm.edu	37	10	115412793	115412793	+	Silent	SNP	A	A	G	rs3737322	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	90	52	78	0	0.577778	0	A|0.676;G|0.324	0.324	strong	.	NRAP	208	.	NM_001261463	exon6	c.T471C	p.Y157Y	TTCTGTATATTCC	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1084821	1084821	+	Silent	SNP	T	T	C	rs10794288	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	121	121	105	0	1	0	T|0.699;C|0.301	0.301	strong	.	MUC2	614	.	NM_002457	exon20	c.T2616C	p.D872D	CTTTGATGGGAAG	.	PASS	Atlas-SNP
MAMDC2	256691	hgsc.bcm.edu	37	9	72723204	72723204	+	Missense_Mutation	SNP	G	G	A	rs139498917	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	125	63	149	0	0.504	0	G|0.999;A|0.001	0.001	strong	.	MAMDC2	55	.	NM_153267	exon3	c.G226A	p.E76K	CAGGCTGAGGAAT	.	PASS	Atlas-SNP
C9orf84	158401	hgsc.bcm.edu	37	9	114490229	114490229	+	Silent	SNP	T	T	G	rs10512411	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	132	65	129	0	0.492424	0	T|0.852;G|0.148	0.148	strong	C9orf84_ENST00000374287,NS,carcinoma,-2,2	C9orf84	207	2	NM_173521	exon11	c.A1326C	p.A442A	TTCTTTTGCCAGA	.	PASS	Atlas-SNP
APOBEC3H	164668	hgsc.bcm.edu	37	22	39496412	39496412	+	Silent	SNP	G	G	C	rs139294	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	58	58	69	0	1	0	G|0.464;C|0.536	0.536	strong	.	APOBEC3H	28	.	NM_001166003	exon2	c.G129C	p.T43T	GCCCACGAGAGGC	.	PASS	Atlas-SNP
CCDC38	120935	hgsc.bcm.edu	37	12	96292170	96292170	+	Missense_Mutation	SNP	C	C	G	rs75959092	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	289	137	358	0	0.474048	0	C|0.917;G|0.083	0.083	strong	.	CCDC38	45	.	NM_182496	exon7	c.G607C	p.V203L	TTTTCACTGCTTG	.	PASS	Atlas-SNP
UBR4	23352	hgsc.bcm.edu	37	1	19500088	19500088	+	Silent	SNP	A	A	G	rs41273197	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	112	59	78	0	0.526786	0	A|0.995;G|0.005	0.005	strong	.	UBR4	415	.	NM_020765	exon23	c.T3010C	p.L1004L	GTATCAAGAAGTA	.	PASS	Atlas-SNP
RSBN1L	222194	hgsc.bcm.edu	37	7	77365770	77365770	+	Silent	SNP	A	A	G	rs3764824	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	28	75	0	0.451613	0	A|0.466;G|0.534	0.534	strong	.	RSBN1L	74	.	NM_198467	exon2	c.A630G	p.E210E	AAAAGAAAGAGAA	.	PASS	Atlas-SNP
CWF19L2	143884	hgsc.bcm.edu	37	11	107309826	107309826	+	Silent	SNP	C	C	T	rs201136952	by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	32	8	44	0	0.25	0	C|1.000;T|0.000	0.000	strong	CWF19L2_ENST00000282251,NS,carcinoma,0,2	CWF19L2	135	2	NM_152434	exon6	c.G654A	p.S218S	AGTAATCGATGAC	.	PASS	Atlas-SNP
OR2T34	127068	hgsc.bcm.edu	37	1	248737595	248737595	+	Missense_Mutation	SNP	A	A	G	rs79056151	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	448	94	369	0	0.209821	0	A|0.500;G|0.500	0.500	weak	OR2T34,NS,carcinoma,0,2	OR2T34	72	2	NM_001001821	exon1	c.T464C	p.V155A	CCCAAAACCCAGC	.	scavenged	Atlas-SNP
ZNF280C	55609	hgsc.bcm.edu	37	X	129349295	129349295	+	Silent	SNP	T	T	G	rs209238	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	21	74	0	0.259259	0	0|0.003;G|0.509	0.509	strong	.	ZNF280C	63	.	NM_017666	exon15	c.A1851C	p.G617G	GTGAATTCCCCGA	.	PASS	Atlas-SNP
TACC2	10579	hgsc.bcm.edu	37	10	123846860	123846860	+	Silent	SNP	C	C	T	rs11599291	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	90	38	85	0	0.422222	0	C|0.767;T|0.233	0.233	strong	TACC2,colon,carcinoma,0,1	TACC2	271	1	NM_206862	exon4	c.C4845T	p.P1615P	TGGTCCCGGGGAC	.	PASS	Atlas-SNP
PRKCI	5584	hgsc.bcm.edu	37	3	169988286	169988286	+	Silent	SNP	C	C	T	rs56257047	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69	33	87	0	0.478261	0	C|0.886;T|0.114	0.114	strong	.	PRKCI	82	.	NM_002740	exon6	c.C528T	p.L176L	CAAACTCTTGGTT	.	PASS	Atlas-SNP
UHRF1BP1	54887	hgsc.bcm.edu	37	6	34789443	34789443	+	Missense_Mutation	SNP	C	C	G	rs369670668		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	114	14	115	0	0.122807	0	.	.	weak	.	UHRF1BP1	102	.	NM_017754	exon2	c.C58G	p.L20V	AAGAATCTTTCCC	.	PASS	Atlas-SNP
COL20A1	57642	hgsc.bcm.edu	37	20	61944253	61944253	+	Silent	SNP	G	G	A	rs376373104		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	156	73	144	0	0.467949	0	.	.	weak	.	COL20A1	137	.	NM_020882	exon16	c.G2043A	p.T681T	GATCACGTGGACG	.	PASS	Atlas-SNP
MEGF11	84465	hgsc.bcm.edu	37	15	66411441	66411441	+	Missense_Mutation	SNP	C	C	T	rs16949528	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	34	22	34	0	0.647059	0	C|0.642;T|0.358	0.358	strong	.	MEGF11	70	.	NM_032445	exon4	c.G284A	p.S95N	TCTCCGCTCTCAT	.	PASS	Atlas-SNP
DNAH6	1768	hgsc.bcm.edu	37	2	84880695	84880695	+	Silent	SNP	G	G	A	rs12992282	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48	17	68	0	0.354167	0	G|0.925;A|0.075	0.075	strong	.	DNAH6	194	.	NM_001370	exon34	c.G5331A	p.G1777G	ACTTGGGATAGAA	.	PASS	Atlas-SNP
AHRR	57491	hgsc.bcm.edu	37	5	434722	434722	+	Missense_Mutation	SNP	G	G	C	rs34453673	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85	43	77	0	0.505882	0	G|0.808;C|0.192	0.192	strong	AHRR,colon,carcinoma,0,1	AHRR	67	1	NM_020731	exon12	c.G1933C	p.D645H	CCCACAGACGGCC	.	PASS	Atlas-SNP
QRICH2	84074	hgsc.bcm.edu	37	17	74289908	74289908	+	Silent	SNP	A	A	G	rs6501883	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	30	76	0	0.37037	0	A|0.557;G|0.443	0.443	strong	.	QRICH2	143	.	NM_032134	exon4	c.T402C	p.S134S	TTCCCTACTGGAA	.	PASS	Atlas-SNP
CALD1	800	hgsc.bcm.edu	37	7	134645319	134645319	+	Silent	SNP	C	C	T	rs2230186	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	123	66	169	0	0.536585	0	C|0.964;T|0.036	0.036	strong	.	CALD1	150	.	NM_033138	exon13	c.C2235T	p.R745R	TAGCCGCATCAAT	.	PASS	Atlas-SNP
ZNF461	92283	hgsc.bcm.edu	37	19	37129806	37129806	+	Missense_Mutation	SNP	G	G	A	rs61746529	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	58	30	61	0	0.517241	0	G|0.967;A|0.033	0.033	strong	.	ZNF461	73	.	NM_153257	exon6	c.C1441T	p.H481Y	GTGAATGAAGTCT	.	PASS	Atlas-SNP
SDC2	6383	hgsc.bcm.edu	37	8	97605800	97605800	+	Silent	SNP	C	C	T	rs1126681	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	28	56	0	0.528302	0	C|0.804;T|0.196	0.196	strong	SDC2,NS,carcinoma,0,2	SDC2	33	2	NM_002998	exon2	c.C153T	p.Y51Y	TGACTACGCTTCT	.	PASS	Atlas-SNP
TTI1	9675	hgsc.bcm.edu	37	20	36624780	36624780	+	Missense_Mutation	SNP	C	C	T	rs34900517	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	23	12	32	0	0.521739	0	C|0.975;T|0.025	0.025	strong	.	TTI1	104	.	NM_014657	exon8	c.G3083A	p.R1028K	TACCTCCTGGCAG	.	PASS	Atlas-SNP
CFHR1	3078	hgsc.bcm.edu	37	1	196801078	196801078	+	Silent	SNP	A	A	T	rs61743621	byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	494	205	264	0	0.41498	0	A|0.604;T|0.396	0.396	strong	CFHR1,right_upper_lobe,carcinoma,+1,1	CFHR1	47	1	NM_002113	exon6	c.A942T	p.R314R	ATTGCGAACAACA	.	PASS	Atlas-SNP
LGALS9	3965	hgsc.bcm.edu	37	17	25970642	25970642	+	Missense_Mutation	SNP	A	A	T	rs361498	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	259	120	249	0	0.46332	0	A|0.874;T|0.126	0.126	strong	.	LGALS9	29	.	NM_009587	exon5	c.A536T	p.Q179L	GCAGACAAAAAGT	.	PASS	Atlas-SNP
WDR62	284403	hgsc.bcm.edu	37	19	36593915	36593915	+	Missense_Mutation	SNP	T	T	G	rs61741470	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	116	58	110	0	0.5	0	T|0.959;G|0.041	0.041	strong	.	WDR62	102	.	NM_001083961	exon28	c.T3401G	p.M1134R	AGCTCATGGACCG	.	PASS	Atlas-SNP
ZNF567	163081	hgsc.bcm.edu	37	19	37209866	37209866	+	Silent	SNP	T	T	C	rs34642314	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	29	65	0	0.537037	0	T|0.917;C|0.083	0.083	strong	.	ZNF567	61	.	NM_152603	exon4	c.T147C	p.A49A	GAAAGCTGAAGAC	.	PASS	Atlas-SNP
TOP3A	7156	hgsc.bcm.edu	37	17	18193941	18193941	+	Silent	SNP	G	G	A	rs2230154	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91	48	70	0	0.527473	0	G|0.757;A|0.243	0.243	strong	TOP3A,NS,carcinoma,0,1	TOP3A	85	1	NM_004618	exon13	c.C1527T	p.D509D	CTCCCCGTCCACC	.	PASS	Atlas-SNP
SACS	26278	hgsc.bcm.edu	37	13	23930055	23930055	+	Missense_Mutation	SNP	A	A	T	rs2031640	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	200	94	226	1	0.47	0.00442478	A|0.907;T|0.093	0.093	strong	.	SACS	871	.	NM_014363	exon8	c.T696A	p.N232K	TTTGAGATTCCAA	.	PASS	Atlas-SNP
INTS1	26173	hgsc.bcm.edu	37	7	1533513	1533513	+	Silent	SNP	A	A	G	rs2251226	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	188	95	202	1	0.505319	0.00495049	A|0.379;G|0.621	0.621	strong	.	INTS1	145	.	NM_001080453	exon15	c.T1945C	p.L649L	CCTCCAAAATGGG	.	PASS	Atlas-SNP
HSD17B14	51171	hgsc.bcm.edu	37	19	49339098	49339098	+	Missense_Mutation	SNP	T	T	C	rs8110220	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	38	16	49	0	0.421053	0	C|0.335;N|0.001	0.335	strong	.	HSD17B14	25	.	NM_016246	exon2	c.A91G	p.N31D	CGCTGTTCACTGA	.	PASS	Atlas-SNP
C2orf54	79919	hgsc.bcm.edu	37	2	241834907	241834907	+	Missense_Mutation	SNP	C	C	T	rs4359646	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	103	42	112	0	0.407767	0	C|0.838;T|0.162	0.162	strong	.	C2orf54	14	.	NM_001085437	exon1	c.G508A	p.A170T	CTGGTGCGATGAG	.	PASS	Atlas-SNP
PSMD3	5709	hgsc.bcm.edu	37	17	38146154	38146154	+	Silent	SNP	T	T	C	rs9916279	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	40	28	33	0	0.7	0	T|0.798;C|0.202	0.202	strong	.	PSMD3	56	.	NM_002809	exon5	c.T849C	p.N283N	CAACAATGAGTGG	.	PASS	Atlas-SNP
TULP3	7289	hgsc.bcm.edu	37	12	3049698	3049698	+	Missense_Mutation	SNP	T	T	C	rs998814	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	39	91	0	0.527027	0	A|0.008;C|0.256	0.256	strong	.	TULP3	45	.	NM_001160408	exon12	c.T1312C	p.C438R	CCAGAATGTATCC	.	PASS	Atlas-SNP
LLGL1	3996	hgsc.bcm.edu	37	17	18137141	18137141	+	Missense_Mutation	SNP	A	A	G	rs2290505	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	97	49	86	0	0.505155	0	A|0.229;G|0.771	0.771	strong	LLGL1,rectum,carcinoma,0,1	LLGL1	61	1	NM_004140	exon5	c.A442G	p.S148G	GCTGCCAGCGACA	.	PASS	Atlas-SNP
TACC2	10579	hgsc.bcm.edu	37	10	123846485	123846485	+	Silent	SNP	A	A	G	rs4751871	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	26	61	0	0.490566	0	A|0.762;G|0.238	0.238	strong	.	TACC2	271	.	NM_206862	exon4	c.A4470G	p.Q1490Q	TCTGCAAGATCCA	.	PASS	Atlas-SNP
MOB3C	148932	hgsc.bcm.edu	37	1	47080665	47080665	+	Missense_Mutation	SNP	C	C	T	rs11211328	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94	39	115	0	0.414894	0	C|0.743;T|0.257	0.257	strong	.	MOB3C	1	.	NM_145279	exon1	c.G84A	p.M28I	CTCATCCATCCCG	.	PASS	Atlas-SNP
RTN3	10313	hgsc.bcm.edu	37	11	63449125	63449125	+	Missense_Mutation	SNP	C	C	A	rs11551944	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	45	22	41	0	0.488889	0	C|0.903;A|0.097	0.097	strong	RTN3_ENST00000356000,NS,carcinoma,0,3	RTN3	104	3	NM_201428	exon1	c.C17A	p.A6E	CGTCGGCGGCCAC	.	PASS	Atlas-SNP
TAS2R31	259290	hgsc.bcm.edu	37	12	11183708	11183708	+	Missense_Mutation	SNP	T	T	C	rs80125932	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	158	25	192	0	0.158228	0	T|0.871;C|0.129	0.129	strong	.	TAS2R31	24	.	NM_176885	exon1	c.A227G	p.Y76C	ACACTATAAAAAG	.	PASS	Atlas-SNP
AKAP6	9472	hgsc.bcm.edu	37	14	33293531	33293531	+	Missense_Mutation	SNP	T	T	A	rs4647899	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	128	62	154	0	0.484375	0	T|0.722;A|0.278	0.278	strong	.	AKAP6	308	.	NM_004274	exon13	c.T6512A	p.F2171Y	CTTGTTTCTCTAG	.	PASS	Atlas-SNP
TGFBI	7045	hgsc.bcm.edu	37	5	135388663	135388663	+	Silent	SNP	A	A	G	rs1054124	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	133	58	135	0	0.43609	0	A|0.650;G|0.350	0.350	strong	.	TGFBI	76	.	NM_000358	exon8	c.A981G	p.V327V	GTCTGTAGAGACC	.	PASS	Atlas-SNP
CYP4A22	284541	hgsc.bcm.edu	37	1	47607281	47607281	+	Missense_Mutation	SNP	C	C	T	rs12564525	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	146	72	140	0	0.493151	0	C|0.715;T|0.285	0.285	strong	.	CYP4A22	60	.	NM_001010969	exon3	c.C376T	p.R126W	GCTCCACGGATTG	.	PASS	Atlas-SNP
COL18A1	80781	hgsc.bcm.edu	37	21	46924389	46924389	+	Silent	SNP	C	C	T	rs11544971	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	18	11	25	0	0.611111	0	C|0.985;T|0.015	0.015	strong	.	COL18A1	129	.	NM_030582	exon33	c.C3327T	p.G1109G	CGGGGGCGGCGGT	.	PASS	Atlas-SNP
CLPSL1	340204	hgsc.bcm.edu	37	6	35755658	35755658	+	Silent	SNP	A	A	G	rs12211728	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	45	55	0	0.833333	0	A|0.641;G|0.359	0.359	strong	.	.	.	.	NM_001010886	exon3	c.A237G	p.Q79Q	TGGCCAATATAGA	.	PASS	Atlas-SNP
ULK4	54986	hgsc.bcm.edu	37	3	41952852	41952852	+	Missense_Mutation	SNP	T	T	C	rs35263917	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	195	97	211	0	0.497436	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
PCDHGB3	56102	hgsc.bcm.edu	37	5	140750517	140750517	+	Silent	SNP	C	C	T	rs78666647	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	132	63	135	0	0.477273	0	C|0.977;T|0.023	0.023	strong	.	PCDHGB3	168	.	NM_018924	exon1	c.C556T	p.L186L	GAGAACCTGGATG	.	PASS	Atlas-SNP
PVRL1	5818	hgsc.bcm.edu	37	11	119549473	119549473	+	Missense_Mutation	SNP	C	C	T	rs200377205	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	40	9	34	0	0.225	0	C|0.996;T|0.005	0.005	weak	.	PVRL1	133	.	NM_002855	exon2	c.G82A	p.V28I	AGTGGACGCCTGG	.	PASS	Atlas-SNP
ABRA	137735	hgsc.bcm.edu	37	8	107782335	107782335	+	Silent	SNP	G	G	A	rs11996457	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	37	70	1	0.493333	0.0142857	G|0.710;A|0.290	0.290	strong	ABRA,NS,adenoma,0,1	ABRA	57	1	NM_139166	exon1	c.C84T	p.S28S	GGCCAAGCTGATG	.	scavenged	Atlas-SNP
ITSN1	6453	hgsc.bcm.edu	37	21	35239562	35239562	+	Missense_Mutation	SNP	A	A	G	rs56279221	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	124	68	70	0	0.548387	0	A|0.937;G|0.063	0.063	strong	.	ITSN1	166	.	NM_003024	exon33	c.A4100G	p.K1367R	GGTGTAAAGGGAT	.	PASS	Atlas-SNP
USP36	57602	hgsc.bcm.edu	37	17	76814782	76814782	+	Silent	SNP	G	G	A	rs35273233	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	99	99	106	0	1	0	G|0.848;A|0.152	0.152	strong	.	USP36	243	.	NM_025090	exon10	c.C990T	p.R330R	GGCAAAGCGCTTG	.	PASS	Atlas-SNP
LAMA5	3911	hgsc.bcm.edu	37	20	60897772	60897772	+	Missense_Mutation	SNP	T	T	C	rs6143021	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72	22	83	0	0.305556	0	T|0.787;C|0.213	0.213	strong	.	LAMA5	268	.	NM_005560	exon46	c.A6107G	p.H2036R	CCGCTGTGGGGGT	.	PASS	Atlas-SNP
HSPG2	3339	hgsc.bcm.edu	37	1	22163390	22163390	+	Silent	SNP	G	G	A	rs35444472	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	24	11	34	0	0.458333	0	A|0.098;C|0.000;G|0.902;T|0.000	0.098	strong	.	HSPG2	311	.	NM_005529	exon75	c.C10260T	p.H3420H	AGCACAGTGGAAC	.	PASS	Atlas-SNP
ACSF2	80221	hgsc.bcm.edu	37	17	48539035	48539035	+	Silent	SNP	T	T	C	rs9674937	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	140	61	147	0	0.435714	0	T|0.644;C|0.356	0.356	strong	.	ACSF2	46	.	NM_025149	exon4	c.T495C	p.Y165Y	GGAGTATGTCCTC	.	PASS	Atlas-SNP
HNRNPCL1	343069	hgsc.bcm.edu	37	1	12907533	12907533	+	Missense_Mutation	SNP	T	T	C	rs141872266	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	197	49	166	0	0.248731	0	T|0.959;C|0.041	0.041	strong	HNRNPCL1,NS,carcinoma,0,1	HNRNPCL1	68	1	NM_001013631	exon2	c.A610G	p.I204V	TTTCAATTTTTTC	.	PASS	Atlas-SNP
FFAR3	2865	hgsc.bcm.edu	37	19	35850520	35850520	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	932	10	723	2	0.0107296	0.00276625	.	.	none	FFAR3,NS,carcinoma,-1,1	FFAR3	40	1	NM_005304	exon2	c.T728C	p.V243A	ACAACGTGTCCCA	.	scavenged	Atlas-SNP
RPAP1	26015	hgsc.bcm.edu	37	15	41829230	41829230	+	Silent	SNP	A	A	G	rs721772	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	16	117	0	0.225352	0	A|0.592;G|0.408	0.408	strong	.	RPAP1	111	.	NM_015540	exon2	c.T94C	p.L32L	TCACCAACTGCAC	.	PASS	Atlas-SNP
ENTPD6	955	hgsc.bcm.edu	37	20	25187213	25187213	+	Missense_Mutation	SNP	G	G	A	rs2076559	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	77	27	92	0	0.350649	0	G|0.702;A|0.298	0.298	strong	.	ENTPD6	57	.	NM_001247	exon2	c.G41A	p.S14N	AAACGAGCTACAT	.	PASS	Atlas-SNP
ZNF366	167465	hgsc.bcm.edu	37	5	71757266	71757266	+	Missense_Mutation	SNP	T	T	C	rs74460472	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	31	52	0	0.596154	0	T|0.950;C|0.050	0.050	strong	.	ZNF366	108	.	NM_152625	exon2	c.A58G	p.K20E	TCTTCTTCACAGC	.	PASS	Atlas-SNP
PPARGC1A	10891	hgsc.bcm.edu	37	4	23815662	23815662	+	Missense_Mutation	SNP	C	C	T	rs8192678	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	36	99	0	0.486486	0	C|0.724;T|0.276	0.276	strong	.	PPARGC1A	129	.	NM_013261	exon8	c.G1444A	p.G482S	GTTCACCGGTCTT	.	PASS	Atlas-SNP
SYNDIG1L	646658	hgsc.bcm.edu	37	14	74876181	74876181	+	Silent	SNP	T	T	G	rs12590672	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51	25	51	0	0.490196	0	T|0.508;G|0.492	0.492	strong	.	SYNDIG1L	24	.	NM_001105579	exon2	c.A267C	p.T89T	GAAGCTTGTCTCA	.	PASS	Atlas-SNP
EP400	57634	hgsc.bcm.edu	37	12	132504639	132504639	+	Silent	SNP	C	C	T	rs147615479	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48	30	57	0	0.625	0	C|0.994;T|0.006	0.006	strong	.	EP400	370	.	NM_015409	exon22	c.C4323T	p.T1441T	TCGCACCGTGGCT	.	PASS	Atlas-SNP
ZNF860	344787	hgsc.bcm.edu	37	3	32031962	32031962	+	Missense_Mutation	SNP	A	A	G	rs1808125	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	27	26	41	0	0.962963	0	A|0.545;G|0.455	0.455	strong	ZNF860_ENST00000360311,NS,carcinoma,0,6	ZNF860	96	6	NM_001137674	exon2	c.A1391G	p.H464R	CCTTCCATCACAA	.	PASS	Atlas-SNP
VPS13C	54832	hgsc.bcm.edu	37	15	62253791	62253791	+	Missense_Mutation	SNP	T	T	C	rs2303405	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	56	27	59	1	0.482143	0.0169492	T|0.942;C|0.058	0.058	strong	VPS13C,NS,carcinoma,0,1	VPS13C	506	1	NM_020821	exon35	c.A3905G	p.Y1302C	TACCTATAAAGTG	.	scavenged	Atlas-SNP
ITIH5	80760	hgsc.bcm.edu	37	10	7622009	7622009	+	Missense_Mutation	SNP	G	G	A	rs41298373	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	26	10	25	0	0.384615	0	G|0.929;A|0.071	0.071	strong	.	ITIH5	343	.	NM_001001851	exon9	c.C1127T	p.A376V	TGCAGGGCCCCGT	.	PASS	Atlas-SNP
STPG2	285555	hgsc.bcm.edu	37	4	98902403	98902403	+	Missense_Mutation	SNP	T	T	C	rs76740552	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	92	56	134	0	0.608696	0	T|0.994;C|0.006	0.006	strong	.	.	.	.	NM_174952	exon6	c.A679G	p.K227E	AAGACTTGAGAGC	.	PASS	Atlas-SNP
MCM9	254394	hgsc.bcm.edu	37	6	119137011	119137011	+	Missense_Mutation	SNP	G	G	A	rs35917528	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	30	15	25	0	0.5	0	G|0.926;A|0.074	0.074	strong	.	MCM9	73	.	NM_017696	exon12	c.C2408T	p.P803L	TCTCCTGGTGATG	.	PASS	Atlas-SNP
BCL2A1	597	hgsc.bcm.edu	37	15	80263217	80263217	+	Missense_Mutation	SNP	C	C	T	rs3826007	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	209	115	200	1	0.550239	0.005	C|0.805;T|0.195	0.195	strong	.	BCL2A1	28	.	NM_001114735	exon1	c.G245A	p.G82D	ATGATGCCGTCTT	.	PASS	Atlas-SNP
PIK3CG	5294	hgsc.bcm.edu	37	7	106524689	106524689	+	Silent	SNP	C	C	T	rs2230460	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	119	60	104	0	0.504202	0	C|0.901;N|0.000	.	strong	.	PIK3CG	279	.	NM_002649	exon9	c.C2850T	p.D950D	CAATGACAATATT	.	PASS	Atlas-SNP
DNASE1L3	1776	hgsc.bcm.edu	37	3	58191266	58191266	+	Silent	SNP	C	C	T	rs2070117	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	113	54	110	0	0.477876	0	C|0.747;T|0.253	0.253	strong	.	DNASE1L3	36	.	NM_004944	exon3	c.G252A	p.T84T	GTTGTACGTTATG	.	PASS	Atlas-SNP
LRRC37A2	474170	hgsc.bcm.edu	37	17	44626866	44626866	+	Missense_Mutation	SNP	T	T	C	rs62073248		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	158	61	72	0	0.386076	0	.	.	weak	LRRC37A2,NS,carcinoid-endocrine_tumour,0,1	LRRC37A2	37	1	NM_001006607	exon9	c.T4361C	p.L1454P	CTGACCTGTCCCC	.	scavenged	Atlas-SNP
IPO4	79711	hgsc.bcm.edu	37	14	24653523	24653523	+	Missense_Mutation	SNP	G	G	C	rs11550452	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	95	40	90	0	0.421053	0	G|0.693;C|0.307	0.307	strong	.	IPO4	74	.	NM_024658	exon17	c.C1738G	p.P580A	AGTCAGGGTCGTC	.	PASS	Atlas-SNP
DNAH5	1767	hgsc.bcm.edu	37	5	13864728	13864728	+	Silent	SNP	C	C	A	rs6554827	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	102	51	105	0	0.5	0	C|0.626;A|0.374	0.374	strong	DNAH5,NS,carcinoma,0,1	DNAH5	868	1	NM_001369	exon28	c.G4374T	p.R1458R	CAAGGCCCGGGGA	.	PASS	Atlas-SNP
LGMN	5641	hgsc.bcm.edu	37	14	93199080	93199080	+	Missense_Mutation	SNP	C	C	T	rs2236264	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93	46	95	0	0.494624	0	T|0.202;G|0.005	0.202	strong	.	LGMN	28	.	NM_005606	exon2	c.G52A	p.V18I	TAGGAACGGCACC	.	PASS	Atlas-SNP
TRPV1	7442	hgsc.bcm.edu	37	17	3486702	3486702	+	Missense_Mutation	SNP	G	G	A	rs224534	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	25	75	0	0.480769	0	G|0.613;A|0.387	0.387	strong	.	TRPV1	99	.	NM_018727	exon9	c.C1406T	p.T469I	TCTCCAGTTTTTT	.	PASS	Atlas-SNP
GRHL2	79977	hgsc.bcm.edu	37	8	102570830	102570830	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	119	33	101	0	0.277311	0	.	.	none	GRHL2,right_lower_lobe,carcinoma,0,1	GRHL2	68	1	NM_024915	exon4	c.G468A	p.T156T	AATCACGGTGGTG	.	PASS	Atlas-SNP
PBOV1	59351	hgsc.bcm.edu	37	6	138539315	138539315	+	Missense_Mutation	SNP	A	A	G	rs6927706	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	236	110	221	0	0.466102	0	A|0.855;G|0.145	0.145	strong	.	PBOV1	12	.	NM_021635	exon1	c.T218C	p.I73T	TGTTCTATGGAAT	.	PASS	Atlas-SNP
WAPAL	23063	hgsc.bcm.edu	37	10	88277457	88277457	+	Missense_Mutation	SNP	C	C	T	rs10887621	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	128	70	101	0	0.546875	0	C|0.796;T|0.204	0.204	strong	.	WAPAL	81	.	NM_015045	exon2	c.G370A	p.V124I	CTTCAACGACCAC	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179406191	179406191	+	Missense_Mutation	SNP	C	C	T	rs3731749	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	179	95	206	0	0.530726	0	C|0.822;T|0.178	0.178	strong	.	TTN	18412	.	NM_001267550	exon350	c.G97613A	p.R32538H	TCTTTGCGCTCCA	.	PASS	Atlas-SNP
OR51G1	79324	hgsc.bcm.edu	37	11	4945233	4945233	+	Missense_Mutation	SNP	C	C	T	rs35264256	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48	20	56	0	0.416667	0	C|0.912;T|0.088	0.088	strong	.	OR51G1	74	.	NM_001005237	exon1	c.G337A	p.E113K	ATGACTCCATTGA	.	PASS	Atlas-SNP
SYT15	83849	hgsc.bcm.edu	37	10	46969312	46969312	+	Missense_Mutation	SNP	G	G	A	rs55894256	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	65	17	98	0	0.261538	0	G|0.950;A|0.050	0.050	strong	SYT15_ENST00000416127,NS,carcinoma,0,3	SYT15	165	3	NM_031912	exon2	c.C149T	p.T50I	GCAGCTGTGGTGG	.	PASS	Atlas-SNP
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32629868	32629868	+	Silent	SNP	A	A	G	rs1049088	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72	16	55	0	0.222222	0	G|0.171;A|0.829	0.171	strong	.	HLA-DQB1	15	.	NM_002123	exon3	c.T537C	p.L179L	CCTAATAAGGGGG	.	PASS	Atlas-SNP
KLHL38	340359	hgsc.bcm.edu	37	8	124663987	124663987	+	Missense_Mutation	SNP	C	C	G	rs16898691	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	29	75	0	0.557692	0	C|0.903;G|0.097	0.097	strong	.	KLHL38	81	.	NM_001081675	exon1	c.G1180C	p.G394R	CCTGCCCTTCTCC	.	PASS	Atlas-SNP
PTGS2	5743	hgsc.bcm.edu	37	1	186648197	186648197	+	Silent	SNP	C	C	G	rs5277	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	101	51	108	1	0.504951	0.00925926	C|0.882;G|0.118	0.118	strong	PTGS2_ENST00000367468,NS,carcinoma,0,1	PTGS2	144	1	NM_000963	exon3	c.G306C	p.V102V	TGTCAACACATAA	.	scavenged	Atlas-SNP
AKAP1	8165	hgsc.bcm.edu	37	17	55182878	55182878	+	Missense_Mutation	SNP	C	C	T	rs17761023	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	108	57	125	0	0.527778	0	C|0.928;T|0.072	0.072	strong	AKAP1,NS,carcinoma,-1,1	AKAP1	73	1	NM_001242902	exon3	c.C53T	p.A18V	TGCTGGCGCTCCT	.	PASS	Atlas-SNP
LANCL3	347404	hgsc.bcm.edu	37	X	37518806	37518806	+	Silent	SNP	C	C	T	rs12009345	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72	18	55	0	0.25	0	C|0.681;0|0.003	.	strong	.	LANCL3	42	.	NM_001170331	exon3	c.C789T	p.S263S	GCAGAGCGTGGAC	.	PASS	Atlas-SNP
PPP2R5A	5525	hgsc.bcm.edu	37	1	212515613	212515613	+	Silent	SNP	C	C	T	rs1774249	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	95	52	97	0	0.547368	0	C|0.701;T|0.299	0.299	strong	.	PPP2R5A	48	.	NM_006243	exon4	c.C564T	p.F188F	GAAATTCGTACAA	.	PASS	Atlas-SNP
ANAPC1	64682	hgsc.bcm.edu	37	2	112615933	112615933	+	Silent	SNP	T	T	C	rs78683369	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	211	66	304	0	0.312796	0	.	.	weak	ANAPC1,NS,carcinoma,0,1	ANAPC1	116	1	NM_022662	exon11	c.A1308G	p.L436L	CCCACATAGGTCA	.	PASS	Atlas-SNP
SEC24C	9632	hgsc.bcm.edu	37	10	75506674	75506674	+	Silent	SNP	T	T	C	rs2306325	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93	48	80	0	0.516129	0	T|0.851;C|0.149	0.149	strong	SEC24C,NS,carcinoma,0,1	SEC24C	86	1	NM_198597	exon2	c.T84C	p.Y28Y	CAGCTATGGTGGG	.	PASS	Atlas-SNP
TIAM2	26230	hgsc.bcm.edu	37	6	155458562	155458562	+	Silent	SNP	C	C	T	rs374521659		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	33	89	0	0.383721	0	.	.	weak	.	TIAM2	161	.	NM_012454	exon4	c.C1446T	p.T482T	AGAAACCGCCGAG	.	PASS	Atlas-SNP
FCRL3	115352	hgsc.bcm.edu	37	1	157670258	157670258	+	Missense_Mutation	SNP	G	G	C	rs201961888	by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	132	43	163	0	0.325758	0	G|1.000;C|0.000	0.000	strong	.	FCRL3	163	.	NM_052939	exon2	c.C22G	p.L8V	GGATCAGCAGCAG	.	PASS	Atlas-SNP
ABP1	26	hgsc.bcm.edu	37	7	150557622	150557622	+	Silent	SNP	G	G	A	rs12179	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	21	61	0	0.333333	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
FANCI	55215	hgsc.bcm.edu	37	15	89804043	89804043	+	Missense_Mutation	SNP	C	C	T	rs17803620	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	112	45	117	0	0.401786	0	C|0.726;T|0.274	0.274	strong	.	FANCI	129	.	NM_001113378	exon4	c.C257T	p.A86V	AAATAGCGTCTGA	.	PASS	Atlas-SNP
HIST1H2BK	85236	hgsc.bcm.edu	37	6	27114488	27114488	+	Silent	SNP	G	G	C	rs12207760	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	103	12	106	0	0.116505	0	G|0.965;C|0.035	0.035	strong	HIST1H2BK_ENST00000396891,NS,carcinoma,0,2	HIST1H2BK	68	2	NM_080593	exon1	c.C90G	p.R30R	GCGCTTGCGCTTC	.	PASS	Atlas-SNP
PCNXL4	64430	hgsc.bcm.edu	37	14	60591887	60591887	+	Missense_Mutation	SNP	G	G	A	rs167437	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	284	282	279	0	0.992958	0	G|0.700;A|0.300	0.300	strong	.	.	.	.	NM_022495	exon8	c.G2296A	p.G766S	GTTTACGGTGGTG	.	PASS	Atlas-SNP
SPESP1	246777	hgsc.bcm.edu	37	15	69238392	69238392	+	Silent	SNP	T	T	C	rs3743092	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	156	66	135	0	0.423077	0	T|0.988;C|0.012	0.012	strong	.	SPESP1	39	.	NM_145658	exon2	c.T519C	p.Y173Y	TCCATATGTTACC	.	PASS	Atlas-SNP
EXD3	54932	hgsc.bcm.edu	37	9	140262426	140262426	+	Missense_Mutation	SNP	C	C	T	rs11533158	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44	44	28	0	1	0	C|0.308;T|0.692	0.692	strong	EXD3_ENST00000340951,colon,carcinoma,0,2	EXD3	86	2	NM_017820	exon6	c.G478A	p.A160T	ACGTCGCGCCCAG	.	PASS	Atlas-SNP
CARD9	64170	hgsc.bcm.edu	37	9	139266405	139266405	+	Silent	SNP	G	G	A	rs10781499	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	115	114	136	0	0.991304	0	G|0.634;A|0.366	0.366	strong	CARD9,NS,carcinoma,0,1	CARD9	47	1	NM_052813	exon2	c.C126T	p.P42P	ATCATCGGGGTTC	.	PASS	Atlas-SNP
SBNO2	22904	hgsc.bcm.edu	37	19	1127615	1127615	+	Silent	SNP	G	G	C	rs2074915	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	25	13	33	0	0.52	0	G|0.810;C|0.190	0.190	strong	SBNO2_ENST00000250872,NS,carcinoma,0,2	SBNO2	112	2	NM_014963	exon5	c.C429G	p.S143S	GTGGGTGGAGGGG	.	PASS	Atlas-SNP
ARNTL2	56938	hgsc.bcm.edu	37	12	27540204	27540204	+	Missense_Mutation	SNP	A	A	G	rs71541528	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	36	66	0	0.507042	0	A|0.970;G|0.030	0.030	strong	.	ARNTL2	54	.	NM_020183	exon7	c.A608G	p.K203R	GAGGAAAAATTCT	.	PASS	Atlas-SNP
SPTBN1	6711	hgsc.bcm.edu	37	2	54858664	54858664	+	Silent	SNP	C	C	T	rs2229503	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	58	32	67	0	0.551724	0	C|0.857;T|0.143	0.143	strong	.	SPTBN1	378	.	NM_003128	exon16	c.C3480T	p.N1160N	GGAGAACAGACAA	.	PASS	Atlas-SNP
FRMPD1	22844	hgsc.bcm.edu	37	9	37745413	37745413	+	Silent	SNP	G	G	A	rs3747541	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	97	49	77	0	0.505155	0	G|0.618;A|0.382	0.382	strong	.	FRMPD1	237	.	NM_014907	exon16	c.G3384A	p.E1128E	GGAGGAGTCTAGG	.	PASS	Atlas-SNP
PRKX	5613	hgsc.bcm.edu	37	X	3592797	3592797	+	Silent	SNP	C	C	A	rs56037462	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	101	27	56	0	0.267327	0	C|0.992;A|0.008	0.008	strong	.	PRKX	29	.	NM_005044	exon2	c.G177T	p.T59T	CCCGAACGTCCCA	.	PASS	Atlas-SNP
CPNE7	27132	hgsc.bcm.edu	37	16	89662990	89662990	+	Silent	SNP	T	T	C	rs694285	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	29	28	42	0	0.965517	0	T|0.654;C|0.346	0.346	strong	CPNE7,caecum,carcinoma,0,1	CPNE7	56	1	NM_014427	exon17	c.T1863C	p.G621G	CCTGGGTGTCCCT	.	PASS	Atlas-SNP
FLT1	2321	hgsc.bcm.edu	37	13	28964198	28964198	+	Silent	SNP	C	C	T	rs17537350	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	52	87	0	0.597701	0	C|0.951;T|0.049	0.049	strong	FLT1_ENST00000541932,colon,carcinoma,-1,2	FLT1	393	2	NM_002019	exon13	c.G1704A	p.T568T	TCCTTCCGTCGGC	.	PASS	Atlas-SNP
GPR98	84059	hgsc.bcm.edu	37	5	90024735	90024735	+	Missense_Mutation	SNP	G	G	A	rs2366928	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	104	46	94	0	0.442308	0	G|0.203;A|0.797	0.797	strong	.	GPR98	605	.	NM_032119	exon49	c.G10411A	p.E3471K	TTTGCCGAAAATG	.	PASS	Atlas-SNP
DCAF13	25879	hgsc.bcm.edu	37	8	104432545	104432545	+	Missense_Mutation	SNP	A	A	G	rs3134253	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	122	63	97	0	0.516393	0	A|0.768;G|0.232	0.232	strong	.	DCAF13	66	.	NM_015420	exon2	c.A580G	p.I194V	GAATATATAAGAG	.	PASS	Atlas-SNP
TGIF1	7050	hgsc.bcm.edu	37	18	3457539	3457539	+	Silent	SNP	A	A	G	rs2229337	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	101	39	104	0	0.386139	0	A|0.856;G|0.144	0.144	strong	.	TGIF1	41	.	NM_170695	exon3	c.A807G	p.P269P	GACCCCATTTCAT	.	PASS	Atlas-SNP
C11orf35	256329	hgsc.bcm.edu	37	11	557584	557584	+	Silent	SNP	G	G	A	rs11822657	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	28	73	0	0.41791	0	G|0.939;A|0.061	0.061	strong	.	C11orf35	22	.	NM_173573	exon6	c.C612T	p.A204A	GGTGGGGGCCTGA	.	PASS	Atlas-SNP
TNFRSF4	7293	hgsc.bcm.edu	37	1	1147422	1147422	+	Silent	SNP	C	C	T	rs17568	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	89	89	100	0	1	0	C|0.674;T|0.326	0.326	strong	.	TNFRSF4	12	.	NM_003327	exon5	c.G534A	p.E178E	CTGGGTCTCCTGG	.	PASS	Atlas-SNP
PRR22	163154	hgsc.bcm.edu	37	19	5783634	5783634	+	Silent	SNP	T	T	C	rs2446210	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	92	49	112	0	0.532609	0	T|0.612;C|0.388	0.388	strong	.	PRR22	25	.	NM_001134316	exon3	c.A624G	p.P208P	GGCGTCTGGGGGC	.	PASS	Atlas-SNP
CD101	9398	hgsc.bcm.edu	37	1	117576522	117576522	+	Missense_Mutation	SNP	A	A	T	rs34223095	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	65	36	83	0	0.553846	0	A|0.960;T|0.040	0.040	strong	.	CD101	95	.	NM_001256109	exon9	c.A2865T	p.L955F	CCCTTTACTCTAT	.	PASS	Atlas-SNP
ITGAX	3687	hgsc.bcm.edu	37	16	31374535	31374535	+	Missense_Mutation	SNP	C	C	G	rs2230429	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	88	88	75	0	1	0	C|0.671;G|0.329	0.329	strong	.	ITGAX	198	.	NM_000887	exon14	c.C1550G	p.P517R	GCCACCCCTGGGG	.	PASS	Atlas-SNP
SLC16A11	162515	hgsc.bcm.edu	37	17	6946357	6946357	+	Missense_Mutation	SNP	C	C	A	rs75636181	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	28	17	68	0	0.607143	0	C|0.967;A|0.033	0.033	strong	SLC16A11,NS,carcinoma,0,1	SLC16A11	25	1	NM_153357	exon2	c.G310T	p.A104S	GGCGGGCCCCCCA	.	PASS	Atlas-SNP
CYP2C8	1558	hgsc.bcm.edu	37	10	96798749	96798749	+	Missense_Mutation	SNP	T	T	C	rs10509681	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	42	93	0	0.552632	0	T|0.946;C|0.054	0.054	strong	.	CYP2C8	73	.	NM_000770	exon8	c.A1196G	p.K399R	AATTCTTTGTCAT	.	PASS	Atlas-SNP
BMS1	9790	hgsc.bcm.edu	37	10	43316099	43316099	+	Silent	SNP	T	T	C	rs61736599	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	322	171	326	0	0.531056	0	T|0.913;C|0.087	0.087	strong	.	BMS1	132	.	NM_014753	exon17	c.T2913C	p.Y971Y	AAAGTATACCCCA	.	PASS	Atlas-SNP
OR6B1	135946	hgsc.bcm.edu	37	7	143701516	143701516	+	Missense_Mutation	SNP	C	C	T	rs7787378	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	90	41	89	0	0.455556	0	C|0.853;N|0.000	.	strong	OR6B1,NS,carcinoma,-1,3	OR6B1	60	3	NM_001005281	exon1	c.C427T	p.R143C	TGCTTCCGCCTCG	.	PASS	Atlas-SNP
ZNF99	7652	hgsc.bcm.edu	37	19	22940899	22940899	+	Silent	SNP	G	G	A	rs59017672	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55	28	49	0	0.509091	0	A|0.316;G|0.683;T|0.001	0.316	strong	.	ZNF99	273	.	NM_001080409	exon4	c.C1812T	p.H604H	TGAGAAGTGGTTA	.	PASS	Atlas-SNP
CD200R1	131450	hgsc.bcm.edu	37	3	112643952	112643952	+	Silent	SNP	C	C	T	rs72491121	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	191	89	221	1	0.465969	0.00452489	C|0.954;T|0.046	0.046	strong	.	CD200R1	91	.	NM_138806	exon6	c.G858A	p.L286L	TTTCAACAACCAA	.	PASS	Atlas-SNP
FYCO1	79443	hgsc.bcm.edu	37	3	46008087	46008087	+	Silent	SNP	G	G	A	rs13079869	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	166	88	155	0	0.53012	0	G|0.920;A|0.080	0.080	strong	.	FYCO1	115	.	NM_024513	exon8	c.C2739T	p.C913C	CAGTGCGCAAACC	.	PASS	Atlas-SNP
EPPK1	83481	hgsc.bcm.edu	37	8	144943384	144943384	+	Silent	SNP	G	G	A	rs189024404	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48	30	37	0	0.625	0	G|0.988;A|0.012	0.012	strong	.	EPPK1	199	.	NM_031308	exon1	c.C4038T	p.L1346L	TGGCACGAGCCCC	.	PASS	Atlas-SNP
MRPL23	6150	hgsc.bcm.edu	37	11	1977552	1977552	+	Missense_Mutation	SNP	G	G	A	rs12812	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	40	18	39	0	0.45	0	G|0.874;A|0.126	0.126	strong	MRPL23,NS,carcinoma,0,1	MRPL23	14	1	NM_021134	exon5	c.G364A	p.A122T	GGCAGCGCTGCCG	.	PASS	Atlas-SNP
VSIG10	54621	hgsc.bcm.edu	37	12	118506186	118506186	+	Silent	SNP	A	A	T	rs67405503	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	190	97	217	0	0.510526	0	A|0.602;T|0.398	0.398	strong	.	VSIG10	41	.	NM_019086	exon8	c.T1563A	p.L521L	ACCTTGAAGATCC	.	PASS	Atlas-SNP
ZBTB20	26137	hgsc.bcm.edu	37	3	114058008	114058008	+	Silent	SNP	G	G	T	rs139619357	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	104	45	126	0	0.432692	0	G|0.999;T|0.001	0.001	strong	.	ZBTB20	157	.	NM_001164342	exon5	c.C2070A	p.T690T	AGGGGGGGTCCCA	.	PASS	Atlas-SNP
TNRC18	84629	hgsc.bcm.edu	37	7	5353253	5353253	+	Silent	SNP	G	G	T	rs140781391	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83	53	84	0	0.638554	0	G|0.907;T|0.093	0.093	strong	.	TNRC18	311	.	NM_001080495	exon27	c.C7269A	p.A2423A	TGCTGGGGCCAGG	.	PASS	Atlas-SNP
CARD8	22900	hgsc.bcm.edu	37	19	48722180	48722180	+	Silent	SNP	C	C	T	rs10500299	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	136	73	150	0	0.536765	0	C|0.758;T|0.242	0.242	strong	.	CARD8	53	.	NM_001184900	exon9	c.G1251A	p.E417E	AGTAATCTCAAGT	.	PASS	Atlas-SNP
TAS2R20	259295	hgsc.bcm.edu	37	12	11150214	11150214	+	Silent	SNP	G	G	A	rs11054142	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	58	28	73	0	0.482759	0	G|0.672;A|0.328	0.328	strong	.	TAS2R20	17	.	NM_176889	exon1	c.C261T	p.A87A	TGCCCAGGCATTA	.	PASS	Atlas-SNP
FLNC	2318	hgsc.bcm.edu	37	7	128477472	128477472	+	Silent	SNP	T	T	C	rs2291560	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49	15	47	0	0.306122	0	T|0.879;C|0.121	0.121	strong	.	FLNC	339	.	NM_001127487	exon4	c.T720C	p.I240I	GGAGATTGTGGAC	.	PASS	Atlas-SNP
UBASH3A	53347	hgsc.bcm.edu	37	21	43824106	43824106	+	Missense_Mutation	SNP	A	A	G	rs2277798	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	147	146	112	0	0.993197	0	A|0.427;G|0.573	0.573	strong	.	UBASH3A	72	.	NM_018961	exon1	c.A52G	p.S18G	CTCAAGAGCCGCA	.	PASS	Atlas-SNP
RNF213	57674	hgsc.bcm.edu	37	17	78355494	78355494	+	Missense_Mutation	SNP	C	C	G	rs61745599	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	35	22	38	0	0.628571	0	C|0.938;G|0.062	0.062	strong	.	RNF213	766	.	NM_001256071	exon57	c.C13945G	p.L4649V	CGCAGGCTTCTCC	.	PASS	Atlas-SNP
SSR3	6747	hgsc.bcm.edu	37	3	156266774	156266774	+	Silent	SNP	C	C	T	rs9296	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	30	61	0	0.47619	0	C|0.865;T|0.135	0.135	strong	.	SSR3	17	.	NM_007107	exon3	c.G279A	p.E93E	AGCATCCTCCCTC	.	PASS	Atlas-SNP
OR2T34	127068	hgsc.bcm.edu	37	1	248737511	248737511	+	Missense_Mutation	SNP	A	A	G	rs74461933		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	361	93	319	1	0.257618	0.0031348	.	.	weak	OR2T34,NS,haematopoietic_neoplasm,0,2	OR2T34	72	2	NM_001001821	exon1	c.T548C	p.F183S	TCACAGAAAAAAC	.	scavenged	Atlas-SNP
SCN9A	6335	hgsc.bcm.edu	37	2	167145142	167145142	+	Silent	SNP	A	A	G	rs13414203	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	13	11	39	0	0.846154	0	A|0.652;G|0.348	0.348	strong	.	SCN9A	296	.	NM_002977	exon10	c.T1119C	p.A373A	GCCAGCAGCACGC	.	PASS	Atlas-SNP
LRP1B	53353	hgsc.bcm.edu	37	2	141259283	141259283	+	Silent	SNP	G	G	A	rs35296183	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	27	22	38	0	0.814815	0	G|0.847;A|0.153	0.153	strong	.	LRP1B	1315	.	NM_018557	exon55	c.C8823T	p.D2941D	TTGACAGTCTTGA	.	PASS	Atlas-SNP
DUSP10	11221	hgsc.bcm.edu	37	1	221912808	221912808	+	Silent	SNP	T	T	C	rs1136448	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	130	127	120	0	0.976923	0	T|0.678;C|0.322	0.322	strong	.	DUSP10	64	.	NM_007207	exon2	c.A279G	p.Q93Q	TTGGGTTTGGGCC	.	PASS	Atlas-SNP
CEP44	80817	hgsc.bcm.edu	37	4	175238508	175238508	+	Silent	SNP	C	C	T	rs17358230	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	40	98	0	0.47619	0	C|0.975;T|0.025	0.025	strong	.	CEP44	35	.	NM_001040157	exon12	c.C1147T	p.L383L	GAGTTACTGAAAT	.	PASS	Atlas-SNP
ICAM5	7087	hgsc.bcm.edu	37	19	10402938	10402938	+	Missense_Mutation	SNP	G	G	A	rs1056538	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55	28	40	0	0.509091	0	G|0.719;A|0.281	0.281	strong	.	ICAM5	53	.	NM_003259	exon4	c.G901A	p.V301I	CAGCTGGTCTGCA	.	PASS	Atlas-SNP
NOP9	161424	hgsc.bcm.edu	37	14	24773387	24773387	+	Silent	SNP	T	T	C	rs2144494	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60	24	52	0	0.4	0	T|0.835;C|0.165	0.165	strong	.	.	.	.	NM_174913	exon8	c.T1551C	p.L517L	GTCCCTTGCCCAA	.	PASS	Atlas-SNP
TSHZ3	57616	hgsc.bcm.edu	37	19	31770506	31770506	+	Missense_Mutation	SNP	C	C	T	rs111618794	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	41	19	71	0	0.463415	0	C|0.998;T|0.002	0.002	strong	TSHZ3_ENST00000240587,NS,carcinoma,+2,1	TSHZ3	549	1	NM_020856	exon2	c.G193A	p.A65T	ACTCGGCGGCCGG	.	PASS	Atlas-SNP
MBD3L2	125997	hgsc.bcm.edu	37	19	7051588	7051588	+	Silent	SNP	G	G	A	rs76206324	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	178	77	54	0	0.432584	0	G|0.855;A|0.145	0.145	strong	.	MBD3L2	2	.	NM_144614	exon2	c.G582A	p.Q194Q	CTTGCAGGCAGAC	.	PASS	Atlas-SNP
SWT1	54823	hgsc.bcm.edu	37	1	185240474	185240474	+	Missense_Mutation	SNP	A	A	G	rs12041704	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	145	66	184	0	0.455172	0	A|0.637;G|0.363	0.363	strong	SWT1,NS,carcinoma,0,1	SWT1	88	1	NM_017673	exon17	c.A2461G	p.N821D	AACAGTAATTATC	.	PASS	Atlas-SNP
ZNF763	284390	hgsc.bcm.edu	37	19	12089903	12089903	+	Silent	SNP	G	G	A	rs112017572	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	19	13	17	0	0.684211	0	G|0.941;A|0.059	0.059	strong	ZNF763,caecum,carcinoma,+2,3	ZNF763	31	3	NM_001012753	exon4	c.G1173A	p.A391A	GAATGCGCTCTGG	.	PASS	Atlas-SNP
SLC4A7	9497	hgsc.bcm.edu	37	3	27442336	27442336	+	Silent	SNP	G	G	A	rs3736312	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	131	63	130	0	0.480916	0	G|0.828;A|0.172	0.172	strong	.	SLC4A7	119	.	NM_003615	exon16	c.C2319T	p.N773N	GCTGGGGTTTGGA	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48	20	45	0	0.416667	0	A|0.446;G|0.554	0.554	strong	.	PRX	151	.	NM_181882	exon7	c.T2645C	p.V882A	CCCTCCACCCGCT	.	PASS	Atlas-SNP
LXN	56925	hgsc.bcm.edu	37	3	158388780	158388780	+	Missense_Mutation	SNP	T	T	C	rs8455	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	190	57	209	0	0.3	0	C|0.557;N|0.000	0.557	strong	.	LXN	14	.	NM_020169	exon2	c.A158G	p.H53R	TTAAGGTGATACT	.	PASS	Atlas-SNP
ZNF705B	100132396	hgsc.bcm.edu	37	8	7808219	7808219	+	Missense_Mutation	SNP	A	A	T	rs2740676		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	182	79	98	0	0.434066	0	T|1.000;|0.000	1.000	weak	ZNF705B_ENST00000443676,NS,carcinoma,0,4	ZNF705B	10	4	NM_001193630	exon6	c.A268T	p.I90L	CACATGATATCCA	.	scavenged	Atlas-SNP
ZNF799	90576	hgsc.bcm.edu	37	19	12502787	12502787	+	Missense_Mutation	SNP	G	G	A	rs12974755	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	234	121	237	0	0.517094	0	G|0.898;A|0.102	0.102	strong	.	ZNF799	111	.	NM_001080821	exon4	c.C425T	p.T142M	TTATGCGTATCTG	.	PASS	Atlas-SNP
TMC1	117531	hgsc.bcm.edu	37	9	75303653	75303653	+	Silent	SNP	C	C	T	rs2589615	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48	27	51	0	0.5625	0	C|0.478;T|0.522	0.522	strong	.	TMC1	87	.	NM_138691	exon6	c.C45T	p.D15D	AGAAGACGAGACT	.	PASS	Atlas-SNP
DNHD1	144132	hgsc.bcm.edu	37	11	6524072	6524072	+	Missense_Mutation	SNP	A	A	C	rs11605196	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85	35	82	0	0.411765	0	A|0.862;C|0.138	0.138	strong	.	DNHD1	198	.	NM_173589	exon3	c.A836C	p.Q279P	ATAGCCAGGTGAT	.	PASS	Atlas-SNP
LBP	3929	hgsc.bcm.edu	37	20	36989381	36989381	+	Silent	SNP	G	G	A	rs2232596	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	95	55	100	0	0.578947	0	G|0.400;A|0.599	0.599	strong	.	LBP	60	.	NM_004139	exon6	c.G612A	p.S204S	GAAATCGGTGTCC	.	PASS	Atlas-SNP
MAGEC3	139081	hgsc.bcm.edu	37	X	140967165	140967165	+	Missense_Mutation	SNP	T	T	C	rs11095909	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	191	137	149	1	0.717277	0.00671141	T|0.639;C|0.361	0.361	strong	.	MAGEC3	228	.	NM_138702	exon3	c.T463C	p.S155P	ACCCTTTCCCTTC	.	PASS	Atlas-SNP
TAF1L	138474	hgsc.bcm.edu	37	9	32631369	32631369	+	Silent	SNP	C	C	T	rs10971047	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	328	162	317	0	0.493902	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
QRICH2	84074	hgsc.bcm.edu	37	17	74288421	74288421	+	Missense_Mutation	SNP	A	A	G	rs6501878	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	26	65	0	0.38806	0	A|0.636;G|0.364	0.364	strong	.	QRICH2	143	.	NM_032134	exon4	c.T1889C	p.I630T	TGAACTATACCAG	.	PASS	Atlas-SNP
PREX1	57580	hgsc.bcm.edu	37	20	47258763	47258763	+	Missense_Mutation	SNP	C	C	T	rs16993997	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	166	76	134	0	0.457831	0	C|0.855;N|0.001	.	strong	PREX1,NS,carcinoma,+2,1	PREX1	441	1	NM_020820	exon29	c.G3718A	p.V1240I	TCATGACTGGCCC	.	PASS	Atlas-SNP
LRRC38	126755	hgsc.bcm.edu	37	1	13802325	13802325	+	Missense_Mutation	SNP	T	T	C	rs3013105	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57	31	47	0	0.54386	0	C|0.487;N|0.000	0.487	strong	LRRC38,NS,meningioma,0,1	LRRC38	12	1	NM_001010847	exon2	c.A874G	p.K292E	CATCCTTGTCCTC	.	PASS	Atlas-SNP
CLEC10A	10462	hgsc.bcm.edu	37	17	6979179	6979179	+	Silent	SNP	A	A	G	rs364569	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83	42	91	0	0.506024	0	A|0.544;G|0.456	0.456	strong	.	CLEC10A	40	.	NM_182906	exon7	c.T546C	p.P182P	GTTGACAGGGCAG	.	PASS	Atlas-SNP
USHBP1	83878	hgsc.bcm.edu	37	19	17367354	17367354	+	Silent	SNP	G	G	A	rs141680124	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	31	60	0	0.574074	0	G|0.992;A|0.008	0.008	strong	.	USHBP1	85	.	NM_031941	exon9	c.C1396T	p.L466L	TCCCCAGAATGGC	.	PASS	Atlas-SNP
ARHGEF10L	55160	hgsc.bcm.edu	37	1	17981184	17981184	+	Silent	SNP	A	A	C	rs35255680	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69	27	59	0	0.391304	0	A|0.800;C|0.200	0.200	strong	.	ARHGEF10L	219	.	NM_018125	exon23	c.A2448C	p.A816A	CTCAGCAGTCAGC	.	PASS	Atlas-SNP
ZNF808	388558	hgsc.bcm.edu	37	19	53056953	53056953	+	Missense_Mutation	SNP	G	G	A	rs329965	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	69	122	0	0.821429	0	G|0.792;A|0.208	0.208	strong	.	ZNF808	81	.	NM_001039886	exon5	c.G784A	p.D262N	AAATGTGATGTAT	.	PASS	Atlas-SNP
AXDND1	126859	hgsc.bcm.edu	37	1	179452275	179452275	+	Silent	SNP	G	G	A	rs10494520	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	113	45	115	0	0.39823	0	G|0.807;A|0.193	0.193	strong	AXDND1,colon,carcinoma,+1,1	AXDND1	142	1	NM_144696	exon18	c.G2010A	p.A670A	CCAAGCGTATATA	.	PASS	Atlas-SNP
SPOCK1	6695	hgsc.bcm.edu	37	5	136834138	136834138	+	Missense_Mutation	SNP	T	T	C	rs111393448	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	41	20	44	0	0.487805	0	T|0.991;C|0.009	0.009	strong	.	SPOCK1	58	.	NM_004598	exon2	c.A110G	p.N37S	AGGAAATTGCCGT	.	PASS	Atlas-SNP
PTGFR	5737	hgsc.bcm.edu	37	1	78958491	78958491	+	Silent	SNP	C	C	T	rs35227129	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	29	69	0	0.439394	0	C|0.937;T|0.063	0.063	strong	.	PTGFR	121	.	NM_000959	exon2	c.C63T	p.T21T	CACAACCTGCCAG	.	PASS	Atlas-SNP
USP7	7874	hgsc.bcm.edu	37	16	8989511	8989511	+	Silent	SNP	C	C	T	rs61731196	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	38	94	0	0.452381	0	C|0.994;T|0.006	0.006	strong	.	USP7	116	.	NM_003470	exon27	c.G2907A	p.T969T	TCGAAACGTCCGG	.	PASS	Atlas-SNP
MTERFD2	130916	hgsc.bcm.edu	37	2	242039210	242039210	+	Missense_Mutation	SNP	G	G	A	rs143756138	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93	42	79	0	0.451613	0	G|0.999;A|0.001	0.001	strong	.	MTERFD2	33	.	NM_182501	exon2	c.C121T	p.R41C	GTTTGCGCAACAA	.	PASS	Atlas-SNP
FOXN3	1112	hgsc.bcm.edu	37	14	89878620	89878620	+	Silent	SNP	G	G	A	rs148222339	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	70	36	75	0	0.514286	0	G|0.997;A|0.003	0.003	strong	.	FOXN3	78	.	NM_005197	exon2	c.C201T	p.H67H	GCTCTCGTGCAGC	.	PASS	Atlas-SNP
OR4D6	219983	hgsc.bcm.edu	37	11	59224885	59224885	+	Missense_Mutation	SNP	G	G	C	rs1453542	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	120	119	139	0	0.991667	0	G|0.782;C|0.218	0.218	strong	.	OR4D6	65	.	NM_001004708	exon1	c.G452C	p.S151T	GGGTGAGTGGTGG	.	PASS	Atlas-SNP
TRAF3	7187	hgsc.bcm.edu	37	14	103371930	103371930	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	102	3	114	0	0.0294118	0	.	.	none	TRAF3,colon,carcinoma,-1,1	TRAF3	60	1	NM_145725	exon12	c.C1516T	p.R506C	TCTCGACGTCATT	.	scavenged	Atlas-SNP
C6orf70	55780	hgsc.bcm.edu	37	6	170181516	170181516	+	Silent	SNP	A	A	G	rs2274952	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	116	54	106	0	0.465517	0	A|0.974;G|0.026	0.026	strong	.	C6orf70	63	.	NM_018341	exon18	c.A1944G	p.T648T	TCTTACACATACA	.	PASS	Atlas-SNP
PAK7	57144	hgsc.bcm.edu	37	20	9520142	9520142	+	Silent	SNP	G	G	A	rs12329540	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	109	42	124	0	0.385321	0	G|0.907;A|0.093	0.093	strong	.	PAK7	194	.	NM_177990	exon10	c.C2127T	p.I709I	GGGGACGATGCAA	.	PASS	Atlas-SNP
SOWAHD	347454	hgsc.bcm.edu	37	X	118893413	118893413	+	Silent	SNP	T	T	C	rs2782225	bycluster;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	42	17	27	0	0.404762	0	T|0.366;C|0.634	0.634	strong	.	.	.	.	NM_001105576	exon1	c.T783C	p.S261S	CAGCAGTGGCACC	.	PASS	Atlas-SNP
SAGE1	55511	hgsc.bcm.edu	37	X	134994005	134994005	+	Missense_Mutation	SNP	T	T	C	rs4829799	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	115	25	84	0	0.217391	0	0|0.015;C|0.189	0.189	strong	.	SAGE1	160	.	NM_018666	exon18	c.T2414C	p.L805S	TGTCTTTGGTGGA	.	PASS	Atlas-SNP
WDR92	116143	hgsc.bcm.edu	37	2	68364478	68364478	+	Missense_Mutation	SNP	T	T	C	rs13009282	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	107	58	113	1	0.542056	0.00884956	T|0.804;C|0.196	0.196	strong	WDR92,NS,carcinoma,0,1	WDR92	21	1	NM_001256476	exon6	c.A721G	p.M241V	TTCTCATGTCAAA	.	scavenged	Atlas-SNP
TACC2	10579	hgsc.bcm.edu	37	10	123842523	123842523	+	Missense_Mutation	SNP	G	G	A	rs11200385	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	24	12	19	0	0.5	0	G|0.763;A|0.237	0.237	strong	.	TACC2	271	.	NM_206862	exon4	c.G508A	p.V170I	GCTGCCGTCCCCA	.	PASS	Atlas-SNP
OR10A2	341276	hgsc.bcm.edu	37	11	6891113	6891113	+	Missense_Mutation	SNP	A	A	G	rs74424652		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	227	87	212	0	0.38326	0	.	.	weak	.	OR10A2	55	.	NM_001004460	exon1	c.A128G	p.H43R	TGCTACACAGCCC	.	PASS	Atlas-SNP
POU5F1B	5462	hgsc.bcm.edu	37	8	128428638	128428638	+	Missense_Mutation	SNP	G	G	A	rs75641460	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	65	50	69	0	0.769231	0	.	.	weak	.	POU5F1B	32	.	NM_001159542	exon1	c.G527A	p.G176E	TATTTGGGAAGGT	.	PASS	Atlas-SNP
PPP2R3A	5523	hgsc.bcm.edu	37	3	135720673	135720673	+	Silent	SNP	T	T	C	rs9872542	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83	42	83	0	0.506024	0	T|0.802;C|0.198	0.198	strong	.	PPP2R3A	114	.	NM_002718	exon2	c.T333C	p.D111D	AAAGGATATTGCA	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	67	74	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
DNAH10	196385	hgsc.bcm.edu	37	12	124417973	124417973	+	Silent	SNP	C	C	T	rs56219209	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57	27	43	0	0.473684	0	C|0.985;T|0.015	0.015	strong	.	DNAH10	888	.	NM_207437	exon76	c.C13038T	p.N4346N	GAAGAACGGCTGG	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	62	67	0	0.96875	0	G|0.677;T|0.323	0.323	strong	.	CPA4	47	.	NM_016352	exon9	c.G907T	p.G303C	TTCAAGGGCTTCA	.	PASS	Atlas-SNP
C1orf101	257044	hgsc.bcm.edu	37	1	244735858	244735858	+	Silent	SNP	A	A	G	rs10927267	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	115	53	96	0	0.46087	0	A|0.783;G|0.217	0.217	strong	C1orf101_ENST00000366534,NS,carcinoma,0,2	C1orf101	158	2	NM_173807	exon11	c.A1734G	p.T578T	TTTCACAACAAAA	.	PASS	Atlas-SNP
PLEKHH1	57475	hgsc.bcm.edu	37	14	68041061	68041061	+	Missense_Mutation	SNP	G	G	A	rs61534804	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	58	34	64	0	0.586207	0	G|0.898;A|0.102	0.102	strong	.	PLEKHH1	118	.	NM_020715	exon14	c.G2029A	p.G677R	GCCACCGGGCCTC	.	PASS	Atlas-SNP
CATSPERD	257062	hgsc.bcm.edu	37	19	5778597	5778597	+	Silent	SNP	C	C	G	rs2305926	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	130	55	138	0	0.423077	0	C|0.978;G|0.022	0.022	strong	TMEM146,NS,carcinoma,0,1	.	.	1	NM_152784	exon22	c.C2307G	p.V769V	GACGGTCTGCCAG	.	PASS	Atlas-SNP
OCA2	4948	hgsc.bcm.edu	37	15	28235773	28235773	+	Silent	SNP	C	C	T	rs1800404	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	51	58	0	0.944444	0	C|0.469;T|0.530	0.530	strong	OCA2,colon,adenoma,-1,1	OCA2	173	1	NM_000275	exon10	c.G1065A	p.A355A	CATGGCCGCCAGA	.	PASS	Atlas-SNP
PRAMEF2	65122	hgsc.bcm.edu	37	1	12919064	12919064	+	Missense_Mutation	SNP	T	T	G	rs3204790	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	219	70	161	3	0.319635	0.0186335	T|0.824;G|0.176	0.176	strong	PRAMEF2,NS,carcinoma,0,1	PRAMEF2	85	1	NM_023014	exon2	c.T200G	p.V67G	CTCTGGTATCGCT	.	scavenged	Atlas-SNP
SMEK1	55671	hgsc.bcm.edu	37	14	91948043	91948043	+	Silent	SNP	T	T	C	rs17127374	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	229	228	254	0	0.995633	0	T|0.932;C|0.068	0.068	strong	.	SMEK1	94	.	NM_032560	exon5	c.A792G	p.T264T	TCTGTATGTCTGA	.	PASS	Atlas-SNP
KRTAP12-1	353332	hgsc.bcm.edu	37	21	46101934	46101934	+	Silent	SNP	G	G	A	rs56135164	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	141	64	128	0	0.453901	0	G|0.954;A|0.046	0.046	strong	.	KRTAP12-1	9	.	NM_181686	exon1	c.C105T	p.C35C	GGGCACGCACACG	.	PASS	Atlas-SNP
SPRR3	6707	hgsc.bcm.edu	37	1	152975715	152975715	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55	14	82	0	0.254545	0	.	.	none	SPRR3,colon,carcinoma,0,3	SPRR3	45	3	NM_001097589	exon2	c.C219T	p.G73G	GCCAGGCTGTACC	.	PASS	Atlas-SNP
VPS9D1	9605	hgsc.bcm.edu	37	16	89783205	89783205	+	Silent	SNP	G	G	A	rs118114589	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	29	60	0	0.557692	0	G|0.988;A|0.012	0.012	strong	.	.	.	.	NM_004913	exon3	c.C201T	p.D67D	GGAGGTGTCGGGG	.	PASS	Atlas-SNP
GM2A	2760	hgsc.bcm.edu	37	5	150639409	150639409	+	Missense_Mutation	SNP	A	A	G	rs153477	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72	72	81	0	1	0	A|0.380;G|0.620	0.620	strong	.	GM2A	24	.	NM_001167607	exon2	c.A175G	p.I59V	CCCATCATCGTTC	.	PASS	Atlas-SNP
HN1	51155	hgsc.bcm.edu	37	17	73142764	73142764	+	Missense_Mutation	SNP	G	G	A	rs62620707	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82	82	97	0	1	0	G|0.983;A|0.017	0.017	strong	HN1_ENST00000409753,NS,carcinoma,0,1	HN1	17	1	NM_016185	exon4	c.C313T	p.H105Y	TACCATGAATATC	.	PASS	Atlas-SNP
FREM1	158326	hgsc.bcm.edu	37	9	14801710	14801710	+	Missense_Mutation	SNP	C	C	A	rs35870000	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	219	112	246	1	0.511416	0.00406504	C|0.719;A|0.281	0.281	strong	.	FREM1	261	.	NM_144966	exon21	c.G3634T	p.A1212S	GGTTGGCTGGCTG	.	PASS	Atlas-SNP
OR52N1	79473	hgsc.bcm.edu	37	11	5809548	5809548	+	Missense_Mutation	SNP	G	G	A	rs7948009	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	97	48	125	0	0.494845	0	G|0.440;A|0.560	0.560	strong	.	OR52N1	70	.	NM_001001913	exon1	c.C499T	p.R167C	GAAGGCGCTTGGT	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	50	29	45	0	0.58	0	G|0.791;C|0.208	0.208	strong	.	C1QTNF6	32	.	NM_182486	exon2	c.C125G	p.P42R	ACCATAGGGATCT	.	PASS	Atlas-SNP
CACNA1B	774	hgsc.bcm.edu	37	9	140918181	140918181	+	Missense_Mutation	SNP	A	A	G	rs11137342	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	18	89	0	0.253521	0	A|0.972;G|0.028	0.028	strong	.	CACNA1B	266	.	NM_001243812	exon19	c.A2986G	p.T996A	AAGGAGACCACGG	.	PASS	Atlas-SNP
OR51E1	143503	hgsc.bcm.edu	37	11	4674343	4674343	+	Missense_Mutation	SNP	G	G	A	rs139501861	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	138	74	143	1	0.536232	0.00699301	G|0.996;A|0.004	0.004	strong	OR51E1,caecum,carcinoma,-1,1	OR51E1	67	1	NM_152430	exon2	c.G587A	p.R196Q	ATATCCGGGTCAA	.	scavenged	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9060125	9060125	+	Silent	SNP	G	G	A	rs12972088	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	121	56	136	0	0.46281	0	G|0.760;A|0.240	0.240	strong	.	MUC16	4315	.	NM_024690	exon3	c.C27321T	p.H9107H	AGTTGAGTGGGTC	.	PASS	Atlas-SNP
GGCX	2677	hgsc.bcm.edu	37	2	85780107	85780107	+	Silent	SNP	G	G	A	rs10179904	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	131	91	168	0	0.694656	0	G|0.893;A|0.107	0.107	strong	.	GGCX	44	.	NM_000821	exon9	c.C1242T	p.T414T	ACGGTAGGTGATC	.	PASS	Atlas-SNP
INPP4A	3631	hgsc.bcm.edu	37	2	99149946	99149946	+	Silent	SNP	G	G	A	rs2278211	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	22	75	0	0.349206	0	G|0.779;N|0.000	.	strong	.	INPP4A	205	.	NM_004027	exon5	c.G258A	p.T86T	ACAGACGGAGATC	.	PASS	Atlas-SNP
AKAP1	8165	hgsc.bcm.edu	37	17	55183792	55183792	+	Missense_Mutation	SNP	G	G	A	rs35359994	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	65	41	62	0	0.630769	0	G|0.949;A|0.051	0.051	strong	.	AKAP1	73	.	NM_001242902	exon3	c.G967A	p.G323S	GAGGAGGGCTTGG	.	PASS	Atlas-SNP
ACSM2A	123876	hgsc.bcm.edu	37	16	20488696	20488696	+	Silent	SNP	A	A	G	rs79385757	byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	535	171	533	0	0.319626	0	A|0.333;G|0.667	0.667	strong	.	ACSM2A	120	.	NM_001010845	exon10	c.A1104G	p.L368L	GGGATTAACTTGC	.	PASS	Atlas-SNP
MKRN1	23608	hgsc.bcm.edu	37	7	140158851	140158851	+	Missense_Mutation	SNP	C	C	G	rs2272095	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	36	100	0	0.418605	0	C|0.819;G|0.181	0.181	strong	.	MKRN1	35	.	NM_013446	exon4	c.G727C	p.V243L	GCAGGACCTGCAG	.	PASS	Atlas-SNP
ARFGAP3	26286	hgsc.bcm.edu	37	22	43203137	43203137	+	Silent	SNP	C	C	T	rs738535	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	36	35	44	0	0.972222	0	C|0.641;T|0.359	0.359	strong	.	ARFGAP3	48	.	NM_014570	exon14	c.G1353A	p.S451S	ACTTGCCGACAGC	.	PASS	Atlas-SNP
NPC2	10577	hgsc.bcm.edu	37	14	74951269	74951269	+	Missense_Mutation	SNP	T	T	C	rs142075589	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	25	46	0	0.531915	0	T|1.000;C|0.000	0.000	strong	.	NPC2	9	.	NM_006432	exon3	c.A212G	p.K71R	ACGGCCTTGCTGC	.	PASS	Atlas-SNP
GRM4	2914	hgsc.bcm.edu	37	6	34003685	34003685	+	Silent	SNP	T	T	C	rs2228623	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	13	57	0	0.154762	0	T|0.822;C|0.178	0.178	strong	.	GRM4	317	.	NM_000841	exon9	c.A2202G	p.T734T	GTCGAGTGTCCGC	.	PASS	Atlas-SNP
TPPP	11076	hgsc.bcm.edu	37	5	665295	665295	+	Silent	SNP	A	A	G	rs61731455	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	78	35	76	0	0.448718	0	A|0.870;G|0.130	0.130	strong	TPPP,caecum,carcinoma,0,1	TPPP	24	1	NM_007030	exon4	c.T582C	p.D194D	CACCAGATCCACG	.	PASS	Atlas-SNP
GPR112	139378	hgsc.bcm.edu	37	X	135431358	135431358	+	Silent	SNP	C	C	T	rs5930933	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83	58	71	0	0.698795	0	C|0.507;0|0.003	.	strong	.	GPR112	459	.	NM_153834	exon6	c.C5493T	p.P1831P	TCTACCCTCTTTG	.	PASS	Atlas-SNP
QRICH2	84074	hgsc.bcm.edu	37	17	74303550	74303550	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	97	4	129	0	0.0412371	0	.	.	none	.	QRICH2	143	.	NM_032134	exon1	c.C32T	p.A11V	ACCCTGGCAAAGC	.	PASS	Atlas-SNP
TRIM27	5987	hgsc.bcm.edu	37	6	28891176	28891176	+	Silent	SNP	T	T	C	rs2230683	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	35	21	55	0	0.6	0	T|0.950;C|0.050	0.050	strong	.	TRIM27	26	.	NM_006510	exon1	c.A234G	p.V78V	CTGCTTTACCAGT	.	PASS	Atlas-SNP
TYR	7299	hgsc.bcm.edu	37	11	89017961	89017961	+	Missense_Mutation	SNP	G	G	A	rs1126809	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	162	159	182	0	0.981481	0	G|0.831;A|0.169	0.169	strong	TYR,NS,carcinoma,+1,1	TYR	130	1	NM_000372	exon4	c.G1205A	p.R402Q	GGCTCCGAAGGCA	.	PASS	Atlas-SNP
LRSAM1	90678	hgsc.bcm.edu	37	9	130219669	130219669	+	Silent	SNP	C	C	T	rs2243906	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	32	78	0	0.395062	0	C|0.416;T|0.584	0.584	strong	.	LRSAM1	40	.	NM_001005373	exon6	c.C249T	p.I83I	AACCATCAAGGTA	.	PASS	Atlas-SNP
SCPEP1	59342	hgsc.bcm.edu	37	17	55079471	55079471	+	Silent	SNP	T	T	C	rs12940187	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	40	84	0	0.493827	0	T|0.884;C|0.116	0.116	strong	.	SCPEP1	35	.	NM_021626	exon12	c.T1225C	p.L409L	AAATCTTTGGAAA	.	PASS	Atlas-SNP
LMF1	64788	hgsc.bcm.edu	37	16	920870	920870	+	Missense_Mutation	SNP	C	C	T	rs35168378	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	34	16	27	0	0.470588	0	C|0.976;T|0.024	0.024	strong	.	LMF1	42	.	NM_022773	exon8	c.G1091A	p.R364Q	GCACGCCGCACCA	.	PASS	Atlas-SNP
KIF4A	24137	hgsc.bcm.edu	37	X	69573639	69573639	+	Silent	SNP	C	C	T	rs1199429	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	145	101	106	0	0.696552	0	0|0.003;T|0.145	0.145	strong	.	KIF4A	118	.	NM_012310	exon15	c.C1656T	p.P552P	GCAGCCCATTCAG	.	PASS	Atlas-SNP
ZNF30	90075	hgsc.bcm.edu	37	19	35422808	35422808	+	Missense_Mutation	SNP	C	C	T	rs10422961	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	54	55	0	1	0	C|0.700;T|0.300	0.300	strong	ZNF30,colon,carcinoma,0,1	ZNF30	44	1	NM_001099438	exon3	c.C71T	p.S24F	CCTTCTCCCAGCA	.	PASS	Atlas-SNP
EMILIN3	90187	hgsc.bcm.edu	37	20	39991171	39991171	+	Silent	SNP	G	G	A	rs61739307	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	37	17	44	0	0.459459	0	G|0.883;A|0.117	0.117	strong	EMILIN3,rectum,carcinoma,0,1	EMILIN3	63	1	NM_052846	exon4	c.C1038T	p.A346A	GCTGGCGGCCTGA	.	PASS	Atlas-SNP
SOGA3	387104	hgsc.bcm.edu	37	6	127797374	127797374	+	Silent	SNP	G	G	A	rs3734450	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	47	86	0	0.626667	0	G|0.678;A|0.322	0.322	strong	C6orf174,colon,carcinoma,0,1	.	.	1	NM_001012279	exon6	c.C1797T	p.N599N	CAGGATGTTGGCT	.	PASS	Atlas-SNP
CXXC5	51523	hgsc.bcm.edu	37	5	139060486	139060486	+	Silent	SNP	G	G	A	rs356445	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	26	14	23	0	0.538462	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
EFHB	151651	hgsc.bcm.edu	37	3	19961331	19961331	+	Silent	SNP	T	T	C	rs2929362	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	168	76	214	0	0.452381	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
AKAP3	10566	hgsc.bcm.edu	37	12	4735737	4735737	+	Silent	SNP	A	A	G	rs2072358	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	178	85	194	0	0.477528	0	G|0.259;A|0.741	0.259	strong	.	AKAP3	212	.	NM_006422	exon4	c.T2331C	p.L777L	CCATTGAAGGACG	.	PASS	Atlas-SNP
NVL	4931	hgsc.bcm.edu	37	1	224482084	224482084	+	Missense_Mutation	SNP	C	C	T	rs34631151	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55	30	56	0	0.545455	0	C|0.969;T|0.031	0.031	strong	.	NVL	74	.	NM_002533	exon12	c.G1210A	p.V404I	CTAGGACCCGGGC	.	PASS	Atlas-SNP
DUSP27	92235	hgsc.bcm.edu	37	1	167097739	167097739	+	Missense_Mutation	SNP	C	C	A	rs2281959	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	58	29	47	0	0.5	0	C|0.639;A|0.361	0.361	strong	.	DUSP27	235	.	NM_001080426	exon5	c.C3371A	p.T1124N	GAAGCACTGACAG	.	PASS	Atlas-SNP
MYO3A	53904	hgsc.bcm.edu	37	10	26286159	26286159	+	Silent	SNP	G	G	T	rs12257119	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	145	65	138	0	0.448276	0	G|0.902;T|0.098	0.098	strong	.	MYO3A	371	.	NM_017433	exon6	c.G480T	p.T160T	GACCACGGAAGGT	.	PASS	Atlas-SNP
MIOX	55586	hgsc.bcm.edu	37	22	50926768	50926768	+	Silent	SNP	C	C	T	rs2232883	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	27	63	0	0.442623	0	C|0.878;T|0.122	0.122	strong	.	MIOX	21	.	NM_017584	exon5	c.C405T	p.P135P	GGAGCCCCAGGTA	.	PASS	Atlas-SNP
PITRM1	10531	hgsc.bcm.edu	37	10	3200292	3200292	+	Missense_Mutation	SNP	G	G	A	rs3182535	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	21	72	0	0.446809	0	G|0.356;A|0.644	0.644	strong	.	PITRM1	109	.	NM_014889	exon11	c.C1190T	p.A397V	TTCTCCGCAATCC	.	PASS	Atlas-SNP
IGHMBP2	3508	hgsc.bcm.edu	37	11	68705674	68705674	+	Missense_Mutation	SNP	C	C	A	rs17612126	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91	13	87	0	0.142857	0	C|0.791;A|0.209	0.209	strong	.	IGHMBP2	83	.	NM_002180	exon14	c.C2636A	p.T879K	TGCCCACGGAGGA	.	PASS	Atlas-SNP
PIGB	9488	hgsc.bcm.edu	37	15	55619796	55619796	+	Missense_Mutation	SNP	T	T	C	rs2290344	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79	47	91	0	0.594937	0	T|0.805;C|0.195	0.195	strong	.	PIGB	36	.	NM_004855	exon4	c.T485C	p.M162T	CATTAATGAAGCA	.	PASS	Atlas-SNP
ZNF311	282890	hgsc.bcm.edu	37	6	28963861	28963861	+	Silent	SNP	G	G	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	107	79	91	0	0.738318	0	.	.	none	.	ZNF311	59	.	NM_001010877	exon7	c.C918G	p.T306T	ACACTGGGTGCAA	.	PASS	Atlas-SNP
DNALI1	7802	hgsc.bcm.edu	37	1	38023316	38023316	+	Missense_Mutation	SNP	C	C	T	rs11749	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	18	60	0	0.339623	0	C|0.786;G|0.000;N|0.000;T|0.213	0.213	strong	.	DNALI1	25	.	NM_003462	exon2	c.C260T	p.A87V	AGCAGGCAGAAGA	.	PASS	Atlas-SNP
ARMS2	387715	hgsc.bcm.edu	37	10	124214355	124214355	+	Nonsense_Mutation	SNP	C	C	T	rs2736911	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	148	77	119	0	0.52027	0	C|0.869;T|0.131	0.131	strong	ARMS2_ENST00000528446,NS,carcinoma,-1,1	ARMS2	7	1	NM_001099667	exon1	c.C112T	p.R38X	ACTCTGCGAGAGT	.	PASS	Atlas-SNP
PGBD1	84547	hgsc.bcm.edu	37	6	28268824	28268824	+	Missense_Mutation	SNP	A	A	G	rs33932084	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	44	59	0	0.709677	0	A|0.939;G|0.061	0.061	strong	.	PGBD1	106	.	NM_001184743	exon7	c.A1193G	p.N398S	AACCCAATTTTCC	.	PASS	Atlas-SNP
LEPR	3953	hgsc.bcm.edu	37	1	66102257	66102257	+	Silent	SNP	G	G	A	rs1805096	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	42	41	64	0	0.97619	0	G|0.516;A|0.484	0.484	strong	.	LEPR	284	.	NM_002303	exon20	c.G3057A	p.P1019P	TTCTCCGTTGAAG	.	PASS	Atlas-SNP
ZNF414	84330	hgsc.bcm.edu	37	19	8578035	8578035	+	Missense_Mutation	SNP	T	T	C	rs8100431	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	24	79	0	0.444444	0	T|0.673;C|0.327	0.327	strong	.	ZNF414	25	.	NM_032370	exon2	c.A194G	p.Q65R	CCCTGCTGCATCC	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	121	52	101	0	0.429752	0	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	.	PASS	Atlas-SNP
MCRS1	10445	hgsc.bcm.edu	37	12	49952668	49952668	+	Silent	SNP	G	G	A	rs2303305	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	24	12	18	0	0.5	0	G|0.892;A|0.108	0.108	strong	.	MCRS1	40	.	NM_001012300	exon13	c.C1299T	p.L433L	GCCACAGAGCACC	.	PASS	Atlas-SNP
DYNC2H1	79659	hgsc.bcm.edu	37	11	103229027	103229027	+	Silent	SNP	T	T	C	rs2566913	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	99	87	73	0	0.878788	0	T|0.488;C|0.512	0.512	strong	.	DYNC2H1	246	.	NM_001080463	exon84	c.T12117C	p.D4039D	ATTTGATAGAGAA	.	PASS	Atlas-SNP
FN1	2335	hgsc.bcm.edu	37	2	216229692	216229692	+	Silent	SNP	A	A	G	rs11651	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73	41	72	0	0.561644	0	A|0.771;G|0.229	0.229	strong	FN1_ENST00000354785,NS,carcinoma,0,2	FN1	521	2	NM_212482	exon44	c.T7161C	p.Y2387Y	ATCATCATAACAC	.	PASS	Atlas-SNP
EPHA1	2041	hgsc.bcm.edu	37	7	143088584	143088584	+	Missense_Mutation	SNP	C	C	T	rs139482378	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	104	52	121	0	0.5	0	C|0.999;T|0.001	0.001	strong	EPHA1,NS,carcinoma,-1,1	EPHA1	193	1	NM_005232	exon18	c.G2897A	p.R966H	AGAATGCGCTTCT	.	PASS	Atlas-SNP
ACSM2A	123876	hgsc.bcm.edu	37	16	20494408	20494408	+	Missense_Mutation	SNP	C	C	T	rs1133607	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	177	89	160	0	0.502825	0	C|0.880;T|0.120	0.120	strong	ACSM2A,NS,carcinoma,+1,1	ACSM2A	120	1	NM_001010845	exon14	c.C1538T	p.S513L	TGGCCTCGCAGTT	.	PASS	Atlas-SNP
OR13H1	347468	hgsc.bcm.edu	37	X	130678596	130678596	+	Silent	SNP	C	C	G	rs17316625	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	167	114	124	0	0.682635	0	C|0.787;0|0.015	.	strong	.	OR13H1	41	.	NM_001004486	exon1	c.C549G	p.L183L	CTCCCTCATTAAG	.	PASS	Atlas-SNP
DND1	373863	hgsc.bcm.edu	37	5	140050894	140050894	+	Missense_Mutation	SNP	G	G	C	rs201638404	byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	470	105	332	1	0.223404	0.00301205	G|0.979;C|0.021	0.021	strong	DND1,NS,carcinoma,-1,1	DND1	15	1	NM_194249	exon4	c.C1046G	p.T349S	ACCATGGTACCTG	.	scavenged	Atlas-SNP
LTF	4057	hgsc.bcm.edu	37	3	46480801	46480801	+	Silent	SNP	A	A	G	rs9110	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	195	97	231	0	0.497436	0	T|0.000;G|0.435;C|0.000;A|0.565	0.435	strong	.	LTF	98	.	NM_002343	exon15	c.T1894C	p.L632L	GGAGCAACACCTG	.	PASS	Atlas-SNP
PPP1R26	9858	hgsc.bcm.edu	37	9	138377657	138377657	+	Missense_Mutation	SNP	T	T	C	rs1808998	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	25	15	28	0	0.6	0	T|0.653;C|0.347	0.347	strong	.	.	.	.	NM_014811	exon4	c.T1301C	p.M434T	AGACCATGGACCC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195505746	195505746	+	Silent	SNP	T	T	G	rs369426870		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	70	21	90	0	0.3	0	.	.	weak	.	MUC4	1505	.	NM_018406	exon2	c.A12705C	p.T4235T	GTGACCTGTGGAT	.	PASS	Atlas-SNP
TAS1R2	80834	hgsc.bcm.edu	37	1	19175846	19175846	+	Missense_Mutation	SNP	T	T	C	rs28374389	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55	27	73	0	0.490909	0	T|0.832;C|0.168	0.168	strong	.	TAS1R2	134	.	NM_152232	exon4	c.A1456G	p.I486V	TGTTGATGGTGTG	.	PASS	Atlas-SNP
RAD9A	5883	hgsc.bcm.edu	37	11	67164791	67164791	+	Silent	SNP	T	T	C	rs872110	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	11	66	0	0.207547	0	T|0.653;C|0.347	0.347	strong	.	RAD9A	15	.	NM_004584	exon10	c.T1014C	p.G338G	CCCCGGTCCCCAC	.	PASS	Atlas-SNP
GAB4	128954	hgsc.bcm.edu	37	22	17450929	17450929	+	Missense_Mutation	SNP	C	C	T	rs61741409	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	119	62	137	0	0.521008	0	C|0.972;T|0.028	0.028	strong	.	GAB4	95	.	NM_001037814	exon4	c.G841A	p.A281T	ATTCTGCATTGTG	.	PASS	Atlas-SNP
CYP2C8	1558	hgsc.bcm.edu	37	10	96827030	96827030	+	Missense_Mutation	SNP	C	C	T	rs11572080	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	90	49	116	0	0.544444	0	C|0.931;T|0.069	0.069	strong	.	CYP2C8	73	.	NM_000770	exon3	c.G416A	p.R139K	ATGCTCCTCTTCC	.	PASS	Atlas-SNP
OR8G2	26492	hgsc.bcm.edu	37	11	124095884	124095884	+	Missense_Mutation	SNP	A	A	G	rs2466614	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	150	122	143	0	0.813333	0	A|0.893;G|0.107	0.107	strong	.	.	.	.	NM_001007249	exon1	c.A487G	p.I163V	GTTTACATTTTAG	.	PASS	Atlas-SNP
CCDC132	55610	hgsc.bcm.edu	37	7	92985252	92985252	+	Silent	SNP	T	T	C	rs2374639	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79	31	70	0	0.392405	0	C|0.320;N|0.000	0.320	strong	.	CCDC132	136	.	NM_017667	exon27	c.T2635C	p.L879L	ATGCAATTGGATT	.	PASS	Atlas-SNP
SALL4	57167	hgsc.bcm.edu	37	20	50407966	50407966	+	Silent	SNP	C	C	T	rs13038893	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	46	14	39	0	0.304348	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
NEK10	152110	hgsc.bcm.edu	37	3	27326097	27326097	+	Silent	SNP	G	G	T	rs11129280	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69	22	89	0	0.318841	0	G|0.774;T|0.226	0.226	strong	.	NEK10	271	.	NM_199347	exon23	c.C2010A	p.T670T	ACTAACGGTTACT	.	PASS	Atlas-SNP
TMEM176B	28959	hgsc.bcm.edu	37	7	150493495	150493495	+	Missense_Mutation	SNP	G	G	A	rs11546671	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	32	17	43	0	0.53125	0	G|0.973;A|0.027	0.027	strong	.	TMEM176B	36	.	NM_014020	exon2	c.C163T	p.P55S	TGGAAGGCACAGT	.	PASS	Atlas-SNP
TCP10L2	401285	hgsc.bcm.edu	37	6	167592576	167592576	+	Silent	SNP	G	G	A	rs60976240	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	53	43	0	1	0	G|0.424;A|0.576	0.576	strong	.	TCP10L2	41	.	NM_001145121	exon6	c.G735A	p.T245T	CGCCACGCTGCAG	.	PASS	Atlas-SNP
HIST1H4I	8294	hgsc.bcm.edu	37	6	27107302	27107302	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	141	93	116	0	0.659574	0	.	.	none	.	HIST1H4I	26	.	NM_003495	exon1	c.C215G	p.T72S	CCGTGACCTACAC	.	PASS	Atlas-SNP
TUBA3E	112714	hgsc.bcm.edu	37	2	130952725	130952725	+	Missense_Mutation	SNP	C	C	T	rs74378236	byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	129	17	237	0	0.131783	0	C|0.500;T|0.500	0.500	strong	.	TUBA3E	73	.	NM_207312	exon3	c.G302A	p.S101N	TAATTACTGGCTG	.	PASS	Atlas-SNP
OR8G2	26492	hgsc.bcm.edu	37	11	124096275	124096275	+	Missense_Mutation	SNP	T	T	C	rs2512268	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	199	162	171	0	0.81407	0	T|0.891;C|0.109	0.109	strong	.	.	.	.	NM_001007249	exon1	c.T878C	p.I293T	ATACTATTGTTGT	.	PASS	Atlas-SNP
C3orf30	152405	hgsc.bcm.edu	37	3	118865801	118865801	+	Silent	SNP	C	C	T	rs4077931	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	37	16	56	0	0.432432	0	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	.	PASS	Atlas-SNP
KRT3	3850	hgsc.bcm.edu	37	12	53186088	53186088	+	Missense_Mutation	SNP	G	G	C	rs3887954	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	105	44	111	0	0.419048	0	G|0.565;C|0.435	0.435	strong	.	KRT3	65	.	NM_057088	exon5	c.C1123G	p.R375G	GTGCACGAACTTC	.	PASS	Atlas-SNP
TAS2R1	50834	hgsc.bcm.edu	37	5	9629529	9629529	+	Missense_Mutation	SNP	G	G	A	rs2234233	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	35	14	41	0	0.4	0	G|0.878;A|0.122	0.122	strong	TAS2R1,NS,carcinoma,0,1	TAS2R1	84	1	NM_019599	exon1	c.C616T	p.R206W	TTTGCCGGGTGTG	.	PASS	Atlas-SNP
KIAA2026	158358	hgsc.bcm.edu	37	9	5969249	5969249	+	Silent	SNP	A	A	G	rs10739080	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68	68	82	0	1	0	A|0.421;G|0.579	0.579	strong	.	KIAA2026	231	.	NM_001017969	exon3	c.T982C	p.L328L	GTTCCAATTCGTA	.	PASS	Atlas-SNP
RNF183	138065	hgsc.bcm.edu	37	9	116060124	116060124	+	Missense_Mutation	SNP	T	T	C	rs3750534	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	147	77	114	0	0.52381	0	T|0.603;C|0.397	0.397	strong	.	RNF183	11	.	NM_145051	exon2	c.A341G	p.Q114R	TAGACTTGAGGCT	.	PASS	Atlas-SNP
DCHS2	54798	hgsc.bcm.edu	37	4	155410909	155410909	+	Silent	SNP	A	A	G	rs35172627	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	101	39	116	0	0.386139	0	A|0.843;G|0.157	0.157	strong	.	DCHS2	594	.	NM_001142552	exon1	c.T1599C	p.N533N	TTGGTCATTGAGG	.	PASS	Atlas-SNP
IQUB	154865	hgsc.bcm.edu	37	7	123097468	123097468	+	Silent	SNP	T	T	C	rs10234745	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	78	33	91	0	0.423077	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
SLIT3	6586	hgsc.bcm.edu	37	5	168093522	168093522	+	Silent	SNP	G	G	A	rs1048307	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	27	55	0	0.574468	0	G|0.834;A|0.166	0.166	strong	.	SLIT3	224	.	NM_001271946	exon36	c.C4530T	p.D1510D	GGAGCCGTCCGTG	.	PASS	Atlas-SNP
SPNS3	201305	hgsc.bcm.edu	37	17	4391153	4391153	+	Silent	SNP	A	A	G	rs333122	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	96	34	78	1	0.354167	0.0128205	A|0.784;G|0.216	0.216	strong	SPNS3,NS,carcinoma,0,1	SPNS3	52	1	NM_182538	exon12	c.A1503G	p.L501L	AGGCCTACTTTCG	.	scavenged	Atlas-SNP
MZF1	7593	hgsc.bcm.edu	37	19	59082605	59082605	+	Missense_Mutation	SNP	C	C	T	rs3752109	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57	28	68	0	0.491228	0	C|0.795;T|0.205	0.205	strong	.	MZF1	37	.	NM_198055	exon2	c.G152A	p.R51H	TCATAGCGGAAGC	.	PASS	Atlas-SNP
C5orf20	140947	hgsc.bcm.edu	37	5	134782443	134782443	+	Missense_Mutation	SNP	T	T	C	rs113429044	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	58	24	65	0	0.413793	0	T|0.902;C|0.098	0.098	strong	.	C5orf20	16	.	NM_130848	exon1	c.A356G	p.K119R	CCTGTCTTCCTTC	.	PASS	Atlas-SNP
USP40	55230	hgsc.bcm.edu	37	2	234432017	234432017	+	Missense_Mutation	SNP	A	A	G	rs838543	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	131	129	134	0	0.984733	0	T|0.001;G|0.188	0.188	strong	.	USP40	174	.	NM_018218	exon15	c.T2033C	p.V678A	GGAAAGACATGTG	.	PASS	Atlas-SNP
FSIP1	161835	hgsc.bcm.edu	37	15	39910404	39910404	+	Missense_Mutation	SNP	G	G	A	rs12908846	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	40	92	0	0.45977	0	G|0.862;A|0.138	0.138	strong	.	FSIP1	53	.	NM_152597	exon11	c.C1231T	p.L411F	CCAGAAGACACTT	.	PASS	Atlas-SNP
MED13L	23389	hgsc.bcm.edu	37	12	116403920	116403920	+	Silent	SNP	G	G	A	rs3088260	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	105	52	120	0	0.495238	0	G|0.936;A|0.064	0.064	strong	.	MED13L	193	.	NM_015335	exon29	c.C6354T	p.P2118P	AGCCTGGGGACAC	.	PASS	Atlas-SNP
PLEC	5339	hgsc.bcm.edu	37	8	144993377	144993377	+	Silent	SNP	A	A	G	rs6992333	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	34	78	0	0.515152	0	A|0.544;G|0.456	0.456	strong	.	PLEC	1144	.	NM_201380	exon32	c.T11023C	p.L3675L	GGCGCAAGCCCGT	.	PASS	Atlas-SNP
TAP2	6891	hgsc.bcm.edu	37	6	32797297	32797297	+	Silent	SNP	T	T	C	rs241441	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	12	70	0	0.169014	0	T|0.748;C|0.252	0.252	strong	.	TAP2	98	.	NM_018833	exon11	c.A1812G	p.G604G	CTGGCTTCCCTTC	.	PASS	Atlas-SNP
HNF1A	6927	hgsc.bcm.edu	37	12	121435342	121435342	+	Silent	SNP	C	C	T	rs2259820	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	117	116	70	0	0.991453	0	C|0.718;T|0.282	0.282	strong	.	HNF1A	302	.	NM_000545	exon7	c.C1375T	p.L459L	ACCACCCTGCAGC	.	PASS	Atlas-SNP
ANGPTL4	51129	hgsc.bcm.edu	37	19	8436164	8436164	+	Missense_Mutation	SNP	C	C	T	rs1044250	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60	31	34	0	0.516667	0	C|0.730;T|0.270	0.270	strong	.	ANGPTL4	21	.	NM_139314	exon6	c.C797T	p.T266M	GCATCACGGGGGA	.	PASS	Atlas-SNP
CRISPLD2	83716	hgsc.bcm.edu	37	16	84900645	84900645	+	Missense_Mutation	SNP	G	G	A	rs149615348	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	24	79	0	0.444444	0	G|0.994;A|0.006	0.006	strong	.	CRISPLD2	36	.	NM_031476	exon7	c.G852A	p.M284I	CTACATGAGTGAG	.	PASS	Atlas-SNP
GRM1	2911	hgsc.bcm.edu	37	6	146755324	146755324	+	Missense_Mutation	SNP	T	T	C	rs6923492	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	25	73	0	0.462963	0	T|0.420;C|0.580	0.580	strong	.	GRM1	419	.	NM_000838	exon9	c.T2977C	p.S993P	CTGCCGTCCCACC	.	PASS	Atlas-SNP
FAM220A	84792	hgsc.bcm.edu	37	7	6370406	6370406	+	Missense_Mutation	SNP	C	C	T	rs3750040	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	35	57	0	0.564516	0	C|0.381;T|0.619	0.619	strong	.	.	.	.	NM_001037163	exon2	c.G380A	p.R127Q	TCTCGCCGCCCCA	.	PASS	Atlas-SNP
LPPR3	0	hgsc.bcm.edu	37	19	814680	814680	+	Silent	SNP	G	G	T	rs56944467	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	12	5	25	0	0.416667	0	G|0.886;T|0.114	0.114	strong	.	.	.	.	NM_024888	exon6	c.C669A	p.A223A	GTGAGGGGCCGGA	.	PASS	Atlas-SNP
PREX1	57580	hgsc.bcm.edu	37	20	47273726	47273726	+	Missense_Mutation	SNP	C	C	T	rs55904123	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	40	24	38	0	0.6	0	C|0.849;T|0.151	0.151	strong	PREX1_ENST00000396220,NS,adenoma,0,2	PREX1	441	2	NM_020820	exon18	c.G1975A	p.V659M	CAGCCACCTGGGT	.	PASS	Atlas-SNP
ACO1	48	hgsc.bcm.edu	37	9	32425910	32425910	+	Silent	SNP	A	A	G	rs3780473	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	103	56	93	0	0.543689	0	G|0.346;N|0.000	0.346	strong	.	ACO1	149	.	NM_002197	exon11	c.A1263G	p.E421E	CACTGAATTCACC	.	PASS	Atlas-SNP
NANS	54187	hgsc.bcm.edu	37	9	100823135	100823135	+	Missense_Mutation	SNP	G	G	C	rs1058446	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	144	72	101	0	0.5	0	G|0.775;C|0.225	0.225	strong	.	NANS	24	.	NM_018946	exon2	c.G204C	p.E68D	CTTGGAGAGGCCA	.	PASS	Atlas-SNP
C1orf94	84970	hgsc.bcm.edu	37	1	34663208	34663208	+	Missense_Mutation	SNP	C	C	G	rs1382602	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	42	67	0	0.552632	0	C|0.612;G|0.387	0.387	strong	.	C1orf94	156	.	NM_001134734	exon2	c.C703G	p.Q235E	AACTTGCAAGTCA	.	PASS	Atlas-SNP
CCDC144NL	339184	hgsc.bcm.edu	37	17	20798992	20798992	+	Silent	SNP	C	C	T	rs8073465	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	134	60	149	0	0.447761	0	C|0.883;T|0.117	0.117	strong	.	CCDC144NL	34	.	NM_001004306	exon1	c.G342A	p.K114K	TTACCTCTTCTTC	.	PASS	Atlas-SNP
CWC27	10283	hgsc.bcm.edu	37	5	64267595	64267595	+	Silent	SNP	T	T	C	rs2278351	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	119	73	120	0	0.613445	0	T|0.708;C|0.292	0.292	strong	.	CWC27	47	.	NM_005869	exon12	c.T1108C	p.L370L	GAAGCTTTGAGGA	.	PASS	Atlas-SNP
LIPC	3990	hgsc.bcm.edu	37	15	58860963	58860963	+	Silent	SNP	C	C	A	rs6074	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	32	49	0	0.615385	0	C|0.856;A|0.144	0.144	strong	.	LIPC	56	.	NM_000236	exon9	c.C1437A	p.T479T	CCCAACCCAGGAA	.	PASS	Atlas-SNP
CYP2D6	1565	hgsc.bcm.edu	37	22	42523539	42523539	+	Silent	SNP	A	A	G	rs28371726	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	217	5	267	4	0.0230415	0.0149813	A|0.959;G|0.041	0.041	strong	CYP2D6_ENST00000360608,NS,carcinoma,0,4	CYP2D6	104	4	NM_000106	exon7	c.T1083C	p.H361H	CACCTCATGAATC	.	scavenged	Atlas-SNP
MLF1	4291	hgsc.bcm.edu	37	3	158320597	158320597	+	Silent	SNP	T	T	C	rs4875	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	89	39	109	0	0.438202	0	T|0.426;C|0.574	0.574	strong	.	MLF1	62	.	NM_001195432	exon8	c.T663C	p.S221S	CATAGGTGATGCT	.	PASS	Atlas-SNP
GAREM	64762	hgsc.bcm.edu	37	18	30050356	30050356	+	Silent	SNP	C	C	T	rs11664566	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	42	22	75	0	0.52381	0	C|0.784;T|0.216	0.216	strong	.	.	.	.	NM_022751	exon1	c.G36A	p.K12K	CACATCCTTGAGG	.	PASS	Atlas-SNP
NGEF	25791	hgsc.bcm.edu	37	2	233785015	233785015	+	Silent	SNP	G	G	A	rs778354	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	43	25	41	0	0.581395	0	G|0.244;A|0.756	0.756	strong	NGEF_ENST00000264051,colon,carcinoma,0,2	NGEF	198	2	NM_019850	exon5	c.C807T	p.P269P	CTCCTCGGGCTGT	.	PASS	Atlas-SNP
USHBP1	83878	hgsc.bcm.edu	37	19	17366278	17366278	+	Silent	SNP	T	T	C	rs4430871	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	37	37	60	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
KIAA1217	56243	hgsc.bcm.edu	37	10	24790393	24790393	+	Silent	SNP	A	A	G	rs1112284	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	43	74	0	0.565789	0	A|0.581;C|0.007	.	strong	.	KIAA1217	235	.	NM_019590	exon9	c.A1920G	p.S640S	CACCTCAGCCATC	.	PASS	Atlas-SNP
MKRN3	7681	hgsc.bcm.edu	37	15	23811592	23811592	+	Silent	SNP	C	C	T	rs2239669	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55	32	66	0	0.581818	0	C|0.745;A|0.002	.	strong	.	MKRN3	155	.	NM_005664	exon1	c.C663T	p.P221P	TGCCCCCGAGGCT	.	PASS	Atlas-SNP
RAI1	10743	hgsc.bcm.edu	37	17	17707105	17707105	+	Silent	SNP	T	T	C	rs3818717	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83	44	68	0	0.53012	0	T|0.635;C|0.365	0.365	strong	.	RAI1	121	.	NM_030665	exon4	c.T5601C	p.I1867I	CACCATTGGGTGC	.	PASS	Atlas-SNP
KRT1	3848	hgsc.bcm.edu	37	12	53072370	53072370	+	Silent	SNP	C	C	T	rs2741155	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	195	90	170	0	0.461538	0	C|0.994;T|0.006	0.006	strong	KRT1,NS,carcinoma,0,1	KRT1	110	1	NM_006121	exon2	c.G762A	p.S254S	CAGTTCCGAATCC	.	PASS	Atlas-SNP
DAXX	1616	hgsc.bcm.edu	37	6	33288271	33288271	+	Silent	SNP	A	A	G	rs1059231	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	30	22	40	0	0.733333	0	A|0.778;G|0.222	0.222	strong	.	DAXX	111	.	NM_001141970	exon4	c.T1173C	p.Y391Y	CATTGCATATTTG	.	PASS	Atlas-SNP
PM20D1	148811	hgsc.bcm.edu	37	1	205819039	205819039	+	Silent	SNP	C	C	T	rs11540016	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	37	74	0	0.552239	0	C|0.902;T|0.098	0.098	strong	.	PM20D1	56	.	NM_152491	exon1	c.G162A	p.A54A	TTTCAGCGCCTCT	.	PASS	Atlas-SNP
ZFYVE1	53349	hgsc.bcm.edu	37	14	73459917	73459917	+	Silent	SNP	C	C	T	rs2333016	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	59	17	45	0	0.288136	0	C|0.689;T|0.311	0.311	strong	.	ZFYVE1	67	.	NM_021260	exon4	c.G1137A	p.E379E	TAGCTGCTCCAAA	.	PASS	Atlas-SNP
PZP	5858	hgsc.bcm.edu	37	12	9334571	9334571	+	Silent	SNP	C	C	T	rs3741849	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	104	45	110	0	0.432692	0	C|0.886;T|0.114	0.114	strong	PZP_ENST00000381997,colon,carcinoma,-1,2	PZP	422	2	NM_002864	exon14	c.G1689A	p.K563K	GCTCACCTTGTTG	.	PASS	Atlas-SNP
ADAM28	10863	hgsc.bcm.edu	37	8	24171051	24171051	+	Silent	SNP	C	C	T	rs6996616	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	169	82	158	0	0.485207	0	C|0.809;T|0.191	0.191	strong	.	ADAM28	100	.	NM_014265	exon6	c.C534T	p.H178H	GGCCCACGATTTG	.	PASS	Atlas-SNP
CIITA	4261	hgsc.bcm.edu	37	16	11001691	11001691	+	Missense_Mutation	SNP	C	C	T	rs13330686	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	46	23	51	0	0.5	0	C|0.935;T|0.065	0.065	strong	.	CIITA	92	.	NM_000246	exon11	c.C2342T	p.S781L	CTGCCTCGGTGGA	.	PASS	Atlas-SNP
CCDC168	643677	hgsc.bcm.edu	37	13	103400729	103400729	+	Missense_Mutation	SNP	G	G	A	rs12583104	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	127	127	216	0	1	0	G|0.314;A|0.686	0.686	strong	.	.	.	.	NM_001146197	exon4	c.C2318T	p.P773L	CTTCCTGGGGAAA	.	PASS	Atlas-SNP
STX6	10228	hgsc.bcm.edu	37	1	180953853	180953853	+	Silent	SNP	A	A	G	rs3747957	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	113	113	134	0	1	0	A|0.439;G|0.561	0.561	strong	.	STX6	21	.	NM_005819	exon7	c.T651C	p.N217N	CATCACATTGTCC	.	PASS	Atlas-SNP
AMPD1	270	hgsc.bcm.edu	37	1	115236057	115236057	+	Nonsense_Mutation	SNP	G	G	A	rs17602729	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	185	88	166	0	0.475676	0	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
ZBTB4	57659	hgsc.bcm.edu	37	17	7366619	7366619	+	Missense_Mutation	SNP	T	T	C	rs34914463	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69	30	95	0	0.434783	0	T|0.942;C|0.058	0.058	strong	.	ZBTB4	163	.	NM_001128833	exon4	c.A1682G	p.N561S	CGTGGATTCCGGC	.	PASS	Atlas-SNP
CEP44	80817	hgsc.bcm.edu	37	4	175225452	175225452	+	Missense_Mutation	SNP	G	G	A	rs4695918	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	126	47	140	0	0.373016	0	G|0.520;A|0.480	0.480	strong	.	CEP44	35	.	NM_001040157	exon6	c.G439A	p.G147S	CCTTTGGGCAATG	.	PASS	Atlas-SNP
C12orf71	728858	hgsc.bcm.edu	37	12	27235279	27235279	+	Silent	SNP	G	G	A	rs12228215	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	198	96	188	0	0.484848	0	G|0.955;A|0.045	0.045	strong	.	C12orf71	20	.	NM_001080406	exon1	c.C138T	p.S46S	ACCCTTGGAAGGT	.	PASS	Atlas-SNP
MLPH	79083	hgsc.bcm.edu	37	2	238434434	238434434	+	Missense_Mutation	SNP	C	C	T	rs11883500	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	107	36	113	0	0.336449	0	C|0.832;T|0.168	0.168	strong	.	MLPH	41	.	NM_001042467	exon7	c.C866T	p.T289I	TGGGGACTGCTGC	.	PASS	Atlas-SNP
MMRN2	79812	hgsc.bcm.edu	37	10	88717154	88717154	+	Missense_Mutation	SNP	C	C	T	rs3750823	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	25	53	0	0.471698	0	C|0.595;T|0.405	0.405	strong	MMRN2,NS,carcinoma,0,1	MMRN2	49	1	NM_024756	exon1	c.G145A	p.G49S	CCTTGCCGGTGTC	.	PASS	Atlas-SNP
PLEC	5339	hgsc.bcm.edu	37	8	144995494	144995494	+	Missense_Mutation	SNP	C	C	T	rs76803079		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	35	24	35	0	0.685714	0	.	.	weak	.	PLEC	1144	.	NM_201380	exon32	c.G8906A	p.R2969H	TAGCCGCGCCGGT	.	PASS	Atlas-SNP
TACC2	10579	hgsc.bcm.edu	37	10	123845211	123845211	+	Missense_Mutation	SNP	G	G	A	rs11200387	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	35	15	33	0	0.428571	0	G|0.826;A|0.174	0.174	strong	.	TACC2	271	.	NM_206862	exon4	c.G3196A	p.A1066T	GCGCCCGCCAGCC	.	PASS	Atlas-SNP
AKAP6	9472	hgsc.bcm.edu	37	14	33014869	33014869	+	Missense_Mutation	SNP	C	C	T	rs3742926	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	88	43	64	0	0.488636	0	C|0.859;T|0.141	0.141	strong	.	AKAP6	308	.	NM_004274	exon4	c.C1010T	p.A337V	ATGCTGCTCAACC	.	PASS	Atlas-SNP
ALMS1	7840	hgsc.bcm.edu	37	2	73829372	73829372	+	Silent	SNP	C	C	T	rs1052162	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	132	89	249	0	0.674242	0	C|0.663;T|0.337	0.337	strong	.	ALMS1	384	.	NM_015120	exon20	c.C12172T	p.L4058L	AAGCGCCTGAAGT	.	PASS	Atlas-SNP
CCDC137	339230	hgsc.bcm.edu	37	17	79638805	79638805	+	Missense_Mutation	SNP	C	C	T	rs11150805	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	106	42	83	0	0.396226	0	C|0.863;T|0.137	0.137	strong	.	CCDC137	27	.	NM_199287	exon4	c.C529T	p.R177W	GTCCGACGGAAAA	.	PASS	Atlas-SNP
KDELC1	79070	hgsc.bcm.edu	37	13	103450973	103450973	+	Silent	SNP	T	T	C	rs7994595	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49	18	58	0	0.367347	0	T|0.916;C|0.084	0.084	strong	.	KDELC1	66	.	NM_024089	exon1	c.A48G	p.P16P	GAGTGCTGGAACT	.	PASS	Atlas-SNP
LILRB5	10990	hgsc.bcm.edu	37	19	54755922	54755922	+	Missense_Mutation	SNP	C	C	T	rs34889610	bycluster;alternate_allele	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	123	45	127	0	0.365854	0	TG|1.000;|0.000	.	alt	.	LILRB5	176	.	NM_001081442	exon12	c.G1624A	p.A542T	CCCGAGCATCCAT	.	PASS	Atlas-SNP
POLR2B	5431	hgsc.bcm.edu	37	4	57876955	57876955	+	Silent	SNP	G	G	A	rs1718878	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	207	98	213	0	0.47343	0	G|0.635;A|0.365	0.365	strong	.	POLR2B	108	.	NM_000938	exon12	c.G1590A	p.A530A	GATGGCGTATATT	.	PASS	Atlas-SNP
ATL2	64225	hgsc.bcm.edu	37	2	38537579	38537579	+	Missense_Mutation	SNP	T	T	C	rs34873284	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	97	58	107	0	0.597938	0	T|0.967;C|0.033	0.033	strong	.	ATL2	49	.	NM_001135673	exon8	c.A815G	p.N272S	TGTTGATTTTGTT	.	PASS	Atlas-SNP
ZNF587	84914	hgsc.bcm.edu	37	19	58371259	58371259	+	Silent	SNP	A	A	G	rs75951435	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	224	20	198	0	0.0892857	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	.	PASS	Atlas-SNP
KIAA1731	85459	hgsc.bcm.edu	37	11	93460160	93460160	+	Missense_Mutation	SNP	A	A	C	rs67879380	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	210	172	183	0	0.819048	0	A|0.852;C|0.148	0.148	strong	.	KIAA1731	173	.	NM_033395	exon24	c.A6518C	p.E2173A	GTTTTGAACAGCT	.	PASS	Atlas-SNP
LOXL2	4017	hgsc.bcm.edu	37	8	23225559	23225559	+	Silent	SNP	G	G	A	rs1063577	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55	29	67	0	0.527273	0	G|0.861;A|0.139	0.139	strong	.	LOXL2	97	.	NM_002318	exon2	c.C306T	p.Y102Y	CTCCACGTAGCCC	.	PASS	Atlas-SNP
PSMB9	5698	hgsc.bcm.edu	37	6	32825090	32825090	+	Missense_Mutation	SNP	G	G	A	rs17587	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	41	37	42	0	0.902439	0	G|0.760;A|0.240	0.240	strong	.	PSMB9	16	.	NM_002800	exon3	c.G179A	p.R60H	ACGAGCGCATCTA	.	PASS	Atlas-SNP
TAS2R20	259295	hgsc.bcm.edu	37	12	11150319	11150319	+	Silent	SNP	T	T	C	rs11054143	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	192	80	194	0	0.416667	0	T|0.678;C|0.322	0.322	strong	.	TAS2R20	17	.	NM_176889	exon1	c.A156G	p.A52A	GGAGACTGCCAGA	.	PASS	Atlas-SNP
KRTAP10-9	386676	hgsc.bcm.edu	37	21	46047418	46047418	+	Silent	SNP	C	C	T	rs8126553	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	134	53	129	0	0.395522	0	C|0.234;T|0.766	0.766	strong	.	KRTAP10-9	24	.	NM_198690	exon1	c.C330T	p.C110C	GTGCTGCGTGCCC	.	PASS	Atlas-SNP
TNXB	7148	hgsc.bcm.edu	37	6	32035694	32035694	+	Silent	SNP	C	C	T	rs1150756	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	103	78	103	0	0.757282	0	C|0.959;T|0.041	0.041	strong	.	TNXB	553	.	NM_019105	exon18	c.G6288A	p.P2096P	CAGGAGCGGCTCC	.	PASS	Atlas-SNP
KLHDC4	54758	hgsc.bcm.edu	37	16	87782322	87782322	+	Missense_Mutation	SNP	G	G	C	rs3751727	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	70	28	51	0	0.4	0	G|0.974;C|0.026	0.026	strong	.	KLHDC4	45	.	NM_001184856	exon5	c.C463G	p.L155V	CCCAGAGATCCTT	.	PASS	Atlas-SNP
INTS1	26173	hgsc.bcm.edu	37	7	1542697	1542697	+	Silent	SNP	G	G	A	rs3752714	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	137	73	111	0	0.532847	0	G|0.412;A|0.588	0.588	strong	INTS1,NS,carcinoma,0,1	INTS1	145	1	NM_001080453	exon3	c.C189T	p.A63A	CAACGCGGCCGCC	.	PASS	Atlas-SNP
MYH13	8735	hgsc.bcm.edu	37	17	10222310	10222310	+	Missense_Mutation	SNP	G	G	A	rs200861648	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	138	56	155	0	0.405797	0	G|1.000;A|0.000	0.000	strong	MYH13_ENST00000252172,right_upper_lobe,carcinoma,0,2	MYH13	533	2	NM_003802	exon27	c.C3535T	p.R1179C	CCCTGCGCATTTT	.	PASS	Atlas-SNP
RRP7A	27341	hgsc.bcm.edu	37	22	42912097	42912097	+	Missense_Mutation	SNP	C	C	T	rs11553441	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82	43	48	0	0.52439	0	C|0.893;T|0.107	0.107	strong	.	RRP7A	25	.	NM_015703	exon3	c.G262A	p.V88I	ACTCTACAGACTG	.	PASS	Atlas-SNP
NUP153	9972	hgsc.bcm.edu	37	6	17688798	17688798	+	Silent	SNP	G	G	A	rs1065057	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	17	73	0	0.195402	0	G|0.720;C|0.000;N|0.000;A|0.279	0.279	strong	.	NUP153	116	.	NM_005124	exon2	c.C163T	p.L55L	TTTGTAGCCACCC	.	PASS	Atlas-SNP
CCDC158	339965	hgsc.bcm.edu	37	4	77255210	77255210	+	Silent	SNP	C	C	T	rs113022439	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	140	140	138	0	1	0	C|0.984;T|0.016	0.016	strong	.	CCDC158	114	.	NM_001042784	exon18	c.G2775A	p.K925K	CTCTGTCTTGCTC	.	PASS	Atlas-SNP
TDRD10	126668	hgsc.bcm.edu	37	1	154516477	154516477	+	Missense_Mutation	SNP	G	G	A	rs12750774	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	92	92	87	0	1	0	G|0.809;A|0.191	0.191	strong	TDRD10,NS,carcinoma,+1,3	TDRD10	48	3	NM_182499	exon9	c.G542A	p.R181Q	GCTTCCGAGACCT	.	PASS	Atlas-SNP
NLRP4	147945	hgsc.bcm.edu	37	19	56369313	56369313	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	152	2	149	0	0.0131579	0	.	.	none	NLRP4_ENST00000301295,colon,carcinoma,-1,1	NLRP4	331	1	NM_134444	exon3	c.C554T	p.T185M	TGTACACGTTCTA	.	scavenged	Atlas-SNP
PCDHB10	56126	hgsc.bcm.edu	37	5	140573709	140573709	+	Missense_Mutation	SNP	G	G	C	rs17844577	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	155	38	222	0	0.245161	0	G|0.943;C|0.057	0.057	strong	PCDHB10,NS,carcinoma,+2,2	PCDHB10	177	2	NM_018930	exon1	c.G1584C	p.E528D	TTTCGAGTTCCGC	.	PASS	Atlas-SNP
DISP1	84976	hgsc.bcm.edu	37	1	223178478	223178478	+	Missense_Mutation	SNP	G	G	A	rs9441940	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	117	41	111	0	0.350427	0	A|0.123;G|0.877;T|0.000	0.123	strong	.	DISP1	145	.	NM_032890	exon10	c.G3739A	p.A1247T	AGTGACGCTGGCT	.	PASS	Atlas-SNP
HMBOX1	79618	hgsc.bcm.edu	37	8	28827928	28827928	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	4	52	0	0.045977	0	.	.	none	.	HMBOX1	34	.	NM_024567	exon4	c.A392T	p.K131M	ATGGAAAGATGTC	.	PASS	Atlas-SNP
CILP2	148113	hgsc.bcm.edu	37	19	19654117	19654117	+	Silent	SNP	G	G	C	rs7252453	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	160	78	152	0	0.4875	0	G|0.754;C|0.246	0.246	strong	.	CILP2	84	.	NM_153221	exon7	c.G1038C	p.L346L	GGAGCTGCGGGGA	.	PASS	Atlas-SNP
MFHAS1	9258	hgsc.bcm.edu	37	8	8749729	8749729	+	Silent	SNP	G	G	C	rs3748141	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	18	8	31	0	0.444444	0	G|0.840;C|0.160	0.160	strong	.	MFHAS1	58	.	NM_004225	exon1	c.C840G	p.L280L	GGAGGAGAGGTTG	.	PASS	Atlas-SNP
TFDP3	51270	hgsc.bcm.edu	37	X	132351703	132351703	+	Missense_Mutation	SNP	C	C	A	rs35745873	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	28	71	0	0.333333	0	C|0.978;A|0.022	0.022	strong	.	TFDP3	92	.	NM_016521	exon1	c.G585T	p.Q195H	ACAGTTCTGAGCC	.	PASS	Atlas-SNP
TNFRSF8	943	hgsc.bcm.edu	37	1	12198297	12198297	+	Silent	SNP	T	T	C	rs476488	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	34	68	0	0.453333	0	A|0.005;C|0.259	0.259	strong	.	TNFRSF8	70	.	NM_001243	exon14	c.T1347C	p.S449S	GAGGAGTGGTGCG	.	PASS	Atlas-SNP
SLC37A2	219855	hgsc.bcm.edu	37	11	124947149	124947149	+	Silent	SNP	G	G	A	rs12276567	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	144	128	113	0	0.888889	0	G|0.679;A|0.321	0.321	strong	SLC37A2_ENST00000403796,NS,adenoma,0,3	SLC37A2	105	3	NM_001145290	exon3	c.G165A	p.S55S	CTGCTCGGAGCAG	.	PASS	Atlas-SNP
KEAP1	9817	hgsc.bcm.edu	37	19	10602344	10602344	+	Missense_Mutation	SNP	G	G	A	rs147613351	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98	43	115	0	0.438776	0	G|1.000;A|0.000	0.000	strong	.	KEAP1	182	.	NM_012289	exon3	c.C1234T	p.P412S	TACGGGGCACGCT	.	PASS	Atlas-SNP
ZNF804A	91752	hgsc.bcm.edu	37	2	185801756	185801756	+	Missense_Mutation	SNP	G	G	A	rs61739288	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	32	64	0	0.432432	0	G|0.932;A|0.068	0.068	strong	.	ZNF804A	322	.	NM_194250	exon4	c.G1633A	p.G545S	AACACAGGTCAGA	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179583496	179583496	+	Missense_Mutation	SNP	T	T	G	rs16866465	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82	44	58	0	0.536585	0	T|0.778;G|0.222	0.222	strong	.	TTN	18412	.	NM_001267550	exon84	c.A24431C	p.E8144A	CCACTTTCTAATG	.	PASS	Atlas-SNP
PRSS3	5646	hgsc.bcm.edu	37	9	33799103	33799103	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	210	9	176	0	0.0428571	0	.	.	none	.	PRSS3	79	.	NM_007343	exon5	c.G840A	p.K280K	CTGGAAGAACAGG	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228505739	228505739	+	Missense_Mutation	SNP	G	G	A	rs3795801	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	183	64	179	0	0.349727	0	G|0.828;A|0.172	0.172	strong	.	OBSCN	2142	.	NM_001271223	exon64	c.G16867A	p.G5623S	CAGCCCGGTGGGC	.	PASS	Atlas-SNP
RBM19	9904	hgsc.bcm.edu	37	12	114386639	114386639	+	Silent	SNP	A	A	G	rs7966348	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	42	93	0	0.518519	0	A|0.823;G|0.177	0.177	strong	RBM19,NS,carcinoma,0,1	RBM19	117	1	NM_001146699	exon10	c.T1275C	p.Y425Y	CCTACCATATTTG	.	PASS	Atlas-SNP
ZFYVE26	23503	hgsc.bcm.edu	37	14	68252852	68252852	+	Missense_Mutation	SNP	A	A	T	rs112787369	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	36	76	0	0.679245	0	A|0.967;T|0.033	0.033	strong	.	ZFYVE26	223	.	NM_015346	exon17	c.T3118A	p.S1040T	TGGCTGACATAAG	.	PASS	Atlas-SNP
WDR81	124997	hgsc.bcm.edu	37	17	1640793	1640793	+	Silent	SNP	C	C	T	rs8077638	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	142	77	130	0	0.542253	0	C|0.789;T|0.211	0.211	strong	WDR81_ENST00000437219,colon,carcinoma,0,6	WDR81	180	6	NM_001163809	exon10	c.C5640T	p.S1880S	CGGCAGCGAGGTG	.	PASS	Atlas-SNP
OTOP1	133060	hgsc.bcm.edu	37	4	4199083	4199083	+	Missense_Mutation	SNP	T	T	G	rs34666677	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	102	47	143	0	0.460784	0	T|0.925;G|0.075	0.075	strong	.	OTOP1	118	.	NM_177998	exon5	c.A1478C	p.K493T	ATGTCCTTGCCCT	.	PASS	Atlas-SNP
LRIG3	121227	hgsc.bcm.edu	37	12	59282702	59282702	+	Silent	SNP	T	T	C	rs17533647	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	106	50	116	0	0.471698	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
FAM120AOS	158293	hgsc.bcm.edu	37	9	96209943	96209943	+	Missense_Mutation	SNP	T	T	C	rs10821128	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	131	130	137	0	0.992366	0	T|0.734;C|0.266	0.266	strong	.	FAM120AOS	13	.	NM_198841	exon3	c.A721G	p.K241E	TTTTCTTTGAGAC	.	PASS	Atlas-SNP
SPAG16	79582	hgsc.bcm.edu	37	2	214794743	214794743	+	Missense_Mutation	SNP	A	A	C	rs12623569	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	129	63	180	0	0.488372	0	A|0.722;C|0.278	0.278	strong	.	SPAG16	134	.	NM_024532	exon12	c.A1274C	p.K425T	TATGTAAAGGCGA	.	PASS	Atlas-SNP
CD8A	925	hgsc.bcm.edu	37	2	87016506	87016506	+	Silent	SNP	A	A	G	rs3020726	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	46	80	0	0.741935	0	A|0.873;G|0.127	0.127	strong	.	CD8A	28	.	NM_001145873	exon7	c.T565C	p.L189L	CGGCCAAGGGCGC	.	PASS	Atlas-SNP
SLC5A9	200010	hgsc.bcm.edu	37	1	48708278	48708278	+	Silent	SNP	G	G	A	rs75538709	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	37	62	0	0.560606	0	G|0.920;A|0.080	0.080	strong	.	SLC5A9	82	.	NM_001135181	exon14	c.G1902A	p.E634E	CCAGGAGCAGCCT	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83	26	110	1	0.313253	0.00909091	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	.	scavenged	Atlas-SNP
PIGQ	9091	hgsc.bcm.edu	37	16	630902	630902	+	Silent	SNP	C	C	G	rs1045274	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	45	19	43	0	0.422222	0	C|0.846;G|0.154	0.154	strong	PIGQ,NS,carcinoma,0,1	PIGQ	43	1	NM_148920	exon9	c.C1461G	p.L487L	TCTGCTCGTGGAC	.	PASS	Atlas-SNP
TACC2	10579	hgsc.bcm.edu	37	10	123844503	123844503	+	Missense_Mutation	SNP	C	C	T	rs10887063	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	40	24	48	0	0.6	0	C|0.791;T|0.209	0.209	strong	.	TACC2	271	.	NM_206862	exon4	c.C2488T	p.L830F	AAGCATCTCCAGC	.	PASS	Atlas-SNP
CERS5	91012	hgsc.bcm.edu	37	12	50529736	50529736	+	Silent	SNP	G	G	A	rs3741562	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	65	35	78	0	0.538462	0	G|0.679;A|0.321	0.321	strong	.	.	.	.	NM_147190	exon7	c.C753T	p.D251D	CAAGAAGTCTGAG	.	PASS	Atlas-SNP
AKAP13	11214	hgsc.bcm.edu	37	15	86122875	86122875	+	Missense_Mutation	SNP	A	A	C	rs34434221	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49	24	42	0	0.489796	0	A|0.978;C|0.022	0.022	strong	.	AKAP13	394	.	NM_007200	exon7	c.A1576C	p.K526Q	ACAAGTAAGCCTG	.	PASS	Atlas-SNP
FUT8	2530	hgsc.bcm.edu	37	14	66136163	66136163	+	Missense_Mutation	SNP	C	C	A	rs35949016	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	167	81	169	3	0.48503	0.0177515	C|0.875;A|0.125	0.125	strong	FUT8,NS,carcinoma,0,1	FUT8	101	1	NM_178155	exon7	c.C800A	p.T267K	CATGCACAGACAG	.	scavenged	Atlas-SNP
ZNF469	84627	hgsc.bcm.edu	37	16	88500957	88500957	+	Missense_Mutation	SNP	C	C	T	rs76389306	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	35	74	0	0.472973	0	C|0.998;T|0.002	0.002	strong	.	ZNF469	121	.	NM_001127464	exon2	c.C6995T	p.P2332L	CAGGGCCGGACTC	.	PASS	Atlas-SNP
AIPL1	23746	hgsc.bcm.edu	37	17	6331803	6331803	+	Silent	SNP	T	T	C	rs8075035	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	46	31	25	0	0.673913	0	T|0.391;C|0.609	0.609	strong	.	AIPL1	34	.	NM_014336	exon3	c.A300G	p.L100L	CCGGGATAGGATG	.	PASS	Atlas-SNP
MCAM	4162	hgsc.bcm.edu	37	11	119181170	119181170	+	Silent	SNP	T	T	C	rs2249466	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	52	48	0	1	0	T|0.279;C|0.721	0.721	strong	MCAM,NS,carcinoma,0,1	MCAM	57	1	NM_006500	exon15	c.A1800G	p.L600L	CGGGGGTAGCGTG	.	PASS	Atlas-SNP
SPANXN2	494119	hgsc.bcm.edu	37	X	142795438	142795438	+	Silent	SNP	G	G	T	rs5908761	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	139	50	88	0	0.359712	0	G|0.764;T|0.236	0.236	strong	.	SPANXN2	67	.	NM_001009615	exon2	c.C240A	p.P80P	TTGGACGGGATTG	.	PASS	Atlas-SNP
STAB2	55576	hgsc.bcm.edu	37	12	104136316	104136316	+	Silent	SNP	C	C	T	rs2292688	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	155	72	136	0	0.464516	0	C|0.892;T|0.108	0.108	strong	.	STAB2	370	.	NM_017564	exon56	c.C6015T	p.F2005F	GAGATTCGGGCCT	.	PASS	Atlas-SNP
LILRB3	11025	hgsc.bcm.edu	37	19	54725913	54725913	+	Missense_Mutation	SNP	C	C	T	rs199822090	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	131	69	210	0	0.526718	0	C|0.931;T|0.069	0.069	strong	.	LILRB3	67	.	NM_006864	exon4	c.G445A	p.G149R	GATATCCCTTCTG	.	PASS	Atlas-SNP
MSGN1	343930	hgsc.bcm.edu	37	2	17998001	17998001	+	Silent	SNP	C	C	T	rs201149255	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	77	33	67	0	0.428571	0	C|0.999;T|0.001	0.001	strong	MSGN1,NS,carcinoma,+1,1	MSGN1	39	1	NM_001105569	exon1	c.C216T	p.G72G	GCACGGCGGGGCC	.	PASS	Atlas-SNP
PPP2R3A	5523	hgsc.bcm.edu	37	3	135745762	135745762	+	Missense_Mutation	SNP	C	C	T	rs9826032	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69	36	92	0	0.521739	0	C|0.992;T|0.008	0.008	strong	.	PPP2R3A	114	.	NM_002718	exon3	c.C2084T	p.P695L	CGGTTCCCCATGT	.	PASS	Atlas-SNP
KANSL1	284058	hgsc.bcm.edu	37	17	44248814	44248814	+	Silent	SNP	G	G	A	rs1881194	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	384	384	227	1	1	0.00440529	G|0.848;A|0.152	0.152	strong	.	.	.	.	NM_001193466	exon2	c.C696T	p.S232S	GACAGAGGATTTG	.	PASS	Atlas-SNP
SPON2	10417	hgsc.bcm.edu	37	4	1165764	1165764	+	Silent	SNP	C	C	T	rs11538062	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	23	143	0	0.343284	0	C|0.870;T|0.130	0.130	strong	.	SPON2	22	.	NM_012445	exon2	c.G96A	p.E32E	GATGGACTCTCCC	.	PASS	Atlas-SNP
MMP3	4314	hgsc.bcm.edu	37	11	102713620	102713620	+	Missense_Mutation	SNP	T	T	C	rs679620	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57	57	53	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
DUSP8	1850	hgsc.bcm.edu	37	11	1580173	1580173	+	Silent	SNP	C	C	A	rs17854342	alternate_allele	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	119	34	119	0	0.285714	0	.	.	alt	.	DUSP8	22	.	NM_004420	exon4	c.G483T	p.L161L	GCGGGTCAGGCCC	.	PASS	Atlas-SNP
SYNJ2	8871	hgsc.bcm.edu	37	6	158499302	158499302	+	Silent	SNP	G	G	T	rs2296507	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	119	119	138	0	1	0	G|0.446;T|0.554	0.554	strong	.	SYNJ2	111	.	NM_003898	exon18	c.G2556T	p.A852A	ACAAGCGTCTGAT	.	PASS	Atlas-SNP
PRR14L	253143	hgsc.bcm.edu	37	22	32112461	32112461	+	Missense_Mutation	SNP	T	T	C	rs140081	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	113	55	89	0	0.486726	0	T|0.684;C|0.316	0.316	strong	.	PRR14L	198	.	NM_173566	exon4	c.A1364G	p.N455S	CTAGAGTTCCCTG	.	PASS	Atlas-SNP
ZNF518B	85460	hgsc.bcm.edu	37	4	10447907	10447907	+	Missense_Mutation	SNP	C	C	T	rs72648876	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	152	70	149	0	0.460526	0	C|0.983;T|0.017	0.017	strong	.	ZNF518B	116	.	NM_053042	exon3	c.G46A	p.G16R	TATGTCCGCCGTT	.	PASS	Atlas-SNP
MTDH	92140	hgsc.bcm.edu	37	8	98725970	98725970	+	Silent	SNP	G	G	A	rs2331652	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	23	12	26	0	0.521739	0	G|0.950;A|0.050	0.050	strong	MTDH,NS,carcinoma,0,1	MTDH	54	1	NM_178812	exon9	c.G1353A	p.K451K	GAAGAAGCAAGGT	.	PASS	Atlas-SNP
MROH1	727957	hgsc.bcm.edu	37	8	145223239	145223239	+	Missense_Mutation	SNP	C	C	T	rs374952645		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	36	9	31	0	0.25	0	.	.	weak	.	.	.	.	NM_001099280	exon4	c.C64T	p.P22S	AAGGACCCCCTGG	.	PASS	Atlas-SNP
MUC21	394263	hgsc.bcm.edu	37	6	30954709	30954709	+	Missense_Mutation	SNP	G	G	A	rs11756238	bycluster;byfrequency;by2hit2allele;byhapmap	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	95	6	99	3	0.0631579	0.030303	G|0.989;A|0.011	0.011	strong	MUC21,colon,carcinoma,-1,2	MUC21	98	2	NM_001010909	exon2	c.G757A	p.G253S	GGGGCCGGCACAG	.	scavenged	Atlas-SNP
CLRN3	119467	hgsc.bcm.edu	37	10	129690837	129690837	+	Missense_Mutation	SNP	G	G	T	rs35890579	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79	38	50	0	0.481013	0	G|0.966;T|0.034	0.034	strong	.	CLRN3	27	.	NM_152311	exon1	c.C212A	p.P71Q	TTCTTTGGTTCTG	.	PASS	Atlas-SNP
CCDC88C	440193	hgsc.bcm.edu	37	14	91760522	91760522	+	Silent	SNP	C	C	T	rs12891713	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	164	68	158	0	0.414634	0	C|0.823;T|0.177	0.177	strong	.	CCDC88C	192	.	NM_001080414	exon23	c.G4107A	p.Q1369Q	CATGTACTGCTTC	.	PASS	Atlas-SNP
DPP3	10072	hgsc.bcm.edu	37	11	66276576	66276576	+	Missense_Mutation	SNP	G	G	A	rs12421620	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	59	10	60	0	0.169492	0	G|0.975;A|0.025	0.025	strong	.	DPP3	61	.	NM_130443	exon18	c.G2068A	p.E690K	GAATACGAGGCGT	.	PASS	Atlas-SNP
POR	5447	hgsc.bcm.edu	37	7	75615287	75615287	+	Silent	SNP	G	G	A	rs1057870	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51	32	80	0	0.627451	0	G|0.826;A|0.174	0.174	strong	.	POR	46	.	NM_000941	exon14	c.G1716A	p.S572S	CCGCTCGGATGAG	.	PASS	Atlas-SNP
ATP1A4	480	hgsc.bcm.edu	37	1	160134056	160134056	+	Missense_Mutation	SNP	G	G	A	rs17368402	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	444	215	443	1	0.484234	0.00225734	G|0.934;A|0.066	0.066	strong	.	ATP1A4	167	.	NM_144699	exon7	c.G889A	p.E297K	GAGATCGAACACT	.	PASS	Atlas-SNP
PTER	9317	hgsc.bcm.edu	37	10	16547058	16547058	+	Silent	SNP	A	A	G	rs7904014	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	147	61	133	0	0.414966	0	A|0.428;G|0.572	0.572	strong	.	PTER	40	.	NM_030664	exon5	c.A738G	p.Q246Q	TGCTCAACTTGGC	.	PASS	Atlas-SNP
TAF1C	9013	hgsc.bcm.edu	37	16	84212779	84212779	+	Missense_Mutation	SNP	G	G	A	rs2230131	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	58	28	52	0	0.482759	0	G|0.840;A|0.160	0.160	strong	.	TAF1C	60	.	NM_005679	exon14	c.C2378T	p.P793L	GAGGGCGGGGTCG	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55	20	50	0	0.363636	0	T|0.829;G|0.171	0.171	strong	.	NCOA7	92	.	NM_001199619	exon17	c.T2826G	p.D942E	ATTTGATTGAAAT	.	PASS	Atlas-SNP
EIF2S3	1968	hgsc.bcm.edu	37	X	24073761	24073761	+	Silent	SNP	C	C	T	rs36018672	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	182	176	132	1	0.967033	0.00757576	C|0.514;T|0.486	0.486	strong	.	EIF2S3	31	.	NM_001415	exon2	c.C99T	p.H33H	TTCACACGAAGTT	.	PASS	Atlas-SNP
MANSC4	100287284	hgsc.bcm.edu	37	12	27915944	27915944	+	Silent	SNP	A	A	G	rs11049124	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	273	126	289	0	0.461538	0	A|0.859;G|0.141	0.141	strong	.	MANSC4	9	.	NM_001146221	exon3	c.T750C	p.P250P	GAGTCCAGGTGGA	.	PASS	Atlas-SNP
PKP3	11187	hgsc.bcm.edu	37	11	403658	403658	+	Missense_Mutation	SNP	G	G	C	rs147657735	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	28	17	26	0	0.607143	0	G|0.999;C|0.001	0.001	strong	PKP3,NS,lymphoid_neoplasm,0,1	PKP3	36	1	NM_007183	exon10	c.G1964C	p.R655P	AGGAGCGTATTCT	.	PASS	Atlas-SNP
COL22A1	169044	hgsc.bcm.edu	37	8	139824057	139824057	+	Silent	SNP	G	G	A	rs10101430	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	157	156	171	0	0.993631	0	G|0.507;A|0.493	0.493	strong	.	COL22A1	390	.	NM_152888	exon9	c.C1434T	p.C478C	AGCTGGGCAGGAG	.	PASS	Atlas-SNP
CNTNAP3B	728577	hgsc.bcm.edu	37	9	43876040	43876040	+	Missense_Mutation	SNP	C	C	A	rs80251176		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	524	277	891	12	0.528626	0.013468	A|1.000;|0.000	1.000	weak	CNTNAP3B,NS,carcinoma,0,1	CNTNAP3B	37	1	NM_001201380	exon14	c.C2132A	p.S711Y	ACACTTCCTGGGG	.	scavenged	Atlas-SNP
TTLL10	254173	hgsc.bcm.edu	37	1	1115503	1115503	+	Missense_Mutation	SNP	T	T	C	rs111751804	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	116	52	99	0	0.448276	0	T|0.985;C|0.015	0.015	strong	.	TTLL10	66	.	NM_001130045	exon6	c.T289C	p.C97R	GGACACTGTGGGC	.	PASS	Atlas-SNP
DLEC1	9940	hgsc.bcm.edu	37	3	38125705	38125705	+	Silent	SNP	G	G	A	rs7652276	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	104	49	106	0	0.471154	0	G|0.644;A|0.356	0.356	strong	.	DLEC1	278	.	NM_007337	exon7	c.G1230A	p.P410P	CCTCCCGCCTTCC	.	PASS	Atlas-SNP
MIA3	375056	hgsc.bcm.edu	37	1	222833538	222833538	+	Silent	SNP	C	C	G	rs2291835	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	108	107	86	0	0.990741	0	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	.	PASS	Atlas-SNP
PPL	5493	hgsc.bcm.edu	37	16	4933939	4933939	+	Missense_Mutation	SNP	G	G	C	rs2037912	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	151	69	145	0	0.456954	0	G|0.581;C|0.419	0.419	strong	.	PPL	168	.	NM_002705	exon22	c.C4717G	p.Q1573E	GGTTTTGCCTCTC	.	PASS	Atlas-SNP
DDX60L	91351	hgsc.bcm.edu	37	4	169279364	169279364	+	Silent	SNP	C	C	T	rs11736382	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	39	16	51	0	0.410256	0	C|0.960;T|0.040	0.040	strong	.	DDX60L	116	.	NM_001012967	exon38	c.G5055A	p.L1685L	TTGACTCAATTGT	.	PASS	Atlas-SNP
FUT3	2525	hgsc.bcm.edu	37	19	5844792	5844792	+	Missense_Mutation	SNP	A	A	C	rs28362459	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	150	150	142	1	1	0.00704225	A|0.832;C|0.168	0.168	strong	FUT3,NS,carcinoma,0,1	FUT3	30	1	NM_001097640	exon3	c.T59G	p.L20R	AATAGCAGTGCGG	.	PASS	Atlas-SNP
SAMM50	25813	hgsc.bcm.edu	37	22	44379822	44379822	+	Silent	SNP	T	T	C	rs10452	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	125	66	107	0	0.528	0	T|0.352;C|0.648	0.648	strong	.	SAMM50	30	.	NM_015380	exon12	c.T1017C	p.L339L	TTACCTTGGGGGA	.	PASS	Atlas-SNP
SEZ6L	23544	hgsc.bcm.edu	37	22	26688838	26688838	+	Silent	SNP	C	C	T	rs17304075	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	28	75	0	0.368421	0	C|0.919;T|0.081	0.081	strong	SEZ6L,NS,carcinoma,+2,1	SEZ6L	174	1	NM_001184777	exon2	c.C561T	p.D187D	GCTGGACCGAAAG	.	PASS	Atlas-SNP
PARP3	10039	hgsc.bcm.edu	37	3	51978552	51978552	+	Silent	SNP	C	C	T	rs142065339	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	38	88	0	0.44186	0	C|0.996;T|0.004	0.004	strong	PARP3_ENST00000398755,right_lower_lobe,carcinoma,+1,2	PARP3	90	2	NM_001003931	exon4	c.C480T	p.I160I	ACTTATCGAAGTA	.	PASS	Atlas-SNP
APCDD1	147495	hgsc.bcm.edu	37	18	10487918	10487918	+	Silent	SNP	C	C	T	rs3185480	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	29	71	0	0.467742	0	C|0.613;T|0.387	0.387	strong	.	APCDD1	57	.	NM_153000	exon5	c.C1428T	p.L476L	GGACCTCGCAGAA	.	PASS	Atlas-SNP
TEX10	54881	hgsc.bcm.edu	37	9	103064530	103064530	+	Silent	SNP	G	G	A	rs7472	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	41	104	0	0.476744	0	G|0.502;A|0.498	0.498	strong	.	TEX10	99	.	NM_017746	exon15	c.C2733T	p.F911F	CACGTTGAAGCAG	.	PASS	Atlas-SNP
AVIL	10677	hgsc.bcm.edu	37	12	58204648	58204648	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	132	6	91	0	0.0454545	0	.	.	none	.	AVIL	60	.	NM_006576	exon5	c.T509C	p.V170A	ATGATGACTTTCC	.	PASS	Atlas-SNP
LAIR1	3903	hgsc.bcm.edu	37	19	54867572	54867572	+	Silent	SNP	C	C	T	rs7257187	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	58	22	60	0	0.37931	0	C|0.734;T|0.266	0.266	strong	.	LAIR1	44	.	NM_002287	exon9	c.G708A	p.T236T	GGTGTCCGTCTCT	.	PASS	Atlas-SNP
TF	7018	hgsc.bcm.edu	37	3	133474328	133474328	+	Silent	SNP	G	G	A	rs12769	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	26	55	0	0.419355	0	G|0.727;A|0.273	0.273	strong	.	TF	116	.	NM_001063	exon5	c.G624A	p.S208S	CTACTCGGGAGCC	.	PASS	Atlas-SNP
IL9R	3581	hgsc.bcm.edu	37	X	155239827	155239827	+	Missense_Mutation	SNP	A	A	G	rs3865220		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	90	38	151	0	0.422222	0	.	.	weak	.	IL9R	73	.	NM_002186	exon9	c.A1319G	p.N440S	GCAACAACAACAA	.	PASS	Atlas-SNP
PSG5	5673	hgsc.bcm.edu	37	19	43680037	43680037	+	Missense_Mutation	SNP	T	T	A	rs1135901	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	14	14	51	0	1	0	T|0.792;A|0.208	0.208	strong	PSG5,colon,carcinoma,0,2	PSG5	58	2	NM_002781	exon3	c.A694T	p.T232S	TCAGGGTGACTGG	.	PASS	Atlas-SNP
POLQ	10721	hgsc.bcm.edu	37	3	121251922	121251922	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	237	66	228	0	0.278481	0	.	.	none	.	POLQ	273	.	NM_199420	exon6	c.T875C	p.L292P	TCCAAAAGCGGTA	.	PASS	Atlas-SNP
PLXNC1	10154	hgsc.bcm.edu	37	12	94642023	94642023	+	Silent	SNP	C	C	T	rs2230756	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	129	61	131	0	0.472868	0	C|0.932;T|0.068	0.068	strong	.	PLXNC1	135	.	NM_005761	exon14	c.C2613T	p.N871N	CTTCAACATTTCC	.	PASS	Atlas-SNP
CXXC11	285093	hgsc.bcm.edu	37	2	242814009	242814009	+	Missense_Mutation	SNP	G	G	A	rs7420371	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	31	20	45	0	0.645161	0	G|0.729;A|0.271	0.271	strong	.	.	.	.	NM_173821	exon2	c.G302A	p.G101E	CACCCGGGGACTG	.	PASS	Atlas-SNP
PLEKHM1	9842	hgsc.bcm.edu	37	17	43552921	43552921	+	Silent	SNP	C	C	T	rs12452273	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	153	153	154	0	1	0	C|0.865;T|0.135	0.135	strong	.	PLEKHM1	69	.	NM_014798	exon4	c.G468A	p.R156R	AGCATCCCGGAGC	.	PASS	Atlas-SNP
ZSCAN20	7579	hgsc.bcm.edu	37	1	33957130	33957130	+	Silent	SNP	C	C	A	rs3795419	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51	51	56	0	1	0	C|0.824;A|0.176	0.176	strong	ZSCAN20,NS,carcinoma,0,1	ZSCAN20	107	1	NM_145238	exon6	c.C1272A	p.A424A	AGAGGCCGTGGCA	.	PASS	Atlas-SNP
CIT	11113	hgsc.bcm.edu	37	12	120148363	120148363	+	Silent	SNP	C	C	T	rs35490437	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	108	48	142	0	0.444444	0	C|0.969;T|0.031	0.031	strong	.	CIT	535	.	NM_001206999	exon38	c.G4917A	p.T1639T	GGGCAGCGTGCAG	.	PASS	Atlas-SNP
GYPB	2994	hgsc.bcm.edu	37	4	144918712	144918712	+	Missense_Mutation	SNP	C	C	G	rs1132783	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	258	134	246	0	0.51938	0	C|0.822;G|0.178	0.178	strong	.	GYPB	17	.	NM_002100	exon4	c.G251C	p.S84T	CGAATACTGTAAG	.	PASS	Atlas-SNP
MYH9	4627	hgsc.bcm.edu	37	22	36690158	36690158	+	Missense_Mutation	SNP	C	C	T	rs147031322		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49	20	48	0	0.408163	0	C|1.000;T|0.000	0.000	weak	MYH9,rectum,carcinoma,0,1	MYH9	225	1	NM_002473	exon28	c.G3817A	p.D1273N	CCTTGTCGGCCAG	.	PASS	Atlas-SNP
MDFI	4188	hgsc.bcm.edu	37	6	41621271	41621271	+	Silent	SNP	G	G	A	rs2230088	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	36	7	25	0	0.194444	0	G|0.892;A|0.108	0.108	strong	.	MDFI	19	.	NM_005586	exon5	c.G699A	p.L233L	CTGCCTGGAGATC	.	PASS	Atlas-SNP
ZNF285	26974	hgsc.bcm.edu	37	19	44890654	44890654	+	Missense_Mutation	SNP	C	C	T	rs149238831	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100	15	108	0	0.15	0	C|0.995;T|0.005	0.005	strong	.	ZNF285	86	.	NM_152354	exon4	c.G1753A	p.E585K	TCTGCTCATGTAG	.	PASS	Atlas-SNP
IVL	3713	hgsc.bcm.edu	37	1	152882648	152882648	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79	11	82	0	0.139241	0	.	.	none	.	IVL	100	.	NM_005547	exon2	c.A375C	p.E125D	GGAAGAAGAGAAG	.	PASS	Atlas-SNP
PRC1	9055	hgsc.bcm.edu	37	15	91513674	91513674	+	Missense_Mutation	SNP	T	T	C	rs12911192	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	41	70	0	0.488095	0	T|0.954;C|0.046	0.046	strong	.	PRC1	51	.	NM_199413	exon12	c.A1532G	p.Y511C	GAGTGGTAGACTG	.	PASS	Atlas-SNP
FNDC8	54752	hgsc.bcm.edu	37	17	33454198	33454198	+	Missense_Mutation	SNP	G	G	T	rs147725468	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	49	61	0	0.583333	0	G|0.999;T|0.001	0.001	strong	.	FNDC8	28	.	NM_017559	exon2	c.G347T	p.G116V	TGGAGGGGGAGCT	.	PASS	Atlas-SNP
IL10RA	3587	hgsc.bcm.edu	37	11	117869878	117869878	+	Missense_Mutation	SNP	C	C	T	rs2229114	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	116	107	96	0	0.922414	0	C|0.969;T|0.031	0.031	strong	.	IL10RA	46	.	NM_001558	exon7	c.C1259T	p.S420L	GTGGCTCGGCCTT	.	PASS	Atlas-SNP
SH2D4B	387694	hgsc.bcm.edu	37	10	82331292	82331292	+	Silent	SNP	G	G	A	rs72805712	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	43	62	0	0.530864	0	G|0.869;A|0.131	0.131	strong	.	SH2D4B	44	.	NM_207372	exon3	c.G453A	p.K151K	CCGCAAGGCTGCC	.	PASS	Atlas-SNP
CEP192	55125	hgsc.bcm.edu	37	18	13095609	13095609	+	Missense_Mutation	SNP	T	T	C	rs474337	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	104	47	117	0	0.451923	0	T|0.259;C|0.741	0.741	strong	.	CEP192	340	.	NM_032142	exon35	c.T6362C	p.L2121P	CGCCTCTGGATCA	.	PASS	Atlas-SNP
HGD	3081	hgsc.bcm.edu	37	3	120369683	120369683	+	Silent	SNP	G	G	A	rs140977117	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110	62	87	0	0.563636	0	G|0.985;A|0.015	0.015	strong	HGD,NS,carcinoma,0,1	HGD	65	1	NM_000187	exon6	c.C372T	p.D124D	CTTTATGTCTCCA	.	PASS	Atlas-SNP
SPTLC3	55304	hgsc.bcm.edu	37	20	13145471	13145471	+	Missense_Mutation	SNP	G	G	A	rs200308499	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94	28	89	0	0.297872	0	.	.	weak	.	SPTLC3	78	.	NM_018327	exon12	c.G1616A	p.R539H	CAGCACGTCCTGA	.	PASS	Atlas-SNP
GPR112	139378	hgsc.bcm.edu	37	X	135430044	135430044	+	Silent	SNP	T	T	C	rs877761	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	114	75	69	0	0.657895	0	T|0.432;0|0.003	.	strong	.	GPR112	459	.	NM_153834	exon6	c.T4179C	p.T1393T	CAGGACTGTGGAA	.	PASS	Atlas-SNP
GID4	79018	hgsc.bcm.edu	37	17	17948475	17948475	+	Silent	SNP	G	G	A	rs2955355	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	96	44	70	0	0.458333	0	G|0.483;A|0.517	0.517	strong	C17orf39,right_upper_lobe,carcinoma,+2,1	.	.	1	NM_024052	exon2	c.G453A	p.G151G	CACGGGGAACTCT	.	PASS	Atlas-SNP
PSG5	5673	hgsc.bcm.edu	37	19	43679410	43679410	+	Silent	SNP	A	A	G	rs1058467	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	35	35	95	0	1	0	A|0.331;G|0.669	0.669	strong	.	PSG5	58	.	NM_002781	exon4	c.T921C	p.A307A	GCCAGTAGCTGAG	.	PASS	Atlas-SNP
SLC2A2	6514	hgsc.bcm.edu	37	3	170724955	170724955	+	Silent	SNP	C	C	T	rs5404	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	89	28	99	0	0.314607	0	C|0.847;T|0.153	0.153	strong	.	SLC2A2	71	.	NM_000340	exon5	c.G594A	p.T198T	AATGCCCGTGACG	.	PASS	Atlas-SNP
ZNF669	79862	hgsc.bcm.edu	37	1	247267274	247267274	+	Missense_Mutation	SNP	C	C	A	rs4925692	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	30	9	39	0	0.3	0	C|0.780;A|0.220	0.220	strong	.	ZNF669	46	.	NM_024804	exon1	c.G228T	p.E76D	ACAGGGCTCCGGC	.	PASS	Atlas-SNP
PIK3R2	5296	hgsc.bcm.edu	37	19	18273013	18273013	+	Silent	SNP	G	G	A	rs28730848	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	29	53	0	0.557692	0	G|0.964;A|0.036	0.036	strong	.	PIK3R2	48	.	NM_005027	exon8	c.G903A	p.A301A	CCCAGCGCTGCCG	.	PASS	Atlas-SNP
FCGRT	2217	hgsc.bcm.edu	37	19	50017724	50017724	+	Silent	SNP	C	C	T	rs2878342	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49	22	61	0	0.44898	0	C|0.846;T|0.154	0.154	strong	FCGRT,NS,carcinoma,0,1	FCGRT	23	1	NM_001136019	exon4	c.C582T	p.R194R	GGGCCGCGGAAAC	.	PASS	Atlas-SNP
CYP11B1	1584	hgsc.bcm.edu	37	8	143960597	143960597	+	Silent	SNP	G	G	A	rs5283	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	40	78	0	0.526316	0	G|0.668;A|0.332	0.332	strong	.	CYP11B1	128	.	NM_000497	exon2	c.C246T	p.D82D	TCCCAAGTCGTAC	.	PASS	Atlas-SNP
GLTSCR2	29997	hgsc.bcm.edu	37	19	48248924	48248924	+	Silent	SNP	G	G	A	rs3181870	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	136	75	113	0	0.551471	0	G|0.981;A|0.019	0.019	strong	.	GLTSCR2	45	.	NM_015710	exon1	c.G108A	p.R36R	GAGGCGGCGGCGG	.	PASS	Atlas-SNP
CPZ	8532	hgsc.bcm.edu	37	4	8605818	8605818	+	Silent	SNP	C	C	T	rs6852001	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57	29	56	0	0.508772	0	C|0.812;T|0.188	0.188	strong	CPZ,NS,carcinoma,0,1	CPZ	95	1	NM_001014447	exon4	c.C612T	p.C204C	CCGCTGCGCCCAC	.	PASS	Atlas-SNP
WDR44	54521	hgsc.bcm.edu	37	X	117566782	117566782	+	Silent	SNP	C	C	T	rs10521584	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	193	133	135	0	0.689119	0	C|0.842;0|0.014	.	strong	.	WDR44	188	.	NM_001184965	exon13	c.C1776T	p.N592N	TAAAAACGCACCC	.	PASS	Atlas-SNP
IKBKAP	8518	hgsc.bcm.edu	37	9	111663793	111663793	+	Silent	SNP	C	C	T	rs10979605	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94	37	88	0	0.393617	0	C|0.909;T|0.091	0.091	strong	.	IKBKAP	122	.	NM_003640	exon18	c.G1926A	p.T642T	AAATGACGTGATA	.	PASS	Atlas-SNP
ERBB3	2065	hgsc.bcm.edu	37	12	56494991	56494991	+	Silent	SNP	G	G	A	rs2271189	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68	31	53	0	0.455882	0	G|0.703;A|0.297	0.297	strong	.	ERBB3	350	.	NM_001982	exon27	c.G3348A	p.R1116R	GTGTAGGAGCCGG	.	PASS	Atlas-SNP
TAS2R16	50833	hgsc.bcm.edu	37	7	122634843	122634843	+	Silent	SNP	C	C	T	rs1204014	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83	45	86	0	0.542169	0	C|0.884;T|0.116	0.116	strong	TAS2R16,right_lower_lobe,carcinoma,-1,2	TAS2R16	57	2	NM_016945	exon1	c.G846A	p.T282T	TTTCAACGTAGGG	.	PASS	Atlas-SNP
ZNF117	51351	hgsc.bcm.edu	37	7	64439701	64439701	+	Missense_Mutation	SNP	C	C	T	rs3807069	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48	22	51	0	0.458333	0	C|0.612;T|0.388	0.388	strong	.	ZNF117	56	.	NM_015852	exon4	c.G248A	p.C83Y	TTATTACATTGAA	.	PASS	Atlas-SNP
EBI3	10148	hgsc.bcm.edu	37	19	4237067	4237067	+	Silent	SNP	A	A	G	rs4905	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	20	10	30	0	0.5	0	A|0.585;G|0.415	0.415	strong	.	EBI3	15	.	NM_005755	exon5	c.A672G	p.T224T	TGCCACAATGAGC	.	PASS	Atlas-SNP
QRICH2	84074	hgsc.bcm.edu	37	17	74290097	74290097	+	Silent	SNP	T	T	A	rs7225131	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	43	23	52	0	0.534884	0	T|0.574;A|0.426	0.426	strong	QRICH2,NS,adenoma,0,1	QRICH2	143	1	NM_032134	exon4	c.A213T	p.S71S	TGTTTCTGAGCCC	.	PASS	Atlas-SNP
ZDHHC11	79844	hgsc.bcm.edu	37	5	801252	801252	+	Missense_Mutation	SNP	C	C	T	rs142091140	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	137	10	120	0	0.0729927	0	C|0.999;T|0.001	0.001	strong	ZDHHC11_ENST00000424784,NS,carcinoma,0,3	ZDHHC11	97	3	NM_024786	exon12	c.G1209A	p.M403I	AGTTTTCATGGGC	.	scavenged	Atlas-SNP
RPS6KA4	8986	hgsc.bcm.edu	37	11	64127744	64127744	+	Silent	SNP	A	A	G	rs521950	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	18	9	32	0	0.5	0	A|0.713;G|0.287	0.287	strong	.	RPS6KA4	85	.	NM_001006944	exon3	c.A237G	p.Q79Q	GACGCAAGAGCAC	.	PASS	Atlas-SNP
FGD5	152273	hgsc.bcm.edu	37	3	14861103	14861103	+	Missense_Mutation	SNP	G	G	C	rs144016950	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	185	87	191	0	0.47027	0	G|0.999;T|0.001	.	strong	.	FGD5	248	.	NM_152536	exon1	c.G525C	p.E175D	CAGGGAGTGCAGC	.	PASS	Atlas-SNP
MCF2L	23263	hgsc.bcm.edu	37	13	113728781	113728781	+	Silent	SNP	G	G	A	rs3814264	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93	30	121	0	0.322581	0	G|0.809;A|0.191	0.191	strong	.	MCF2L	182	.	NM_001112732	exon10	c.G1020A	p.A340A	CGCAGCGTCCCAG	.	PASS	Atlas-SNP
RPN1	6184	hgsc.bcm.edu	37	3	128344786	128344786	+	Silent	SNP	G	G	A	rs1126828	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80	41	73	0	0.5125	0	G|0.779;A|0.221	0.221	strong	RPN1,NS,carcinoma,0,1	RPN1	39	1	NM_002950	exon7	c.C1206T	p.D402D	AAATGTGTCCAGA	.	PASS	Atlas-SNP
RGS3	5998	hgsc.bcm.edu	37	9	116346287	116346287	+	Silent	SNP	C	C	T	rs3810927	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	77	35	90	0	0.454545	0	C|0.832;T|0.168	0.168	strong	RGS3_ENST00000374140,NS,carcinoma,0,2	RGS3	251	2	NM_144488	exon21	c.C2595T	p.Y865Y	CACCTACAGCCAG	.	PASS	Atlas-SNP
FKBP15	23307	hgsc.bcm.edu	37	9	115931703	115931703	+	Silent	SNP	G	G	A	rs3810910	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	152	151	171	0	0.993421	0	G|0.712;A|0.288	0.288	strong	.	FKBP15	128	.	NM_015258	exon26	c.C3286T	p.L1096L	GGGACAGTCTTGT	.	PASS	Atlas-SNP
MATN1	4146	hgsc.bcm.edu	37	1	31188901	31188901	+	Silent	SNP	A	A	G	rs20566	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	123	59	90	0	0.479675	0	A|0.426;G|0.574	0.574	strong	.	MATN1	28	.	NM_002379	exon5	c.T1062C	p.T354T	AGCCCCAGTCATT	.	PASS	Atlas-SNP
IRAK2	3656	hgsc.bcm.edu	37	3	10276185	10276185	+	Missense_Mutation	SNP	C	C	G	rs11465927	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	114	58	139	0	0.508772	0	C|0.976;G|0.024	0.024	strong	.	IRAK2	113	.	NM_001570	exon11	c.C1315G	p.L439V	GCCTCGCTCTGCT	.	PASS	Atlas-SNP
MFAP2	4237	hgsc.bcm.edu	37	1	17301780	17301780	+	Silent	SNP	A	A	G	rs761422	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	140	60	153	0	0.428571	0	G|0.440;N|0.000	0.440	strong	.	MFAP2	8	.	NM_017459	exon8	c.T432C	p.H144H	CTCCTCATGGGCA	.	PASS	Atlas-SNP
SLC25A46	91137	hgsc.bcm.edu	37	5	110079450	110079450	+	Silent	SNP	T	T	C	rs17446534	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	249	122	196	0	0.48996	0	T|0.938;C|0.062	0.062	strong	.	SLC25A46	33	.	NM_138773	exon3	c.T346C	p.L116L	AATGTATTGGCAC	.	PASS	Atlas-SNP
TAP1	6890	hgsc.bcm.edu	37	6	32816772	32816772	+	Missense_Mutation	SNP	C	C	A	rs41550019	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	97	15	54	0	0.154639	0	G|0.000;C|0.939;A|0.061	0.061	strong	.	TAP1	39	.	NM_000593	exon6	c.G1552T	p.V518L	CCTCCACAGCCTG	.	PASS	Atlas-SNP
RICTOR	253260	hgsc.bcm.edu	37	5	38944635	38944635	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73	4	60	0	0.0547945	0	.	.	none	RICTOR,colon,carcinoma,0,1	RICTOR	182	1	NM_152756	exon36	c.G4826A	p.R1609H	AGTATACGGCACA	.	PASS	Atlas-SNP
ZCCHC16	340595	hgsc.bcm.edu	37	X	111698463	111698463	+	Silent	SNP	C	C	T	rs112035132	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	146	32	109	0	0.219178	0	C|0.941;T|0.059	0.059	strong	.	ZCCHC16	66	.	NM_001004308	exon3	c.C507T	p.L169L	CCTCCTCGCTCAA	.	PASS	Atlas-SNP
CTU2	348180	hgsc.bcm.edu	37	16	88781073	88781073	+	Missense_Mutation	SNP	G	G	A	rs11549835	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	95	49	111	0	0.515789	0	G|0.914;A|0.086	0.086	strong	.	CTU2	66	.	NM_001012759	exon12	c.G1280A	p.R427Q	AGACCCGGACACC	.	PASS	Atlas-SNP
DDX20	11218	hgsc.bcm.edu	37	1	112308972	112308972	+	Silent	SNP	G	G	A	rs197413	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	20	76	0	0.322581	0	G|0.512;A|0.488	0.488	strong	.	DDX20	50	.	NM_007204	exon11	c.G1926A	p.V642V	CCCTGTGTTGGCA	.	PASS	Atlas-SNP
CARS	833	hgsc.bcm.edu	37	11	3028140	3028140	+	Silent	SNP	G	G	A	rs729662	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48	23	44	0	0.479167	0	G|0.727;A|0.273	0.273	strong	.	CARS	114	.	NM_001014437	exon19	c.C2118T	p.P706P	AAGCTCGGGCAGG	.	PASS	Atlas-SNP
GJA9	81025	hgsc.bcm.edu	37	1	39341749	39341749	+	Missense_Mutation	SNP	C	C	T	rs61732191	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	160	2	152	0	0.0125	0	C|0.999;T|0.001	0.001	strong	GJA9,NS,malignant_melanoma,+1,1	GJA9	55	1	NM_030772	exon2	c.G22A	p.G8R	TATCTCCAAGGAG	.	scavenged	Atlas-SNP
B3GNT5	84002	hgsc.bcm.edu	37	3	182988131	182988131	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	156	69	168	0	0.442308	0	.	.	none	.	B3GNT5	26	.	NM_032047	exon2	c.A545G	p.Y182C	ATACCTATTGTCC	.	PASS	Atlas-SNP
TACC2	10579	hgsc.bcm.edu	37	10	123903133	123903133	+	Missense_Mutation	SNP	G	G	A	rs12765679	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	26	44	0	0.5	0	G|0.854;A|0.146	0.146	strong	.	TACC2	271	.	NM_206862	exon7	c.G5746A	p.E1916K	GCTGCAGAACACA	.	PASS	Atlas-SNP
ARHGAP33	115703	hgsc.bcm.edu	37	19	36273308	36273308	+	Silent	SNP	G	G	A	rs35297478	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	26	51	0	0.490566	0	G|0.905;A|0.095	0.095	strong	.	ARHGAP33	102	.	NM_052948	exon13	c.G1119A	p.L373L	GGAGCTGTCTGGC	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	83	97	0	0.988095	0	G|0.552;A|0.448	0.448	strong	.	ARHGAP42	32	.	NM_152432	exon20	c.G2137A	p.V713I	GGAGACGTTTCCC	.	PASS	Atlas-SNP
LIPK	643414	hgsc.bcm.edu	37	10	90490921	90490921	+	Silent	SNP	G	G	A	rs412227	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	42	77	0	0.482759	0	G|0.756;A|0.244	0.244	strong	.	LIPK	50	.	NM_001080518	exon3	c.G405A	p.P135P	ATCACCGGAATAC	.	PASS	Atlas-SNP
KIAA1984	84960	hgsc.bcm.edu	37	9	139694569	139694569	+	Missense_Mutation	SNP	A	A	C	rs7859194	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	13	7	19	0	0.538462	0	A|0.754;C|0.246	0.246	strong	.	KIAA1984	39	.	NM_001039374	exon4	c.A386C	p.D129A	AGCTGGACAGCCT	.	PASS	Atlas-SNP
TMEM5	10329	hgsc.bcm.edu	37	12	64173807	64173807	+	Missense_Mutation	SNP	G	G	A	rs61935924	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	21	21	40	0	1	0	G|0.927;A|0.073	0.073	strong	.	TMEM5	35	.	NM_014254	exon1	c.G67A	p.A23T	CTCTACGCTGCCT	.	PASS	Atlas-SNP
PPP1R18	170954	hgsc.bcm.edu	37	6	30652781	30652781	+	Missense_Mutation	SNP	C	C	T	rs9262143	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	115	89	78	0	0.773913	0	C|0.942;T|0.058	0.058	strong	.	.	.	.	NM_001134870	exon2	c.G1015A	p.G339R	CCTTCCCGGAGTT	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1246941	1246941	+	Missense_Mutation	SNP	A	A	G	rs2672785	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	218	114	237	0	0.522936	0	A|0.673;G|0.327	0.327	strong	MUC5B,NS,malignant_melanoma,-1,4	MUC5B	473	4	NM_002458	exon2	c.A101G	p.E34G	GCTGGGAGAATGC	.	PASS	Atlas-SNP
TSSK1B	83942	hgsc.bcm.edu	37	5	112770027	112770027	+	Silent	SNP	T	T	G	rs26980	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68	37	73	0	0.544118	0	T|0.931;G|0.069	0.069	strong	.	TSSK1B	89	.	NM_032028	exon1	c.A510C	p.A170A	GCTTAATGCCATT	.	PASS	Atlas-SNP
SLC17A9	63910	hgsc.bcm.edu	37	20	61588865	61588865	+	Silent	SNP	C	C	T	rs76379118	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	88	46	90	0	0.522727	0	C|0.958;T|0.042	0.042	strong	.	SLC17A9	54	.	NM_022082	exon3	c.C330T	p.L110L	ACTGCTCGCCCAC	.	PASS	Atlas-SNP
ERBB4	2066	hgsc.bcm.edu	37	2	212251864	212251864	+	Silent	SNP	T	T	C	rs3748962	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	189	92	165	0	0.486772	0	T|0.756;C|0.244	0.244	strong	.	ERBB4	480	.	NM_005235	exon27	c.A3195G	p.V1065V	TCGGTATACAAAC	.	PASS	Atlas-SNP
ANKRD26	22852	hgsc.bcm.edu	37	10	27303605	27303605	+	Missense_Mutation	SNP	A	A	T	rs2274741	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	118	118	120	0	1	0	A|0.712;T|0.288	0.288	strong	.	ANKRD26	179	.	NM_014915	exon31	c.T4542A	p.F1514L	CTCTCTAAACTGC	.	PASS	Atlas-SNP
ESPL1	9700	hgsc.bcm.edu	37	12	53662624	53662624	+	Missense_Mutation	SNP	C	C	A	rs6580942	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	40	39	31	0	0.975	0	C|0.192;A|0.808	0.808	strong	.	ESPL1	158	.	NM_012291	exon2	c.C74A	p.A25D	TGCCCGCCTTGAA	.	PASS	Atlas-SNP
QSOX1	5768	hgsc.bcm.edu	37	1	180159654	180159654	+	Silent	SNP	C	C	T	rs7521513	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82	40	78	0	0.487805	0	C|0.863;T|0.137	0.137	strong	.	QSOX1	79	.	NM_002826	exon10	c.C1227T	p.V409V	GTGGGTCCTCTTC	.	PASS	Atlas-SNP
GABRB1	2560	hgsc.bcm.edu	37	4	47322219	47322219	+	Silent	SNP	C	C	A	rs6284	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83	39	88	0	0.46988	0	C|0.849;A|0.151	0.151	strong	.	GABRB1	107	.	NM_000812	exon5	c.C537A	p.I179I	GGAGATCGAAAGT	.	PASS	Atlas-SNP
TRIM45	80263	hgsc.bcm.edu	37	1	117656088	117656088	+	Missense_Mutation	SNP	A	A	G	rs1289658	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	95	95	103	0	1	0	A|0.549;G|0.451	0.451	strong	.	TRIM45	55	.	NM_025188	exon5	c.T1487C	p.M496T	CTCACCATCACAG	.	PASS	Atlas-SNP
FHOD1	29109	hgsc.bcm.edu	37	16	67281172	67281172	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	11	6	16	0	0.545455	0	.	.	none	.	FHOD1	86	.	NM_013241	exon1	c.G142A	p.A48T	GCAGCGCCCCGTC	.	PASS	Atlas-SNP
SGK1	6446	hgsc.bcm.edu	37	6	134495200	134495200	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	5	72	0	0.0657895	0	.	.	none	.	SGK1	387	.	NM_001143676	exon5	c.C456G	p.I152M	CTTCAAGATGGAC	.	PASS	Atlas-SNP
SNAP25	6616	hgsc.bcm.edu	37	20	10258375	10258375	+	Splice_Site	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	20	5	40	0	0.25	0	.	.	none	.	SNAP25	79	.	NM_130811	exon3	c.114+1G>A	.	GAAGAGGTAAGAA	.	PASS	Atlas-SNP
SLCO4C1	353189	hgsc.bcm.edu	37	5	101575091	101575091	+	Silent	SNP	C	C	T	rs62370437	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	88	48	65	0	0.545455	0	C|0.597;T|0.403	0.403	strong	.	SLCO4C1	113	.	NM_180991	exon12	c.G1878A	p.G626G	AATTGTCCCTAAA	.	PASS	Atlas-SNP
STAT3	6774	hgsc.bcm.edu	37	17	40475330	40475330	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	102	33	87	0	0.323529	0	.	.	none	STAT3,NS,lymphoid_neoplasm,0,1	STAT3	268	1	NM_003150	exon19	c.G1696T	p.D566Y	TATTGTCCAGCCA	.	PASS	Atlas-SNP
CFHR4	10877	hgsc.bcm.edu	37	1	196884258	196884258	+	Silent	SNP	A	A	T	rs379049		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	509	143	354	1	0.280943	0.00282486	.	.	weak	CFHR4_ENST00000367416,right_lower_lobe,carcinoma,+1,2	CFHR4	141	2	NM_001201550	exon9	c.A1530T	p.P510P	ACCACCAAGATGC	.	scavenged	Atlas-SNP
IRS2	8660	hgsc.bcm.edu	37	13	110435914	110435914	+	Silent	SNP	G	G	A	rs12853546	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	19	13	21	0	0.684211	0	G|0.788;A|0.212	0.212	strong	IRS2,NS,carcinoma,0,1	IRS2	44	1	NM_003749	exon1	c.C2487T	p.P829P	CCCCACGGGGGAG	.	PASS	Atlas-SNP
C3orf20	84077	hgsc.bcm.edu	37	3	14724413	14724413	+	Missense_Mutation	SNP	G	G	A	rs9821143	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	44	93	0	0.505747	0	G|0.672;A|0.328	0.328	strong	.	C3orf20	109	.	NM_032137	exon3	c.G193A	p.D65N	CCGTCCGACATCT	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1101649	1101649	+	Silent	SNP	T	T	C	rs7480563	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	54	41	0	1	0	T|0.346;C|0.654	0.654	strong	MUC2_ENST00000441003,NS,carcinoma,0,1	MUC2	614	1	NM_002457	exon43	c.T7650C	p.P2550P	CTGTCCTTTCTAC	.	PASS	Atlas-SNP
DHX9	1660	hgsc.bcm.edu	37	1	182844020	182844020	+	Silent	SNP	C	C	T	rs11332	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55	30	44	0	0.545455	0	C|0.865;T|0.135	0.135	strong	.	DHX9	114	.	NM_001357	exon16	c.C1746T	p.T582T	GATGACCCACTTT	.	PASS	Atlas-SNP
OR10H1	26539	hgsc.bcm.edu	37	19	15918434	15918434	+	Silent	SNP	C	C	A	rs1859299	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	151	70	138	0	0.463576	0	A|0.032;C|0.968	0.032	strong	.	OR10H1	59	.	NM_013940	exon1	c.G414T	p.P138P	GCCCCGCGGGCTC	.	PASS	Atlas-SNP
ALPPL2	251	hgsc.bcm.edu	37	2	233274509	233274509	+	Missense_Mutation	SNP	C	C	G	rs1048995	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	18	9	18	0	0.5	0	C|0.899;G|0.101	0.101	strong	ALPPL2,NS,carcinoma,0,2	ALPPL2	36	2	NM_031313	exon11	c.C1526G	p.P509R	CGGGGCCGTCCGT	.	scavenged	Atlas-SNP
SNAPC4	6621	hgsc.bcm.edu	37	9	139289825	139289825	+	Silent	SNP	A	A	G	rs4266763	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	134	134	188	1	1	0.00531915	A|0.611;G|0.388	0.388	strong	.	SNAPC4	82	.	NM_003086	exon4	c.T396C	p.D132D	TTTGCCATCTTTC	.	PASS	Atlas-SNP
MRPL45	84311	hgsc.bcm.edu	37	17	36453167	36453167	+	Silent	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	20	51	0	0.298507	0	.	.	none	.	MRPL45	27	.	NM_032351	exon1	c.T18C	p.P6P	CATACCTCAAGGG	.	PASS	Atlas-SNP
IDO2	169355	hgsc.bcm.edu	37	8	39840234	39840234	+	Missense_Mutation	SNP	A	A	G	rs4736794	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60	36	72	0	0.6	0	A|0.845;G|0.155	0.155	strong	.	IDO2	78	.	NM_194294	exon5	c.A418G	p.I140V	CCTCCTATCCTGG	.	PASS	Atlas-SNP
STT3B	201595	hgsc.bcm.edu	37	3	31667621	31667621	+	Splice_Site	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	96	2	102	0	0.0208333	0	.	.	none	STT3B,NS,carcinoma,0,1	STT3B	52	1	NM_178862	exon13	c.2073+2T>C	.	TTCGGGTAAGAAA	.	scavenged	Atlas-SNP
OR2T33	391195	hgsc.bcm.edu	37	1	248436655	248436655	+	Silent	SNP	C	C	G	rs140771747		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	516	41	412	0	0.0794574	0	C|0.999;G|0.001	0.001	weak	OR2T33,NS,carcinoma,0,3	OR2T33	133	3	NM_001004695	exon1	c.G462C	p.G154G	CAGGAGCCCGTCA	.	PASS	Atlas-SNP
HSP90AA1	3320	hgsc.bcm.edu	37	14	102552201	102552201	+	Silent	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	155	40	136	0	0.258065	0	.	.	none	.	HSP90AA1	65	.	NM_001017963	exon4	c.T789C	p.A263A	CAAATAAGCAGAA	.	PASS	Atlas-SNP
PJA1	64219	hgsc.bcm.edu	37	X	68381912	68381912	+	Silent	SNP	G	G	A	rs3761646	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	46	31	50	0	0.673913	0	G|0.863;0|0.003	.	strong	.	PJA1	106	.	NM_145119	exon2	c.C1170T	p.G390G	GCTTTCGCCACTG	.	PASS	Atlas-SNP
FAM208B	54906	hgsc.bcm.edu	37	10	5781802	5781802	+	Missense_Mutation	SNP	C	C	A	rs41310221	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	105	58	96	0	0.552381	0	C|0.994;A|0.006	0.006	strong	.	.	.	.	NM_017782	exon13	c.C1669A	p.L557I	AGAAATCTTCACT	.	PASS	Atlas-SNP
CCDC105	126402	hgsc.bcm.edu	37	19	15131330	15131330	+	Missense_Mutation	SNP	G	G	A	rs35352238	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	118	117	110	0	0.991525	0	G|0.758;A|0.242	0.242	strong	.	CCDC105	53	.	NM_173482	exon3	c.G733A	p.V245M	CAAGCCGTGGACC	.	PASS	Atlas-SNP
PTPRD	5789	hgsc.bcm.edu	37	9	8449782	8449782	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	189	57	228	0	0.301587	0	.	.	none	.	PTPRD	1348	.	NM_002839	exon34	c.C3931T	p.P1311S	GTGAAGGGATCTC	.	PASS	Atlas-SNP
SIPA1L3	23094	hgsc.bcm.edu	37	19	38673298	38673298	+	Missense_Mutation	SNP	C	C	G	rs3745945	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79	38	66	0	0.481013	0	C|0.942;G|0.058	0.058	strong	.	SIPA1L3	150	.	NM_015073	exon16	c.C4348G	p.P1450A	AAGCAGCCTGTAC	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110	58	124	1	0.527273	0.00806452	T|0.489;C|0.511	0.511	strong	C10orf116,NS,carcinoma,0,1	.	.	1	NM_006829	exon3	c.T204C	p.I68I	TGGGATTGGGAAA	.	scavenged	Atlas-SNP
GABBR2	9568	hgsc.bcm.edu	37	9	101340316	101340316	+	Silent	SNP	T	T	C	rs3750344	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	42	84	0	0.552632	0	T|0.809;C|0.191	0.191	strong	.	GABBR2	126	.	NM_005458	exon2	c.A360G	p.A120A	TTTTATTGCATCG	.	PASS	Atlas-SNP
OR1S2	219958	hgsc.bcm.edu	37	11	57971201	57971201	+	Silent	SNP	G	G	A	rs11229280	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	139	129	197	1	0.928058	0.00507614	G|0.585;A|0.415	0.415	strong	OR1S2,NS,carcinoma,-2,3	OR1S2	119	3	NM_001004459	exon1	c.C453T	p.A151A	GAACCTGGCCCGC	.	PASS	Atlas-SNP
OGFOD3	79701	hgsc.bcm.edu	37	17	80350331	80350331	+	Silent	SNP	G	G	A	rs11903	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	139	66	155	0	0.47482	0	G|0.764;A|0.236	0.236	strong	.	.	.	.	NM_024648	exon9	c.C903T	p.I301I	GATGGTGATGGCG	.	PASS	Atlas-SNP
LMF1	64788	hgsc.bcm.edu	37	16	921179	921179	+	Missense_Mutation	SNP	G	G	A	rs143076454	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	88	37	91	0	0.420455	0	G|0.988;A|0.012	0.012	strong	.	LMF1	42	.	NM_022773	exon7	c.C1060T	p.R354W	CGGGCCGGGCCCC	.	PASS	Atlas-SNP
TCF7L1	83439	hgsc.bcm.edu	37	2	85536415	85536415	+	Missense_Mutation	SNP	G	G	A	rs11547160	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	38	68	0	0.716981	0	G|0.963;A|0.037	0.037	strong	.	TCF7L1	44	.	NM_031283	exon12	c.G1597A	p.G533R	TCCTCTGGGCAGA	.	PASS	Atlas-SNP
TAS1R2	80834	hgsc.bcm.edu	37	1	19175944	19175944	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	92	4	86	0	0.0434783	0	.	.	none	.	TAS1R2	134	.	NM_152232	exon4	c.G1358A	p.W453X	CATTGCCACTGGA	.	PASS	Atlas-SNP
CD276	80381	hgsc.bcm.edu	37	15	73996066	73996066	+	Missense_Mutation	SNP	G	G	A	rs11574483	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98	48	94	0	0.489796	0	G|0.889;A|0.111	0.111	strong	CD276,NS,carcinoma,0,1	CD276	29	1	NM_001024736	exon5	c.G800A	p.R267H	CCCTGCGCTGCTC	.	PASS	Atlas-SNP
MMP3	4314	hgsc.bcm.edu	37	11	102713447	102713447	+	Silent	SNP	G	G	C	rs41380244	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	124	15	101	0	0.120968	0	G|0.915;C|0.085	0.085	strong	.	MMP3	60	.	NM_002422	exon2	c.C306G	p.T102T	AGGAAAGGTTCTG	.	PASS	Atlas-SNP
SOX30	11063	hgsc.bcm.edu	37	5	157078475	157078475	+	Silent	SNP	C	C	G	rs3749797	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	195	85	208	1	0.435897	0.00480769	C|0.825;G|0.175	0.175	strong	SOX30,NS,carcinoma,0,1	SOX30	67	1	NM_178424	exon1	c.G612C	p.P204P	GGCTGCCGGGCTT	.	scavenged	Atlas-SNP
HIST1H1B	3009	hgsc.bcm.edu	37	6	27835272	27835272	+	Silent	SNP	T	T	C	rs200948	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	66	71	0	0.868421	0	T|0.896;C|0.104	0.104	strong	.	HIST1H1B	54	.	NM_005322	exon1	c.A36G	p.P12P	CGGCGCTGGGGTG	.	PASS	Atlas-SNP
PCNXL4	64430	hgsc.bcm.edu	37	14	60591829	60591829	+	Silent	SNP	T	T	C	rs308990	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	261	258	214	0	0.988506	0	T|0.723;C|0.277	0.277	strong	.	.	.	.	NM_022495	exon8	c.T2238C	p.F746F	TTATTTTAGTTTA	.	PASS	Atlas-SNP
ZNF99	7652	hgsc.bcm.edu	37	19	22941191	22941191	+	Missense_Mutation	SNP	T	T	A	rs11667397	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	17	8	16	0	0.470588	0	T|0.834;A|0.166	0.166	strong	.	ZNF99	273	.	NM_001080409	exon4	c.A1520T	p.K507I	CAAGGTTTCTCTT	.	PASS	Atlas-SNP
DCHS2	54798	hgsc.bcm.edu	37	4	155412464	155412464	+	Missense_Mutation	SNP	C	C	T	rs13149269	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68	66	60	0	0.970588	0	C|0.653;N|0.001	.	strong	.	DCHS2	594	.	NM_001142552	exon1	c.G44A	p.R15Q	GCCCGCCGCTGCT	.	PASS	Atlas-SNP
COL18A1	80781	hgsc.bcm.edu	37	21	46924383	46924383	+	Silent	SNP	C	C	T	rs11544970	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	22	13	29	0	0.590909	0	C|0.975;T|0.025	0.025	strong	.	COL18A1	129	.	NM_030582	exon33	c.C3321T	p.P1107P	GGAGCCCGGGGGC	.	PASS	Atlas-SNP
SLC2A4RG	56731	hgsc.bcm.edu	37	20	62373707	62373707	+	Missense_Mutation	SNP	G	G	T	rs8957	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	90	44	72	0	0.488889	0	G|0.242;T|0.758	0.758	strong	SLC2A4RG,NS,carcinoma,0,1	SLC2A4RG	20	1	NM_020062	exon6	c.G699T	p.E233D	GCCTGAGCAGAGT	.	PASS	Atlas-SNP
SGK223	0	hgsc.bcm.edu	37	8	8176554	8176554	+	Missense_Mutation	SNP	C	C	T	rs12549973	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	25	13	17	0	0.52	0	C|0.701;T|0.299	0.299	strong	.	.	.	.	NM_001080826	exon5	c.G3331A	p.A1111T	GCTCCGCCTGGTG	.	PASS	Atlas-SNP
KLHL26	55295	hgsc.bcm.edu	37	19	18775077	18775077	+	Silent	SNP	C	C	T	rs1076235	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	26	16	16	0	0.615385	0	C|0.625;T|0.375	0.375	strong	KLHL26,NS,carcinoma,0,1	KLHL26	43	1	NM_018316	exon2	c.C90T	p.A30A	CACGGCCGACAAG	.	PASS	Atlas-SNP
GIMAP2	26157	hgsc.bcm.edu	37	7	150389593	150389593	+	Silent	SNP	T	T	C	rs1860871	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110	59	126	0	0.536364	0	T|0.910;C|0.090	0.090	strong	.	GIMAP2	39	.	NM_015660	exon3	c.T219C	p.I73I	AGAGATTGTCATT	.	PASS	Atlas-SNP
RBMXL3	139804	hgsc.bcm.edu	37	X	114426385	114426385	+	Missense_Mutation	SNP	G	G	A	rs80194951	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	160	48	151	0	0.3	0	G|0.929;A|0.071	0.071	strong	.	RBMXL3	83	.	NM_001145346	exon1	c.G2381A	p.R794H	GAGGCCGCTCACC	.	PASS	Atlas-SNP
MTHFR	4524	hgsc.bcm.edu	37	1	11854896	11854896	+	Silent	SNP	G	G	A	rs2066462	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	122	68	103	0	0.557377	0	G|0.910;A|0.090	0.090	strong	.	MTHFR	65	.	NM_005957	exon7	c.C1056T	p.S352S	GTGGGCGCTGAGA	.	PASS	Atlas-SNP
SLC4A7	9497	hgsc.bcm.edu	37	3	27472936	27472936	+	Missense_Mutation	SNP	C	C	T	rs3755652	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	147	78	170	0	0.530612	0	C|0.843;T|0.157	0.157	strong	.	SLC4A7	119	.	NM_003615	exon7	c.G976A	p.E326K	GACTCTCTTGGGA	.	PASS	Atlas-SNP
C9orf123	90871	hgsc.bcm.edu	37	9	7799606	7799606	+	Silent	SNP	C	C	A	rs14059	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	43	43	46	0	1	0	C|0.639;A|0.361	0.361	strong	.	C9orf123	7	.	NM_033428	exon1	c.G129T	p.L43L	CTTCAACAGGCGG	.	PASS	Atlas-SNP
OR2W5	441932	hgsc.bcm.edu	37	1	247655102	247655102	+	Missense_Mutation	SNP	G	G	A	rs143904230	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94	60	76	0	0.638298	0	G|0.989;A|0.011	0.011	strong	.	OR2W5	97	.	NM_001004698	exon1	c.G673A	p.G225S	AGCCGCGGTGCTG	.	PASS	Atlas-SNP
SPDYE1	285955	hgsc.bcm.edu	37	7	44047066	44047066	+	Missense_Mutation	SNP	T	T	C	rs79154079		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	127	29	155	0	0.228346	0	.	.	weak	.	SPDYE1	29	.	NM_175064	exon5	c.T832C	p.C278R	CGCCGTTGCATGA	.	PASS	Atlas-SNP
FBN3	84467	hgsc.bcm.edu	37	19	8159339	8159339	+	Missense_Mutation	SNP	G	G	C	rs34167077	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55	27	37	0	0.490909	0	G|0.937;C|0.063	0.063	strong	.	FBN3	300	.	NM_032447	exon46	c.C5896G	p.H1966D	TGCAGTGGTCACT	.	PASS	Atlas-SNP
NOS1	4842	hgsc.bcm.edu	37	12	117672544	117672544	+	Missense_Mutation	SNP	G	G	A	rs375069851		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68	26	72	0	0.382353	0	.	.	weak	NOS1,caecum,carcinoma,0,2	NOS1	240	2	NM_001204218	exon22	c.C3163T	p.R1055C	GGAGACGCACGAA	.	PASS	Atlas-SNP
GPRIN1	114787	hgsc.bcm.edu	37	5	176026143	176026143	+	Silent	SNP	C	C	T	rs77245696	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94	30	132	0	0.319149	0	C|0.778;T|0.222	0.222	strong	.	GPRIN1	77	.	NM_052899	exon2	c.G693A	p.R231R	CTCCTTCCTCGGT	.	PASS	Atlas-SNP
BST1	683	hgsc.bcm.edu	37	4	15720553	15720553	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79	38	82	0	0.481013	0	.	.	none	.	BST1	30	.	NM_004334	exon7	c.T728C	p.M243T	GCAGCATGAAAGT	.	PASS	Atlas-SNP
SPNS3	201305	hgsc.bcm.edu	37	17	4391132	4391132	+	Silent	SNP	C	C	T	rs2291743	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	92	37	84	0	0.402174	0	C|0.793;T|0.207	0.207	strong	SPNS3,NS,carcinoma,0,1	SPNS3	52	1	NM_182538	exon12	c.C1482T	p.N494N	CAGCAACGACCTG	.	PASS	Atlas-SNP
OR2F2	135948	hgsc.bcm.edu	37	7	143632618	143632618	+	Missense_Mutation	SNP	C	C	T	rs61744352	byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	96	92	110	0	0.958333	0	C|0.403;T|0.597	0.597	strong	.	OR2F2	63	.	NM_001004685	exon1	c.C293T	p.A98V	GCTGTGCAGCCCA	.	PASS	Atlas-SNP
ACOXL	55289	hgsc.bcm.edu	37	2	111691147	111691147	+	Silent	SNP	G	G	A	rs3761711	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	124	61	116	0	0.491935	0	G|0.971;A|0.029	0.029	strong	.	ACOXL	93	.	NM_001142807	exon12	c.G987A	p.A329A	GGTGGCGGGGCTG	.	PASS	Atlas-SNP
CCDC122	160857	hgsc.bcm.edu	37	13	44411421	44411421	+	Missense_Mutation	SNP	C	C	T	rs79782223	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	232	57	135	0	0.24569	0	C|0.963;T|0.037	0.037	strong	.	CCDC122	21	.	NM_144974	exon7	c.G817A	p.E273K	GTTACTCTTGCAT	.	PASS	Atlas-SNP
KCNQ2	3785	hgsc.bcm.edu	37	20	62046278	62046278	+	Silent	SNP	G	G	C	rs1801545	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	89	52	107	0	0.58427	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
SERPINA9	327657	hgsc.bcm.edu	37	14	94933695	94933695	+	Missense_Mutation	SNP	G	G	A	rs17090921	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	29	52	0	0.453125	0	G|0.689;A|0.311	0.311	strong	.	SERPINA9	105	.	NM_175739	exon3	c.C707T	p.P236L	TATTCAGGGTGAA	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	111	88	107	0	0.792793	0	A|0.004;C|0.245	0.245	strong	.	HIST1H3I	28	.	NM_003533	exon1	c.A348G	p.K116K	GACGCGTTTGGCG	.	PASS	Atlas-SNP
PYGL	5836	hgsc.bcm.edu	37	14	51383432	51383432	+	Silent	SNP	G	G	A	rs2075643	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94	51	93	0	0.542553	0	G|0.807;A|0.193	0.193	strong	.	PYGL	77	.	NM_002863	exon9	c.C1020T	p.D340D	GTGAGTGTCATTC	.	PASS	Atlas-SNP
CAB39L	81617	hgsc.bcm.edu	37	13	49951193	49951193	+	Silent	SNP	T	T	C	rs8002858	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	219	119	154	0	0.543379	0	T|0.454;C|0.546	0.546	strong	.	CAB39L	35	.	NM_030925	exon3	c.A186G	p.P62P	TTCTGTTGGGGGT	.	PASS	Atlas-SNP
COL4A1	1282	hgsc.bcm.edu	37	13	110838814	110838814	+	Silent	SNP	A	A	G	rs61749897	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	30	45	0	0.576923	0	A|0.900;G|0.100	0.100	strong	.	COL4A1	372	.	NM_001845	exon26	c.T1815C	p.P605P	TCCTGGAGGCCCA	.	PASS	Atlas-SNP
DTYMK	1841	hgsc.bcm.edu	37	2	242618050	242618050	+	Silent	SNP	A	A	G	rs1131195	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57	18	65	0	0.315789	0	A|0.622;G|0.378	0.378	strong	.	DTYMK	9	.	NM_012145	exon4	c.T345C	p.D115D	ACACCAATCTAGG	.	PASS	Atlas-SNP
ESPNL	339768	hgsc.bcm.edu	37	2	239039183	239039183	+	Missense_Mutation	SNP	G	G	A	rs73102303	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	45	24	70	0	0.533333	0	G|0.871;A|0.129	0.129	strong	ESPNL,NS,carcinoma,0,1	ESPNL	63	1	NM_194312	exon9	c.G1828A	p.V610M	AAGGGCGTGCATG	.	PASS	Atlas-SNP
TMEM254	80195	hgsc.bcm.edu	37	10	81841692	81841692	+	Missense_Mutation	SNP	G	G	T	rs1932574	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57	35	73	0	0.614035	0	G|0.607;T|0.393	0.393	strong	.	TMEM254	1	.	NM_001270371	exon3	c.G278T	p.C93F	CCTCCTGTGCAAT	.	PASS	Atlas-SNP
PAIP2B	400961	hgsc.bcm.edu	37	2	71415619	71415619	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80	54	143	0	0.675	0	.	.	none	.	PAIP2B	7	.	NM_020459	exon4	c.A362G	p.E121G	TACTTCTCTCCTG	.	PASS	Atlas-SNP
OR4K17	390436	hgsc.bcm.edu	37	14	20585769	20585769	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	205	95	267	0	0.463415	0	.	.	none	.	OR4K17	58	.	NM_001004715	exon1	c.C204T	p.V68V	TGTGGTCACAGTT	.	PASS	Atlas-SNP
KLK1	3816	hgsc.bcm.edu	37	19	51323676	51323676	+	Missense_Mutation	SNP	C	C	T	rs5515	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	114	58	122	0	0.508772	0	C|0.947;T|0.053	0.053	strong	.	KLK1	27	.	NM_002257	exon3	c.G230A	p.R77H	TTGTGGCGACCCA	.	PASS	Atlas-SNP
BPI	671	hgsc.bcm.edu	37	20	36946848	36946848	+	Missense_Mutation	SNP	G	G	A	rs4358188	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	151	149	130	0	0.986755	0	G|0.558;A|0.442	0.442	strong	BPI,NS,carcinoma,0,1	BPI	67	1	NM_001725	exon6	c.G646A	p.E216K	TCCTCCGAGCTGC	.	PASS	Atlas-SNP
MEF2D	4209	hgsc.bcm.edu	37	1	156446903	156446903	+	Silent	SNP	T	T	C	rs2274317	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85	80	83	1	0.941176	0.0120482	A|0.000;C|0.551;T|0.449	0.551	strong	MEF2D,colon,adenoma,-1,1	MEF2D	43	1	NM_005920	exon7	c.A756G	p.P252P	TGGGGGTGGAGAC	.	scavenged	Atlas-SNP
KIAA0556	23247	hgsc.bcm.edu	37	16	27752135	27752135	+	Silent	SNP	C	C	T	rs12447120	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	38	75	0	0.5	0	C|0.837;T|0.163	0.163	strong	.	KIAA0556	348	.	NM_015202	exon15	c.C2517T	p.D839D	CTCAGACATCTTT	.	PASS	Atlas-SNP
PALLD	23022	hgsc.bcm.edu	37	4	169606649	169606649	+	Missense_Mutation	SNP	C	C	A	rs62333891	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	36	103	0	0.413793	0	C|0.887;A|0.113	0.113	strong	.	PALLD	179	.	NM_001166108	exon6	c.C1274A	p.T425N	GTCCAACTTCATA	.	PASS	Atlas-SNP
DSC3	1825	hgsc.bcm.edu	37	18	28586964	28586964	+	Silent	SNP	A	A	G	rs1313586	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	92	49	112	0	0.532609	0	A|0.478;G|0.521	0.521	strong	DSC3,NS,carcinoma,0,1	DSC3	225	1	NM_024423	exon12	c.T1797C	p.P599P	TTCATCAGGATCA	.	PASS	Atlas-SNP
INPP5E	56623	hgsc.bcm.edu	37	9	139328551	139328551	+	Silent	SNP	T	T	C	rs10870199	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	26	13	18	0	0.5	0	T|0.894;C|0.106	0.106	strong	.	INPP5E	18	.	NM_019892	exon3	c.A972G	p.P324P	CTCGGCTGGGAGC	.	PASS	Atlas-SNP
MRGPRG	386746	hgsc.bcm.edu	37	11	3239366	3239366	+	Silent	SNP	G	G	A	rs145777944	by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	49	93	0	0.563218	0	G|1.000;A|0.000	0.000	strong	.	MRGPRG	6	.	NM_001164377	exon1	c.C678T	p.F226F	CAGCAGGAAGTTC	.	PASS	Atlas-SNP
STK17B	9262	hgsc.bcm.edu	37	2	197021276	197021276	+	Silent	SNP	T	T	C	rs10931726	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	229	84	196	0	0.366812	0	T|0.540;C|0.460	0.460	strong	STK17B,NS,carcinoma,-1,1	STK17B	28	1	NM_004226	exon3	c.A222G	p.R74R	TTCTGCTCGACAA	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	43	32	55	0	0.744186	0	G|0.687;C|0.313	0.313	strong	.	ALMS1	384	.	NM_015120	exon8	c.G6851C	p.R2284P	TTGCCCGTTTCAG	.	PASS	Atlas-SNP
CDRT1	374286	hgsc.bcm.edu	37	17	15496727	15496727	+	Missense_Mutation	SNP	T	T	G	rs79385100	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	174	101	203	0	0.58046	0	T|0.825;G|0.175	0.175	strong	.	CDRT1	83	.	NM_006382	exon11	c.A1930C	p.N644H	TCCCATTGAAGAA	.	PASS	Atlas-SNP
SPATA4	132851	hgsc.bcm.edu	37	4	177113836	177113836	+	Silent	SNP	C	C	T	rs6832177	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	141	64	150	1	0.453901	0.00666667	C|0.701;T|0.299	0.299	strong	SPATA4,NS,carcinoma,-1,1	SPATA4	44	1	NM_144644	exon4	c.G630A	p.A210A	GAACTCCGCTTTA	.	scavenged	Atlas-SNP
GAD1	2571	hgsc.bcm.edu	37	2	171678625	171678625	+	Silent	SNP	T	T	C	rs769404	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	36	36	42	0	1	0	T|0.654;C|0.346	0.346	strong	GAD1,colon,carcinoma,0,1	GAD1	79	1	NM_000817	exon3	c.T111C	p.H37H	GGCCCATGGATGC	.	PASS	Atlas-SNP
POC5	134359	hgsc.bcm.edu	37	5	75003678	75003678	+	Missense_Mutation	SNP	T	T	C	rs2307111	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	180	180	221	0	1	0	T|0.429;C|0.571	0.571	strong	.	POC5	82	.	NM_001099271	exon3	c.A107G	p.H36R	GCATAATGAAGCA	.	PASS	Atlas-SNP
PIM1	5292	hgsc.bcm.edu	37	6	37138946	37138946	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55	8	53	0	0.145455	0	.	.	none	.	PIM1	71	.	NM_001243186	exon4	c.G559A	p.V187M	AAGAAGGTGAGCT	.	PASS	Atlas-SNP
QRICH2	84074	hgsc.bcm.edu	37	17	74289839	74289839	+	Silent	SNP	G	G	A	rs6501881	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	138	59	138	0	0.427536	0	G|0.579;A|0.421	0.421	strong	.	QRICH2	143	.	NM_032134	exon4	c.C471T	p.G157G	TGGCACGCCAGCT	.	PASS	Atlas-SNP
HIST1H2AE	3012	hgsc.bcm.edu	37	6	26217245	26217245	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	25	89	0	0.308642	0	.	.	none	.	HIST1H2AE	25	.	NM_021052	exon1	c.G43A	p.A15T	GCAAAAGCTAAAA	.	PASS	Atlas-SNP
NUGGC	389643	hgsc.bcm.edu	37	8	27903069	27903069	+	Missense_Mutation	SNP	C	C	T	rs13279787	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	120	54	108	0	0.45	0	C|0.625;N|0.000	.	strong	.	.	.	.	NM_001010906	exon12	c.G1421A	p.S474N	TTGAAACTATCTG	.	PASS	Atlas-SNP
CACNA1F	778	hgsc.bcm.edu	37	X	49081230	49081230	+	Missense_Mutation	SNP	C	C	T	rs141010716	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69	47	55	0	0.681159	0	C|0.997;T|0.003	0.003	strong	.	CACNA1F	218	.	NM_005183	exon14	c.G1903A	p.V635I	TGGTGACCTTAAA	.	PASS	Atlas-SNP
LILRA6	79168	hgsc.bcm.edu	37	19	54745665	54745665	+	Missense_Mutation	SNP	C	C	T	rs1052966	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	537	63	661	0	0.117318	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
SMCR8	140775	hgsc.bcm.edu	37	17	18219742	18219742	+	Silent	SNP	G	G	A	rs34824853	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	65	26	61	0	0.4	0	G|0.950;A|0.050	0.050	strong	.	SMCR8	62	.	NM_144775	exon1	c.G639A	p.T213T	AGAAACGGAGATC	.	PASS	Atlas-SNP
PCDHB7	56129	hgsc.bcm.edu	37	5	140554481	140554481	+	Missense_Mutation	SNP	G	G	T	rs1811237	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	125	36	131	0	0.288	0	G|0.758;T|0.242	0.242	strong	PCDHB7,NS,carcinoma,0,1	PCDHB7	231	1	NM_018940	exon1	c.G2065T	p.V689L	TACCTGGTGGTGG	.	PASS	Atlas-SNP
GRIK4	2900	hgsc.bcm.edu	37	11	120531044	120531044	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51	20	34	0	0.392157	0	.	.	none	GRIK4,colon,NS,0,1	GRIK4	149	1	NM_014619	exon1	c.C17T	p.A6V	TCTCGGCGCCTTT	.	PASS	Atlas-SNP
DSPP	1834	hgsc.bcm.edu	37	4	88536460	88536460	+	Silent	SNP	C	C	T	rs199691318	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	12	71	0	0.157895	0	.	.	weak	.	DSPP	174	.	NM_014208	exon5	c.C2646T	p.S882S	TGATAGCAGTGAC	.	PASS	Atlas-SNP
CPNE7	27132	hgsc.bcm.edu	37	16	89661807	89661807	+	Silent	SNP	C	C	T	rs12445560	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	102	52	96	0	0.509804	0	C|0.937;T|0.063	0.063	strong	.	CPNE7	56	.	NM_014427	exon16	c.C1560T	p.G520G	GGACGGCGTGGTG	.	PASS	Atlas-SNP
DHX32	55760	hgsc.bcm.edu	37	10	127530325	127530325	+	Silent	SNP	T	T	C	rs3208565	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	42	91	0	0.5	0	T|0.521;C|0.479	0.479	strong	DHX32,NS,carcinoma,0,1	DHX32	67	1	NM_018180	exon7	c.A1530G	p.A510A	CATGGCTGCGATT	.	PASS	Atlas-SNP
ZHX3	23051	hgsc.bcm.edu	37	20	39831725	39831725	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	340	5	296	2	0.0147059	0.00675676	.	.	none	ZHX3,lower_third,carcinoma,-1,1	ZHX3	78	1	NM_015035	exon3	c.T1832C	p.F611S	GGTGTGAAGTCAG	.	scavenged	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29912098	29912098	+	Silent	SNP	G	G	A	rs142475339	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	124	26	120	0	0.209677	0	G|0.871;A|0.129	0.129	strong	.	HLA-A	89	.	NM_001242758	exon4	c.G819A	p.V273V	GGTGGTGCCTTCT	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	26	13	23	0	0.5	0	T|0.783;C|0.217	0.217	strong	.	BRF1	102	.	NM_001242790	exon4	c.A600G	p.P200P	CCTGACTGGGCAG	.	PASS	Atlas-SNP
DDX55	57696	hgsc.bcm.edu	37	12	124104049	124104049	+	Silent	SNP	A	A	G	rs15587	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	35	8	58	0	0.228571	0	A|0.701;G|0.299	0.299	strong	.	DDX55	51	.	NM_020936	exon13	c.A1404G	p.G468G	GAGAGGAAAGCAG	.	PASS	Atlas-SNP
KRT6C	286887	hgsc.bcm.edu	37	12	52863213	52863213	+	Missense_Mutation	SNP	C	C	T	rs412533	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	30	89	0	0.405405	0	C|0.723;T|0.277	0.277	strong	.	KRT6C	55	.	NM_173086	exon8	c.G1441A	p.V481I	GTCCAACGCCTTC	.	PASS	Atlas-SNP
CCDC102A	92922	hgsc.bcm.edu	37	16	57552088	57552088	+	Silent	SNP	T	T	C	rs28756858	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	46	46	57	0	1	0	A|0.000;C|0.268;T|0.732	0.268	strong	.	CCDC102A	22	.	NM_033212	exon6	c.A1140G	p.A380A	GACCTGTGCCCGC	.	PASS	Atlas-SNP
TMCC2	9911	hgsc.bcm.edu	37	1	205238530	205238530	+	Silent	SNP	C	C	T	rs1779411	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	46	26	34	0	0.565217	0	C|0.784;T|0.216	0.216	strong	.	TMCC2	89	.	NM_014858	exon3	c.C1200T	p.G400G	TGGGGGCGGCGTG	.	PASS	Atlas-SNP
FAM110D	79927	hgsc.bcm.edu	37	1	26488019	26488019	+	Silent	SNP	G	G	A	rs3748857	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	29	28	29	0	0.965517	0	G|0.753;A|0.247	0.247	strong	.	.	.	.	NM_024869	exon2	c.G237A	p.P79P	GCTGCCGAGGCCT	.	PASS	Atlas-SNP
RBM23	55147	hgsc.bcm.edu	37	14	23371055	23371055	+	Missense_Mutation	SNP	G	G	C	rs1127066	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	39	68	0	0.549296	0	G|0.760;C|0.240	0.240	strong	.	RBM23	44	.	NM_001077351	exon13	c.C1284G	p.F428L	GAGCTGGAAACAC	.	PASS	Atlas-SNP
C1orf127	148345	hgsc.bcm.edu	37	1	11009703	11009703	+	Missense_Mutation	SNP	C	C	T	rs1281012	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	29	61	0	0.537037	0	C|0.907;T|0.093	0.093	strong	.	C1orf127	134	.	NM_001170754	exon11	c.G1268A	p.R423Q	GAAGGCCGGTGCA	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179412966	179412966	+	Silent	SNP	G	G	A	rs35445420	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94	45	103	0	0.478723	0	G|0.985;A|0.015	0.015	strong	.	TTN	18412	.	NM_001267550	exon339	c.C93387T	p.S31129S	GACTGCGGAGGAT	.	PASS	Atlas-SNP
GPR139	124274	hgsc.bcm.edu	37	16	20043236	20043236	+	Missense_Mutation	SNP	T	T	C	rs149441644	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	117	61	124	0	0.521368	0	T|0.996;C|0.004	0.004	strong	.	GPR139	75	.	NM_001002911	exon2	c.A883G	p.M295V	CTGCCATGGTGCG	.	PASS	Atlas-SNP
PRDM16	63976	hgsc.bcm.edu	37	1	3328659	3328659	+	Missense_Mutation	SNP	C	C	T	rs2493292	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48	19	61	0	0.395833	0	C|0.868;T|0.132	0.132	strong	.	PRDM16	147	.	NM_022114	exon9	c.C1898T	p.P633L	GCGACCCTGACAA	.	PASS	Atlas-SNP
GNPTAB	79158	hgsc.bcm.edu	37	12	102224436	102224436	+	Silent	SNP	C	C	T	rs4764655	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51	23	81	0	0.45098	0	C|0.900;T|0.100	0.100	strong	.	GNPTAB	120	.	NM_024312	exon1	c.G18A	p.L6L	TCTCTGCAGGAGC	.	PASS	Atlas-SNP
EFCAB7	84455	hgsc.bcm.edu	37	1	63999868	63999868	+	Missense_Mutation	SNP	T	T	C	rs6657480	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	43	101	0	0.581081	0	T|0.741;C|0.259	0.259	strong	.	EFCAB7	45	.	NM_032437	exon6	c.T785C	p.M262T	AGTTAATGGAGCC	.	PASS	Atlas-SNP
STRN3	29966	hgsc.bcm.edu	37	14	31381351	31381351	+	Missense_Mutation	SNP	T	T	C	rs2273171	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	106	47	102	0	0.443396	0	C|0.414;N|0.000	0.414	strong	STRN3,NS,carcinoma,0,1	STRN3	117	1	NM_001083893	exon11	c.A1412G	p.N471S	TTGGGATTCCATG	.	PASS	Atlas-SNP
CCDC168	643677	hgsc.bcm.edu	37	13	103394003	103394003	+	Missense_Mutation	SNP	G	G	A	rs1449707	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	56	56	91	0	1	0	G|0.336;A|0.664	0.664	strong	.	.	.	.	NM_001146197	exon4	c.C9044T	p.T3015I	TGGCAAGTCTTCT	.	PASS	Atlas-SNP
TMEM63A	9725	hgsc.bcm.edu	37	1	226034774	226034774	+	Silent	SNP	C	C	T	rs2292559	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	103	45	93	0	0.436893	0	C|0.957;T|0.043	0.043	strong	.	TMEM63A	75	.	NM_014698	exon24	c.G2391A	p.T797T	ACTGCCCGTGGCG	.	PASS	Atlas-SNP
EPS8	2059	hgsc.bcm.edu	37	12	15776095	15776095	+	Silent	SNP	C	C	T	rs1126786	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	129	63	119	0	0.488372	0	T|0.130;G|0.153;C|0.674;A|0.042	0.130	strong	.	EPS8	70	.	NM_004447	exon20	c.G2352A	p.L784L	TACCTCCAATGCA	.	PASS	Atlas-SNP
XIRP2	129446	hgsc.bcm.edu	37	2	168108357	168108357	+	Silent	SNP	A	A	G	rs1842233	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	37	81	0	0.440476	0	G|0.309;N|0.001	0.309	strong	.	XIRP2	914	.	NM_152381	exon9	c.A10455G	p.Q3485Q	GTGGCAAGAGAGT	.	PASS	Atlas-SNP
ARHGEF10	9639	hgsc.bcm.edu	37	8	1905132	1905132	+	Silent	SNP	G	G	A	rs3735876	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	105	52	104	0	0.495238	0	G|0.648;A|0.352	0.352	strong	.	ARHGEF10	255	.	NM_014629	exon29	c.G3738A	p.S1246S	AGATTCGCTGGGA	.	PASS	Atlas-SNP
MAGEB6	158809	hgsc.bcm.edu	37	X	26212477	26212477	+	Missense_Mutation	SNP	G	G	C	rs145782491	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	44	50	0	0.656716	0	G|0.990;C|0.010	0.010	strong	.	MAGEB6	91	.	NM_173523	exon2	c.G514C	p.G172R	GCCGAGGGTGAAG	.	PASS	Atlas-SNP
SUN2	25777	hgsc.bcm.edu	37	22	39134715	39134715	+	Silent	SNP	T	T	C	rs1062687	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	52	59	0	1	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
LAMTOR2	28956	hgsc.bcm.edu	37	1	156025096	156025096	+	Silent	SNP	C	C	T	rs7541	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	56	32	59	0	0.571429	0	C|0.895;T|0.105	0.105	strong	.	LAMTOR2	13	.	NM_001145264	exon2	c.C111T	p.Y37Y	TGGTTACGGGGAC	.	PASS	Atlas-SNP
SLFN5	162394	hgsc.bcm.edu	37	17	33592323	33592323	+	Missense_Mutation	SNP	C	C	G	rs113644060	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	140	64	127	0	0.457143	0	C|0.975;G|0.025	0.025	strong	.	SLFN5	92	.	NM_144975	exon5	c.C2092G	p.P698A	CTCCCCCCTCCCT	.	PASS	Atlas-SNP
RPH3AL	9501	hgsc.bcm.edu	37	17	63683	63683	+	Missense_Mutation	SNP	G	G	A	rs117190076	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	40	21	51	0	0.525	0	G|0.957;A|0.043	0.043	strong	.	RPH3AL	18	.	NM_006987	exon10	c.C908T	p.A303V	GCGTCAGCAGCGG	.	PASS	Atlas-SNP
PTCRA	171558	hgsc.bcm.edu	37	6	42891022	42891022	+	Missense_Mutation	SNP	G	G	A	rs9471966	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	149	70	118	0	0.469799	0	G|0.729;A|0.271	0.271	strong	.	PTCRA	24	.	NM_138296	exon2	c.G316A	p.V106I	CCTTTGGTCTGCC	.	PASS	Atlas-SNP
CD27	939	hgsc.bcm.edu	37	12	6554263	6554263	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	25	9	37	0	0.36	0	.	.	none	.	CD27	17	.	NM_001242	exon1	c.T2C	p.M1T	GGACCATGGCACG	.	PASS	Atlas-SNP
GIPC1	10755	hgsc.bcm.edu	37	19	14589378	14589378	+	Silent	SNP	C	C	T	rs1127307	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	111	54	116	0	0.486486	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
CD226	10666	hgsc.bcm.edu	37	18	67531642	67531642	+	Missense_Mutation	SNP	T	T	C	rs763361	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85	35	112	0	0.411765	0	C|0.456;N|0.000	0.456	strong	CD226,NS,adenoma,0,1	CD226	51	1	NM_006566	exon7	c.A919G	p.S307G	GTTGACTGGTAGA	.	PASS	Atlas-SNP
DHX34	9704	hgsc.bcm.edu	37	19	47883126	47883126	+	Missense_Mutation	SNP	C	C	T	rs151213663	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	40	21	68	0	0.525	0	C|0.994;T|0.006	0.006	strong	.	DHX34	98	.	NM_014681	exon14	c.C2866T	p.R956W	CTGGACCGGCAGC	.	PASS	Atlas-SNP
TMEM2	23670	hgsc.bcm.edu	37	9	74360234	74360234	+	Missense_Mutation	SNP	C	C	T	rs25688	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48	21	48	0	0.4375	0	C|0.937;T|0.063	0.063	strong	.	TMEM2	112	.	NM_001135820	exon4	c.G734A	p.R245K	AGGGTCCTTGCCA	.	PASS	Atlas-SNP
LRRC8B	23507	hgsc.bcm.edu	37	1	90049040	90049040	+	Silent	SNP	A	A	G	rs36084789	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	113	63	78	0	0.557522	0	A|0.813;G|0.187	0.187	strong	.	LRRC8B	49	.	NM_015350	exon5	c.A831G	p.P277P	TGTTCCATATTTT	.	PASS	Atlas-SNP
KIAA0556	23247	hgsc.bcm.edu	37	16	27772880	27772880	+	Missense_Mutation	SNP	G	G	A	rs61742593	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	33	12	37	0	0.363636	0	G|0.975;A|0.025	0.025	strong	.	KIAA0556	348	.	NM_015202	exon19	c.G3778A	p.E1260K	CTCCCCGAGTACT	.	PASS	Atlas-SNP
PISD	23761	hgsc.bcm.edu	37	22	32015766	32015766	+	Silent	SNP	G	G	A	rs41282571	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	187	97	167	0	0.518717	0	A|0.028;C|0.000;G|0.972	0.028	strong	.	PISD	53	.	NM_014338	exon9	c.C960T	p.F320F	CGTCACGAAGCTG	.	PASS	Atlas-SNP
GJB3	2707	hgsc.bcm.edu	37	1	35250840	35250840	+	Silent	SNP	G	G	A	rs61732640	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	223	3	232	0	0.0134529	0	G|0.969;A|0.031	0.031	strong	GJB3,NS,carcinoma,+1,1	GJB3	40	1	NM_001005752	exon2	c.G477A	p.P159P	TATGCCGCGCCTG	.	scavenged	Atlas-SNP
CACNA1F	778	hgsc.bcm.edu	37	X	49081291	49081291	+	Silent	SNP	G	G	A	rs2235127	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110	32	65	0	0.290909	0	G|0.623;A|0.377	0.377	strong	.	CACNA1F	218	.	NM_005183	exon14	c.C1842T	p.G614G	CATGGCGCCCACC	.	PASS	Atlas-SNP
TTLL10	254173	hgsc.bcm.edu	37	1	1120431	1120431	+	Missense_Mutation	SNP	G	G	A	rs1320571	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	163	87	135	1	0.533742	0.00740741	G|0.839;A|0.161	0.161	strong	TTLL10_ENST00000379290,NS,haematopoietic_neoplasm,0,6	TTLL10	66	6	NM_001130045	exon13	c.G1343A	p.S448N	ACATCAGTGACAC	.	scavenged	Atlas-SNP
POTEC	388468	hgsc.bcm.edu	37	18	14542931	14542931	+	Missense_Mutation	SNP	C	C	T	rs45554841	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	234	43	236	0	0.183761	0	C|0.857;T|0.143	0.143	strong	POTEC,NS,carcinoma,0,1	POTEC	129	1	NM_001137671	exon1	c.G215A	p.C72Y	CCCCTGCAGCAGG	.	PASS	Atlas-SNP
TLR10	81793	hgsc.bcm.edu	37	4	38774889	38774889	+	Missense_Mutation	SNP	T	T	C	rs4129009	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	178	76	165	0	0.426966	0	T|0.840;C|0.160	0.160	strong	.	TLR10	87	.	NM_001017388	exon2	c.A2323G	p.I775V	CATTAATAGCAGC	.	PASS	Atlas-SNP
CLCNKA	1187	hgsc.bcm.edu	37	1	16355287	16355287	+	Missense_Mutation	SNP	C	C	G	rs45588635	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	60	79	0	0.983607	0	C|0.981;G|0.019	0.019	strong	.	CLCNKA	56	.	NM_004070	exon11	c.C1000G	p.L334V	ACCTTGCTTCTCG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195511686	195511686	+	Silent	SNP	G	G	T	rs201950480	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	190	31	158	1	0.163158	0.00632911	G|0.998;T|0.002	0.002	weak	MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	NM_018406	exon2	c.C6765A	p.T2255T	AAGAGGGGTGGTG	.	scavenged	Atlas-SNP
GLT1D1	144423	hgsc.bcm.edu	37	12	129360498	129360498	+	Silent	SNP	G	G	A	rs482401	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	118	54	100	0	0.457627	0	G|0.706;A|0.294	0.294	strong	.	GLT1D1	48	.	NM_144669	exon2	c.G108A	p.K36K	TTTGAAGGATGCC	.	PASS	Atlas-SNP
HTR1D	3352	hgsc.bcm.edu	37	1	23519633	23519633	+	Silent	SNP	A	A	G	rs6300	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	45	81	0	0.517241	0	A|0.854;G|0.146	0.146	strong	.	HTR1D	36	.	NM_000864	exon1	c.T1080C	p.N360N	CTCTTCATTAAAC	.	PASS	Atlas-SNP
VASH2	79805	hgsc.bcm.edu	37	1	213147400	213147400	+	Missense_Mutation	SNP	G	G	A	rs35976699	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48	28	26	0	0.583333	0	G|0.977;A|0.023	0.023	strong	.	VASH2	55	.	NM_024749	exon5	c.G851A	p.R284Q	TCGGCCGGCGAGA	.	PASS	Atlas-SNP
COL6A5	256076	hgsc.bcm.edu	37	3	130104153	130104153	+	Missense_Mutation	SNP	G	G	A	rs149308947	by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	56	23	75	0	0.410714	0	G|1.000;A|0.000	0.000	strong	.	COL6A5	205	.	NM_153264	exon5	c.G1807A	p.D603N	AACTTTGATGCTT	.	PASS	Atlas-SNP
USP17L7	392197	hgsc.bcm.edu	37	8	11989986	11989986	+	Missense_Mutation	SNP	G	G	C	rs9694757	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	120	32	122	0	0.266667	0	G|0.910;C|0.090	0.090	strong	.	.	.	.	NM_001256869	exon1	c.C1533G	p.S511R	CCTGGTGCTCCCT	.	PASS	Atlas-SNP
CLPSL1	340204	hgsc.bcm.edu	37	6	35748931	35748931	+	Missense_Mutation	SNP	T	T	C	rs34109614	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	131	99	154	0	0.755725	0	C|0.301;G|0.000;T|0.698	0.301	strong	.	.	.	.	NM_001010886	exon1	c.T44C	p.F15S	TCTTCTTCTTTCT	.	PASS	Atlas-SNP
KIF1B	23095	hgsc.bcm.edu	37	1	10397567	10397567	+	Missense_Mutation	SNP	A	A	G	rs2297881	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	183	93	154	0	0.508197	0	A|0.963;G|0.037	0.037	strong	.	KIF1B	242	.	NM_015074	exon29	c.A3260G	p.Y1087C	CAGAGTATGCAGA	.	PASS	Atlas-SNP
ADAMTS7	11173	hgsc.bcm.edu	37	15	79067065	79067065	+	Missense_Mutation	SNP	G	G	A	rs201460425		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73	11	94	0	0.150685	0	G|0.999;A|0.001	0.001	weak	ADAMTS7,NS,carcinoma,+2,2	ADAMTS7	142	2	NM_014272	exon12	c.C1777T	p.P593S	CAGCAGGGCAGGC	.	scavenged	Atlas-SNP
CHD8	57680	hgsc.bcm.edu	37	14	21878110	21878110	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	2	99	0	0.0232558	0	.	.	none	CHD8_ENST00000430710,colon,carcinoma,-1,2	CHD8	339	2	NM_001170629	exon10	c.C2264T	p.P755L	TCATAGGGCAGAG	.	scavenged	Atlas-SNP
KDM4C	23081	hgsc.bcm.edu	37	9	7103816	7103816	+	Silent	SNP	C	C	T	rs3763651	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100	44	114	0	0.44	0	C|0.456;T|0.544	0.544	strong	.	KDM4C	186	.	NM_001146694	exon18	c.C2556T	p.D852D	TGATGACTGGCCT	.	PASS	Atlas-SNP
FMN2	56776	hgsc.bcm.edu	37	1	240370941	240370941	+	Silent	SNP	T	T	C	rs4997329	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	17	117	4	0.278689	0.034188	T|0.863;C|0.137	0.137	strong	FMN2,caecum,carcinoma,0,1	FMN2	451	1	NM_020066	exon5	c.T2829C	p.P943P	AATACCTCCTCCG	.	scavenged	Atlas-SNP
MAML3	55534	hgsc.bcm.edu	37	4	140811081	140811081	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69	4	89	1	0.057971	0.011236	.	.	none	MAML3_ENST00000509479,NS,carcinoma,0,2	MAML3	192	2	NM_018717	exon2	c.G1509A	p.Q503Q	CTGCTGCTGCTGC	.	scavenged	Atlas-SNP
GPC6	10082	hgsc.bcm.edu	37	13	94482567	94482567	+	Missense_Mutation	SNP	G	G	A	rs369251626		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	127	77	94	0	0.606299	0	.	.	weak	.	GPC6	102	.	NM_005708	exon3	c.G480A	p.M160I	GGAAATGCTCAAT	.	PASS	Atlas-SNP
NLRP1	22861	hgsc.bcm.edu	37	17	5487164	5487164	+	Silent	SNP	C	C	G	rs884367	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	38	65	0	0.506667	0	C|0.812;G|0.188	0.188	strong	.	NLRP1	358	.	NM_033007	exon1	c.G114C	p.S38S	CTCACCCGAAGAG	.	PASS	Atlas-SNP
ZC3H3	23144	hgsc.bcm.edu	37	8	144522388	144522388	+	Missense_Mutation	SNP	A	A	T	rs2272753	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	34	62	0	0.447368	0	A|0.879;T|0.121	0.121	strong	.	ZC3H3	75	.	NM_015117	exon11	c.T2638A	p.S880T	GGGATGAGGAGGA	.	PASS	Atlas-SNP
LEPR	3953	hgsc.bcm.edu	37	1	66036441	66036441	+	Missense_Mutation	SNP	A	A	G	rs1137100	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	19	69	0	0.283582	0	A|0.705;G|0.295	0.295	strong	.	LEPR	284	.	NM_001003680	exon4	c.A326G	p.K109R	AAGGAAAGACATT	.	PASS	Atlas-SNP
COL19A1	1310	hgsc.bcm.edu	37	6	70890224	70890224	+	Silent	SNP	G	G	A	rs2273948	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	148	74	132	0	0.5	0	G|0.939;A|0.061	0.061	strong	.	COL19A1	232	.	NM_001858	exon43	c.G2688A	p.G896G	CCCAGGGCCTCCA	.	PASS	Atlas-SNP
DISP1	84976	hgsc.bcm.edu	37	1	223178561	223178561	+	Silent	SNP	A	A	C	rs9441941	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	123	57	143	0	0.463415	0	A|0.467;C|0.533	0.533	strong	DISP1,NS,carcinoma,0,1	DISP1	145	1	NM_032890	exon10	c.A3822C	p.P1274P	CTGCCCAGATGCC	.	PASS	Atlas-SNP
ABCC1	4363	hgsc.bcm.edu	37	16	16138322	16138322	+	Silent	SNP	T	T	C	rs246221	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94	51	106	0	0.542553	0	T|0.563;C|0.437	0.437	strong	.	ABCC1	156	.	NM_004996	exon8	c.T825C	p.V275V	GAAGGTTGTGTAC	.	PASS	Atlas-SNP
TLE3	7090	hgsc.bcm.edu	37	15	70345626	70345626	+	Silent	SNP	C	C	T	rs1057865	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	150	66	153	0	0.44	0	C|0.639;T|0.361	0.361	strong	.	TLE3	104	.	NM_005078	exon17	c.G1923A	p.T641T	GCGCACCGTGTTG	.	PASS	Atlas-SNP
MUTYH	4595	hgsc.bcm.edu	37	1	45797505	45797505	+	Missense_Mutation	SNP	C	C	G	rs3219489	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	37	14	25	0	0.378378	0	C|0.710;G|0.290	0.290	strong	.	MUTYH	38	.	NM_001128425	exon12	c.G1014C	p.Q338H	GTGGCACTGTCCA	.	PASS	Atlas-SNP
UQCC	55245	hgsc.bcm.edu	37	20	33971914	33971914	+	Missense_Mutation	SNP	C	C	T	rs4911494	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	169	82	160	0	0.485207	0	C|0.456;T|0.544	0.544	strong	.	UQCC	41	.	NM_018244	exon3	c.G152A	p.R51Q	CATGCTCGGGACT	.	PASS	Atlas-SNP
DOK6	220164	hgsc.bcm.edu	37	18	67365668	67365668	+	Silent	SNP	A	A	G	rs4426448	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98	51	107	0	0.520408	0	A|0.522;G|0.478	0.478	strong	.	DOK6	56	.	NM_152721	exon5	c.A438G	p.T146T	GCCTACACCAAAC	.	PASS	Atlas-SNP
PTPRS	5802	hgsc.bcm.edu	37	19	5210782	5210782	+	Silent	SNP	G	G	A	rs1143698	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	88	87	67	0	0.988636	0	G|0.667;A|0.333	0.333	strong	PTPRS,NS,carcinoma,0,1	PTPRS	169	1	NM_002850	exon34	c.C5269T	p.L1757L	CCGCCAGCGGCCC	.	PASS	Atlas-SNP
BCL2A1	597	hgsc.bcm.edu	37	15	80263406	80263406	+	Missense_Mutation	SNP	C	C	T	rs1138357	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	119	54	151	0	0.453782	0	C|0.708;T|0.292	0.292	strong	.	BCL2A1	28	.	NM_001114735	exon1	c.G56A	p.C19Y	AGGACGCACTGCA	.	PASS	Atlas-SNP
COL15A1	1306	hgsc.bcm.edu	37	9	101778265	101778265	+	Missense_Mutation	SNP	G	G	T	rs2297603	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	30	66	0	0.46875	0	G|0.909;T|0.091	0.091	strong	COL15A1,brain,glioma,0,1	COL15A1	211	1	NM_001855	exon11	c.G1511T	p.G504V	GTCCTGGTGATGA	.	PASS	Atlas-SNP
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32557489	32557489	+	Missense_Mutation	SNP	A	A	T	rs199514452	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	233	18	127	8	0.0772532	0.0629921	A|0.864;T|0.136	0.136	strong	HLA-DRB1,colon,carcinoma,0,1	HLA-DRB1	41	1	NM_002124	exon1	c.T31A	p.C11S	TCATGCAGGAGCC	.	scavenged	Atlas-SNP
FOXRED2	80020	hgsc.bcm.edu	37	22	36900806	36900806	+	Missense_Mutation	SNP	A	A	G	rs760718	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82	82	85	0	1	0	A|0.435;G|0.565	0.565	strong	.	FOXRED2	48	.	NM_001102371	exon3	c.T535C	p.F179L	CTACAAAGAGGAC	.	PASS	Atlas-SNP
CAPN9	10753	hgsc.bcm.edu	37	1	230923313	230923313	+	Missense_Mutation	SNP	C	C	T	rs12731961	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	106	60	81	0	0.566038	0	C|0.793;T|0.207	0.207	strong	.	CAPN9	116	.	NM_006615	exon13	c.C1564T	p.R522W	GAGCAGCGGTTTC	.	PASS	Atlas-SNP
PRAMEF22	653606	hgsc.bcm.edu	37	1	13036639	13036639	+	Silent	SNP	C	C	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	1091	29	1123	9	0.0265811	0.00801425	.	.	none	PRAMEF22,NS,carcinoma,+2,2	PRAMEF22	13	2	NM_001100631	exon2	c.C711A	p.R237R	TCTTCGCAAACTC	.	scavenged	Atlas-SNP
TMEM105	284186	hgsc.bcm.edu	37	17	79287477	79287477	+	Missense_Mutation	SNP	G	G	A	rs9916085	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	95	50	110	0	0.526316	0	G|0.882;A|0.118	0.118	strong	.	TMEM105	19	.	NM_178520	exon3	c.C364T	p.R122W	CACCCCGGCCCCA	.	PASS	Atlas-SNP
ATP10D	57205	hgsc.bcm.edu	37	4	47525054	47525054	+	Missense_Mutation	SNP	T	T	C	rs7683838	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	46	22	63	0	0.478261	0	T|0.869;C|0.131	0.131	strong	.	ATP10D	168	.	NM_020453	exon4	c.T511C	p.C171R	GACCGATGCTGGA	.	PASS	Atlas-SNP
KIAA1614	57710	hgsc.bcm.edu	37	1	180905352	180905352	+	Silent	SNP	C	C	T	rs3795505	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82	42	83	0	0.512195	0	C|0.668;T|0.332	0.332	strong	.	KIAA1614	75	.	NM_020950	exon5	c.C2307T	p.S769S	AGAAAGCCACGAG	.	PASS	Atlas-SNP
SLC38A5	92745	hgsc.bcm.edu	37	X	48317386	48317386	+	Missense_Mutation	SNP	A	A	G	rs17281188	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	109	19	88	0	0.174312	0	A|0.906;0|0.027	.	strong	.	SLC38A5	98	.	NM_033518	exon17	c.T1352C	p.M451T	ACGGCCATGAAGA	.	PASS	Atlas-SNP
ZNF154	7710	hgsc.bcm.edu	37	19	58213693	58213693	+	Silent	SNP	C	C	T	rs61730373	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	167	83	167	0	0.497006	0	C|0.843;T|0.157	0.157	strong	ZNF154,caecum,carcinoma,-1,2	ZNF154	34	2	NM_001085384	exon3	c.G624A	p.R208R	AACTCTCCGGTGC	.	PASS	Atlas-SNP
COL6A1	1291	hgsc.bcm.edu	37	21	47423507	47423507	+	Silent	SNP	G	G	A	rs71336107	alternate_allele	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91	60	64	0	0.659341	0	ATC|0.500;GTT|0.500	.	alt	COL6A1,NS,carcinoma,0,2	COL6A1	101	2	NM_001848	exon35	c.G2667A	p.A889A	GCGGGCGTCGCTG	.	PASS	Atlas-SNP
VSTM2B	342865	hgsc.bcm.edu	37	19	30020752	30020752	+	Silent	SNP	C	C	T	rs61731469	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	133	61	127	0	0.458647	0	C|0.973;T|0.027	0.027	strong	.	VSTM2B	15	.	NM_001146339	exon4	c.C324T	p.I108I	TGACATCTCACAC	.	PASS	Atlas-SNP
PLXNA2	5362	hgsc.bcm.edu	37	1	208390086	208390086	+	Silent	SNP	G	G	C	rs1664227	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	32	19	29	0	0.59375	0	G|0.664;C|0.336	0.336	strong	.	PLXNA2	178	.	NM_025179	exon2	c.C1182G	p.T394T	CGCCTTGGTGCAC	.	PASS	Atlas-SNP
C11orf93	120376	hgsc.bcm.edu	37	11	111179054	111179054	+	Silent	SNP	A	A	G	rs3087587	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	65	68	0	0.77381	0	G|0.408;N|0.000	0.408	strong	.	C11orf93	10	.	NM_001271458	exon5	c.A648G	p.A216A	CCAGGCAGCAGAG	.	PASS	Atlas-SNP
CSF1R	1436	hgsc.bcm.edu	37	5	149460355	149460355	+	Silent	SNP	G	G	A	rs41287102	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	151	70	149	0	0.463576	0	G|0.994;A|0.006	0.006	strong	.	CSF1R	250	.	NM_005211	exon3	c.C282T	p.S94S	GGCGGCGCTGCCT	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	53	44	0	1	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
KRTAP10-5	386680	hgsc.bcm.edu	37	21	45999753	45999753	+	Missense_Mutation	SNP	C	C	G	rs464424	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	35	20	51	0	0.571429	0	C|0.913;G|0.087	0.087	strong	.	KRTAP10-5	43	.	NM_198694	exon1	c.G703C	p.V235L	TGGGCACGCAGCA	.	PASS	Atlas-SNP
ZNF341	84905	hgsc.bcm.edu	37	20	32376748	32376748	+	Silent	SNP	C	C	T	rs34260449	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	142	75	180	0	0.528169	0	C|0.985;T|0.015	0.015	strong	.	ZNF341	73	.	NM_032819	exon13	c.C1911T	p.H637H	GATCCACGAGCCC	.	PASS	Atlas-SNP
WWC1	23286	hgsc.bcm.edu	37	5	167850748	167850748	+	Silent	SNP	A	A	G	rs12054944	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55	55	66	0	1	0	A|0.448;G|0.552	0.552	strong	WWC1,NS,carcinoma,0,2	WWC1	98	2	NM_015238	exon11	c.A1485G	p.S495S	GCCCTCAGGCTGC	.	PASS	Atlas-SNP
C19orf12	83636	hgsc.bcm.edu	37	19	30193721	30193721	+	Silent	SNP	G	G	A	rs10424582	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	137	135	121	0	0.985401	0	G|0.297;A|0.703	0.703	strong	.	C19orf12	16	.	NM_001031726	exon3	c.C357T	p.T119T	CAGCGCGGTCAGC	.	PASS	Atlas-SNP
PTPN13	5783	hgsc.bcm.edu	37	4	87622624	87622624	+	Missense_Mutation	SNP	G	G	A	rs61730646	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	109	44	134	0	0.40367	0	G|0.995;A|0.005	0.005	strong	.	PTPN13	203	.	NM_006264	exon7	c.G865A	p.G289S	ATCCCTGGCATTG	.	PASS	Atlas-SNP
ABCD4	5826	hgsc.bcm.edu	37	14	74759006	74759006	+	Missense_Mutation	SNP	C	C	T	rs3742801	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	41	21	34	0	0.512195	0	C|0.710;T|0.290	0.290	strong	.	ABCD4	54	.	NM_005050	exon11	c.G1102A	p.E368K	CCCACTCGCTCTC	.	PASS	Atlas-SNP
P2RY2	5029	hgsc.bcm.edu	37	11	72946020	72946020	+	Silent	SNP	C	C	T	rs1783596	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	81	81	0	1	0	C|0.425;T|0.575	0.575	strong	.	P2RY2	54	.	NM_176071	exon3	c.C816T	p.R272R	CTTCCGCTCGCTG	.	PASS	Atlas-SNP
KIAA1731	85459	hgsc.bcm.edu	37	11	93402006	93402006	+	Silent	SNP	A	A	G	rs61743303	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	96	74	97	1	0.770833	0.0103093	A|0.867;G|0.133	0.133	strong	KIAA1731_ENST00000325212,NS,carcinoma,0,1	KIAA1731	173	1	NM_033395	exon4	c.A342G	p.A114A	GCGGGCAGCAGAA	.	scavenged	Atlas-SNP
SLC22A25	387601	hgsc.bcm.edu	37	11	62984868	62984868	+	Missense_Mutation	SNP	T	T	C	rs11231409	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	31	49	0	0.5	0	T|0.610;C|0.390	0.390	strong	.	SLC22A25	87	.	NM_199352	exon4	c.A748G	p.S250G	CCAGGCTTCCCAG	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179458591	179458591	+	Missense_Mutation	SNP	C	C	T	rs2288569	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	44	60	0	0.505747	0	C|0.818;T|0.182	0.182	strong	TTN_ENST00000359218,NS,carcinoma,-1,5	TTN	18412	5	NM_001267550	exon298	c.G58436A	p.R19479H	CCAGGACGGTCTG	.	PASS	Atlas-SNP
PLEKHM1	9842	hgsc.bcm.edu	37	17	43545893	43545893	+	Silent	SNP	T	T	C	rs1879581	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83	83	105	0	1	0	T|0.863;C|0.137	0.137	strong	.	PLEKHM1	69	.	NM_014798	exon5	c.A990G	p.T330T	GATCTCTGTTTCT	.	PASS	Atlas-SNP
FLNC	2318	hgsc.bcm.edu	37	7	128484816	128484816	+	Silent	SNP	A	A	G	rs3734973	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	41	84	0	0.476744	0	A|0.663;G|0.337	0.337	strong	FLNC,caecum,carcinoma,+2,1	FLNC	339	1	NM_001127487	exon21	c.A3297G	p.V1099V	GACCGTAGAGGGC	.	PASS	Atlas-SNP
MB	4151	hgsc.bcm.edu	37	22	36007075	36007075	+	Silent	SNP	C	C	T	rs7293	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	162	71	130	0	0.438272	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
CBLB	868	hgsc.bcm.edu	37	3	105389153	105389153	+	Silent	SNP	A	A	G	rs11713094	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	118	57	89	0	0.483051	0	A|0.789;G|0.211	0.211	strong	.	CBLB	118	.	NM_170662	exon18	c.T2613C	p.P871P	TCTAGCAGGAGGC	.	PASS	Atlas-SNP
SPZ1	84654	hgsc.bcm.edu	37	5	79616083	79616083	+	Missense_Mutation	SNP	G	G	C	rs1862136	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91	91	119	0	1	0	G|0.244;C|0.756	0.756	strong	.	SPZ1	60	.	NM_032567	exon1	c.G49C	p.V17L	AAAACCGTTAACC	.	PASS	Atlas-SNP
DNAH6	1768	hgsc.bcm.edu	37	2	84924823	84924823	+	Missense_Mutation	SNP	T	T	C	rs78190897	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	35	25	65	0	0.714286	0	T|0.868;C|0.132	0.132	strong	.	DNAH6	194	.	NM_001370	exon47	c.T7649C	p.V2550A	AAGAAGTAGGAAT	.	PASS	Atlas-SNP
SLC13A4	26266	hgsc.bcm.edu	37	7	135406176	135406176	+	Silent	SNP	A	A	G	rs4596594	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	138	73	141	0	0.528986	0	A|0.531;G|0.469	0.469	strong	SLC13A4,rectum,carcinoma,0,1	SLC13A4	56	1	NM_012450	exon2	c.T195C	p.L65L	CGGGTAAAGGAAG	.	PASS	Atlas-SNP
HPS1	3257	hgsc.bcm.edu	37	10	100190920	100190920	+	Silent	SNP	G	G	A	rs1801287	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	149	78	157	0	0.52349	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
TSPAN2	10100	hgsc.bcm.edu	37	1	115604798	115604798	+	Silent	SNP	C	C	T	rs10776795	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	240	113	245	0	0.470833	0	C|0.686;T|0.314	0.314	strong	TSPAN2,NS,carcinoma,0,1	TSPAN2	37	1	NM_005725	exon3	c.G228A	p.G76G	GCAGCACCCGAAG	.	PASS	Atlas-SNP
AASDH	132949	hgsc.bcm.edu	37	4	57204777	57204777	+	Missense_Mutation	SNP	A	A	C	rs8340	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	223	116	224	0	0.520179	0	C|0.176;N|0.000	0.176	strong	AASDH,NS,carcinoma,0,1	AASDH	101	1	NM_181806	exon15	c.T3088G	p.Y1030D	CATTGTAGTTATG	.	PASS	Atlas-SNP
ANO7	50636	hgsc.bcm.edu	37	2	242163538	242163538	+	Silent	SNP	G	G	A	rs115620538	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	136	73	132	0	0.536765	0	G|0.974;A|0.026	0.026	strong	.	ANO7	136	.	NM_001001891	exon25	c.G2772A	p.T924T	CTTCACGGTTCCC	.	PASS	Atlas-SNP
MED16	10025	hgsc.bcm.edu	37	19	871222	871222	+	Silent	SNP	G	G	A	rs8100258	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	59	58	56	0	0.983051	0	G|0.860;A|0.140	0.140	strong	.	MED16	61	.	NM_005481	exon13	c.C2130T	p.D710D	CGCCTCGTCCGGC	.	PASS	Atlas-SNP
CDCA4	55038	hgsc.bcm.edu	37	14	105478159	105478159	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80	33	57	0	0.4125	0	.	.	none	.	CDCA4	18	.	NM_017955	exon2	c.G108A	p.S36S	CAGGAGCGACTGC	.	PASS	Atlas-SNP
C1orf172	126695	hgsc.bcm.edu	37	1	27278553	27278553	+	Missense_Mutation	SNP	G	G	A	rs3010109	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	121	53	144	0	0.438017	0	G|0.894;A|0.106	0.106	strong	.	C1orf172	38	.	NM_152365	exon2	c.C319T	p.R107W	ATCCCCGCACACA	.	PASS	Atlas-SNP
TUBA3E	112714	hgsc.bcm.edu	37	2	130952038	130952038	+	Missense_Mutation	SNP	G	G	A	rs13000721	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	102	16	204	1	0.156863	0.00490196	G|0.676;A|0.324	0.324	strong	TUBA3E,NS,carcinoma,0,8	TUBA3E	73	8	NM_207312	exon4	c.C377T	p.A126V	AGATCCGCCTGAG	.	scavenged	Atlas-SNP
ENTHD2	146705	hgsc.bcm.edu	37	17	79205736	79205736	+	Silent	SNP	G	G	A	rs11655759	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	129	57	108	0	0.44186	0	G|0.729;A|0.271	0.271	strong	.	.	.	.	NM_144679	exon8	c.C612T	p.S204S	CAGGTCGCTGTTC	.	PASS	Atlas-SNP
SERHL2	253190	hgsc.bcm.edu	37	22	42970004	42970004	+	Silent	SNP	G	G	C	rs147451679	byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	436	57	382	0	0.130734	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
PCDHB10	56126	hgsc.bcm.edu	37	5	140572668	140572668	+	Silent	SNP	C	C	T	rs597064	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	33	122	0	0.383721	0	C|0.561;T|0.439	0.439	strong	.	PCDHB10	177	.	NM_018930	exon1	c.C543T	p.N181N	TATTAACATTAGT	.	PASS	Atlas-SNP
PTBP1	5725	hgsc.bcm.edu	37	19	804396	804396	+	Silent	SNP	C	C	T	rs3180287	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	34	13	41	0	0.382353	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
PCDHGA2	56113	hgsc.bcm.edu	37	5	140720954	140720954	+	Missense_Mutation	SNP	T	T	C	rs66823521	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	221	98	242	0	0.443439	0	T|0.910;C|0.090	0.090	strong	PCDHG_cluster,NS,carcinoma,-2,2	PCDHGA2	205	2	NM_018915	exon1	c.T2416C	p.F806L	GAAACGTTTTCTC	.	PASS	Atlas-SNP
PARP1	142	hgsc.bcm.edu	37	1	226589958	226589958	+	Silent	SNP	G	G	A	rs1805404	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51	25	38	0	0.490196	0	G|0.811;A|0.189	0.189	strong	PARP1,colon,carcinoma,-1,1	PARP1	100	1	NM_001618	exon2	c.C243T	p.D81D	CTGCTGGTCATCC	.	PASS	Atlas-SNP
PMPCA	23203	hgsc.bcm.edu	37	9	139311471	139311471	+	Silent	SNP	C	C	T	rs3812581	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	112	62	68	0	0.553571	0	C|0.785;T|0.215	0.215	strong	.	PMPCA	29	.	NM_015160	exon7	c.C702T	p.N234N	GATCAACCGAGAG	.	PASS	Atlas-SNP
C5orf60	285679	hgsc.bcm.edu	37	5	179071947	179071947	+	Silent	SNP	A	A	G	rs4645306	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	202	64	153	0	0.316832	0	A|0.743;G|0.257	0.257	strong	.	C5orf60	24	.	NM_001142306	exon1	c.T75C	p.I25I	TGTACCAATAACA	.	PASS	Atlas-SNP
NPY5R	4889	hgsc.bcm.edu	37	4	164272703	164272703	+	Silent	SNP	G	G	A	rs11946004	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	135	63	110	0	0.466667	0	G|0.899;A|0.101	0.101	strong	.	NPY5R	101	.	NM_006174	exon4	c.G1278A	p.G426G	ATATGGGTTTCTT	.	PASS	Atlas-SNP
ASPM	259266	hgsc.bcm.edu	37	1	197070442	197070442	+	Missense_Mutation	SNP	G	G	T	rs3762271	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	58	58	70	0	1	0	G|0.722;T|0.278	0.278	strong	.	ASPM	444	.	NM_018136	exon18	c.C7939A	p.L2647I	CTCTAAGGTGGAG	.	PASS	Atlas-SNP
RBM19	9904	hgsc.bcm.edu	37	12	114374887	114374887	+	Missense_Mutation	SNP	T	T	C	rs2290787	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	158	84	138	0	0.531646	0	A|0.076;C|0.019;T|0.905	0.019	strong	RBM19,NS,carcinoma,0,1	RBM19	117	1	NM_001146699	exon16	c.A1993G	p.T665A	GGGCTGTGCTGGA	.	PASS	Atlas-SNP
PSME4	23198	hgsc.bcm.edu	37	2	54161756	54161756	+	Missense_Mutation	SNP	T	T	C	rs146618010	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	22	65	0	0.415094	0	T|1.000;C|0.000	0.000	weak	.	PSME4	247	.	NM_014614	exon8	c.A943G	p.I315V	CGGTGATCCATAT	.	PASS	Atlas-SNP
SYCE1	93426	hgsc.bcm.edu	37	10	135368590	135368590	+	Missense_Mutation	SNP	T	T	C	rs3737031	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	145	80	136	0	0.551724	0	T|0.856;C|0.144	0.144	strong	SYCE1_ENST00000343131,NS,carcinoma,0,1	SYCE1	81	1	NM_001143764	exon13	c.A962G	p.H321R	GCTTGGTGTGCAG	.	PASS	Atlas-SNP
GCNT4	51301	hgsc.bcm.edu	37	5	74324902	74324902	+	Missense_Mutation	SNP	C	C	T	rs4704166	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	36	17	38	0	0.472222	0	C|0.657;G|0.000;T|0.343	0.343	strong	GCNT4,NS,carcinoma,0,1	GCNT4	46	1	NM_016591	exon1	c.G961A	p.V321I	CTTGAACGATGGA	.	PASS	Atlas-SNP
TRIM69	140691	hgsc.bcm.edu	37	15	45047402	45047402	+	Missense_Mutation	SNP	A	A	G	rs17588988	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	96	72	124	0	0.75	0	A|0.936;G|0.064	0.064	strong	.	TRIM69	47	.	NM_182985	exon2	c.A311G	p.K104R	AGATTAAGAAGTT	.	PASS	Atlas-SNP
NAMPT	10135	hgsc.bcm.edu	37	7	105903904	105903904	+	Silent	SNP	T	T	C	rs2302559	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	257	257	325	1	1	0.00307692	T|0.374;C|0.626	0.626	strong	.	NAMPT	37	.	NM_005746	exon7	c.A903G	p.S301S	ACTTCTTGATACT	.	PASS	Atlas-SNP
PGAP1	80055	hgsc.bcm.edu	37	2	197712710	197712710	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	38	13	44	0	0.342105	0	.	.	none	PGAP1,caecum,carcinoma,-1,3	PGAP1	84	3	NM_024989	exon21	c.A1913C	p.K638T	TCAACTTTGTATG	.	PASS	Atlas-SNP
FUT3	2525	hgsc.bcm.edu	37	19	5843784	5843784	+	Missense_Mutation	SNP	A	A	T	rs3894326	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	133	62	124	0	0.466165	0	A|0.935;T|0.065	0.065	strong	.	FUT3	30	.	NM_001097640	exon3	c.T1067A	p.I356K	GCCGCTATGCTGC	.	PASS	Atlas-SNP
METTL21A	151194	hgsc.bcm.edu	37	2	208477852	208477852	+	Missense_Mutation	SNP	G	G	A	rs2551949	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	121	55	164	0	0.454545	0	G|0.142;A|0.858	0.858	strong	.	METTL21A	24	.	NM_145280	exon4	c.C575T	p.T192I	CTCACAGTAAATT	.	PASS	Atlas-SNP
ZNF407	55628	hgsc.bcm.edu	37	18	72344509	72344509	+	Missense_Mutation	SNP	G	G	A	rs7227263	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80	36	73	0	0.45	0	G|0.910;A|0.090	0.090	strong	.	ZNF407	231	.	NM_001146190	exon1	c.G1534A	p.G512R	GACTCCGGGCTGC	.	PASS	Atlas-SNP
PLXNB3	5365	hgsc.bcm.edu	37	X	153043896	153043896	+	Silent	SNP	G	G	A	rs144872102	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	47	62	0	0.618421	0	G|0.999;A|0.001	0.001	strong	.	PLXNB3	208	.	NM_001163257	exon35	c.G5589A	p.E1863E	CCAGGAGATGAAC	.	PASS	Atlas-SNP
SENP7	57337	hgsc.bcm.edu	37	3	101177848	101177848	+	Missense_Mutation	SNP	T	T	G	rs6809436	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	120	73	127	0	0.608333	0	T|0.902;G|0.098	0.098	strong	.	SENP7	170	.	NM_020654	exon4	c.A235C	p.K79Q	GTTTTTTATTTTT	.	PASS	Atlas-SNP
RNF19B	127544	hgsc.bcm.edu	37	1	33402515	33402515	+	Silent	SNP	C	C	T	rs35462688	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79	46	93	0	0.582278	0	C|0.947;T|0.053	0.053	strong	.	RNF19B	43	.	NM_153341	exon9	c.G2091A	p.S697S	GGGGGTCGAGGGG	.	PASS	Atlas-SNP
FAM86A	196483	hgsc.bcm.edu	37	16	5145474	5145474	+	Silent	SNP	C	C	T	rs7192650	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	112	110	94	0	0.982143	0	C|0.858;T|0.142	0.142	strong	.	FAM86A	32	.	NM_201400	exon2	c.G138A	p.L46L	CCGCAGCAGCTCA	.	PASS	Atlas-SNP
DND1	373863	hgsc.bcm.edu	37	5	140052320	140052320	+	Missense_Mutation	SNP	T	T	C	rs201446376	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	13	5	11	0	0.384615	0	T|0.983;C|0.016	0.016	strong	DND1,NS,carcinoma,0,1	DND1	15	1	NM_194249	exon3	c.A314G	p.Y105C	GAGCTGTAGCGGG	.	scavenged	Atlas-SNP
GPSM1	26086	hgsc.bcm.edu	37	9	139235526	139235526	+	Nonsense_Mutation	SNP	C	C	A	rs59873903	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	76	63	0	1	0	C|0.774;A|0.226	0.226	strong	.	GPSM1	50	.	NM_015597	exon9	c.C1283A	p.S428X	TGGGATCGAGGCC	.	PASS	Atlas-SNP
EVC	2121	hgsc.bcm.edu	37	4	5754579	5754579	+	Missense_Mutation	SNP	C	C	T	rs28483498	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	102	72	98	0	0.705882	0	C|0.947;T|0.053	0.053	strong	.	EVC	90	.	NM_153717	exon9	c.C1115T	p.T372M	AGAGGACGATGGG	.	PASS	Atlas-SNP
GTF2H3	2967	hgsc.bcm.edu	37	12	124144395	124144395	+	Silent	SNP	A	A	G	rs1051793	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	159	69	139	0	0.433962	0	A|0.577;G|0.423	0.423	strong	.	GTF2H3	20	.	NM_001516	exon11	c.A738G	p.P246P	ACCCCCAGTTCAT	.	PASS	Atlas-SNP
CAPRIN2	65981	hgsc.bcm.edu	37	12	30906358	30906358	+	Missense_Mutation	SNP	G	G	A	rs17688567	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	134	68	125	0	0.507463	0	G|0.953;A|0.047	0.047	strong	.	CAPRIN2	109	.	NM_023925	exon1	c.C340T	p.P114S	GGGAAGGAGATGC	.	PASS	Atlas-SNP
WDR72	256764	hgsc.bcm.edu	37	15	54007512	54007512	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	223	64	223	0	0.286996	0	.	.	none	.	WDR72	177	.	NM_182758	exon5	c.G392T	p.G131V	TATTCTCCACAAC	.	PASS	Atlas-SNP
ARID4A	5926	hgsc.bcm.edu	37	14	58831258	58831258	+	Silent	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85	16	87	0	0.188235	0	.	.	none	.	ARID4A	222	.	NM_002892	exon20	c.A2451C	p.A817A	TGAAGCAGGAAGT	.	PASS	Atlas-SNP
CHML	1122	hgsc.bcm.edu	37	1	241797585	241797585	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	90	47	86	0	0.522222	0	.	.	none	.	CHML	82	.	NM_001821	exon1	c.G1484C	p.C495S	GAAGAACATAATT	.	PASS	Atlas-SNP
EPX	8288	hgsc.bcm.edu	37	17	56272390	56272390	+	Silent	SNP	A	A	G	rs2240815	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	34	73	0	0.539683	0	A|0.474;G|0.526	0.526	strong	.	EPX	95	.	NM_000502	exon6	c.A660G	p.R220R	TGGCCGAGCCCTC	.	PASS	Atlas-SNP
MPHOSPH6	10200	hgsc.bcm.edu	37	16	82203768	82203768	+	Silent	SNP	G	G	T	rs2303261	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51	19	99	0	0.372549	0	G|0.367;T|0.633	0.633	strong	MPHOSPH6,rectum,carcinoma,0,1	MPHOSPH6	16	1	NM_005792	exon1	c.C13A	p.R5R	TCTTTCGCTCGGC	.	PASS	Atlas-SNP
SH3PXD2A	9644	hgsc.bcm.edu	37	10	105362104	105362104	+	Silent	SNP	G	G	A	rs11191741	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	78	77	72	1	0.987179	0.0138889	G|0.718;A|0.282	0.282	strong	SH3PXD2A,NS,neuroblastoma,0,1	SH3PXD2A	90	1	NM_014631	exon14	c.C2787T	p.F929F	CTTGCCGAAGCCC	.	scavenged	Atlas-SNP
ATRNL1	26033	hgsc.bcm.edu	37	10	117061434	117061434	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	107	24	97	0	0.224299	0	.	.	none	.	ATRNL1	219	.	NM_207303	exon17	c.C2699T	p.T900I	ACTGTACAAGCAA	.	PASS	Atlas-SNP
LRRC55	219527	hgsc.bcm.edu	37	11	56949691	56949691	+	Missense_Mutation	SNP	G	G	A	rs12364102	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	113	55	134	0	0.486726	0	G|0.920;A|0.080	0.080	strong	.	LRRC55	52	.	NM_001005210	exon1	c.G324A	p.M108I	GCCAATGGACACC	.	PASS	Atlas-SNP
TPX2	22974	hgsc.bcm.edu	37	20	30354417	30354417	+	Silent	SNP	G	G	A	rs13044019	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73	27	68	0	0.369863	0	G|0.974;A|0.026	0.026	strong	.	TPX2	61	.	NM_012112	exon5	c.G288A	p.P96P	CATTCCGTCAAAT	.	PASS	Atlas-SNP
APPL1	26060	hgsc.bcm.edu	37	3	57303684	57303684	+	Missense_Mutation	SNP	A	A	G	rs11544593	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79	44	85	0	0.556962	0	A|0.892;G|0.108	0.108	strong	.	APPL1	59	.	NM_012096	exon22	c.A2099G	p.E700G	TGGGAGAAGGAGG	.	PASS	Atlas-SNP
ARHGEF18	23370	hgsc.bcm.edu	37	19	7524846	7524846	+	Silent	SNP	C	C	T	rs2287914	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	23	98	0	0.348485	0	C|0.797;T|0.203	0.203	strong	.	ARHGEF18	129	.	NM_001130955	exon10	c.C1854T	p.V618V	GGTGGTCGAGGCC	.	PASS	Atlas-SNP
HRH2	3274	hgsc.bcm.edu	37	5	175110779	175110779	+	Silent	SNP	G	G	A	rs1800689	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	157	75	138	0	0.477707	0	G|0.952;A|0.048	0.048	strong	.	HRH2	108	.	NM_001131055	exon2	c.G543A	p.V181V	TGAAGTGTACGGG	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	141	76	143	0	0.539007	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
TM4SF20	79853	hgsc.bcm.edu	37	2	228243905	228243905	+	Missense_Mutation	SNP	G	G	A	rs7574414	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	102	56	108	0	0.54902	0	G|0.889;A|0.111	0.111	strong	TM4SF20,NS,carcinoma,0,1	TM4SF20	24	1	NM_024795	exon1	c.C80T	p.A27V	GGTATCGCATTGA	.	PASS	Atlas-SNP
USP40	55230	hgsc.bcm.edu	37	2	234386134	234386134	+	Silent	SNP	A	A	G	rs2971863	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	66	60	0	1	0	A|0.746;G|0.254	0.254	strong	.	USP40	174	.	NM_018218	exon31	c.T3648C	p.H1216H	CTGCTCATGGAGG	.	PASS	Atlas-SNP
DNAJB9	4189	hgsc.bcm.edu	37	7	108212353	108212353	+	Silent	SNP	G	G	A	rs1043615	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	108	44	118	0	0.407407	0	G|0.543;A|0.457	0.457	strong	.	DNAJB9	25	.	NM_012328	exon2	c.G183A	p.P61P	GAGCCCGGATGCT	.	PASS	Atlas-SNP
C9orf50	375759	hgsc.bcm.edu	37	9	132377900	132377900	+	Missense_Mutation	SNP	C	C	T	rs918165	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	40	38	40	0	0.95	0	C|0.491;T|0.509	0.509	strong	.	C9orf50	25	.	NM_199350	exon4	c.G743A	p.R248K	TTGAGCCTGGGGA	.	PASS	Atlas-SNP
MYOM2	9172	hgsc.bcm.edu	37	8	2021421	2021421	+	Missense_Mutation	SNP	G	G	T	rs2272720	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80	80	91	0	1	0	G|0.687;T|0.313	0.313	strong	.	MYOM2	251	.	NM_003970	exon10	c.G961T	p.V321L	TCAGACGTGCTGT	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9046876	9046876	+	Missense_Mutation	SNP	G	G	T	rs4804378	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	113	50	85	0	0.442478	0	G|0.807;T|0.193	0.193	strong	.	MUC16	4315	.	NM_024690	exon5	c.C34755A	p.S11585R	CGTTGTGCTGGTT	.	PASS	Atlas-SNP
NOX3	50508	hgsc.bcm.edu	37	6	155775980	155775980	+	Silent	SNP	G	G	T	rs12195525	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51	21	61	0	0.411765	0	G|0.886;T|0.114	0.114	strong	NOX3,rectum,carcinoma,+1,1	NOX3	93	1	NM_015718	exon3	c.C220A	p.R74R	GGTTTCGACTGAC	.	PASS	Atlas-SNP
ARMC4	55130	hgsc.bcm.edu	37	10	28257853	28257853	+	Missense_Mutation	SNP	G	G	C	rs57067036	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	756	374	601	116	0.494709	0.193012	G|0.500;C|0.500	0.500	strong	ARMC4,rectum,NS,0,1	ARMC4	177	1	NM_018076	exon9	c.C1237G	p.R413G	CATACCGAAGTAA	.	scavenged	Atlas-SNP
FCGBP	8857	hgsc.bcm.edu	37	19	40368520	40368520	+	Silent	SNP	G	G	C	rs36079378	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	189	73	119	1	0.386243	0.00840336	G|0.500;C|0.500	0.500	strong	FCGBP,NS,carcinoma,0,1	FCGBP	416	1	NM_003890	exon28	c.C12828G	p.G4276G	GCCAGGGCCCTCG	.	scavenged	Atlas-SNP
BOD1	91272	hgsc.bcm.edu	37	5	173036257	173036257	+	Silent	SNP	A	A	G	rs77014290	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	140	25	123	0	0.178571	0	A|0.981;G|0.019	0.019	strong	BOD1,NS,carcinoma,0,1	BOD1	15	1	NM_138369	exon3	c.T543C	p.S181S	GTCCTGAGATGGA	.	PASS	Atlas-SNP
DCTN5	84516	hgsc.bcm.edu	37	16	23677006	23677006	+	Silent	SNP	A	A	G	rs35586	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	90	89	81	0	0.988889	0	A|0.799;G|0.201	0.201	strong	.	DCTN5	21	.	NM_032486	exon5	c.A408G	p.P136P	ACCTCCAGAAACT	.	PASS	Atlas-SNP
PNPLA5	150379	hgsc.bcm.edu	37	22	44282276	44282276	+	Missense_Mutation	SNP	A	A	G	rs739231	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57	26	56	0	0.45614	0	A|0.572;G|0.428	0.428	strong	.	PNPLA5	46	.	NM_138814	exon6	c.T856C	p.W286R	CCTTCCAGCGTTG	.	PASS	Atlas-SNP
ULK4	54986	hgsc.bcm.edu	37	3	41756986	41756986	+	Missense_Mutation	SNP	A	A	T	rs61744385	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	39	65	0	0.52	0	A|0.770;T|0.230	0.230	strong	.	ULK4	150	.	NM_017886	exon24	c.T2530A	p.L844M	GACACAACTTCAG	.	PASS	Atlas-SNP
SETD6	79918	hgsc.bcm.edu	37	16	58550484	58550484	+	Silent	SNP	G	G	A	rs3743567	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68	33	79	0	0.485294	0	G|0.896;A|0.104	0.104	strong	.	SETD6	27	.	NM_001160305	exon4	c.G579A	p.L193L	CGTGCTGCCCTTC	.	PASS	Atlas-SNP
WHSC1	7468	hgsc.bcm.edu	37	4	1957774	1957774	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93	4	109	0	0.0430108	0	.	.	none	.	WHSC1	180	.	NM_133335	exon15	c.G2740A	p.E914K	AAGCACGAGATTG	.	PASS	Atlas-SNP
KIR3DL1	3811	hgsc.bcm.edu	37	19	55340836	55340836	+	Missense_Mutation	SNP	A	A	G	rs45551936	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	10	10	35	0	1	0	A|0.847;G|0.153	0.153	strong	.	KIR3DL1	174	.	NM_013289	exon7	c.A1021G	p.I341V	CTGCACATTCTGA	.	PASS	Atlas-SNP
OR52E4	390081	hgsc.bcm.edu	37	11	5906203	5906203	+	Missense_Mutation	SNP	T	T	G	rs11823828	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	234	112	231	1	0.478632	0.004329	T|0.612;G|0.388	0.388	strong	.	OR52E4	65	.	NM_001005165	exon1	c.T681G	p.F227L	TGTTTTTCGCCTT	.	PASS	Atlas-SNP
SEMA5B	54437	hgsc.bcm.edu	37	3	122646828	122646828	+	Missense_Mutation	SNP	A	A	G	rs2276774	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	45	65	0	0.535714	0	A|0.858;G|0.142	0.142	strong	.	SEMA5B	303	.	NM_001256347	exon8	c.T821C	p.I274T	TTCTCAATAGTCC	.	PASS	Atlas-SNP
GRIN2B	2904	hgsc.bcm.edu	37	12	13764774	13764774	+	Silent	SNP	G	G	A	rs1805482	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	30	68	0	0.422535	0	G|0.753;A|0.247	0.247	strong	.	GRIN2B	303	.	NM_000834	exon8	c.C1665T	p.S555S	GTCAGCGCTGAAT	.	PASS	Atlas-SNP
CAMKV	79012	hgsc.bcm.edu	37	3	49899795	49899795	+	Silent	SNP	G	G	A	rs3796386	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	140	135	127	0	0.964286	0	G|0.650;A|0.350	0.350	strong	.	CAMKV	84	.	NM_024046	exon2	c.C27T	p.G9G	CTTGTCGCCCAGA	.	PASS	Atlas-SNP
C5orf20	140947	hgsc.bcm.edu	37	5	134782576	134782576	+	Missense_Mutation	SNP	T	T	G	rs1031844	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	50	50	69	2	1	0.0289855	T|0.370;G|0.630	0.630	strong	C5orf20,middle_lobe,carcinoma,+2,1	C5orf20	16	1	NM_130848	exon1	c.A223C	p.T75P	GCAAGGTTTTGTT	.	scavenged	Atlas-SNP
CCHCR1	54535	hgsc.bcm.edu	37	6	31122482	31122482	+	Missense_Mutation	SNP	G	G	A	rs130076	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	55	59	0	0.820895	0	G|0.828;A|0.172	0.172	strong	.	CCHCR1	68	.	NM_001105564	exon4	c.C592T	p.R198W	GGAGCCGGACCTC	.	PASS	Atlas-SNP
VWA3B	200403	hgsc.bcm.edu	37	2	98853173	98853173	+	Missense_Mutation	SNP	G	G	A	rs11889349	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51	20	58	0	0.392157	0	G|0.380;A|0.620	0.620	strong	.	VWA3B	138	.	NM_144992	exon19	c.G2653A	p.V885M	CATGTCGTGTCTA	.	PASS	Atlas-SNP
MXRA5	25878	hgsc.bcm.edu	37	X	3235724	3235724	+	Missense_Mutation	SNP	C	C	T	rs1635242	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	77	76	47	0	0.987013	0	C|0.319;T|0.681	0.681	strong	.	MXRA5	815	.	NM_015419	exon6	c.G5998A	p.G2000S	TGCGGCCCTCCAC	.	PASS	Atlas-SNP
LTF	4057	hgsc.bcm.edu	37	3	46490474	46490474	+	Silent	SNP	G	G	A	rs2230894	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	102	52	112	0	0.509804	0	G|0.814;A|0.186	0.186	strong	.	LTF	98	.	NM_002343	exon9	c.C1092T	p.V364V	CCACACGACCCGC	.	PASS	Atlas-SNP
EPHX1	2052	hgsc.bcm.edu	37	1	226027659	226027659	+	Silent	SNP	C	C	T	rs2292568	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	139	59	127	0	0.42446	0	C|0.950;N|0.001	.	strong	.	EPHX1	57	.	NM_001136018	exon6	c.C852T	p.P284P	GTACCCCGTCAAG	.	PASS	Atlas-SNP
AQP7	364	hgsc.bcm.edu	37	9	33395103	33395103	+	Silent	SNP	G	G	A	rs148012859	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	168	4	178	0	0.0238095	0	A|0.002;G|0.998;T|0.000	0.002	strong	AQP7,NS,carcinoma,0,1	AQP7	58	1	NM_001170	exon3	c.C117T	p.A39A	GAACTCGGCCAGG	.	scavenged	Atlas-SNP
DHRS7C	201140	hgsc.bcm.edu	37	17	9676134	9676134	+	Missense_Mutation	SNP	G	G	A	rs2280490	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	23	22	28	0	0.956522	0	G|0.907;A|0.093	0.093	strong	.	DHRS7C	34	.	NM_001220493	exon5	c.C680T	p.S227L	TGGTACGACCGGA	.	PASS	Atlas-SNP
ANKRD30A	91074	hgsc.bcm.edu	37	10	37451586	37451586	+	Missense_Mutation	SNP	G	G	A	rs12766884	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	202	78	253	0	0.386139	0	G|0.968;A|0.032	0.032	strong	ANKRD30A,right_upper_lobe,carcinoma,+1,3	ANKRD30A	448	3	NM_052997	exon16	c.G1742A	p.G581E	CTCCGGGGAAGCC	.	PASS	Atlas-SNP
SP140	11262	hgsc.bcm.edu	37	2	231149097	231149097	+	Missense_Mutation	SNP	T	T	C	rs4972945	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	156	92	155	0	0.589744	0	T|0.878;C|0.122	0.122	strong	.	SP140	121	.	NM_007237	exon16	c.T1535C	p.M512T	TGAGAATGAGAAG	.	PASS	Atlas-SNP
HNRNPCL1	343069	hgsc.bcm.edu	37	1	12907496	12907496	+	Missense_Mutation	SNP	T	T	C	rs75752931		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	244	58	171	0	0.237705	0	.	.	weak	.	HNRNPCL1	68	.	NM_001013631	exon2	c.A647G	p.K216R	GCATTTTTCACCT	.	PASS	Atlas-SNP
IL33	90865	hgsc.bcm.edu	37	9	6253571	6253571	+	Silent	SNP	C	C	T	rs10975519	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	95	50	110	0	0.526316	0	C|0.633;T|0.367	0.367	strong	.	IL33	27	.	NM_033439	exon6	c.C489T	p.Y163Y	GAGTTACTATGAG	.	PASS	Atlas-SNP
SMG6	23293	hgsc.bcm.edu	37	17	2091765	2091765	+	Missense_Mutation	SNP	C	C	T	rs903160	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	77	38	80	0	0.493506	0	C|0.626;T|0.374	0.374	strong	.	SMG6	97	.	NM_017575	exon11	c.G2914A	p.A972T	GAGCTGCGGCTTG	.	PASS	Atlas-SNP
ERCC6	2074	hgsc.bcm.edu	37	10	50667105	50667105	+	Missense_Mutation	SNP	T	T	C	rs2228529	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	107	61	124	1	0.570093	0.00806452	T|0.826;C|0.173	0.173	strong	ERCC6,NS,carcinoma,0,1	ERCC6	162	1	NM_000124	exon21	c.C4238G	p.P1413R	GCTTCCTGCAGGT	.	scavenged	Atlas-SNP
MROH9	80133	hgsc.bcm.edu	37	1	170934394	170934394	+	Missense_Mutation	SNP	T	T	C	rs16863872	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	113	59	98	0	0.522124	0	T|0.955;C|0.045	0.045	strong	C1orf129_ENST00000367759,NS,carcinoma,-2,2	.	.	2	NM_025063	exon7	c.T478C	p.Y160H	AGAAAATACGTAA	.	PASS	Atlas-SNP
GAB4	128954	hgsc.bcm.edu	37	22	17469026	17469026	+	Silent	SNP	G	G	A	rs5992604	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91	37	75	0	0.406593	0	G|0.617;A|0.383	0.383	strong	.	GAB4	95	.	NM_001037814	exon3	c.C510T	p.H170H	GAGGCCGTGACTG	.	PASS	Atlas-SNP
DTHD1	401124	hgsc.bcm.edu	37	4	36310049	36310049	+	Missense_Mutation	SNP	C	C	T	rs12507599	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79	41	71	0	0.518987	0	C|0.725;T|0.275	0.275	strong	.	DTHD1	63	.	NM_001170700	exon6	c.C1654T	p.R552C	CCATCTCGTCATT	.	PASS	Atlas-SNP
DUSP27	92235	hgsc.bcm.edu	37	1	167097567	167097567	+	Missense_Mutation	SNP	G	G	A	rs61748784	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	108	50	106	0	0.462963	0	G|0.904;A|0.096	0.096	strong	.	DUSP27	235	.	NM_001080426	exon5	c.G3199A	p.D1067N	TCCAGGGACTGGG	.	PASS	Atlas-SNP
CCL14	6358	hgsc.bcm.edu	37	17	34313612	34313612	+	Missense_Mutation	SNP	G	G	A	rs75238886	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	105	46	81	0	0.438095	0	G|0.973;A|0.027	0.027	strong	.	CCL14	22	.	NM_032962	exon1	c.C74T	p.S25F	CGTGAGGAGGATT	.	PASS	Atlas-SNP
CCR3	1232	hgsc.bcm.edu	37	3	46306700	46306700	+	Silent	SNP	T	T	C	rs4987053	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	194	94	180	0	0.484536	0	T|0.903;C|0.097	0.097	strong	.	CCR3	52	.	NM_178328	exon3	c.T114C	p.Y38Y	CTACTATGATGAC	.	PASS	Atlas-SNP
MLF1	4291	hgsc.bcm.edu	37	3	158320703	158320703	+	Missense_Mutation	SNP	C	C	A	rs15967	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80	37	85	0	0.4625	0	T|0.055;G|0.123	.	strong	.	MLF1	62	.	NM_001195432	exon8	c.C769A	p.P257T	GAGAATCCTGGCT	.	PASS	Atlas-SNP
ZNRF3	84133	hgsc.bcm.edu	37	22	29445817	29445817	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	27	110	0	0.313953	0	.	.	none	.	ZNRF3	75	.	NM_001206998	exon8	c.G1648A	p.D550N	GGCAGCGACAGCA	.	PASS	Atlas-SNP
FGFBP3	143282	hgsc.bcm.edu	37	10	93668110	93668110	+	Missense_Mutation	SNP	T	T	A	rs1107947	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	56	27	56	0	0.482143	0	T|0.805;A|0.195	0.195	strong	.	FGFBP3	6	.	NM_152429	exon2	c.A617T	p.E206V	TTGCCCTCGTTGG	.	PASS	Atlas-SNP
PNRC1	10957	hgsc.bcm.edu	37	6	89793894	89793894	+	Silent	SNP	G	G	C	rs1130809	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	102	46	116	0	0.45098	0	G|0.746;C|0.254	0.254	strong	.	PNRC1	17	.	NM_006813	exon2	c.G963C	p.T321T	AAAAACGCTCCTC	.	PASS	Atlas-SNP
INTS1	26173	hgsc.bcm.edu	37	7	1538614	1538614	+	Silent	SNP	G	G	A	rs2289035	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	35	25	37	0	0.714286	0	G|0.492;A|0.508	0.508	strong	.	INTS1	145	.	NM_001080453	exon8	c.C1134T	p.P378P	CACCTTGGGGTTC	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228471379	228471379	+	Silent	SNP	G	G	C	rs56168609	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	145	70	147	0	0.482759	0	G|0.721;C|0.279	0.279	strong	OBSCN_ENST00000570156,NS,carcinoma,+1,4	OBSCN	2142	4	NM_001271223	exon38	c.G10200C	p.R3400R	CCTGCGGCTCACC	.	PASS	Atlas-SNP
GSDMC	56169	hgsc.bcm.edu	37	8	130760850	130760850	+	Missense_Mutation	SNP	A	A	G	rs4144738	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	109	41	139	0	0.376147	0	A|0.363;G|0.637	0.637	strong	GSDMC,NS,carcinoma,0,1	GSDMC	71	1	NM_031415	exon14	c.T1424C	p.M475T	AGCTCCATCCTAA	.	PASS	Atlas-SNP
SEMA6C	10500	hgsc.bcm.edu	37	1	151110832	151110832	+	Silent	SNP	G	G	A	rs72708441	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	135	61	140	0	0.451852	0	G|0.947;A|0.053	0.053	strong	.	SEMA6C	70	.	NM_001178061	exon8	c.C507T	p.C169C	AAAGGGGCATCGA	.	PASS	Atlas-SNP
TBCD	6904	hgsc.bcm.edu	37	17	80887244	80887244	+	Silent	SNP	T	T	C	rs1127986	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48	24	50	0	0.5	0	T|0.751;C|0.249	0.249	strong	.	TBCD	94	.	NM_005993	exon32	c.T2859C	p.D953D	GTCCGATGTGGCC	.	PASS	Atlas-SNP
SLC45A1	50651	hgsc.bcm.edu	37	1	8390384	8390384	+	Silent	SNP	G	G	C	rs56125713	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	39	78	0	0.448276	0	G|0.867;C|0.133	0.133	strong	.	SLC45A1	85	.	NM_001080397	exon4	c.G831C	p.L277L	CACCCTGAGCGTC	.	PASS	Atlas-SNP
HSPA9	3313	hgsc.bcm.edu	37	5	137892170	137892170	+	Silent	SNP	G	G	A	rs10117	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94	42	82	0	0.446809	0	G|0.442;A|0.558	0.558	strong	.	HSPA9	49	.	NM_004134	exon16	c.C1933T	p.L645L	GCTTCAGTGATGC	.	PASS	Atlas-SNP
DST	667	hgsc.bcm.edu	37	6	56505175	56505175	+	Silent	SNP	T	T	A	rs113432929	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	132	70	136	0	0.530303	0	T|0.997;A|0.003	0.003	strong	.	DST	1427	.	NM_001723	exon4	c.A645T	p.S215S	CATCCCTGATGAC	.	PASS	Atlas-SNP
MARCH4	57574	hgsc.bcm.edu	37	2	217148417	217148417	+	Silent	SNP	C	C	A	rs876771	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68	42	99	0	0.617647	0	C|0.576;A|0.424	0.424	strong	.	MARCH4	50	.	NM_020814	exon2	c.G552T	p.S184S	CTTGACCGAGCCA	.	PASS	Atlas-SNP
ZNF81	347344	hgsc.bcm.edu	37	X	47774599	47774599	+	Missense_Mutation	SNP	C	C	T	rs186251256	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	279	197	198	0	0.706093	0	C|0.992;T|0.008	0.008	strong	.	ZNF81	60	.	NM_007137	exon5	c.C554T	p.S185L	TTCTTTCACAGAA	.	PASS	Atlas-SNP
ADAM19	8728	hgsc.bcm.edu	37	5	156936364	156936364	+	Missense_Mutation	SNP	T	T	C	rs1422795	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98	47	71	0	0.479592	0	T|0.592;C|0.408	0.408	strong	.	ADAM19	216	.	NM_033274	exon9	c.A850G	p.S284G	TCCAACTGAGAAA	.	PASS	Atlas-SNP
CDCA7L	55536	hgsc.bcm.edu	37	7	21956405	21956405	+	Silent	SNP	G	G	A	rs1128250	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49	8	78	0	0.163265	0	G|0.773;A|0.227	0.227	strong	CDCA7L,caecum,carcinoma,0,1	CDCA7L	56	1	NM_018719	exon2	c.C132T	p.C44C	ACTATCGCAGCTC	.	PASS	Atlas-SNP
MTHFR	4524	hgsc.bcm.edu	37	1	11863057	11863057	+	Silent	SNP	G	G	A	rs2066470	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	78	44	95	0	0.564103	0	G|0.910;A|0.090	0.090	strong	.	MTHFR	65	.	NM_005957	exon2	c.C117T	p.P39P	CCGCTCGGGGTCC	.	PASS	Atlas-SNP
PPP1R26	9858	hgsc.bcm.edu	37	9	138377853	138377853	+	Silent	SNP	A	A	G	rs2004074	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48	21	44	1	0.4375	0.0227273	A|0.691;G|0.309	0.309	strong	KIAA0649,colon,carcinoma,0,1	.	.	1	NM_014811	exon4	c.A1497G	p.V499V	CCCTGTAGAGGGC	.	scavenged	Atlas-SNP
RANBP6	26953	hgsc.bcm.edu	37	9	6012347	6012347	+	Silent	SNP	T	T	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79	29	81	0	0.367089	0	.	.	none	.	RANBP6	127	.	NM_012416	exon1	c.A3261T	p.V1087V	TTGTGATACACAT	.	PASS	Atlas-SNP
PCDHGA4	56111	hgsc.bcm.edu	37	5	140735361	140735361	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72	31	80	0	0.430556	0	.	.	none	.	PCDHGA4	150	.	NM_018917	exon1	c.C594T	p.R198R	GGAACGCGCTCTA	.	PASS	Atlas-SNP
MAP7D2	256714	hgsc.bcm.edu	37	X	20071046	20071046	+	Missense_Mutation	SNP	T	T	C	rs34519770	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	156	115	91	0	0.737179	0	T|0.544;C|0.456	0.456	strong	.	MAP7D2	165	.	NM_152780	exon5	c.A545G	p.N182S	CGTTTATTCATGG	.	PASS	Atlas-SNP
TBX4	9496	hgsc.bcm.edu	37	17	59560685	59560685	+	Silent	SNP	C	C	T	rs2270150	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	104	51	88	0	0.490385	0	C|0.880;T|0.120	0.120	strong	.	TBX4	69	.	NM_018488	exon8	c.C1446T	p.V482V	TCAGGTCCGAGAG	.	PASS	Atlas-SNP
TMEM51	55092	hgsc.bcm.edu	37	1	15541607	15541607	+	Silent	SNP	T	T	C	rs3820065	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	24	10	26	0	0.416667	0	T|0.843;C|0.157	0.157	strong	.	TMEM51	28	.	NM_018022	exon2	c.T24C	p.N8N	GGCCAATGGCTCG	.	PASS	Atlas-SNP
DSP	1832	hgsc.bcm.edu	37	6	7584617	7584617	+	Silent	SNP	C	C	T	rs2076300	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	14	87	0	0.162791	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
MRGPRD	116512	hgsc.bcm.edu	37	11	68748003	68748003	+	Silent	SNP	T	T	C	rs34847539	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55	54	64	0	0.981818	0	T|0.325;C|0.675	0.675	strong	.	MRGPRD	53	.	NM_198923	exon1	c.A453G	p.T151T	ACAGAGTGTCCAC	.	PASS	Atlas-SNP
ADD1	118	hgsc.bcm.edu	37	4	2906707	2906707	+	Missense_Mutation	SNP	G	G	T	rs4961	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	103	38	126	0	0.368932	0	G|0.800;T|0.200	0.200	strong	.	ADD1	56	.	NM_014190	exon10	c.G1378T	p.G460W	GAGGAAGGGCAGA	.	PASS	Atlas-SNP
C9orf66	157983	hgsc.bcm.edu	37	9	214864	214864	+	Missense_Mutation	SNP	C	C	T	rs2236547	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	29	15	35	0	0.517241	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
TEP1	7011	hgsc.bcm.edu	37	14	20852029	20852029	+	Missense_Mutation	SNP	A	A	G	rs1760904	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	6	6	2	0	1	0	A|0.367;G|0.633	0.633	strong	.	TEP1	224	.	NM_007110	exon25	c.T3583C	p.S1195P	CTAATGATGCCAC	.	PASS	Atlas-SNP
MAPKAP1	79109	hgsc.bcm.edu	37	9	128246786	128246786	+	Silent	SNP	G	G	A	rs2070113	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	199	97	199	0	0.487437	0	G|0.819;T|0.001	.	strong	.	MAPKAP1	68	.	NM_001006617	exon9	c.C1143T	p.H381H	GTAATGGTGGCTG	.	PASS	Atlas-SNP
SLC17A4	10050	hgsc.bcm.edu	37	6	25776949	25776949	+	Missense_Mutation	SNP	G	G	A	rs11754288	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	194	43	199	0	0.221649	0	G|0.711;A|0.289	0.289	strong	.	SLC17A4	79	.	NM_005495	exon9	c.G1114A	p.A372T	TTCACTGCCATTG	.	PASS	Atlas-SNP
PIK3C2G	5288	hgsc.bcm.edu	37	12	18499636	18499636	+	Silent	SNP	C	C	T	rs17847788	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	109	39	136	0	0.357798	0	C|0.869;T|0.131	0.131	strong	PIK3C2G_ENST00000433979,brain,glioma,0,3	PIK3C2G	315	3	NM_004570	exon11	c.C1491T	p.Y497Y	TGTCTACTGTAAC	.	PASS	Atlas-SNP
MBL2	4153	hgsc.bcm.edu	37	10	54531242	54531242	+	Missense_Mutation	SNP	G	G	A	rs5030737	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	128	66	108	0	0.515625	0	G|0.957;A|0.043	0.043	strong	.	MBL2	55	.	NM_000242	exon1	c.C154T	p.R52C	CATCACGCCCATC	.	PASS	Atlas-SNP
WDR31	114987	hgsc.bcm.edu	37	9	116082647	116082647	+	Missense_Mutation	SNP	C	C	G	rs41307479	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	115	57	114	0	0.495652	0	C|0.850;G|0.150	0.150	strong	.	WDR31	23	.	NM_001012361	exon9	c.G770C	p.C257S	GCTTCACAGCCTT	.	PASS	Atlas-SNP
MYOM1	8736	hgsc.bcm.edu	37	18	3176063	3176063	+	Silent	SNP	C	C	T	rs2230162	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	34	118	0	0.459459	0	T|0.164;G|0.282	0.164	strong	.	MYOM1	192	.	NM_003803	exon6	c.G999A	p.G333G	GTGCATCCCATAT	.	PASS	Atlas-SNP
KRT72	140807	hgsc.bcm.edu	37	12	52986187	52986187	+	Missense_Mutation	SNP	T	T	C	rs12833456	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	28	86	0	0.444444	0	C|0.351;N|0.000	0.351	strong	.	KRT72	70	.	NM_001146225	exon4	c.A791G	p.Y264C	CCTTCATAAAGGC	.	PASS	Atlas-SNP
NME8	51314	hgsc.bcm.edu	37	7	37936530	37936530	+	Silent	SNP	T	T	C	rs3213975	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	42	97	0	0.688525	0	T|0.770;C|0.230	0.230	strong	.	.	.	.	NM_016616	exon17	c.T1603C	p.L535L	AGACGATTGATGG	.	PASS	Atlas-SNP
DHDH	27294	hgsc.bcm.edu	37	19	49442933	49442933	+	Silent	SNP	T	T	C	rs2270939	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	41	23	35	0	0.560976	0	T|0.623;C|0.377	0.377	strong	.	DHDH	35	.	NM_014475	exon4	c.T594C	p.S198S	GATTTCTGTCGTG	.	PASS	Atlas-SNP
MAP3K6	9064	hgsc.bcm.edu	37	1	27687466	27687466	+	Missense_Mutation	SNP	G	G	T	rs35659744	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	33	63	0	0.622642	0	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	.	PASS	Atlas-SNP
STARD13	90627	hgsc.bcm.edu	37	13	33704065	33704065	+	Missense_Mutation	SNP	T	T	C	rs3742321	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	33	12	56	0	0.363636	0	T|0.811;C|0.189	0.189	strong	.	STARD13	100	.	NM_178006	exon5	c.A749G	p.K250R	GTGGGCTTCTCAT	.	PASS	Atlas-SNP
CES3	23491	hgsc.bcm.edu	37	16	66997756	66997756	+	Missense_Mutation	SNP	T	T	C	rs71647892	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	140	70	110	0	0.5	0	T|0.993;C|0.007	0.007	strong	.	CES3	56	.	NM_024922	exon4	c.T478C	p.Y160H	ACCTCCTACGATG	.	PASS	Atlas-SNP
LRP1B	53353	hgsc.bcm.edu	37	2	141259376	141259376	+	Silent	SNP	G	G	A	rs35164907	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51	40	51	0	0.784314	0	G|0.818;A|0.182	0.182	strong	.	LRP1B	1315	.	NM_018557	exon55	c.C8730T	p.C2910C	ATTGTCGCAAAGA	.	PASS	Atlas-SNP
CAND2	23066	hgsc.bcm.edu	37	3	12859004	12859004	+	Missense_Mutation	SNP	A	A	C	rs3732678	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94	93	83	0	0.989362	0	A|0.402;C|0.597;G|0.000	0.597	strong	.	CAND2	138	.	NM_001162499	exon10	c.A2573C	p.H858P	CAGGCCACCAGCG	.	PASS	Atlas-SNP
SERPINA3	12	hgsc.bcm.edu	37	14	95081081	95081081	+	Silent	SNP	A	A	G	rs17826465	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	25	79	0	0.378788	0	A|0.935;G|0.065	0.065	strong	.	SERPINA3	78	.	NM_001085	exon2	c.A303G	p.K101K	TCTCAAAGGCCTC	.	PASS	Atlas-SNP
IRAK2	3656	hgsc.bcm.edu	37	3	10264480	10264480	+	Missense_Mutation	SNP	C	C	G	rs3844283	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	89	42	105	0	0.47191	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
ZNF275	10838	hgsc.bcm.edu	37	X	152610985	152610985	+	Silent	SNP	T	T	C	rs3213466	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	39	38	27	0	0.974359	0	0|0.006;C|0.479	0.479	strong	.	ZNF275	44	.	NM_001080485	exon3	c.T39C	p.P13P	CGTTCCTGTTTTA	.	PASS	Atlas-SNP
PRRC2B	84726	hgsc.bcm.edu	37	9	134350323	134350323	+	Missense_Mutation	SNP	C	C	G	rs10736851	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	41	41	39	0	1	0	C|0.230;G|0.770	0.770	strong	.	PRRC2B	266	.	NM_013318	exon15	c.C2807G	p.T936S	GCAGGACCCGGAG	.	PASS	Atlas-SNP
NEB	4703	hgsc.bcm.edu	37	2	152420361	152420361	+	Silent	SNP	C	C	T	rs145252235	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	23	63	0	0.310811	0	C|0.989;T|0.011	0.011	strong	.	NEB	1697	.	NM_001271208	exon118	c.G18555A	p.K6185K	AGCATGCTTGGCT	.	PASS	Atlas-SNP
KANSL1	284058	hgsc.bcm.edu	37	17	44108906	44108906	+	Missense_Mutation	SNP	A	A	G	rs34579536	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	66	80	0	1	0	A|0.860;G|0.140	0.140	strong	KIAA1267,colon,carcinoma,0,1	.	.	1	NM_001193466	exon15	c.T3254C	p.I1085T	GGGACAATGGGAG	.	PASS	Atlas-SNP
DYTN	391475	hgsc.bcm.edu	37	2	207572133	207572133	+	Silent	SNP	A	A	C	rs67248530	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	170	82	138	0	0.482353	0	A|0.951;C|0.049	0.049	strong	.	DYTN	168	.	NM_001093730	exon3	c.T189G	p.S63S	TGCCTGAGAAAGT	.	PASS	Atlas-SNP
PRG4	10216	hgsc.bcm.edu	37	1	186276661	186276661	+	Missense_Mutation	SNP	A	A	G	rs61831150	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57	48	74	1	0.842105	0.0135135	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	.	scavenged	Atlas-SNP
PRICKLE4	29964	hgsc.bcm.edu	37	6	41754576	41754576	+	Silent	SNP	C	C	T	rs9381093	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51	42	45	0	0.823529	0	C|0.588;T|0.412	0.412	strong	.	PRICKLE4	29	.	NM_013397	exon8	c.C864T	p.L288L	ACTCCTCGCTGCT	.	PASS	Atlas-SNP
TMEM2	23670	hgsc.bcm.edu	37	9	74355028	74355028	+	Silent	SNP	A	A	G	rs25690	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	31	57	0	0.5	0	A|0.936;G|0.064	0.064	strong	.	TMEM2	112	.	NM_001135820	exon5	c.T1155C	p.T385T	ATCCACAGTATAA	.	PASS	Atlas-SNP
CFHR1	3078	hgsc.bcm.edu	37	1	196799691	196799691	+	Silent	SNP	G	G	A	rs56411312	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	337	127	226	0	0.376855	0	G|0.878;A|0.122	0.122	strong	.	CFHR1	47	.	NM_002113	exon5	c.G669A	p.P223P	ATTCCCGTTGTCA	.	PASS	Atlas-SNP
TBC1D16	125058	hgsc.bcm.edu	37	17	77984141	77984141	+	Silent	SNP	C	C	T	rs35922784	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	124	63	98	0	0.508065	0	C|0.729;T|0.271	0.271	strong	.	TBC1D16	48	.	NM_019020	exon3	c.G597A	p.G199G	CTCCCGCCCCTCC	.	PASS	Atlas-SNP
SGCA	6442	hgsc.bcm.edu	37	17	48247689	48247689	+	Silent	SNP	C	C	T	rs1801191	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	104	46	106	0	0.442308	0	C|0.911;T|0.089	0.089	strong	.	SGCA	35	.	NM_000023	exon7	c.C933T	p.V311V	CTATGTCATGTGC	.	PASS	Atlas-SNP
GK2	2712	hgsc.bcm.edu	37	4	80329343	80329343	+	Silent	SNP	T	T	C	rs6837906	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	33	20	37	0	0.606061	0	T|0.803;C|0.197	0.197	strong	.	GK2	102	.	NM_033214	exon1	c.A12G	p.P4P	TGTCTTTGGGGCT	.	PASS	Atlas-SNP
SNAPC4	6621	hgsc.bcm.edu	37	9	139272502	139272502	+	Silent	SNP	T	T	C	rs3812565	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	24	8	50	1	0.333333	0.02	T|0.670;C|0.330	0.330	strong	SNAPC4,caecum,carcinoma,0,1	SNAPC4	82	1	NM_003086	exon21	c.A3777G	p.L1259L	CTGGGGTAGGGGC	.	scavenged	Atlas-SNP
KBTBD12	166348	hgsc.bcm.edu	37	3	127642814	127642814	+	Missense_Mutation	SNP	G	G	C	rs61268888	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	148	59	152	0	0.398649	0	G|0.846;C|0.154	0.154	strong	.	KBTBD12	41	.	NM_207335	exon1	c.G910C	p.V304L	GATCCTGTATCAC	.	PASS	Atlas-SNP
FAM186A	121006	hgsc.bcm.edu	37	12	50727811	50727811	+	Missense_Mutation	SNP	C	C	T	rs6580742	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	204	106	203	0	0.519608	0	C|0.920;T|0.080	0.080	strong	.	FAM186A	181	.	NM_001145475	exon5	c.G6579A	p.M2193I	GCTCAGCATCATG	.	PASS	Atlas-SNP
FBP1	2203	hgsc.bcm.edu	37	9	97369151	97369151	+	Silent	SNP	G	G	A	rs1042144	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	125	58	135	0	0.464	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
CXCL14	9547	hgsc.bcm.edu	37	5	134914455	134914455	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	23	7	52	0	0.304348	0	.	.	none	.	CXCL14	13	.	NM_004887	exon1	c.C50T	p.A17V	GCGGCCGCCAGGA	.	PASS	Atlas-SNP
CLIC5	53405	hgsc.bcm.edu	37	6	46047458	46047458	+	Silent	SNP	C	C	T	rs3734207	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	96	52	90	0	0.541667	0	C|0.815;T|0.185	0.185	strong	.	CLIC5	48	.	NM_001114086	exon1	c.G522A	p.E174E	GTAAATCTCAGGG	.	PASS	Atlas-SNP
C6orf118	168090	hgsc.bcm.edu	37	6	165715405	165715405	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	29	9	28	0	0.310345	0	.	.	none	.	C6orf118	116	.	NM_144980	exon2	c.G406A	p.A136T	GAGAGGCCTGGGG	.	PASS	Atlas-SNP
GDPD4	220032	hgsc.bcm.edu	37	11	76954833	76954833	+	Missense_Mutation	SNP	G	G	A	rs11237146	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	78	11	64	0	0.141026	0	G|0.770;A|0.229	0.229	strong	.	GDPD4	49	.	NM_182833	exon12	c.C1147T	p.H383Y	CCACATGCTGAAA	.	PASS	Atlas-SNP
HBS1L	10767	hgsc.bcm.edu	37	6	135323873	135323873	+	Missense_Mutation	SNP	C	C	T	rs34860737	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	111	2	106	0	0.018018	0	C|0.999;T|0.001	0.001	strong	HBS1L,NS,carcinoma,+1,1	HBS1L	75	1	NM_006620	exon5	c.G538A	p.G180R	CTTACCCAGGCAC	.	scavenged	Atlas-SNP
DNLZ	728489	hgsc.bcm.edu	37	9	139256541	139256541	+	Missense_Mutation	SNP	C	C	T	rs3812554	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	65	31	76	0	0.476923	0	C|0.926;T|0.074	0.074	strong	.	DNLZ	8	.	NM_001080849	exon3	c.G460A	p.A154T	TGGGGGCCCCTGC	.	PASS	Atlas-SNP
INPP4B	8821	hgsc.bcm.edu	37	4	143235865	143235865	+	Silent	SNP	C	C	G	rs3756122	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	131	66	143	0	0.503817	0	C|0.877;G|0.123	0.123	strong	.	INPP4B	132	.	NM_003866	exon9	c.G423C	p.G141G	ACTTACCCCAACT	.	PASS	Atlas-SNP
CDHR2	54825	hgsc.bcm.edu	37	5	175998246	175998246	+	Silent	SNP	T	T	C	rs17078320	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94	46	79	0	0.489362	0	T|0.732;C|0.268	0.268	strong	.	CDHR2	152	.	NM_017675	exon6	c.T348C	p.D116D	GGAAGATAGAAAC	.	PASS	Atlas-SNP
ADCY8	114	hgsc.bcm.edu	37	8	132002770	132002770	+	Silent	SNP	G	G	A	rs2228950	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73	33	68	0	0.452055	0	G|0.701;A|0.299	0.299	strong	.	ADCY8	291	.	NM_001115	exon2	c.C979T	p.L327L	TGAATAGCACTGC	.	PASS	Atlas-SNP
TMEM214	54867	hgsc.bcm.edu	37	2	27260469	27260469	+	Missense_Mutation	SNP	G	G	A	rs1124649	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	125	59	124	0	0.472	0	G|0.713;A|0.287	0.287	strong	.	TMEM214	41	.	NM_017727	exon9	c.G1051A	p.V351M	CTGAAAGTGCTGG	.	PASS	Atlas-SNP
P2RX7	5027	hgsc.bcm.edu	37	12	121622304	121622304	+	Missense_Mutation	SNP	A	A	C	rs3751143	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49	27	45	0	0.55102	0	A|0.826;C|0.174	0.174	strong	.	P2RX7	53	.	NM_002562	exon13	c.A1487C	p.E496A	TGGAGGAGCTGTG	.	PASS	Atlas-SNP
ZNF462	58499	hgsc.bcm.edu	37	9	109689859	109689859	+	Silent	SNP	T	T	C	rs3814540	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	97	48	93	0	0.494845	0	T|0.525;C|0.475	0.475	strong	.	ZNF462	322	.	NM_021224	exon3	c.T3666C	p.N1222N	GGCCAATGCAGAT	.	PASS	Atlas-SNP
CCDC157	550631	hgsc.bcm.edu	37	22	30772686	30772686	+	Silent	SNP	C	C	T	rs2286442	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	90	32	94	0	0.355556	0	C|0.898;T|0.102	0.102	strong	.	CCDC157	86	.	NM_001017437	exon12	c.C2211T	p.G737G	ACCTGGCCGGGGA	.	PASS	Atlas-SNP
ZNF462	58499	hgsc.bcm.edu	37	9	109773145	109773145	+	Missense_Mutation	SNP	A	A	T	rs10217192	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	58	33	48	0	0.568965	0	A|0.879;T|0.121	0.121	strong	.	ZNF462	322	.	NM_021224	exon13	c.A7355T	p.H2452L	AAATCCACCCAAA	.	PASS	Atlas-SNP
MGA	23269	hgsc.bcm.edu	37	15	41988709	41988709	+	Missense_Mutation	SNP	A	A	G	rs199666635	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	40	28	63	0	0.7	0	.	.	weak	.	MGA	264	.	NM_001080541	exon3	c.A1501G	p.M501V	TCTTCTATGTTGG	.	PASS	Atlas-SNP
TLR8	51311	hgsc.bcm.edu	37	X	12937804	12937804	+	Silent	SNP	C	C	T	rs5744080	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	103	71	78	0	0.68932	0	C|0.402;0|0.003	.	strong	.	TLR8	134	.	NM_138636	exon2	c.C645T	p.H215H	TTCACACGTGCCA	.	PASS	Atlas-SNP
CIITA	4261	hgsc.bcm.edu	37	16	11001256	11001256	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	105	41	121	0	0.390476	0	.	.	none	.	CIITA	92	.	NM_000246	exon11	c.C1907T	p.T636M	CCTCCACGCTCAC	.	PASS	Atlas-SNP
PCDHB11	56125	hgsc.bcm.edu	37	5	140579367	140579367	+	Missense_Mutation	SNP	G	G	A	rs917535	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	46	23	62	0	0.5	0	G|0.931;A|0.069	0.069	strong	PCDHB11,NS,carcinoma,+1,1	PCDHB11	162	1	NM_018931	exon1	c.G20A	p.R7H	GGACACGCACTCA	.	PASS	Atlas-SNP
RBMXL3	139804	hgsc.bcm.edu	37	X	114425923	114425923	+	Missense_Mutation	SNP	C	C	A	rs142223554	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	130	30	128	0	0.230769	0	C|0.930;A|0.070	0.070	strong	.	RBMXL3	83	.	NM_001145346	exon1	c.C1919A	p.A640D	TTGATGCCAACAG	.	PASS	Atlas-SNP
FAM214A	56204	hgsc.bcm.edu	37	15	52901284	52901284	+	Silent	SNP	T	T	C	rs58018557	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73	25	53	0	0.342466	0	T|0.652;C|0.348	0.348	strong	.	.	.	.	NM_019600	exon6	c.A1827G	p.S609S	GGAAGTTGATAAA	.	PASS	Atlas-SNP
OR2T2	401992	hgsc.bcm.edu	37	1	248616408	248616408	+	Missense_Mutation	SNP	C	C	T	rs73147579	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	667	137	822	0	0.205397	0	C|0.875;T|0.125	0.125	strong	OR2T2,NS,carcinoma,-2,1	OR2T2	73	1	NM_001004136	exon1	c.C310T	p.L104F	ATCTTCCTCTACC	.	PASS	Atlas-SNP
ARSG	22901	hgsc.bcm.edu	37	17	66364749	66364749	+	Silent	SNP	T	T	C	rs1558877	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	74	82	0	1	0	T|0.481;C|0.519	0.519	strong	.	ARSG	55	.	NM_001267727	exon7	c.T765C	p.P255P	CTTACCTGTGACT	.	PASS	Atlas-SNP
HOXC9	3225	hgsc.bcm.edu	37	12	54394497	54394497	+	Silent	SNP	C	C	T	rs2241820	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	15	5	16	0	0.333333	0	C|0.388;T|0.612	0.612	strong	.	HOXC9	25	.	NM_006897	exon1	c.C525T	p.A175A	GAAGGCCGACCTG	.	PASS	Atlas-SNP
CACNG6	59285	hgsc.bcm.edu	37	19	54515415	54515415	+	Missense_Mutation	SNP	G	G	C	rs12980121	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	25	15	39	0	0.6	0	G|0.953;C|0.047	0.047	strong	.	CACNG6	42	.	NM_145814	exon4	c.G755C	p.C252S	CCCTCTGTCCCAA	.	PASS	Atlas-SNP
KLK12	43849	hgsc.bcm.edu	37	19	51535130	51535130	+	Splice_Site	SNP	A	A	G	rs3745540	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	24	74	1	0.324324	0.0135135	A|0.476;G|0.524	0.524	strong	KLK12,NS,carcinoma,0,2	KLK12	30	2	NM_145894	exon5	c.457+2T>C	.	CCCCTTACTCCGT	.	scavenged	Atlas-SNP
NPBWR1	2831	hgsc.bcm.edu	37	8	53852871	53852871	+	Missense_Mutation	SNP	A	A	T	rs33977775	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	39	24	37	0	0.615385	0	A|0.907;T|0.093	0.093	strong	.	NPBWR1	38	.	NM_005285	exon1	c.A404T	p.Y135F	ACCGCTACCTGGT	.	PASS	Atlas-SNP
INPP4A	3631	hgsc.bcm.edu	37	2	99172244	99172244	+	Missense_Mutation	SNP	A	A	G	rs2278206	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	29	18	43	0	0.62069	0	A|0.729;G|0.271	0.271	strong	.	INPP4A	205	.	NM_001134224	exon17	c.A1810G	p.T604A	CCCTCCACTGCAT	.	PASS	Atlas-SNP
SLC5A12	159963	hgsc.bcm.edu	37	11	26692742	26692742	+	Silent	SNP	G	G	A	rs7128823	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	171	80	159	0	0.467836	0	G|0.686;A|0.314	0.314	strong	.	SLC5A12	134	.	NM_178498	exon15	c.C1764T	p.N588N	GAGTCCGTTCTGT	.	PASS	Atlas-SNP
GBF1	8729	hgsc.bcm.edu	37	10	104140350	104140350	+	Missense_Mutation	SNP	G	G	A	rs11191274	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	114	63	99	0	0.552632	0	G|0.918;A|0.082	0.082	strong	.	GBF1	142	.	NM_004193	exon38	c.G5077A	p.G1693S	GGAGGCGGCCCCT	.	PASS	Atlas-SNP
ATHL1	80162	hgsc.bcm.edu	37	11	293188	293188	+	Silent	SNP	T	T	C	rs12801980	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	56	25	62	0	0.446429	0	C|0.344;N|0.000	0.344	strong	.	ATHL1	88	.	NM_025092	exon8	c.T1296C	p.H432H	GTACCATTCAGGG	.	PASS	Atlas-SNP
APITD1-CORT	100526739	hgsc.bcm.edu	37	1	10511544	10511544	+	Silent	SNP	C	C	T	rs628462	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	168	165	135	0	0.982143	0	C|0.685;T|0.315	0.315	strong	CORT,colon,carcinoma,0,2	.	.	2	NM_198544	exon5	c.C387T	p.A129A	GGAAGCCCGGGAG	.	PASS	Atlas-SNP
DNAH8	1769	hgsc.bcm.edu	37	6	38690860	38690860	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	107	30	90	0	0.280374	0	.	.	none	.	DNAH8	1239	.	NM_001206927	exon2	c.C275T	p.P92L	CGCGACCGGTTCA	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9086819	9086819	+	Silent	SNP	G	G	A	rs1823056	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	131	63	110	0	0.480916	0	G|0.811;A|0.189	0.189	strong	.	MUC16	4315	.	NM_024690	exon1	c.C4996T	p.L1666L	TTTCCAGTGCCAT	.	PASS	Atlas-SNP
MUC13	56667	hgsc.bcm.edu	37	3	124627024	124627024	+	Missense_Mutation	SNP	T	T	G	rs1127233	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	121	120	149	1	0.991736	0.00671141	T|0.752;G|0.248	0.248	strong	MUC13,colon,carcinoma,0,1	MUC13	57	1	NM_033049	exon11	c.A1506C	p.R502S	GCTGTGTCTTGAA	.	PASS	Atlas-SNP
C1orf63	57035	hgsc.bcm.edu	37	1	25570081	25570081	+	Missense_Mutation	SNP	T	T	C	rs1043879	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	188	79	217	0	0.420213	0	T|0.831;C|0.169	0.169	strong	.	C1orf63	17	.	NM_020317	exon4	c.A716G	p.E239G	GGTTTTTCATTGG	.	PASS	Atlas-SNP
ZNF180	7733	hgsc.bcm.edu	37	19	44981375	44981375	+	Silent	SNP	T	T	C	rs954314	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	108	108	90	0	1	0	T|0.760;C|0.240	0.240	strong	ZNF180,caecum,carcinoma,0,1	ZNF180	103	1	NM_013256	exon5	c.A1323G	p.Q441Q	TCCACATTGATTG	.	PASS	Atlas-SNP
THBS1	7057	hgsc.bcm.edu	37	15	39880358	39880358	+	Silent	SNP	C	C	T	rs2228261	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80	39	95	0	0.4875	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
ZNF770	54989	hgsc.bcm.edu	37	15	35273620	35273620	+	Silent	SNP	C	C	T	rs4923849	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	45	26	35	0	0.577778	0	C|0.523;T|0.477	0.477	strong	.	ZNF770	64	.	NM_014106	exon3	c.G2016A	p.Q672Q	AGTAAGCTGATGT	.	PASS	Atlas-SNP
ZNF804A	91752	hgsc.bcm.edu	37	2	185801597	185801597	+	Missense_Mutation	SNP	A	A	G	rs61739290	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	161	78	158	0	0.484472	0	A|0.947;G|0.053	0.053	strong	.	ZNF804A	322	.	NM_194250	exon4	c.A1474G	p.I492V	GAAGACATTTGCA	.	PASS	Atlas-SNP
CAND1	55832	hgsc.bcm.edu	37	12	67699536	67699536	+	Silent	SNP	G	G	A	rs17781675	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	56	22	58	0	0.392857	0	G|0.959;A|0.041	0.041	strong	.	CAND1	100	.	NM_018448	exon10	c.G2088A	p.E696E	AGATGAGCTCCCA	.	PASS	Atlas-SNP
OXNAD1	92106	hgsc.bcm.edu	37	3	16312564	16312564	+	Silent	SNP	C	C	T	rs842259	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	99	99	94	0	1	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
ITGAD	3681	hgsc.bcm.edu	37	16	31429879	31429879	+	Missense_Mutation	SNP	T	T	C	rs150615624	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	33	64	0	0.44	0	T|1.000;C|0.000	0.000	strong	.	ITGAD	154	.	NM_005353	exon23	c.T2774C	p.I925T	CCATGATCAGCAG	.	PASS	Atlas-SNP
CDRT1	374286	hgsc.bcm.edu	37	17	15510988	15510988	+	Missense_Mutation	SNP	T	T	C	rs62070402	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	144	62	147	0	0.430556	0	T|0.810;C|0.190	0.190	strong	.	CDRT1	83	.	NM_006382	exon6	c.A1132G	p.N378D	ACAGGTTGTACTC	.	PASS	Atlas-SNP
MRPL22	29093	hgsc.bcm.edu	37	5	154320820	154320820	+	Silent	SNP	C	C	T	rs115393757	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	125	76	130	0	0.608	0	C|0.995;T|0.005	0.005	strong	.	MRPL22	18	.	NM_014180	exon2	c.C72T	p.A24A	GCTGGCCTTGGGG	.	PASS	Atlas-SNP
EYS	346007	hgsc.bcm.edu	37	6	66044927	66044927	+	Missense_Mutation	SNP	T	T	C	rs61753610	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	88	43	98	0	0.488636	0	T|0.875;C|0.125	0.125	strong	.	EYS	527	.	NM_001142801	exon11	c.A1712G	p.Q571R	TTTTCTTGATCAT	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228526011	228526011	+	Silent	SNP	C	C	T	rs11577699	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51	23	74	0	0.45098	0	C|0.879;T|0.121	0.121	strong	.	OBSCN	2142	.	NM_001271223	exon79	c.C19893T	p.A6631A	GGGGGCCGCTGAG	.	PASS	Atlas-SNP
MAGEB4	4115	hgsc.bcm.edu	37	X	30261158	30261158	+	Silent	SNP	G	G	C	rs2856733	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	105	105	55	0	1	0	0|0.003;C|0.849	0.849	strong	.	MAGEB4	75	.	NM_002367	exon1	c.G906C	p.L302L	CCCACTGCTTTAT	.	PASS	Atlas-SNP
GRM1	2911	hgsc.bcm.edu	37	6	146755842	146755842	+	Silent	SNP	C	C	A	rs9373491	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	31	14	19	0	0.451613	0	C|0.428;A|0.572	0.572	strong	.	GRM1	419	.	NM_000838	exon9	c.C3495A	p.P1165P	CTCCCCCGTGTCC	.	PASS	Atlas-SNP
CEACAM20	125931	hgsc.bcm.edu	37	19	45017249	45017249	+	Missense_Mutation	SNP	T	T	C	rs1465723	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	58	57	71	0	0.982759	0	T|0.864;C|0.136	0.136	strong	.	CEACAM20	31	.	NM_001102600	exon7	c.A1409G	p.Y470C	CTGATGTAGAGAA	.	PASS	Atlas-SNP
DNAH2	146754	hgsc.bcm.edu	37	17	7680159	7680159	+	Silent	SNP	G	G	A	rs62059684	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49	21	56	0	0.428571	0	G|0.764;A|0.236	0.236	strong	.	DNAH2	498	.	NM_020877	exon31	c.G5010A	p.A1670A	GACAGCGAAGGAG	.	PASS	Atlas-SNP
FMR1	2332	hgsc.bcm.edu	37	X	146993715	146993715	+	Silent	SNP	G	G	T	rs111485627	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	123	27	89	0	0.219512	0	C|0.000;G|0.987;T|0.013	0.013	strong	.	FMR1	93	.	NM_002024	exon1	c.G18T	p.V6V	GGTGGTGGAAGTG	.	PASS	Atlas-SNP
ABCC4	10257	hgsc.bcm.edu	37	13	95858978	95858978	+	Silent	SNP	T	T	C	rs2274405	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68	68	62	0	1	0	T|0.367;C|0.633	0.633	strong	ABCC4_ENST00000376887,NS,carcinoma,0,1	ABCC4	248	1	NM_005845	exon8	c.A969G	p.S323S	GAAAAATGAAGCC	.	PASS	Atlas-SNP
NPAP1	23742	hgsc.bcm.edu	37	15	24923390	24923390	+	Silent	SNP	C	C	T	rs60574723	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72	39	84	0	0.541667	0	C|0.605;T|0.395	0.395	strong	.	.	.	.	NM_018958	exon1	c.C2376T	p.F792F	TGATTTCCTGAGC	.	PASS	Atlas-SNP
TAPBPL	55080	hgsc.bcm.edu	37	12	6562810	6562810	+	Missense_Mutation	SNP	A	A	G	rs2532500	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100	46	90	0	0.46	0	A|0.344;G|0.656	0.656	strong	.	TAPBPL	21	.	NM_018009	exon3	c.A493G	p.T165A	AGGGTCACCAAGA	.	PASS	Atlas-SNP
CLDN8	9073	hgsc.bcm.edu	37	21	31587793	31587793	+	Missense_Mutation	SNP	A	A	G	rs686364	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	124	60	80	0	0.483871	0	T|0.003;G|0.402	0.402	strong	.	CLDN8	40	.	NM_199328	exon1	c.T451C	p.S151P	CTATTGAGTTATA	.	PASS	Atlas-SNP
PANK4	55229	hgsc.bcm.edu	37	1	2441358	2441358	+	Missense_Mutation	SNP	T	T	C	rs2494620	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	136	136	157	1	1	0.00636943	T|0.615;C|0.385	0.385	strong	PANK4,NS,lymphoid_neoplasm,0,2	PANK4	64	2	NM_018216	exon18	c.A2051G	p.Q684R	TCTTCCTGGAGCG	.	PASS	Atlas-SNP
TAPBPL	55080	hgsc.bcm.edu	37	12	6562753	6562753	+	Missense_Mutation	SNP	A	A	G	rs2532501	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	105	49	114	0	0.466667	0	A|0.341;G|0.659	0.659	strong	.	TAPBPL	21	.	NM_018009	exon3	c.A436G	p.M146V	GCCAACATGCAGG	.	PASS	Atlas-SNP
ABCD1	215	hgsc.bcm.edu	37	X	153005605	153005605	+	Silent	SNP	G	G	A	rs41314153	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	16	56	0	0.216216	0	G|0.916;A|0.084	0.084	strong	.	ABCD1	59	.	NM_000033	exon6	c.G1548A	p.L516L	CTCCCTGTTCCGG	.	PASS	Atlas-SNP
ACSM5	54988	hgsc.bcm.edu	37	16	20441020	20441020	+	Missense_Mutation	SNP	G	G	A	rs12932087	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	19	42	0	0.404255	0	G|0.913;A|0.087	0.087	strong	.	ACSM5	101	.	NM_017888	exon8	c.G1022A	p.R341K	GCCTGAGGCACTG	.	PASS	Atlas-SNP
MDM2	4193	hgsc.bcm.edu	37	12	69233215	69233215	+	Silent	SNP	A	A	G	rs769412	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	38	126	0	0.452381	0	A|0.927;G|0.073	0.073	strong	.	MDM2	92	.	NM_002392	exon11	c.A1080G	p.E360E	AGCTGAAGAGGGC	.	PASS	Atlas-SNP
EP400	57634	hgsc.bcm.edu	37	12	132528724	132528724	+	Silent	SNP	C	C	T	rs61944617	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	43	70	0	0.581081	0	C|0.996;T|0.004	0.004	strong	.	EP400	370	.	NM_015409	exon35	c.C6453T	p.D2151D	TCAGGACGCAGTG	.	PASS	Atlas-SNP
SLC4A2	6522	hgsc.bcm.edu	37	7	150761314	150761314	+	Missense_Mutation	SNP	G	G	A	rs2303929	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	123	122	134	1	0.99187	0.00746269	G|0.779;A|0.221	0.221	strong	SLC4A2,NS,carcinoma,0,1	SLC4A2	98	1	NM_003040	exon3	c.G77A	p.G26E	GCCCTGGGACGCC	.	PASS	Atlas-SNP
OR8B8	26493	hgsc.bcm.edu	37	11	124310622	124310622	+	Silent	SNP	A	A	G	rs4296049	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	16	48	0	0.25	0	A|0.756;G|0.244	0.244	strong	.	OR8B8	76	.	NM_012378	exon1	c.T360C	p.Y120Y	GCGGTCATACGCC	.	PASS	Atlas-SNP
TCF12	6938	hgsc.bcm.edu	37	15	57565432	57565432	+	Silent	SNP	C	C	T	rs77034126	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	121	61	127	0	0.504132	0	C|0.996;T|0.004	0.004	strong	.	TCF12	242	.	NM_207036	exon19	c.C1950T	p.V650V	GGCAGTCATCCTT	.	PASS	Atlas-SNP
SLCO1B1	10599	hgsc.bcm.edu	37	12	21358837	21358837	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94	22	91	0	0.234043	0	.	.	none	SLCO1B1,right_lower_lobe,carcinoma,+1,1	SLCO1B1	151	1	NM_006446	exon11	c.T1367G	p.L456R	TACCACTTTCTTA	.	PASS	Atlas-SNP
UPF1	5976	hgsc.bcm.edu	37	19	18943156	18943156	+	Silent	SNP	G	G	A	rs80065570	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	18	8	17	0	0.444444	0	G|0.966;A|0.034	0.034	strong	.	UPF1	88	.	NM_002911	exon1	c.G138A	p.T46T	GCAGACGCCCCCC	.	PASS	Atlas-SNP
RP1	6101	hgsc.bcm.edu	37	8	55538741	55538741	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44	17	53	0	0.386364	0	.	.	none	.	RP1	429	.	NM_006269	exon4	c.A2299G	p.N767D	ACTCAAAATTCCA	.	PASS	Atlas-SNP
PRDM9	56979	hgsc.bcm.edu	37	5	23527637	23527637	+	Missense_Mutation	SNP	A	A	C	rs61051796	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	77	31	67	2	0.402597	0.0298507	A|0.999;C|0.001	0.001	weak	PRDM9,extremity,malignant_melanoma,0,1	PRDM9	344	1	NM_020227	exon11	c.A2440C	p.S814R	GGCTTTAGCAATA	.	scavenged	Atlas-SNP
XRCC1	7515	hgsc.bcm.edu	37	19	44057574	44057574	+	Missense_Mutation	SNP	G	G	A	rs1799782	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	96	43	103	0	0.447917	0	G|0.905;A|0.095	0.095	strong	.	XRCC1	47	.	NM_006297	exon6	c.C580T	p.R194W	TGATCCGGCTGAA	.	PASS	Atlas-SNP
CNNM4	26504	hgsc.bcm.edu	37	2	97465384	97465384	+	Silent	SNP	C	C	T	rs41286594	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	151	81	152	0	0.536424	0	C|0.986;T|0.014	0.014	strong	.	CNNM4	48	.	NM_020184	exon5	c.C1947T	p.S649S	CCCCTCCGGTGAG	.	PASS	Atlas-SNP
TOPBP1	11073	hgsc.bcm.edu	37	3	133341988	133341988	+	Missense_Mutation	SNP	T	T	C	rs10935070	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93	45	86	0	0.483871	0	T|0.819;C|0.181	0.181	strong	.	TOPBP1	218	.	NM_007027	exon19	c.A3125G	p.N1042S	TTATTATTGGTGG	.	PASS	Atlas-SNP
ABCC11	85320	hgsc.bcm.edu	37	16	48226479	48226479	+	Silent	SNP	C	C	T	rs12443685	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	97	54	122	0	0.556701	0	C|0.860;T|0.140	0.140	strong	.	ABCC11	177	.	NM_033151	exon19	c.G2658A	p.K886K	CGTGACCTTGGTG	.	PASS	Atlas-SNP
ESRRB	2103	hgsc.bcm.edu	37	14	76966275	76966275	+	Missense_Mutation	SNP	T	T	C	rs188462546	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91	50	97	0	0.549451	0	T|0.994;C|0.006	0.006	strong	.	ESRRB	114	.	NM_004452	exon10	c.T1366C	p.F456L	TGCCCCTTCCAAT	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	104	48	90	0	0.461538	0	G|0.752;A|0.248	0.248	strong	.	AKAP7	61	.	NM_016377	exon6	c.G644A	p.S215N	GCAGAAGTTTTAA	.	PASS	Atlas-SNP
STYK1	55359	hgsc.bcm.edu	37	12	10782115	10782115	+	Missense_Mutation	SNP	T	T	C	rs3759259	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94	94	77	0	1	0	T|0.438;C|0.562	0.562	strong	.	STYK1	55	.	NM_018423	exon6	c.A610G	p.S204G	GAAAGCTGAGCAG	.	PASS	Atlas-SNP
HNRNPCL1	343069	hgsc.bcm.edu	37	1	12908005	12908005	+	Silent	SNP	G	G	A	rs141516126	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	220	34	239	0	0.154545	0	G|0.999;A|0.001	0.001	strong	.	HNRNPCL1	68	.	NM_001013631	exon2	c.C138T	p.C46C	AACAGAGCAGCCC	.	PASS	Atlas-SNP
AZU1	566	hgsc.bcm.edu	37	19	830854	830854	+	Silent	SNP	T	T	C	rs595844	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	35	19	44	0	0.542857	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
OR51G1	79324	hgsc.bcm.edu	37	11	4945236	4945236	+	Missense_Mutation	SNP	T	T	C	rs35666095	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49	20	61	0	0.408163	0	T|0.912;C|0.088	0.088	strong	.	OR51G1	74	.	NM_001005237	exon1	c.A334G	p.M112V	ACTCCATTGAAGA	.	PASS	Atlas-SNP
DHRS1	115817	hgsc.bcm.edu	37	14	24760808	24760808	+	Silent	SNP	C	C	T	rs1131941	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73	34	87	0	0.465753	0	C|0.827;T|0.173	0.173	strong	.	DHRS1	21	.	NM_138452	exon7	c.G678A	p.A226A	GGTTTCCGCAGAT	.	PASS	Atlas-SNP
PCNXL3	399909	hgsc.bcm.edu	37	11	65384727	65384727	+	Silent	SNP	C	C	T	rs12790427	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	27	85	0	0.321429	0	C|0.719;T|0.281	0.281	strong	PCNXL3_ENST00000355703,NS,carcinoma,0,1	PCNXL3	140	1	NM_032223	exon3	c.C348T	p.P116P	GGACCCCGGAGTG	.	PASS	Atlas-SNP
MYH11	4629	hgsc.bcm.edu	37	16	15814717	15814717	+	Silent	SNP	C	C	T	rs11648119	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	36	68	0	0.507042	0	C|0.989;T|0.011	0.011	strong	.	MYH11	520	.	NM_001040114	exon34	c.G4791A	p.K1597K	CCTCCTCTTCTCC	.	PASS	Atlas-SNP
NRG3	10718	hgsc.bcm.edu	37	10	84745040	84745040	+	Silent	SNP	A	A	G	rs17101196	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79	50	80	0	0.632911	0	A|0.911;G|0.089	0.089	strong	.	NRG3	301	.	NM_001010848	exon9	c.A1770G	p.P590P	AATGCCAGGGATT	.	PASS	Atlas-SNP
LEFTY1	10637	hgsc.bcm.edu	37	1	226076669	226076669	+	Missense_Mutation	SNP	C	C	T	rs41310561	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	56	34	61	0	0.607143	0	C|0.955;T|0.045	0.045	strong	LEFTY1,NS,carcinoma,0,1	LEFTY1	30	1	NM_020997	exon1	c.G98A	p.R33Q	AGCTGCCGCAGCA	.	PASS	Atlas-SNP
TMEM232	642987	hgsc.bcm.edu	37	5	109973902	109973902	+	Silent	SNP	T	T	G	rs1422495	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	127	59	130	0	0.464567	0	T|0.910;G|0.090	0.090	strong	.	TMEM232	57	.	NM_001039763	exon5	c.A498C	p.A166A	TACCTTTGCTAGC	.	PASS	Atlas-SNP
CCDC176	80127	hgsc.bcm.edu	37	14	74523949	74523949	+	Silent	SNP	G	G	A	rs3742808	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	34	80	0	0.447368	0	G|0.755;A|0.245	0.245	strong	.	.	.	.	NM_025057	exon11	c.G1566A	p.Q522Q	ACCTCAGGAGTCT	.	PASS	Atlas-SNP
PRRC2A	7916	hgsc.bcm.edu	37	6	31603770	31603770	+	Silent	SNP	A	A	G	rs11229	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	112	92	116	0	0.821429	0	A|0.841;G|0.159	0.159	strong	.	PRRC2A	152	.	NM_004638	exon25	c.A5568G	p.Q1856Q	CTCTCAATTACAT	.	PASS	Atlas-SNP
FAM170B	170370	hgsc.bcm.edu	37	10	50339925	50339925	+	Silent	SNP	G	G	A	rs12765281	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	26	9	40	0	0.346154	0	G|0.768;A|0.232	0.232	strong	.	FAM170B	20	.	NM_001164484	exon2	c.C585T	p.D195D	CAGCCAGTCCGGC	.	PASS	Atlas-SNP
ZNF366	167465	hgsc.bcm.edu	37	5	71739602	71739602	+	Missense_Mutation	SNP	G	G	C	rs13188519	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	92	25	79	0	0.271739	0	G|0.916;C|0.084	0.084	strong	.	ZNF366	108	.	NM_152625	exon5	c.C2216G	p.A739G	AGCACTGCTTGTT	.	PASS	Atlas-SNP
RBM12B	389677	hgsc.bcm.edu	37	8	94746049	94746049	+	Missense_Mutation	SNP	T	T	G	rs16916188	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	32	11	51	0	0.34375	0	T|0.964;G|0.036	0.036	strong	.	RBM12B	78	.	NM_203390	exon3	c.A2590C	p.N864H	TAAAATTGTCAGG	.	PASS	Atlas-SNP
AGXT2	64902	hgsc.bcm.edu	37	5	35039437	35039437	+	Silent	SNP	A	A	G	rs2279651	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	193	88	200	0	0.455959	0	A|0.516;G|0.484	0.484	strong	.	AGXT2	89	.	NM_031900	exon3	c.T354C	p.H118H	GTGGCAATGGCCA	.	PASS	Atlas-SNP
CPS1	1373	hgsc.bcm.edu	37	2	211540507	211540507	+	Missense_Mutation	SNP	C	C	A	rs1047891	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	119	59	132	0	0.495798	0	C|0.699;A|0.301	0.301	strong	.	CPS1	485	.	NM_001122633	exon37	c.C4235A	p.T1412N	CTGCCACCCCAGT	.	PASS	Atlas-SNP
WHAMM	123720	hgsc.bcm.edu	37	15	83481880	83481880	+	Missense_Mutation	SNP	A	A	G	rs35270670	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	235	109	204	0	0.46383	0	A|0.847;G|0.153	0.153	strong	.	WHAMM	63	.	NM_001080435	exon2	c.A635G	p.N212S	AAGCCAACACCAT	.	PASS	Atlas-SNP
POLR3A	11128	hgsc.bcm.edu	37	10	79769647	79769647	+	Missense_Mutation	SNP	C	C	A	rs34588967	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	144	63	148	1	0.4375	0.00675676	A|0.005;C|0.990;T|0.006	0.005	strong	POLR3A,NS,carcinoma,-1,2	POLR3A	104	2	NM_007055	exon13	c.G1745T	p.R582L	GGGAGGCGAACTT	.	scavenged	Atlas-SNP
COL4A3BP	10087	hgsc.bcm.edu	37	5	74681773	74681773	+	Silent	SNP	T	T	C	rs698912	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	38	70	0	0.452381	0	T|0.743;C|0.257	0.257	strong	COL4A3BP,NS,carcinoma,0,1	COL4A3BP	72	1	NM_001130105	exon14	c.A1755G	p.E585E	GCAGACTTCATGT	.	PASS	Atlas-SNP
COL6A3	1293	hgsc.bcm.edu	37	2	238243292	238243292	+	Missense_Mutation	SNP	G	G	A	rs1131296	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	102	100	81	0	0.980392	0	G|0.635;A|0.365	0.365	strong	.	COL6A3	608	.	NM_004369	exon41	c.C9206T	p.T3069I	TGGTAGGTGGCTC	.	PASS	Atlas-SNP
TIGD1	200765	hgsc.bcm.edu	37	2	233413842	233413842	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	20	9	17	0	0.45	0	.	.	none	.	TIGD1	17	.	NM_145702	exon1	c.A751G	p.T251A	ATTTAGTATAATT	.	PASS	Atlas-SNP
PODXL	5420	hgsc.bcm.edu	37	7	131193739	131193739	+	Missense_Mutation	SNP	C	C	T	rs3212298	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	394	175	336	0	0.444162	0	C|0.940;T|0.060	0.060	strong	PODXL,NS,malignant_melanoma,+2,2	PODXL	53	2	NM_001018111	exon5	c.G1072A	p.V358I	TCAGGACGAGCTG	.	PASS	Atlas-SNP
PCNT	5116	hgsc.bcm.edu	37	21	47856053	47856053	+	Silent	SNP	C	C	T	rs61735826	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	39	13	47	0	0.333333	0	C|0.974;T|0.026	0.026	strong	.	PCNT	283	.	NM_006031	exon39	c.C8988T	p.A2996A	CCAGGCCGTGGAC	.	PASS	Atlas-SNP
ZNF91	7644	hgsc.bcm.edu	37	19	23542697	23542697	+	Silent	SNP	G	G	C	rs1821845	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	22	22	15	0	1	0	G|0.505;C|0.495	0.495	strong	.	ZNF91	349	.	NM_003430	exon4	c.C3084G	p.G1028G	AGCTTTGCCACAT	.	PASS	Atlas-SNP
RSPH10B	222967	hgsc.bcm.edu	37	7	6005323	6005323	+	Missense_Mutation	SNP	C	C	T	rs200962894	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	1248	514	1034	0	0.411859	0	C|0.950;T|0.050	0.050	strong	RSPH10B,NS,carcinoma,0,2	RSPH10B	28	2	NM_173565	exon4	c.G275A	p.R92H	AGCCCACGAACCT	.	scavenged	Atlas-SNP
ZNF331	55422	hgsc.bcm.edu	37	19	54080067	54080067	+	Missense_Mutation	SNP	T	T	C	rs61744130	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82	45	115	0	0.548781	0	T|0.955;C|0.045	0.045	strong	.	ZNF331	66	.	NM_001253801	exon5	c.T253C	p.C85R	TGGATATGTGAAG	.	PASS	Atlas-SNP
ALDH9A1	223	hgsc.bcm.edu	37	1	165667781	165667781	+	Silent	SNP	T	T	G	rs12408101	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	34	34	62	1	1	0.016129	T|0.850;G|0.150	0.150	strong	ALDH9A1_ENST00000354775,NS,carcinoma,0,1	ALDH9A1	75	1	NM_000696	exon1	c.A15C	p.A5A	CAGGCCTGCTCGG	.	scavenged	Atlas-SNP
PLXNA2	5362	hgsc.bcm.edu	37	1	208391085	208391085	+	Silent	SNP	G	G	A	rs12120681	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	171	90	171	0	0.526316	0	G|0.894;A|0.106	0.106	strong	PLXNA2,colon,carcinoma,-1,1	PLXNA2	178	1	NM_025179	exon2	c.C183T	p.A61A	ATAGACGGCCCCC	.	PASS	Atlas-SNP
CYP4Z1	199974	hgsc.bcm.edu	37	1	47571902	47571902	+	Silent	SNP	C	C	T	rs75156930		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	284	111	321	1	0.390845	0.00311526	.	.	weak	.	CYP4Z1	43	.	NM_178134	exon9	c.C1170T	p.I390I	ACCCATCACCTTT	.	PASS	Atlas-SNP
PCDHB7	56129	hgsc.bcm.edu	37	5	140552585	140552585	+	Missense_Mutation	SNP	G	G	C	rs28470552	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	109	52	115	0	0.477064	0	G|0.929;C|0.071	0.071	strong	.	PCDHB7	231	.	NM_018940	exon1	c.G169C	p.G57R	GGGGTAGGGGAAC	.	PASS	Atlas-SNP
POM121L12	285877	hgsc.bcm.edu	37	7	53103946	53103946	+	Silent	SNP	G	G	C	rs12113170	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	22	22	35	0	1	0	G|0.631;C|0.369	0.369	strong	.	POM121L12	146	.	NM_182595	exon1	c.G582C	p.G194G	CGACGGGCCGTTG	.	PASS	Atlas-SNP
TGS1	96764	hgsc.bcm.edu	37	8	56723557	56723557	+	Missense_Mutation	SNP	T	T	G	rs7823773	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	129	60	106	0	0.465116	0	T|0.844;G|0.156	0.156	strong	.	TGS1	66	.	NM_024831	exon11	c.T2261G	p.F754C	CTTCTTTTTTAAA	.	PASS	Atlas-SNP
NUP210	23225	hgsc.bcm.edu	37	3	13383540	13383540	+	Silent	SNP	A	A	G	rs2271504	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	106	54	102	0	0.509434	0	A|0.369;G|0.631	0.631	strong	.	NUP210	182	.	NM_024923	exon22	c.T3048C	p.F1016F	GTCCATAAAGGGG	.	PASS	Atlas-SNP
IKBKAP	8518	hgsc.bcm.edu	37	9	111663754	111663754	+	Silent	SNP	G	G	A	rs2230791	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98	32	73	0	0.326531	0	G|0.775;T|0.018	.	strong	.	IKBKAP	122	.	NM_003640	exon18	c.C1965T	p.T655T	GGAATGGGTTGTC	.	PASS	Atlas-SNP
PRIMA1	145270	hgsc.bcm.edu	37	14	94245652	94245652	+	Silent	SNP	C	C	T	rs4900195	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	29	28	35	0	0.965517	0	C|0.579;T|0.421	0.421	strong	PRIMA1,rectum,carcinoma,0,1	PRIMA1	21	1	NM_178013	exon3	c.G99A	p.T33T	ACCATGCGTCACC	.	PASS	Atlas-SNP
CLSTN3	9746	hgsc.bcm.edu	37	12	7288432	7288432	+	Missense_Mutation	SNP	A	A	G	rs7302230	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	106	51	114	0	0.481132	0	A|0.964;G|0.036	0.036	strong	.	CLSTN3	84	.	NM_014718	exon5	c.A625G	p.S209G	CAGTACAGTGGTG	.	PASS	Atlas-SNP
CAMTA2	23125	hgsc.bcm.edu	37	17	4875628	4875628	+	Missense_Mutation	SNP	A	A	G	rs16942615	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	21	41	0	0.396226	0	A|0.914;G|0.086	0.086	strong	.	CAMTA2	93	.	NM_001171167	exon16	c.T2776C	p.S926P	CCTTGGAGTTGGT	.	PASS	Atlas-SNP
ALAD	210	hgsc.bcm.edu	37	9	116152915	116152915	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	29	16	40	0	0.551724	0	.	.	none	.	ALAD	36	.	NM_000031	exon6	c.C439T	p.R147C	GCTGGCGGCTCTC	.	PASS	Atlas-SNP
RPS20	6224	hgsc.bcm.edu	37	8	56985814	56985814	+	Silent	SNP	T	T	C	rs1050403	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	22	11	17	0	0.5	0	T|0.863;C|0.137	0.137	strong	.	RPS20	16	.	NM_001146227	exon4	c.A195G	p.T65T	TTTTCTTGTAGTG	.	PASS	Atlas-SNP
LEFTY1	10637	hgsc.bcm.edu	37	1	226074563	226074563	+	Missense_Mutation	SNP	T	T	G	rs360057	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	160	84	170	0	0.525	0	T|0.711;G|0.289	0.289	strong	LEFTY1,colon,carcinoma,0,1	LEFTY1	30	1	NM_020997	exon4	c.A965C	p.D322A	AGCGAGTCAGTCT	.	PASS	Atlas-SNP
SDHA	6389	hgsc.bcm.edu	37	5	256455	256455	+	Missense_Mutation	SNP	C	C	G	rs1126697	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	2	83	0	0.0238095	0	C|0.998;G|0.002	0.002	weak	SDHA,NS,adenocarcinoma,0,1	SDHA	80	1	NM_004168	exon15	c.C1915G	p.L639V	GTCACTCTGGAAT	.	scavenged	Atlas-SNP
NBPF3	84224	hgsc.bcm.edu	37	1	21808159	21808159	+	Silent	SNP	G	G	A	rs74689674	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	165	94	305	1	0.569697	0.00327869	G|0.500;A|0.500	0.500	weak	NBPF3,NS,carcinoma,+1,1	NBPF3	55	1	NM_032264	exon13	c.A1503A	p.P501P	GTATTCGACTCCT	.	scavenged	Atlas-SNP
EMILIN3	90187	hgsc.bcm.edu	37	20	39990614	39990614	+	Missense_Mutation	SNP	C	C	T	rs2235592	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	25	60	0	0.480769	0	C|0.743;T|0.257	0.257	strong	.	EMILIN3	63	.	NM_052846	exon4	c.G1595A	p.S532N	ACGAGGCTGTCCA	.	PASS	Atlas-SNP
PLXNA4	91584	hgsc.bcm.edu	37	7	132192949	132192949	+	Silent	SNP	T	T	C	rs156962	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94	46	103	0	0.489362	0	T|0.598;C|0.402	0.402	strong	PLXNA4_ENST00000359827,NS,carcinoma,0,2	PLXNA4	873	2	NM_001105543	exon2	c.A504G	p.S168S	AAAGACTGAGCCG	.	PASS	Atlas-SNP
C2CD3	26005	hgsc.bcm.edu	37	11	73785326	73785326	+	Silent	SNP	T	T	C	rs4453265	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	118	118	114	1	1	0.00877193	T|0.543;C|0.457	0.457	strong	.	C2CD3	288	.	NM_015531	exon24	c.A4923G	p.V1641V	TCTTTCTACTAGG	.	PASS	Atlas-SNP
COL1A1	1277	hgsc.bcm.edu	37	17	48269167	48269167	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	38	3	29	0	0.0789474	0	.	.	none	COL1A1,NS,carcinoma,-2,2	COL1A1	158	2	NM_000088	exon31	c.C2109T	p.P703P	GTTGCCGGGAGCA	.	scavenged	Atlas-SNP
SAMD10	140700	hgsc.bcm.edu	37	20	62607160	62607160	+	Silent	SNP	C	C	T	rs817343	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	39	15	61	0	0.384615	0	C|0.770;T|0.230	0.230	strong	SAMD10,rectum,carcinoma,0,2	SAMD10	16	2	NM_080621	exon4	c.G471A	p.A157A	CTTCTCCGCATTC	.	PASS	Atlas-SNP
AZU1	566	hgsc.bcm.edu	37	19	830820	830820	+	Missense_Mutation	SNP	G	G	A	rs28626600	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	26	16	33	0	0.615385	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
LRP1B	53353	hgsc.bcm.edu	37	2	141457985	141457985	+	Silent	SNP	T	T	A	rs13431727	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57	17	86	0	0.298246	0	T|0.782;A|0.218	0.218	strong	.	LRP1B	1315	.	NM_018557	exon41	c.A6633T	p.P2211P	CCTTATTGGGGAA	.	PASS	Atlas-SNP
LRRC43	254050	hgsc.bcm.edu	37	12	122674780	122674780	+	Missense_Mutation	SNP	C	C	A	rs11060094	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	147	77	116	0	0.52381	0	C|0.865;A|0.135	0.135	strong	.	LRRC43	105	.	NM_001098519	exon5	c.C766A	p.Q256K	GTGCTGCAGGGAA	.	PASS	Atlas-SNP
TLR8	51311	hgsc.bcm.edu	37	X	12939112	12939112	+	Silent	SNP	G	G	C	rs2407992	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	116	86	106	0	0.741379	0	0|0.007;C|0.613	0.613	strong	.	TLR8	134	.	NM_138636	exon2	c.G1953C	p.L651L	TAGGCTGAAGCAC	.	PASS	Atlas-SNP
CCDC168	643677	hgsc.bcm.edu	37	13	103397583	103397583	+	Missense_Mutation	SNP	C	C	G	rs9582626	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83	83	183	0	1	0	C|0.319;G|0.681	0.681	strong	.	.	.	.	NM_001146197	exon4	c.G5464C	p.A1822P	ACAATGCCTCCTG	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	103	57	90	0	0.553398	0	A|0.425;G|0.575	0.575	strong	.	PKD1L2	361	.	NM_001076780	exon1	c.T217C	p.W73R	GAAACCACTGGGT	.	PASS	Atlas-SNP
LAMC3	10319	hgsc.bcm.edu	37	9	133914570	133914570	+	Silent	SNP	G	G	A	rs2293518	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	77	38	47	0	0.493506	0	G|0.809;A|0.191	0.191	strong	LAMC3,NS,adenoma,0,1	LAMC3	167	1	NM_006059	exon6	c.G1218A	p.T406T	GCCCACGGTGACT	.	PASS	Atlas-SNP
CYP1B1	1545	hgsc.bcm.edu	37	2	38298139	38298139	+	Missense_Mutation	SNP	T	T	C	rs1800440	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	131	131	142	0	1	0	T|0.882;C|0.118	0.118	strong	CYP1B1,colon,carcinoma,0,3	CYP1B1	39	3	NM_000104	exon3	c.A1358G	p.N453S	TCCTTGTTGATGA	.	PASS	Atlas-SNP
PCDHB1	29930	hgsc.bcm.edu	37	5	140433038	140433038	+	Silent	SNP	C	C	T	rs2233594	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	169	87	143	0	0.514793	0	C|0.987;T|0.013	0.013	strong	.	PCDHB1	148	.	NM_013340	exon1	c.C1983T	p.I661I	CAACATCCTGCTG	.	PASS	Atlas-SNP
ARHGEF28	64283	hgsc.bcm.edu	37	5	73163831	73163831	+	Silent	SNP	C	C	T	rs2931423	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	97	52	95	0	0.536082	0	C|0.759;T|0.241	0.241	strong	.	.	.	.	NM_001080479	exon19	c.C2283T	p.G761G	TCCAGGCACCACC	.	PASS	Atlas-SNP
CLEC4F	165530	hgsc.bcm.edu	37	2	71044211	71044211	+	Missense_Mutation	SNP	C	C	T	rs2075221	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	36	22	35	0	0.611111	0	C|0.692;T|0.308	0.308	strong	CLEC4F,caecum,carcinoma,-1,1	CLEC4F	95	1	NM_173535	exon4	c.G302A	p.R101Q	AGCTCTCGCATTT	.	scavenged	Atlas-SNP
ZNF860	344787	hgsc.bcm.edu	37	3	32031615	32031615	+	Missense_Mutation	SNP	A	A	C	rs13064905	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	126	124	219	0	0.984127	0	A|0.614;C|0.386	0.386	strong	.	ZNF860	96	.	NM_001137674	exon2	c.A1044C	p.E348D	TTGTGAAAAGGCT	.	PASS	Atlas-SNP
ANXA1	301	hgsc.bcm.edu	37	9	75775235	75775235	+	Silent	SNP	A	A	G	rs1050305	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79	40	49	0	0.506329	0	A|0.863;G|0.137	0.137	strong	.	ANXA1	27	.	NM_000700	exon5	c.A327G	p.L109L	TGTTTTAGCTCTG	.	PASS	Atlas-SNP
ASAH1	427	hgsc.bcm.edu	37	8	17930772	17930772	+	Missense_Mutation	SNP	C	C	T	rs3753115	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	187	184	408	1	0.983957	0.00245098	C|0.584;T|0.416	0.416	strong	.	ASAH1	71	.	NM_001127505	exon3	c.G187A	p.V63I	TTATAACAGCAGG	.	PASS	Atlas-SNP
EPHB3	2049	hgsc.bcm.edu	37	3	184289152	184289152	+	Silent	SNP	A	A	G	rs13069661	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	302	128	328	1	0.423841	0.00304878	A|0.802;G|0.198	0.198	strong	EPHB3,NS,adenoma,0,1	EPHB3	114	1	NM_004443	exon2	c.A165G	p.T55T	GTGGACATCTCAT	.	PASS	Atlas-SNP
PCDHB6	56130	hgsc.bcm.edu	37	5	140531215	140531215	+	Silent	SNP	C	C	G	rs61730161	byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69	36	60	1	0.521739	0.0166667	C|0.800;G|0.200	0.200	strong	PCDHB6,caecum,carcinoma,+2,2	PCDHB6	161	2	NM_018939	exon1	c.C1377G	p.R459R	CGTCCGCGAGAAC	.	scavenged	Atlas-SNP
GEMIN4	50628	hgsc.bcm.edu	37	17	648157	648157	+	Silent	SNP	G	G	A	rs1045481	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68	33	49	0	0.485294	0	G|0.829;A|0.172	0.172	strong	.	GEMIN4	116	.	NM_015721	exon2	c.C3126T	p.I1042I	AGGGCCGATGCCC	.	PASS	Atlas-SNP
SEC24D	9871	hgsc.bcm.edu	37	4	119736607	119736607	+	Silent	SNP	C	C	T	rs114611353	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73	27	69	0	0.369863	0	C|0.960;T|0.040	0.040	strong	.	SEC24D	96	.	NM_014822	exon5	c.G672A	p.Q224Q	CTTACCCTGCTGC	.	PASS	Atlas-SNP
VSIG4	11326	hgsc.bcm.edu	37	X	65244971	65244971	+	Missense_Mutation	SNP	C	C	T	rs17315645	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	108	30	95	0	0.277778	0	C|0.964;0|0.016	.	strong	.	VSIG4	54	.	NM_001257403	exon6	c.G836A	p.G279E	CTCTTTCCTAGAG	.	PASS	Atlas-SNP
DYNC1H1	1778	hgsc.bcm.edu	37	14	102482399	102482399	+	Silent	SNP	C	C	T	rs17541158	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	23	36	0	0.489362	0	C|0.972;T|0.028	0.028	strong	.	DYNC1H1	395	.	NM_001376	exon36	c.C7449T	p.I2483I	GCAGATCGAGCAG	.	PASS	Atlas-SNP
KIF26A	26153	hgsc.bcm.edu	37	14	104643721	104643721	+	Silent	SNP	C	C	A	rs2487301	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	4	4	10	0	1	0	C|0.566;A|0.434	0.434	strong	.	KIF26A	84	.	NM_015656	exon12	c.C4596A	p.A1532A	TGTGGCCGGTCCC	.	PASS	Atlas-SNP
TSNARE1	203062	hgsc.bcm.edu	37	8	143425354	143425354	+	Missense_Mutation	SNP	C	C	T	rs79460462	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79	41	58	0	0.518987	0	C|0.973;T|0.027	0.027	strong	.	TSNARE1	59	.	NM_145003	exon4	c.G718A	p.E240K	AGCCCTCGGAGGG	.	PASS	Atlas-SNP
DMXL1	1657	hgsc.bcm.edu	37	5	118513876	118513876	+	Missense_Mutation	SNP	G	G	A	rs79460759	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	112	48	143	0	0.428571	0	G|0.958;A|0.042	0.042	strong	.	DMXL1	268	.	NM_005509	exon28	c.G7072A	p.A2358T	TGGTCTGCTGTGT	.	PASS	Atlas-SNP
ZNF596	169270	hgsc.bcm.edu	37	8	195254	195254	+	Missense_Mutation	SNP	C	C	A	rs2074718	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	125	67	147	0	0.536	0	C|0.837;A|0.163	0.163	strong	.	ZNF596	34	.	NM_173539	exon6	c.C407A	p.T136K	TGAGAACGAAACA	.	PASS	Atlas-SNP
TARM1	441864	hgsc.bcm.edu	37	19	54573301	54573301	+	Missense_Mutation	SNP	G	G	A	rs77768804	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60	23	69	1	0.383333	0.0144928	G|0.950;A|0.050	0.050	strong	TARM1,NS,carcinoma,0,2	TARM1	10	2	NM_001135686	exon5	c.C772T	p.R258W	CATTCCGGCTGTA	.	scavenged	Atlas-SNP
LILRB4	11006	hgsc.bcm.edu	37	19	55175740	55175740	+	Silent	SNP	C	C	T	rs3745871	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	96	37	124	0	0.385417	0	C|0.609;N|0.000	.	strong	.	LILRB4	86	.	NM_006847	exon4	c.C459T	p.F153F	CACTTTCCTTCTG	.	PASS	Atlas-SNP
CLCN1	1180	hgsc.bcm.edu	37	7	143042837	143042837	+	Silent	SNP	C	C	T	rs2272251	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	45	26	43	0	0.577778	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
GNB2	2783	hgsc.bcm.edu	37	7	100273936	100273936	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98	10	109	0	0.102041	0	.	.	none	.	GNB2	29	.	NM_005273	exon2	c.C48T	p.N16N	CCGGAACCAGATC	.	PASS	Atlas-SNP
IRF2BP2	359948	hgsc.bcm.edu	37	1	234744250	234744250	+	Silent	SNP	G	G	A	rs8722	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55	25	73	0	0.454545	0	G|0.834;A|0.166	0.166	strong	.	IRF2BP2	37	.	NM_182972	exon1	c.C991T	p.L331L	CAGTCAGGGCCGG	.	PASS	Atlas-SNP
FAM65B	9750	hgsc.bcm.edu	37	6	24843183	24843183	+	Silent	SNP	A	A	G	rs145837095	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	68	72	0	0.781609	0	A|0.998;G|0.002	0.002	strong	FAM65B_ENST00000259698,NS,carcinoma,-1,2	FAM65B	134	2	NM_014722	exon14	c.T1827C	p.N609N	AAGCCCATTAAAA	.	PASS	Atlas-SNP
TNRC6B	23112	hgsc.bcm.edu	37	22	40552119	40552119	+	Missense_Mutation	SNP	G	G	A	rs9611280	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	114	113	104	0	0.991228	0	G|0.943;A|0.057	0.057	strong	TNRC6B_ENST00000301923,lymph_node,lymphoid_neoplasm,0,1	TNRC6B	195	1	NM_001024843	exon4	c.G46A	p.V16M	TTGCAGGTGGAAC	.	PASS	Atlas-SNP
NLRP3	114548	hgsc.bcm.edu	37	1	247588053	247588053	+	Silent	SNP	C	C	T	rs34298354	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	30	69	0	0.491803	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
MAGED1	9500	hgsc.bcm.edu	37	X	51644748	51644748	+	Silent	SNP	C	C	A	rs3199687	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110	27	67	0	0.245455	0	C|0.875;A|0.125	0.125	strong	.	MAGED1	84	.	NM_001005333	exon13	c.C2227A	p.R743R	GAAGCCCGGGCTG	.	PASS	Atlas-SNP
GEMIN2	8487	hgsc.bcm.edu	37	14	39587220	39587220	+	Silent	SNP	C	C	A	rs150986614	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51	21	40	0	0.411765	0	C|0.997;A|0.003	0.003	strong	.	.	.	.	NM_003616	exon3	c.C273A	p.P91P	CCAACCCGCCCCT	.	PASS	Atlas-SNP
DPH3	285381	hgsc.bcm.edu	37	3	16305674	16305674	+	Silent	SNP	C	C	G	rs14080	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	90	90	123	0	1	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
LARGE	9215	hgsc.bcm.edu	37	22	34000460	34000460	+	Silent	SNP	G	G	A	rs36002910	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	104	67	86	0	0.644231	0	G|0.979;A|0.021	0.021	strong	.	LARGE	98	.	NM_004737	exon6	c.C576T	p.P192P	CACAGCGGGCACC	.	PASS	Atlas-SNP
SFT2D1	113402	hgsc.bcm.edu	37	6	166739646	166739646	+	Missense_Mutation	SNP	T	T	C	rs11551053	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	135	68	140	0	0.503704	0	T|0.932;C|0.068	0.068	strong	SFT2D1,colon,carcinoma,+1,2	SFT2D1	12	2	NM_145169	exon5	c.A325G	p.I109V	TAAATATGAAACA	.	PASS	Atlas-SNP
SACS	26278	hgsc.bcm.edu	37	13	23909162	23909162	+	Silent	SNP	A	A	G	rs9552929	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	19	73	0	0.351852	0	A|0.767;G|0.233	0.233	strong	.	SACS	871	.	NM_014363	exon10	c.T8853C	p.V2951V	CTTTACAACATGA	.	PASS	Atlas-SNP
MAP4K4	9448	hgsc.bcm.edu	37	2	102472459	102472459	+	Silent	SNP	A	A	G	rs1139583	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	31	72	0	0.5	0	A|0.881;G|0.119	0.119	strong	.	MAP4K4	111	.	NM_004834	exon13	c.A1254G	p.E418E	GCGGGAAGCTAGA	.	PASS	Atlas-SNP
SERTAD4	56256	hgsc.bcm.edu	37	1	210411429	210411429	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	168	3	146	0	0.0178571	0	.	.	none	SERTAD4,NS,carcinoma,0,1	SERTAD4	53	1	NM_019605	exon2	c.C124T	p.P42S	CCAGGGCCAGCAC	.	scavenged	Atlas-SNP
NEB	4703	hgsc.bcm.edu	37	2	152422087	152422087	+	Silent	SNP	A	A	G	rs2288211	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	132	33	137	0	0.25	0	A|0.732;G|0.268	0.268	strong	NEB,NS,carcinoma,0,1	NEB	1697	1	NM_001271208	exon116	c.T18294C	p.Y6098Y	GTTAGGATAGTTT	.	PASS	Atlas-SNP
SHBG	6462	hgsc.bcm.edu	37	17	7536527	7536527	+	Missense_Mutation	SNP	G	G	A	rs6259	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60	27	68	0	0.45	0	G|0.910;A|0.090	0.090	strong	.	SHBG	21	.	NM_001040	exon8	c.G1066A	p.D356N	GGAGAAGACTCTT	.	PASS	Atlas-SNP
PPARGC1A	10891	hgsc.bcm.edu	37	4	23815681	23815681	+	Silent	SNP	G	G	A	rs17574213	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	36	112	0	0.473684	0	G|0.955;A|0.045	0.045	strong	.	PPARGC1A	129	.	NM_013261	exon8	c.C1425T	p.D475D	TTCGTCGTCAAAA	.	PASS	Atlas-SNP
CDR1	1038	hgsc.bcm.edu	37	X	139866477	139866477	+	Missense_Mutation	SNP	T	T	C	rs41299075	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	226	162	148	0	0.716814	0	T|0.901;C|0.099	0.099	strong	.	CDR1	58	.	NM_004065	exon1	c.A55G	p.I19V	AAGGTATGTCTTC	.	PASS	Atlas-SNP
CDC27	996	hgsc.bcm.edu	37	17	45214604	45214604	+	Missense_Mutation	SNP	A	A	T	rs75661039	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	20	4	8	0	0.2	0	A|0.993;T|0.007	0.007	weak	.	CDC27	337	.	NM_001114091	exon14	c.T1845A	p.H615Q	AAACTCATGCCCT	.	PASS	Atlas-SNP
FAM129B	64855	hgsc.bcm.edu	37	9	130270782	130270782	+	Silent	SNP	G	G	A	rs11545937	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	41	17	47	0	0.414634	0	G|0.957;C|0.000;A|0.043	0.043	strong	.	FAM129B	84	.	NM_022833	exon11	c.C1353T	p.L451L	GTGCAGGAGGGTC	.	PASS	Atlas-SNP
DGKH	160851	hgsc.bcm.edu	37	13	42729441	42729441	+	Silent	SNP	C	C	T	rs3208827	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	248	73	177	0	0.294355	0	C|0.928;T|0.072	0.072	strong	.	DGKH	106	.	NM_001204504	exon5	c.C399T	p.F133F	TCCATTCAGAAGG	.	PASS	Atlas-SNP
FRG2B	441581	hgsc.bcm.edu	37	10	135440203	135440203	+	Missense_Mutation	SNP	A	A	T	rs200661929	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	687	138	633	0	0.200873	0	A|0.986;T|0.014	0.014	strong	FRG2B,NS,haematopoietic_neoplasm,0,1	FRG2B	47	1	NM_001080998	exon1	c.T44A	p.I15N	CACTGGATGGAGG	.	scavenged	Atlas-SNP
GET4	51608	hgsc.bcm.edu	37	7	930689	930689	+	Silent	SNP	C	C	T	rs13171	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	291	156	225	0	0.536082	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
LMOD3	56203	hgsc.bcm.edu	37	3	69168747	69168747	+	Silent	SNP	A	A	G	rs115972674	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57	31	72	0	0.54386	0	A|0.979;G|0.021	0.021	strong	.	LMOD3	92	.	NM_198271	exon2	c.T759C	p.P253P	CATGTCAGGATCA	.	PASS	Atlas-SNP
KDM2B	84678	hgsc.bcm.edu	37	12	121881848	121881848	+	Silent	SNP	G	G	A	rs10849885	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82	48	59	0	0.585366	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
KCNH2	3757	hgsc.bcm.edu	37	7	150649603	150649603	+	Silent	SNP	G	G	A	rs740952	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	135	66	126	0	0.488889	0	A|0.278;G|0.722;T|0.000	0.278	strong	.	KCNH2	157	.	NM_000238	exon6	c.C1467T	p.I489I	GACGGCGATGCGG	.	PASS	Atlas-SNP
FAT2	2196	hgsc.bcm.edu	37	5	150901630	150901630	+	Silent	SNP	G	G	T	rs3734049	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	25	7	33	0	0.28	0	G|0.872;T|0.128	0.128	strong	.	FAT2	465	.	NM_001447	exon18	c.C10524A	p.I3508I	GGGAGGGATGCCA	.	PASS	Atlas-SNP
KAL1	3730	hgsc.bcm.edu	37	X	8504833	8504833	+	Missense_Mutation	SNP	C	C	T	rs808119	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85	85	55	0	1	0	C|0.447;T|0.553	0.553	strong	.	KAL1	78	.	NM_000216	exon11	c.G1600A	p.V534I	AGCCAACAGGCTT	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	161	64	152	0	0.397516	0	T|0.928;C|0.072	0.072	strong	.	FYCO1	115	.	NM_024513	exon8	c.A3001G	p.N1001D	GGGTGTTGAGCTC	.	PASS	Atlas-SNP
CD19	930	hgsc.bcm.edu	37	16	28944700	28944700	+	Silent	SNP	G	G	T	rs35979293	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	37	87	0	0.440476	0	G|0.736;T|0.264	0.264	strong	.	CD19	65	.	NM_001178098	exon4	c.G705T	p.P235P	TCGCCCGGCCAGA	.	PASS	Atlas-SNP
OSBPL7	114881	hgsc.bcm.edu	37	17	45890707	45890707	+	Silent	SNP	C	C	T	rs2301690	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	30	65	0	0.46875	0	C|0.759;T|0.241	0.241	strong	.	OSBPL7	65	.	NM_145798	exon16	c.G1662A	p.K554K	GAAGGGCTTGCAG	.	PASS	Atlas-SNP
ZNF460	10794	hgsc.bcm.edu	37	19	57802911	57802911	+	Silent	SNP	G	G	A	rs36032958	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82	46	95	0	0.560976	0	G|0.947;A|0.053	0.053	strong	.	ZNF460	59	.	NM_006635	exon3	c.G1002A	p.R334R	GGAGAGGCCCTTT	.	PASS	Atlas-SNP
ATP13A4	84239	hgsc.bcm.edu	37	3	193210768	193210768	+	Silent	SNP	A	A	G	rs2130407	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	48	78	0	0.571429	0	A|0.508;G|0.492	0.492	strong	.	ATP13A4	154	.	NM_032279	exon5	c.T471C	p.L157L	AGAACTAAGCCAG	.	PASS	Atlas-SNP
KY	339855	hgsc.bcm.edu	37	3	134322814	134322814	+	Silent	SNP	G	G	C	rs2293294	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	33	69	1	0.464789	0.0144928	G|0.694;C|0.306	0.306	strong	KY_ENST00000423778,NS,carcinoma,0,1	KY	92	1	NM_178554	exon11	c.C1593G	p.G531G	AAACTTGCCTGCA	.	scavenged	Atlas-SNP
ZNF792	126375	hgsc.bcm.edu	37	19	35449409	35449409	+	Silent	SNP	G	G	A	rs2651081	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	65	64	50	0	0.984615	0	G|0.659;A|0.341	0.341	strong	FLJ38451,NS,carcinoma,0,1	ZNF792	46	1	NM_175872	exon4	c.C1350T	p.H450H	ACACCCGTGAGGC	.	PASS	Atlas-SNP
PRICKLE4	29964	hgsc.bcm.edu	37	6	41753084	41753084	+	Silent	SNP	C	C	T	rs9394831	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	52	62	0	0.787879	0	C|0.821;T|0.179	0.179	strong	.	PRICKLE4	29	.	NM_013397	exon6	c.C388T	p.L130L	AGGGAGCTGCTGA	.	PASS	Atlas-SNP
PIWIL4	143689	hgsc.bcm.edu	37	11	94326765	94326765	+	Missense_Mutation	SNP	G	G	C	rs57607909	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	104	18	82	0	0.173077	0	G|0.768;C|0.232	0.232	strong	.	PIWIL4	70	.	NM_152431	exon9	c.G1108C	p.A370P	AGTGAGGCTCAGC	.	PASS	Atlas-SNP
OR2T27	403239	hgsc.bcm.edu	37	1	248813470	248813470	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91	27	84	0	0.296703	0	.	.	none	.	OR2T27	52	.	NM_001001824	exon1	c.C716T	p.A239V	CAGGTGGCCACAG	.	PASS	Atlas-SNP
LDHAL6B	92483	hgsc.bcm.edu	37	15	59500116	59500116	+	Missense_Mutation	SNP	T	T	C	rs3825937	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	106	53	109	0	0.5	0	T|0.679;C|0.321	0.321	strong	.	LDHAL6B	30	.	NM_033195	exon1	c.T977C	p.I326T	CCATAATTAAGGG	.	PASS	Atlas-SNP
SMOC1	64093	hgsc.bcm.edu	37	14	70418881	70418881	+	Silent	SNP	G	G	A	rs3742909	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73	71	86	0	0.972603	0	G|0.784;A|0.216	0.216	strong	.	SMOC1	61	.	NM_001034852	exon2	c.G126A	p.Q42Q	CCCACAGTGCAAC	.	PASS	Atlas-SNP
OR4E2	26686	hgsc.bcm.edu	37	14	22133692	22133692	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	196	95	210	0	0.484694	0	.	.	none	.	OR4E2	44	.	NM_001001912	exon1	c.C396A	p.Y132X	CCACTACCCCAAT	.	PASS	Atlas-SNP
PDHB	5162	hgsc.bcm.edu	37	3	58416535	58416535	+	Silent	SNP	C	C	T	rs1126551	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	131	64	143	0	0.48855	0	C|0.695;T|0.305	0.305	strong	PDHB,NS,carcinoma,0,1	PDHB	19	1	NM_000925	exon6	c.G438A	p.G146G	ATTGGGCCCTCTG	.	PASS	Atlas-SNP
C9orf96	169436	hgsc.bcm.edu	37	9	136268038	136268038	+	Silent	SNP	C	C	T	rs3124748	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	125	59	156	0	0.472	0	C|0.588;T|0.412	0.412	strong	.	C9orf96	77	.	NM_153710	exon14	c.C1371T	p.N457N	GCAGAACGCTGGG	.	PASS	Atlas-SNP
CCDC85A	114800	hgsc.bcm.edu	37	2	56603044	56603044	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	189	45	177	0	0.238095	0	.	.	none	.	CCDC85A	70	.	NM_001080433	exon5	c.C1546T	p.P516S	CAGCAGCCTGAAC	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79	28	97	0	0.35443	0	G|0.835;A|0.165	0.165	strong	.	FAM83A	64	.	NM_032899	exon3	c.G709A	p.A237T	AAATTCGCTGGCC	.	PASS	Atlas-SNP
PITRM1	10531	hgsc.bcm.edu	37	10	3191830	3191830	+	Missense_Mutation	SNP	G	G	C	rs41305673	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	28	69	0	0.4375	0	G|0.972;C|0.028	0.028	strong	.	PITRM1	109	.	NM_014889	exon16	c.C1854G	p.F618L	GCTGCAGAAGAGG	.	PASS	Atlas-SNP
SLC4A1	6521	hgsc.bcm.edu	37	17	42335135	42335135	+	Silent	SNP	C	C	T	rs5017	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	112	62	114	0	0.553571	0	C|0.948;T|0.052	0.052	strong	.	SLC4A1	104	.	NM_000342	exon12	c.G1323A	p.L441L	GGAGATCAGCAGC	.	PASS	Atlas-SNP
BACH2	60468	hgsc.bcm.edu	37	6	90660319	90660319	+	Silent	SNP	T	T	C	rs9451298	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	59	58	50	0	0.983051	0	T|0.695;C|0.305	0.305	strong	BACH2_ENST00000257749,NS,carcinoma,0,3	BACH2	224	3	NM_001170794	exon5	c.A1506G	p.V502V	GATTGGTACCGGG	.	PASS	Atlas-SNP
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32629129	32629129	+	Missense_Mutation	SNP	T	T	C	rs1130432	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44	19	5	0	0.431818	0	T|0.827;C|0.173	0.173	strong	.	HLA-DQB1	15	.	NM_002123	exon4	c.A767G	p.Q256R	CCTTTCTGACTCC	.	PASS	Atlas-SNP
TMPRSS9	360200	hgsc.bcm.edu	37	19	2396556	2396556	+	Silent	SNP	C	C	T	rs7252886	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	37	83	0	0.440476	0	C|0.631;T|0.369	0.369	strong	.	TMPRSS9	79	.	NM_182973	exon2	c.C162T	p.G54G	ACAGGGCTTCCAC	.	PASS	Atlas-SNP
INPP5E	56623	hgsc.bcm.edu	37	9	139327439	139327439	+	Silent	SNP	A	A	G	rs10781542	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	26	61	0	0.5	0	A|0.597;G|0.403	0.403	strong	.	INPP5E	18	.	NM_019892	exon5	c.T1248C	p.T416T	GAAGGAAGTGCCA	.	PASS	Atlas-SNP
ECSIT	51295	hgsc.bcm.edu	37	19	11617020	11617020	+	Silent	SNP	T	T	G	rs34645543	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44	26	32	0	0.590909	0	T|0.999;G|0.001	0.001	strong	.	ECSIT	32	.	NM_016581	exon8	c.A1275C	p.R425R	CTGCTGTCGCTGC	.	PASS	Atlas-SNP
SAGE1	55511	hgsc.bcm.edu	37	X	134994054	134994054	+	Silent	SNP	G	G	A	rs4829584	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85	14	65	0	0.164706	0	0|0.004;A|0.130	0.130	strong	.	SAGE1	160	.	NM_018666	exon18	c.G2463A	p.K821K	GGCAAAGAAAATT	.	PASS	Atlas-SNP
CNDP2	55748	hgsc.bcm.edu	37	18	72178161	72178161	+	Silent	SNP	T	T	C	rs2278159	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	111	52	100	0	0.468468	0	T|0.825;C|0.175	0.175	strong	CNDP2,NS,carcinoma,0,1	CNDP2	55	1	NM_018235	exon6	c.T570C	p.Y190Y	GGACTATGTCTGC	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	174	40	118	0	0.229885	0	A|0.540;0|0.011	.	strong	.	NUP62CL	10	.	NM_017681	exon7	c.T530C	p.I177T	ACTTACATCTCCA	.	PASS	Atlas-SNP
DLEC1	9940	hgsc.bcm.edu	37	3	38081031	38081031	+	Silent	SNP	A	A	T	rs7616776	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	58	29	77	0	0.5	0	A|0.652;T|0.348	0.348	strong	DLEC1_ENST00000346219,NS,carcinoma,0,2	DLEC1	278	2	NM_007337	exon1	c.A315T	p.S105S	GTACTCAGCCGAG	.	PASS	Atlas-SNP
NPTXR	23467	hgsc.bcm.edu	37	22	39222652	39222652	+	Silent	SNP	G	G	A	rs5757299	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	78	77	91	0	0.987179	0	G|0.577;A|0.423	0.423	strong	.	NPTXR	34	.	NM_014293	exon3	c.C951T	p.Y317Y	GAATGCGTAGAGC	.	PASS	Atlas-SNP
SEC16B	89866	hgsc.bcm.edu	37	1	177929940	177929940	+	Silent	SNP	G	G	A	rs7413442	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	174	84	210	0	0.482759	0	G|0.727;A|0.273	0.273	strong	.	SEC16B	92	.	NM_033127	exon7	c.C922T	p.L308L	TGTGCAGTTCAAC	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228407260	228407260	+	Silent	SNP	G	G	A	rs1771484	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	24	59	0	0.510638	0	G|0.718;A|0.282	0.282	strong	.	OBSCN	2142	.	NM_001271223	exon9	c.G2889A	p.E963E	CTGTGAGGCCAGG	.	PASS	Atlas-SNP
ARHGAP24	83478	hgsc.bcm.edu	37	4	86915923	86915923	+	Silent	SNP	G	G	A	rs11547776	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	126	64	114	0	0.507937	0	G|0.791;A|0.209	0.209	strong	ARHGAP24,NS,carcinoma,0,1	ARHGAP24	116	1	NM_001025616	exon9	c.G1116A	p.R372R	TAGTAGGCAGTGC	.	PASS	Atlas-SNP
MTUS1	57509	hgsc.bcm.edu	37	8	17612323	17612323	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	160	2	186	1	0.0125	0.00537634	.	.	none	MTUS1,lower_third,carcinoma,0,1	MTUS1	144	1	NM_001001924	exon2	c.G994A	p.E332K	CCATTTCCTTGTG	.	scavenged	Atlas-SNP
FAM86A	196483	hgsc.bcm.edu	37	16	5140561	5140561	+	Silent	SNP	C	C	T	rs9673770	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80	50	101	0	0.625	0	C|0.896;T|0.104	0.104	strong	FAM86A,NS,carcinoma,0,1	FAM86A	32	1	NM_201400	exon5	c.G348A	p.S116S	GCCTCCCGAGGGC	.	PASS	Atlas-SNP
SIGLEC10	89790	hgsc.bcm.edu	37	19	51919240	51919240	+	Silent	SNP	C	C	T	rs79484306	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	154	39	144	0	0.253247	0	C|0.910;T|0.090	0.090	strong	SIGLEC12_ENST00000439889,NS,carcinoma,-2,2	SIGLEC10	112	2	NM_001171157	exon5	c.G936A	p.G312G	CTTCACCCCGGGC	.	PASS	Atlas-SNP
ARL16	339231	hgsc.bcm.edu	37	17	79650828	79650828	+	Missense_Mutation	SNP	T	T	G	rs8066889	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	26	5	33	0	0.192308	0	T|0.736;G|0.264	0.264	strong	.	ARL16	14	.	NM_001040025	exon1	c.A28C	p.S10R	CGCGGCTCAAGGC	.	PASS	Atlas-SNP
CILP2	148113	hgsc.bcm.edu	37	19	19654189	19654189	+	Silent	SNP	G	G	A	rs45556231	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	145	55	161	0	0.37931	0	G|0.842;A|0.158	0.158	strong	CILP2,NS,carcinoma,0,1	CILP2	84	1	NM_153221	exon7	c.G1110A	p.S370S	GCGCTCGGGCACT	.	PASS	Atlas-SNP
PLEKHM1	9842	hgsc.bcm.edu	37	17	43552537	43552537	+	Silent	SNP	G	G	A	rs71238846	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	127	122	119	1	0.96063	0.00840336	G|0.865;A|0.135	0.135	strong	.	PLEKHM1	69	.	NM_014798	exon4	c.C852T	p.C284C	CTCCTCGCAATGG	.	PASS	Atlas-SNP
TMOD1	7111	hgsc.bcm.edu	37	9	100331188	100331188	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	97	50	102	0	0.515464	0	.	.	none	.	TMOD1	29	.	NM_001166116	exon8	c.A739T	p.M247L	GCTGAGATGCTCA	.	PASS	Atlas-SNP
KIF3B	9371	hgsc.bcm.edu	37	20	30915461	30915461	+	Silent	SNP	T	T	C	rs1129012	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	35	78	0	0.492958	0	A|0.000;C|0.216;G|0.000;T|0.784	0.216	strong	KIF3B,NS,carcinoma,0,1	KIF3B	75	1	NM_004798	exon7	c.T1965C	p.Y655Y	CCGATATAGGGTG	.	PASS	Atlas-SNP
CCDC41	51134	hgsc.bcm.edu	37	12	94761701	94761701	+	Silent	SNP	T	T	C	rs12426243	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	125	53	99	0	0.424	0	T|0.891;C|0.109	0.109	strong	.	CCDC41	59	.	NM_016122	exon11	c.A1212G	p.R404R	TGCTAATCTGTTC	.	PASS	Atlas-SNP
LAT	27040	hgsc.bcm.edu	37	16	28996225	28996225	+	Silent	SNP	T	T	C	rs41301797	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	33	14	41	0	0.424242	0	T|0.500;C|0.500	0.500	weak	.	LAT	22	.	NM_001014989	exon1	c.T43C	p.L15L	CCCGTCTTGGGGG	.	PASS	Atlas-SNP
PIP4K2A	5305	hgsc.bcm.edu	37	10	22839628	22839628	+	Missense_Mutation	SNP	T	T	C	rs2230469	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	127	58	124	0	0.456693	0	T|0.753;C|0.247	0.247	strong	.	PIP4K2A	59	.	NM_005028	exon7	c.A752G	p.N251S	TTCTTGTTGTTGT	.	PASS	Atlas-SNP
CSMD3	114788	hgsc.bcm.edu	37	8	113364696	113364696	+	Silent	SNP	A	A	G	rs11778209	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	137	63	130	0	0.459854	0	A|0.790;G|0.210	0.210	strong	CSMD3_ENST00000343508,NS,carcinoma,-1,2	CSMD3	2325	2	NM_198123	exon39	c.T6204C	p.Y2068Y	AACCATATATCTG	.	PASS	Atlas-SNP
HOXC10	3226	hgsc.bcm.edu	37	12	54379670	54379670	+	Silent	SNP	C	C	T	rs4564384	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	31	89	0	0.382716	0	T|0.070;G|0.000;C|0.929	0.070	strong	.	HOXC10	42	.	NM_017409	exon1	c.C627T	p.P209P	GACCCCCAGCCCC	.	PASS	Atlas-SNP
MADCAM1	8174	hgsc.bcm.edu	37	19	498524	498524	+	Silent	SNP	A	A	G	rs2302217	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57	25	64	1	0.438596	0.015625	A|0.429;G|0.571	0.571	strong	MADCAM1,NS,carcinoma,0,1	MADCAM1	29	1	NM_130760	exon3	c.A366G	p.P122P	CTCCCCAGCAGCC	.	scavenged	Atlas-SNP
ZNF597	146434	hgsc.bcm.edu	37	16	3486738	3486738	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	38	9	43	0	0.236842	0	.	.	none	.	ZNF597	41	.	NM_152457	exon4	c.G961T	p.D321Y	CAGAGTCCTCGTC	.	PASS	Atlas-SNP
SPATA31D4	389761	hgsc.bcm.edu	37	9	84547771	84547771	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	109	45	119	0	0.412844	0	.	.	none	.	.	.	.	NM_001145197	exon4	c.A2695C	p.M899L	CAAAAGATGTTGG	.	PASS	Atlas-SNP
TMPRSS5	80975	hgsc.bcm.edu	37	11	113570385	113570385	+	Missense_Mutation	SNP	C	C	T	rs11601425	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	215	31	147	0	0.144186	0	C|0.946;T|0.054	0.054	strong	.	TMPRSS5	69	.	NM_030770	exon3	c.G137A	p.R46Q	CCACGTCGCATGG	.	PASS	Atlas-SNP
CD276	80381	hgsc.bcm.edu	37	15	74001993	74001993	+	Silent	SNP	T	T	C	rs11552770	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83	40	98	0	0.481928	0	T|0.807;C|0.193	0.193	strong	.	CD276	29	.	NM_001024736	exon8	c.T1509C	p.A503A	AGGAGCTGAGGAC	.	PASS	Atlas-SNP
PDIA5	10954	hgsc.bcm.edu	37	3	122880191	122880191	+	Silent	SNP	T	T	C	rs8935	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	65	30	65	0	0.461538	0	C|0.276;T|0.724	0.276	strong	.	PDIA5	66	.	NM_006810	exon16	c.T1368C	p.C456C	TGACTGTGTCAAA	.	PASS	Atlas-SNP
WDR66	144406	hgsc.bcm.edu	37	12	122369762	122369762	+	Silent	SNP	C	C	T	rs7313748	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	227	111	207	1	0.488987	0.00483092	C|0.713;T|0.287	0.287	strong	.	WDR66	143	.	NM_001178003	exon4	c.C858T	p.N286N	CTACAACGTGTTC	.	PASS	Atlas-SNP
PTPRZ1	5803	hgsc.bcm.edu	37	7	121659234	121659234	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	173	9	172	0	0.0520231	0	.	.	none	.	PTPRZ1	605	.	NM_002851	exon13	c.G4900A	p.E1634K	GAATCCGAGAAGA	.	PASS	Atlas-SNP
PPAN-P2RY11	692312	hgsc.bcm.edu	37	19	10224548	10224548	+	Missense_Mutation	SNP	G	G	A	rs3745601	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	45	19	64	0	0.422222	0	G|0.855;A|0.145	0.145	strong	.	PPAN-P2RY11	81	.	NM_001040664	exon13	c.G1519A	p.A507T	CTGGCCGCCTACC	.	PASS	Atlas-SNP
RCN3	57333	hgsc.bcm.edu	37	19	50045878	50045878	+	Missense_Mutation	SNP	C	C	T	rs34654230	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100	48	71	0	0.48	0	C|0.891;G|0.000;T|0.108	0.108	strong	RCN3,NS,carcinoma,0,1	RCN3	28	1	NM_020650	exon6	c.C748T	p.R250W	CAGTTCCGGGACT	.	PASS	Atlas-SNP
WFIKKN1	117166	hgsc.bcm.edu	37	16	683547	683547	+	Silent	SNP	G	G	A	rs148648187	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	7	5	13	0	0.714286	0	G|0.994;A|0.006	0.006	strong	.	WFIKKN1	30	.	NM_053284	exon2	c.G1137A	p.P379P	CAGCCCGCTGCTG	.	PASS	Atlas-SNP
OR2J3	442186	hgsc.bcm.edu	37	6	29080267	29080267	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	295	17	318	0	0.0576271	0	.	.	none	.	OR2J3	53	.	NM_001005216	exon1	c.G600A	p.L200L	TGAGCTGACCCTC	.	PASS	Atlas-SNP
IBA57	200205	hgsc.bcm.edu	37	1	228362682	228362682	+	Missense_Mutation	SNP	G	G	A	rs2298014	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	34	20	31	0	0.588235	0	G|0.783;A|0.217	0.217	strong	.	IBA57	22	.	NM_001010867	exon2	c.G631A	p.G211S	CCCGGGGGCCGGC	.	PASS	Atlas-SNP
SYNPO2L	79933	hgsc.bcm.edu	37	10	75415677	75415677	+	Missense_Mutation	SNP	C	C	T	rs60632610	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	33	75	0	0.44	0	C|0.845;G|0.000;T|0.155	0.155	strong	.	SYNPO2L	118	.	NM_001114133	exon1	c.G4A	p.G2S	CAGCACCCATCGC	.	PASS	Atlas-SNP
MUC6	4588	hgsc.bcm.edu	37	11	1018316	1018316	+	Silent	SNP	G	G	A	rs201954368		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	268	7	270	0	0.0261194	0	.	.	weak	MUC6_ENST00000421673,NS,carcinoma,0,4	MUC6	408	4	NM_005961	exon31	c.C4485T	p.S1495S	GTGGGTGGACCCT	.	scavenged	Atlas-SNP
DOCK1	1793	hgsc.bcm.edu	37	10	129242515	129242515	+	Silent	SNP	G	G	A	rs11371	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	56	55	60	0	0.982143	0	G|0.667;A|0.333	0.333	strong	.	DOCK1	188	.	NM_001380	exon50	c.G5322A	p.R1774R	ACCAAGGGCCAAG	.	PASS	Atlas-SNP
RAB11B	9230	hgsc.bcm.edu	37	19	8468337	8468337	+	Silent	SNP	C	C	T	rs2230876	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	95	42	90	0	0.442105	0	C|0.701;A|0.004	.	strong	.	RAB11B	15	.	NM_004218	exon5	c.C552T	p.R184R	AGACCGCGCTGCC	.	PASS	Atlas-SNP
CBX2	84733	hgsc.bcm.edu	37	17	77758484	77758484	+	Silent	SNP	G	G	A	rs3751956	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73	73	94	0	1	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
H2AFY2	55506	hgsc.bcm.edu	37	10	71851653	71851653	+	Silent	SNP	G	G	A	rs116804623	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49	22	52	0	0.44898	0	G|0.988;A|0.012	0.012	strong	.	H2AFY2	30	.	NM_018649	exon4	c.G420A	p.T140T	GGCCACGTCAGGC	.	PASS	Atlas-SNP
TLE1	7088	hgsc.bcm.edu	37	9	84205860	84205860	+	Silent	SNP	G	G	A	rs8782	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	117	54	124	0	0.461538	0	G|0.736;A|0.264	0.264	strong	.	TLE1	81	.	NM_005077	exon16	c.C1689T	p.T563T	GCGCGGGGTTGGA	.	PASS	Atlas-SNP
ZNF530	348327	hgsc.bcm.edu	37	19	58117083	58117083	+	Missense_Mutation	SNP	A	A	G	rs9677004	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98	55	101	0	0.561224	0	A|0.716;G|0.284	0.284	strong	.	ZNF530	71	.	NM_020880	exon3	c.A190G	p.T64A	GAGGGGACGCCTT	.	PASS	Atlas-SNP
OR9G9	504191	hgsc.bcm.edu	37	11	56468431	56468431	+	Missense_Mutation	SNP	G	G	A	rs141836537	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	143	22	167	0	0.153846	0	G|1.000;A|0.000	0.000	weak	.	.	.	.	NM_001013358	exon1	c.G568A	p.E190K	TGTGGCGAGAAGG	.	PASS	Atlas-SNP
OR8G5	219865	hgsc.bcm.edu	37	11	124135662	124135662	+	Missense_Mutation	SNP	A	A	G	rs2512166	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	228	186	193	1	0.815789	0.00518135	A|0.887;G|0.113	0.113	strong	.	.	.	.	NM_001005198	exon1	c.A940G	p.T314A	TTTTATACTATTG	.	PASS	Atlas-SNP
LRRC41	10489	hgsc.bcm.edu	37	1	46746164	46746164	+	Missense_Mutation	SNP	C	C	T	rs11542623	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	121	64	130	0	0.528926	0	C|0.869;A|0.002	.	strong	.	LRRC41	74	.	NM_006369	exon6	c.G1825A	p.V609I	TCAGAACGGAGCA	.	PASS	Atlas-SNP
MGAT1	4245	hgsc.bcm.edu	37	5	180218668	180218668	+	Missense_Mutation	SNP	A	A	G	rs634501	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	128	65	95	0	0.507812	0	A|0.273;G|0.727	0.727	strong	MGAT1,NS,carcinoma,0,1	MGAT1	48	1	NM_001114617	exon3	c.T1304C	p.L435P	CACGTCAGTGGGG	.	PASS	Atlas-SNP
GPRC5C	55890	hgsc.bcm.edu	37	17	72436078	72436078	+	Missense_Mutation	SNP	G	G	A	rs148895616	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	29	15	40	0	0.517241	0	G|0.999;A|0.001	0.001	strong	.	GPRC5C	92	.	NM_022036	exon2	c.G298A	p.A100T	CTGGAGGCCGTGG	.	PASS	Atlas-SNP
KIAA0753	9851	hgsc.bcm.edu	37	17	6515454	6515454	+	Missense_Mutation	SNP	C	C	T	rs2289643	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100	44	106	0	0.44	0	C|0.456;T|0.544	0.544	strong	KIAA0753,NS,carcinoma,0,1	KIAA0753	63	1	NM_014804	exon8	c.G1330A	p.D444N	CCGTATCGGGCTG	.	PASS	Atlas-SNP
SNAPC4	6621	hgsc.bcm.edu	37	9	139279173	139279173	+	Silent	SNP	G	G	A	rs10781510	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	50	50	25	0	1	0	G|0.640;A|0.360	0.360	strong	.	SNAPC4	82	.	NM_003086	exon13	c.C1419T	p.V473V	CTTACCGACACCA	.	PASS	Atlas-SNP
HCFC1	3054	hgsc.bcm.edu	37	X	153227753	153227753	+	Silent	SNP	G	G	C	rs372516617		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48	10	26	0	0.208333	0	.	.	weak	.	HCFC1	284	.	NM_005334	exon5	c.C717G	p.T239T	CGTCAGGGTGTCT	.	PASS	Atlas-SNP
ERN2	10595	hgsc.bcm.edu	37	16	23722280	23722280	+	Silent	SNP	G	G	A	rs56342512	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	113	58	134	0	0.513274	0	G|0.944;A|0.056	0.056	strong	.	ERN2	131	.	NM_033266	exon2	c.C297T	p.H99H	TAGTGCGTGGAGA	.	PASS	Atlas-SNP
MXRA5	25878	hgsc.bcm.edu	37	X	3241256	3241256	+	Missense_Mutation	SNP	T	T	C	rs5983119	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	84	76	0	1	0	0|0.003;C|0.749	0.749	strong	.	MXRA5	815	.	NM_015419	exon5	c.A2470G	p.I824V	GAGAAATAGCAGG	.	PASS	Atlas-SNP
MTMR11	10903	hgsc.bcm.edu	37	1	149908108	149908108	+	Silent	SNP	A	A	G	rs1868992	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69	68	72	0	0.985507	0	A|0.617;G|0.382	0.382	strong	.	MTMR11	136	.	NM_001145862	exon2	c.T81C	p.N27N	CATCCTATTTTCC	.	PASS	Atlas-SNP
MARC2	54996	hgsc.bcm.edu	37	1	220928334	220928334	+	Silent	SNP	A	A	G	rs12048193	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	122	52	116	0	0.42623	0	A|0.989;G|0.011	0.011	strong	MOSC2,NS,carcinoma,+2,1	.	.	1	NM_017898	exon2	c.A318G	p.R106R	TGCCCGACAGGAG	.	PASS	Atlas-SNP
C9orf156	51531	hgsc.bcm.edu	37	9	100684757	100684757	+	Missense_Mutation	SNP	A	A	G	rs3183927	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	25	12	40	0	0.48	0	A|0.729;G|0.271	0.271	strong	C9orf156,NS,carcinoma,0,1	C9orf156	35	1	NM_016481	exon1	c.T19C	p.S7P	GCCCCGACTCCTC	.	PASS	Atlas-SNP
OR4D6	219983	hgsc.bcm.edu	37	11	59225221	59225221	+	Missense_Mutation	SNP	T	T	C	rs1453541	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	117	117	118	0	1	0	T|0.689;C|0.311	0.311	strong	OR4D6,NS,carcinoma,-1,2	OR4D6	65	2	NM_001004708	exon1	c.T788C	p.M263T	CCTTCATGACGCT	.	PASS	Atlas-SNP
FCRLB	127943	hgsc.bcm.edu	37	1	161693199	161693199	+	Missense_Mutation	SNP	C	C	T	rs35002732	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	123	64	131	0	0.520325	0	C|0.976;T|0.024	0.024	strong	.	FCRLB	35	.	NM_001002901	exon3	c.C95T	p.T32I	CTTGGACCACCAT	.	PASS	Atlas-SNP
TRERF1	55809	hgsc.bcm.edu	37	6	42236973	42236973	+	Missense_Mutation	SNP	C	C	T	rs61756353	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	90	19	59	0	0.211111	0	C|0.997;T|0.003	0.003	strong	.	TRERF1	124	.	NM_033502	exon5	c.G356A	p.G119D	TGGTAGCCATCAG	.	PASS	Atlas-SNP
SCO2	9997	hgsc.bcm.edu	37	22	50962259	50962259	+	Silent	SNP	G	G	A	rs131811	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	43	90	0	0.581081	0	G|0.958;A|0.042	0.042	strong	.	SCO2	38	.	NM_001169111	exon2	c.C582T	p.S194S	TTTGGTGGAGCCG	.	PASS	Atlas-SNP
SLC39A4	55630	hgsc.bcm.edu	37	8	145642111	145642111	+	Silent	SNP	C	C	G	rs13251676	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	172	99	158	0	0.575581	0	C|0.962;G|0.038	0.038	strong	.	SLC39A4	54	.	NM_130849	exon1	c.G63C	p.T21T	GGACGCCGTCGCC	.	PASS	Atlas-SNP
DNAJC7	7266	hgsc.bcm.edu	37	17	40142302	40142302	+	Silent	SNP	T	T	C	rs1127182	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98	54	69	0	0.55102	0	T|0.894;C|0.106	0.106	strong	.	DNAJC7	51	.	NM_003315	exon6	c.A579G	p.P193P	TGCTTCTGGATAA	.	PASS	Atlas-SNP
LILRB4	11006	hgsc.bcm.edu	37	19	55179145	55179145	+	Missense_Mutation	SNP	A	A	T	rs61738946	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	252	13	183	1	0.0515873	0.00546448	A|0.990;T|0.010	0.010	strong	LILRB4,NS,carcinoma,+2,1	LILRB4	86	1	NM_006847	exon11	c.A1101T	p.R367S	CTCCAGACCTAGG	.	scavenged	Atlas-SNP
ACP1	52	hgsc.bcm.edu	37	2	272203	272203	+	Missense_Mutation	SNP	C	C	T	rs11553746	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	180	93	146	0	0.516667	0	C|0.738;T|0.262	0.262	strong	ACP1_ENST00000272067,NS,carcinoma,+1,1	ACP1	42	1	NM_001040649	exon3	c.C284T	p.T95I	CATTGACAGCGGT	.	PASS	Atlas-SNP
CCDC81	60494	hgsc.bcm.edu	37	11	86123464	86123464	+	Silent	SNP	T	T	C	rs11234644	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	117	95	92	0	0.811966	0	T|0.954;C|0.046	0.046	strong	CCDC81,colon,carcinoma,+1,1	CCDC81	89	1	NM_001156474	exon11	c.T1254C	p.P418P	CAGTCCTGCGCTT	.	PASS	Atlas-SNP
FAM102A	399665	hgsc.bcm.edu	37	9	130742413	130742413	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	15	65	0	0.227273	0	.	.	none	.	FAM102A	32	.	NM_001035254	exon1	c.G4A	p.A2T	AGAAAGCCATGAG	.	PASS	Atlas-SNP
DPY19L2	283417	hgsc.bcm.edu	37	12	63954304	63954304	+	Silent	SNP	T	T	C	rs1054891	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	66	132	0	1	0	T|0.532;C|0.468	0.468	strong	DPY19L2,colon,carcinoma,0,1	DPY19L2	97	1	NM_173812	exon22	c.A2265G	p.L755L	AACCTTTAATACT	.	PASS	Atlas-SNP
PRR18	285800	hgsc.bcm.edu	37	6	166721224	166721224	+	Missense_Mutation	SNP	C	C	G	rs7757150	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	17	17	14	0	1	0	C|0.208;G|0.792	0.792	strong	.	PRR18	4	.	NM_175922	exon1	c.G407C	p.C136S	TTCAGGCAGAAGC	.	PASS	Atlas-SNP
TNFRSF19	55504	hgsc.bcm.edu	37	13	24242166	24242166	+	Missense_Mutation	SNP	C	C	T	rs35041805	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	88	50	81	0	0.568182	0	C|0.981;T|0.019	0.019	strong	.	TNFRSF19	52	.	NM_018647	exon8	c.C784T	p.P262S	TGCAGCCCCAACC	.	PASS	Atlas-SNP
CNGB1	1258	hgsc.bcm.edu	37	16	58001086	58001086	+	Silent	SNP	C	C	T	rs61997250	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	46	20	56	0	0.434783	0	C|0.981;T|0.019	0.019	strong	.	CNGB1	105	.	NM_001297	exon2	c.G105A	p.A35A	CACCTCCGCCTCC	.	PASS	Atlas-SNP
HN1	51155	hgsc.bcm.edu	37	17	73144665	73144665	+	Missense_Mutation	SNP	C	C	A	rs117208625	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	233	113	220	0	0.484979	0	C|0.998;A|0.002	0.002	strong	.	HN1	17	.	NM_016185	exon2	c.G158T	p.G53V	GGTGTCCCAAAGA	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1081757	1081757	+	Missense_Mutation	SNP	G	G	C	rs57737240	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	121	118	136	0	0.975207	0	G|0.707;C|0.293	0.293	strong	.	MUC2	614	.	NM_002457	exon13	c.G1685C	p.S562T	AGTCAAGCTGCCA	.	PASS	Atlas-SNP
S100A7	6278	hgsc.bcm.edu	37	1	153431435	153431435	+	Missense_Mutation	SNP	T	T	G	rs72708760	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	160	77	177	0	0.48125	0	T|0.997;G|0.003	0.003	strong	.	S100A7	23	.	NM_002963	exon2	c.A55C	p.K19Q	TGTATTTGTGAAA	.	PASS	Atlas-SNP
PDCD11	22984	hgsc.bcm.edu	37	10	105194086	105194086	+	Missense_Mutation	SNP	C	C	T	rs2986014	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	28	35	0	0.538462	0	C|0.578;T|0.422	0.422	strong	.	PDCD11	160	.	NM_014976	exon24	c.C3646T	p.L1216F	AAGACCCTCTTAT	.	PASS	Atlas-SNP
SLC16A6	9120	hgsc.bcm.edu	37	17	66267691	66267691	+	Missense_Mutation	SNP	A	A	T	rs7222013	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	127	60	131	0	0.472441	0	A|0.636;T|0.364	0.364	strong	.	SLC16A6	56	.	NM_001174166	exon6	c.T610A	p.F204I	TGATAAAGATGGG	.	PASS	Atlas-SNP
ESF1	51575	hgsc.bcm.edu	37	20	13695607	13695607	+	Missense_Mutation	SNP	T	T	G	rs34414644	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	162	83	161	0	0.512346	0	T|0.915;G|0.085	0.085	strong	.	ESF1	77	.	NM_001276380	exon14	c.A2470C	p.I824L	GATCAATGGACTT	.	PASS	Atlas-SNP
C1orf101	257044	hgsc.bcm.edu	37	1	244715882	244715882	+	Silent	SNP	A	A	G	rs34510134	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	194	86	227	0	0.443299	0	A|0.933;G|0.067	0.067	strong	.	C1orf101	158	.	NM_173807	exon9	c.A795G	p.S265S	TGATTCATTCAAA	.	PASS	Atlas-SNP
CCDC168	643677	hgsc.bcm.edu	37	13	103396716	103396716	+	Missense_Mutation	SNP	C	C	G	rs6491708	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	32	32	62	0	1	0	C|0.327;G|0.673	0.673	strong	.	.	.	.	NM_001146197	exon4	c.G6331C	p.E2111Q	TTTTCTCAGAAAT	.	PASS	Atlas-SNP
KIAA0556	23247	hgsc.bcm.edu	37	16	27692835	27692835	+	Silent	SNP	G	G	A	rs12923861	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	26	13	26	0	0.5	0	G|0.863;A|0.137	0.137	strong	.	KIAA0556	348	.	NM_015202	exon8	c.G924A	p.Q308Q	AGACCAGGAGAGG	.	PASS	Atlas-SNP
NEK5	341676	hgsc.bcm.edu	37	13	52661569	52661569	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	126	65	82	0	0.515873	0	.	.	none	.	NEK5	189	.	NM_199289	exon15	c.G1297A	p.E433K	TTGGCTCGGCAGA	.	PASS	Atlas-SNP
CYP4A22	284541	hgsc.bcm.edu	37	1	47611598	47611598	+	Missense_Mutation	SNP	T	T	C	rs2405599	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	190	92	173	0	0.484211	0	T|0.740;C|0.260	0.260	strong	.	CYP4A22	60	.	NM_001010969	exon10	c.T1283C	p.L428P	CCAACCTAGAGGT	.	PASS	Atlas-SNP
CNTNAP3B	728577	hgsc.bcm.edu	37	9	43915893	43915893	+	Missense_Mutation	SNP	G	G	C	rs62538181		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	138	11	283	0	0.0797101	0	.	.	weak	CNTNAP3B,NS,carcinoma,0,4	CNTNAP3B	37	4	NM_001201380	exon23	c.G3741C	p.M1247I	TGTCATGGGAGGT	.	scavenged	Atlas-SNP
BTNL8	79908	hgsc.bcm.edu	37	5	180377470	180377470	+	Missense_Mutation	SNP	G	G	A	rs113820381	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	35	35	72	0	1	0	G|0.772;A|0.228	0.228	strong	.	BTNL8	114	.	NM_001040462	exon8	c.G1429A	p.A477T	GCCTCTGCAATCC	.	PASS	Atlas-SNP
HFM1	164045	hgsc.bcm.edu	37	1	91782031	91782031	+	Missense_Mutation	SNP	T	T	C	rs11584478	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	96	55	109	0	0.572917	0	T|0.824;C|0.176	0.176	strong	.	HFM1	188	.	NM_001017975	exon26	c.A2815G	p.I939V	ATGTTATACCTGT	.	PASS	Atlas-SNP
ZWILCH	55055	hgsc.bcm.edu	37	15	66821250	66821250	+	Missense_Mutation	SNP	A	A	G	rs11071896	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	148	65	132	0	0.439189	0	A|0.818;G|0.182	0.182	strong	.	ZWILCH	46	.	NM_017975	exon11	c.A1030G	p.S344G	GTTCGGAGTGATC	.	PASS	Atlas-SNP
PHLDB1	23187	hgsc.bcm.edu	37	11	118514625	118514625	+	Silent	SNP	C	C	T	rs11216938	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	71	54	0	0.876543	0	C|0.822;T|0.178	0.178	strong	PHLDB1,rectum,carcinoma,0,1	PHLDB1	103	1	NM_001144758	exon14	c.C2985T	p.S995S	GCTCAGCGTGGCT	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	88	87	110	0	0.988636	0	A|0.479;G|0.521	0.521	strong	.	ARHGAP42	32	.	NM_152432	exon20	c.A2118G	p.S706S	TGCTTCAGTCACT	.	PASS	Atlas-SNP
KLHL35	283212	hgsc.bcm.edu	37	11	75133765	75133765	+	Silent	SNP	G	G	A	rs11539810	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	6	46	0	0.0967742	0	G|0.910;A|0.090	0.090	strong	KLHL35,NS,carcinoma,0,1	KLHL35	15	1	NM_001039548	exon6	c.C1611T	p.G537G	CCGCCCGCCAAGG	.	PASS	Atlas-SNP
ABCC12	94160	hgsc.bcm.edu	37	16	48122582	48122582	+	Missense_Mutation	SNP	G	G	A	rs7193955	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	75	81	0	0.986842	0	G|0.395;A|0.605	0.605	strong	ABCC12,colon,carcinoma,0,1	ABCC12	190	1	NM_033226	exon24	c.C3349T	p.R1117C	CCCCACGGCTGGG	.	PASS	Atlas-SNP
AFAP1	60312	hgsc.bcm.edu	37	4	7783163	7783163	+	Silent	SNP	G	G	A	rs28542374	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	117	116	160	0	0.991453	0	G|0.356;A|0.644	0.644	strong	.	AFAP1	93	.	NM_001134647	exon13	c.C1722T	p.S574S	CTGAGCGGAGGCA	.	PASS	Atlas-SNP
AGXT	189	hgsc.bcm.edu	37	2	241813453	241813453	+	Silent	SNP	G	G	A	rs33958047	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	65	26	69	0	0.4	0	G|0.866;A|0.134	0.134	strong	.	AGXT	50	.	NM_000030	exon6	c.G654A	p.S218S	GACCTCGCTCATC	.	PASS	Atlas-SNP
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32549362	32549362	+	Silent	SNP	G	G	A	rs3200488	byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	153	6	138	0	0.0392157	0	G|0.410;A|0.590	0.590	strong	HLA-DRB1,NS,carcinoma,0,1	HLA-DRB1	41	1	NM_002124	exon3	c.C624T	p.S208S	TGTCACGCTTGGG	.	scavenged	Atlas-SNP
CAPN7	23473	hgsc.bcm.edu	37	3	15276541	15276541	+	Silent	SNP	A	A	G	rs17539942	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	70	36	95	0	0.514286	0	A|0.924;G|0.076	0.076	strong	.	CAPN7	63	.	NM_014296	exon12	c.A1296G	p.K432K	TCACAAAGGAGAT	.	PASS	Atlas-SNP
FAM71F2	346653	hgsc.bcm.edu	37	7	128317658	128317658	+	Missense_Mutation	SNP	C	C	T	rs6467210	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94	45	77	0	0.478723	0	C|0.674;T|0.326	0.326	strong	.	FAM71F2	19	.	NM_001012454	exon3	c.C406T	p.R136W	TACGACCGGCTCC	.	PASS	Atlas-SNP
SFSWAP	6433	hgsc.bcm.edu	37	12	132239988	132239988	+	Silent	SNP	G	G	A	rs139034136	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	28	10	33	0	0.357143	0	G|0.999;A|0.001	0.001	strong	.	SFSWAP	69	.	NM_001261411	exon10	c.G1512A	p.Q504Q	GAAGCAGTTCTTC	.	PASS	Atlas-SNP
ALS2CR8	79800	hgsc.bcm.edu	37	2	203847044	203847044	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	170	52	139	0	0.305882	0	.	.	none	.	ALS2CR8	56	.	NM_024744	exon16	c.G1939A	p.E647K	ATGGACGAGCTGG	.	PASS	Atlas-SNP
CCT3	7203	hgsc.bcm.edu	37	1	156290656	156290656	+	Missense_Mutation	SNP	T	T	C	rs11548200	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	148	69	146	0	0.466216	0	T|0.961;C|0.039	0.039	strong	.	CCT3	61	.	NM_005998	exon7	c.A583G	p.I195V	TTTTTATGTCAAT	.	PASS	Atlas-SNP
TMEM17	200728	hgsc.bcm.edu	37	2	62733189	62733189	+	Missense_Mutation	SNP	C	C	T	rs17854454	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83	33	113	0	0.39759	0	C|0.865;T|0.135	0.135	strong	.	TMEM17	19	.	NM_198276	exon1	c.G76A	p.G26S	CTGGACCGGTCCG	.	PASS	Atlas-SNP
PIK3C2G	5288	hgsc.bcm.edu	37	12	18649057	18649057	+	Missense_Mutation	SNP	C	C	T	rs12312266	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69	28	71	0	0.405797	0	C|0.665;N|0.000	.	strong	.	PIK3C2G	315	.	NM_004570	exon20	c.C2732T	p.P911L	CTAATCCGATGGG	.	PASS	Atlas-SNP
GNL1	2794	hgsc.bcm.edu	37	6	30521137	30521137	+	Silent	SNP	G	G	A	rs2074505	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	76	114	0	1	0	G|0.335;A|0.665	0.665	strong	.	GNL1	47	.	NM_005275	exon6	c.C798T	p.D266D	ACTAGGGTCCTGT	.	PASS	Atlas-SNP
C12orf60	144608	hgsc.bcm.edu	37	12	14976553	14976553	+	Silent	SNP	G	G	C	rs17761825	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	102	49	97	0	0.480392	0	G|0.853;C|0.147	0.147	strong	.	C12orf60	31	.	NM_175874	exon2	c.G684C	p.A228A	AAAAGCGATAAAG	.	PASS	Atlas-SNP
TRIM23	373	hgsc.bcm.edu	37	5	64905256	64905256	+	Silent	SNP	T	T	C	rs17240173	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	230	112	228	0	0.486957	0	T|0.990;C|0.010	0.010	strong	.	TRIM23	73	.	NM_033228	exon6	c.A858G	p.S286S	AATACATGACCGG	.	PASS	Atlas-SNP
LMTK2	22853	hgsc.bcm.edu	37	7	97822115	97822115	+	Missense_Mutation	SNP	T	T	A	rs11765552	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48	25	63	0	0.520833	0	T|0.639;A|0.361	0.361	strong	.	LMTK2	228	.	NM_014916	exon11	c.T2338A	p.L780M	CCAGGCTTGTCTT	.	PASS	Atlas-SNP
MUC6	4588	hgsc.bcm.edu	37	11	1016889	1016889	+	Missense_Mutation	SNP	G	G	A	rs373231068		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	556	21	412	0	0.0377698	0	.	.	weak	MUC6_ENST00000421673,NS,carcinoma,-1,2	MUC6	408	2	NM_005961	exon31	c.C5912T	p.P1971L	GTAGGTGGGGAGT	.	scavenged	Atlas-SNP
RGSL1	353299	hgsc.bcm.edu	37	1	182443014	182443014	+	Missense_Mutation	SNP	G	G	C	rs647224	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	128	55	118	0	0.429688	0	G|0.871;C|0.129	0.129	strong	RGSL2,NS,carcinoma,0,1	RGSL1	111	1	NM_001137669	exon6	c.G768C	p.W256C	GATGTGGCAATTG	.	PASS	Atlas-SNP
NES	10763	hgsc.bcm.edu	37	1	156639753	156639753	+	Silent	SNP	G	G	A	rs11582300	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	178	88	180	0	0.494382	0	G|0.413;A|0.587	0.587	strong	.	NES	196	.	NM_006617	exon4	c.C4227T	p.S1409S	CCCATCGGACTCC	.	PASS	Atlas-SNP
PNPLA5	150379	hgsc.bcm.edu	37	22	44282307	44282307	+	Silent	SNP	G	G	A	rs739232	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	21	48	0	0.403846	0	G|0.598;A|0.402	0.402	strong	.	PNPLA5	46	.	NM_138814	exon6	c.C825T	p.D275D	GTTTCCGTCAGCC	.	PASS	Atlas-SNP
CR1L	1379	hgsc.bcm.edu	37	1	207857254	207857254	+	Missense_Mutation	SNP	A	A	G	rs3085	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110	48	91	0	0.436364	0	A|0.852;G|0.148	0.148	strong	.	CR1L	97	.	NM_175710	exon4	c.A415G	p.I139V	TGCATCATCTCAG	.	PASS	Atlas-SNP
IVL	3713	hgsc.bcm.edu	37	1	152882981	152882981	+	Silent	SNP	A	A	T	rs62637699	byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55	11	42	0	0.2	0	A|0.696;T|0.304	0.304	strong	IVL,colon,carcinoma,+2,2	IVL	100	2	NM_005547	exon2	c.A708T	p.P236P	GCTCCCACAGCAG	.	PASS	Atlas-SNP
C9orf123	90871	hgsc.bcm.edu	37	9	7799653	7799653	+	Missense_Mutation	SNP	G	G	T	rs1127430	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	27	26	27	0	0.962963	0	G|0.647;T|0.353	0.353	strong	.	C9orf123	7	.	NM_033428	exon1	c.C82A	p.P28T	CTGGGGGCGCAGG	.	PASS	Atlas-SNP
ALG8	79053	hgsc.bcm.edu	37	11	77825320	77825320	+	Missense_Mutation	SNP	T	T	C	rs665278	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	89	16	67	0	0.179775	0	T|0.842;C|0.158	0.158	strong	.	ALG8	54	.	NM_024079	exon6	c.A665G	p.N222S	GGTTTATTTGCAG	.	PASS	Atlas-SNP
C9orf84	158401	hgsc.bcm.edu	37	9	114484783	114484783	+	Silent	SNP	A	A	G	rs12352352	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91	38	50	0	0.417582	0	A|0.817;G|0.183	0.183	strong	.	C9orf84	207	.	NM_173521	exon13	c.T1845C	p.P615P	AGCAGTAGGGAGG	.	PASS	Atlas-SNP
HIST1H1E	3008	hgsc.bcm.edu	37	6	26157224	26157224	+	Silent	SNP	G	G	A	rs147799648	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	7	85	1	0.0945946	0.0117647	G|0.999;A|0.001	0.001	strong	HIST1H1E,NS,lymphoid_neoplasm,+2,1	HIST1H1E	69	1	NM_005321	exon1	c.G606A	p.K202K	ACCAAAGACCGCC	.	scavenged	Atlas-SNP
ENTPD7	57089	hgsc.bcm.edu	37	10	101451194	101451194	+	Silent	SNP	A	A	C	rs72832512	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	108	44	105	0	0.407407	0	A|0.978;C|0.022	0.022	strong	.	ENTPD7	44	.	NM_020354	exon8	c.A762C	p.V254V	GACAGTAGGGATA	.	PASS	Atlas-SNP
NDUFAF2	91942	hgsc.bcm.edu	37	5	60241142	60241142	+	Silent	SNP	G	G	A	rs79660491	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	136	103	143	0	0.757353	0	.	.	weak	.	NDUFAF2	10	.	NM_174889	exon1	c.G60A	p.K20K	AGTGAAGGAGCAC	.	PASS	Atlas-SNP
SMG6	23293	hgsc.bcm.edu	37	17	2203025	2203025	+	Missense_Mutation	SNP	T	T	G	rs1885987	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	247	124	227	0	0.502024	0	T|0.736;G|0.264	0.264	strong	SMG6,NS,carcinoma,+1,1	SMG6	97	1	NM_017575	exon2	c.A1022C	p.N341T	GCACTGTTTTTCT	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82	37	83	0	0.451219	0	T|0.669;C|0.331	0.331	strong	.	PRX	151	.	NM_181882	exon7	c.A2763G	p.I921M	TGTCTCTATCATC	.	PASS	Atlas-SNP
DNAH12	201625	hgsc.bcm.edu	37	3	57414097	57414097	+	Missense_Mutation	SNP	T	T	A	rs17793014	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	33	42	0	0.5	0	T|0.739;A|0.261	0.261	strong	.	DNAH12	182	.	NM_178504	exon35	c.A5262T	p.K1754N	CACATATTTAAAA	.	PASS	Atlas-SNP
DCAF16	54876	hgsc.bcm.edu	37	4	17805379	17805379	+	Missense_Mutation	SNP	G	G	A	rs7690457	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	155	67	176	0	0.432258	0	G|0.893;A|0.107	0.107	strong	.	DCAF16	19	.	NM_017741	exon3	c.C386T	p.T129I	GGACTTGTAAGAG	.	PASS	Atlas-SNP
MMP8	4317	hgsc.bcm.edu	37	11	102593248	102593248	+	Missense_Mutation	SNP	T	T	C	rs1940475	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	310	308	267	0	0.993548	0	T|0.417;C|0.583	0.583	strong	MMP8,face,malignant_melanoma,+2,1	MMP8	68	1	NM_002424	exon2	c.A259G	p.K87E	GCTTTTTCATCAT	.	PASS	Atlas-SNP
KRT14	3861	hgsc.bcm.edu	37	17	39742894	39742894	+	Silent	SNP	G	G	A	rs3826551	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	30	20	22	0	0.666667	0	G|0.454;A|0.546	0.546	strong	KRT14,NS,carcinoma,0,3	KRT14	65	3	NM_000526	exon1	c.C193T	p.L65L	CCCCCAGCCCGCA	.	PASS	Atlas-SNP
ENPP2	5168	hgsc.bcm.edu	37	8	120569870	120569870	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	106	5	108	0	0.0471698	0	.	.	none	.	ENPP2	254	.	NM_006209	exon26	c.G2639A	p.R880H	ATGTCACGCACCC	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228486404	228486404	+	Missense_Mutation	SNP	C	C	T	rs56021350	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	12	4	6	0	0.333333	0	C|0.825;T|0.175	0.175	strong	OBSCN_ENST00000570156,NS,carcinoma,0,3	OBSCN	2142	3	NM_001271223	exon49	c.C13196T	p.T4399M	CGGCCACGCTCAC	.	scavenged	Atlas-SNP
ZNF652	22834	hgsc.bcm.edu	37	17	47394825	47394825	+	Missense_Mutation	SNP	G	G	C	rs181916483	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	211	108	226	1	0.511848	0.00442478	G|0.998;C|0.002	0.002	strong	ZNF652,NS,haematopoietic_neoplasm,0,3	ZNF652	54	3	NM_001145365	exon2	c.C263G	p.S88C	ACGTCAGACACTG	.	PASS	Atlas-SNP
FOXQ1	94234	hgsc.bcm.edu	37	6	1313470	1313470	+	Silent	SNP	C	C	T	rs4435985	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	111	16	144	0	0.144144	0	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	.	PASS	Atlas-SNP
SRRM4	84530	hgsc.bcm.edu	37	12	119588962	119588962	+	Missense_Mutation	SNP	G	G	A	rs2723880	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	41	56	0	0.61194	0	G|0.714;A|0.286	0.286	strong	.	SRRM4	131	.	NM_194286	exon10	c.G1217A	p.R406Q	CGTCCCGATCCCC	.	PASS	Atlas-SNP
PCK1	5105	hgsc.bcm.edu	37	20	56137798	56137798	+	Silent	SNP	G	G	A	rs1062600	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	51	60	0	0.980769	0	G|0.633;A|0.367	0.367	strong	.	PCK1	95	.	NM_002591	exon4	c.G453A	p.S151S	GGGCTCGCCTCTG	.	PASS	Atlas-SNP
MRC2	9902	hgsc.bcm.edu	37	17	60769803	60769803	+	Silent	SNP	A	A	G	rs3826537	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60	32	56	0	0.533333	0	A|0.680;G|0.320	0.320	strong	.	MRC2	126	.	NM_006039	exon30	c.A4431G	p.Q1477Q	TGAGCAACAAGAA	.	PASS	Atlas-SNP
INTS6	26512	hgsc.bcm.edu	37	13	51950198	51950198	+	Missense_Mutation	SNP	T	T	C	rs144918317	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	26	67	0	0.298851	0	T|0.999;C|0.001	0.001	strong	.	INTS6	72	.	NM_012141	exon13	c.A1715G	p.K572R	TGTCCTTTCAGAA	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	59	27	41	0	0.457627	0	T|0.868;G|0.132	0.132	strong	.	PTPRZ1	605	.	NM_001206838	exon1	c.T8G	p.I3S	TGCGAATCCTAAA	.	PASS	Atlas-SNP
HTT	3064	hgsc.bcm.edu	37	4	3234980	3234980	+	Missense_Mutation	SNP	G	G	A	rs362272	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	107	34	147	0	0.317757	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
MRGPRX4	117196	hgsc.bcm.edu	37	11	18195348	18195348	+	Missense_Mutation	SNP	C	C	T	rs11024532	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	109	57	104	0	0.522936	0	C|0.817;T|0.183	0.183	strong	.	MRGPRX4	68	.	NM_054032	exon1	c.C545T	p.A182V	CAGTCGCGTGGCT	.	PASS	Atlas-SNP
ABCA7	10347	hgsc.bcm.edu	37	19	1056183	1056183	+	Missense_Mutation	SNP	C	C	T	rs144562001	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	39	20	36	0	0.512821	0	C|0.999;G|0.000;T|0.000	0.000	strong	.	ABCA7	174	.	NM_019112	exon32	c.C4357T	p.R1453C	CTCGACCGTGTCC	.	PASS	Atlas-SNP
OR2T29	343563	hgsc.bcm.edu	37	1	248722624	248722624	+	Missense_Mutation	SNP	C	C	T	rs9439352		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	482	89	480	0	0.184647	0	C|0.250;T|0.750	0.750	weak	.	OR2T29	8	.	NM_001004694	exon1	c.G169A	p.A57T	GGTGGGCGTCACA	.	PASS	Atlas-SNP
FAT2	2196	hgsc.bcm.edu	37	5	150905398	150905398	+	Silent	SNP	C	C	T	rs3734051	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	58	24	48	0	0.413793	0	C|0.776;N|0.000	.	strong	FAT2,colon,carcinoma,-1,2	FAT2	465	2	NM_001447	exon17	c.G10437A	p.P3479P	TCCATCCGGGGTC	.	PASS	Atlas-SNP
STT3A	3703	hgsc.bcm.edu	37	11	125482982	125482982	+	Silent	SNP	T	T	C	rs34079079	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	333	282	292	1	0.846847	0.00342466	T|0.980;C|0.020	0.020	strong	.	STT3A	52	.	NM_152713	exon13	c.T1464C	p.I488I	GTCCATTGTACTA	.	PASS	Atlas-SNP
OR1S2	219958	hgsc.bcm.edu	37	11	57970760	57970760	+	Missense_Mutation	SNP	C	C	T	rs200054918		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91	7	123	0	0.0769231	0	.	.	weak	OR1S2,NS,carcinoma,0,3	OR1S2	119	3	NM_001004459	exon1	c.G894A	p.M298I	GGGGTTCATCATG	.	scavenged	Atlas-SNP
ANGPTL5	253935	hgsc.bcm.edu	37	11	101765654	101765654	+	Missense_Mutation	SNP	G	G	A	rs77315074	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	161	138	119	1	0.857143	0.00840336	G|0.973;A|0.027	0.027	strong	ANGPTL5,NS,carcinoma,+1,1	ANGPTL5	60	1	NM_178127	exon8	c.C803T	p.T268M	AATCTCGTTTCAT	.	PASS	Atlas-SNP
MURC	347273	hgsc.bcm.edu	37	9	103348634	103348634	+	Silent	SNP	G	G	A	rs2780956	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	31	11	28	0	0.354839	0	G|0.649;A|0.351	0.351	strong	.	MURC	43	.	NM_001018116	exon2	c.G996A	p.R332R	AGGAAGGGAAATC	.	PASS	Atlas-SNP
USP15	9958	hgsc.bcm.edu	37	12	62785663	62785663	+	Silent	SNP	T	T	C	rs11174457	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	200	90	252	1	0.45	0.00396825	T|0.933;C|0.067	0.067	strong	USP15,NS,carcinoma,0,1	USP15	105	1	NM_001252078	exon17	c.T2301C	p.A767A	TGCTGCTGAGGTA	.	PASS	Atlas-SNP
PKD1	5310	hgsc.bcm.edu	37	16	2162839	2162839	+	Silent	SNP	T	T	C	rs2099534	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	32	14	24	0	0.4375	0	T|0.971;C|0.029	0.029	strong	PKD1,NS,carcinoma,0,1	PKD1	184	1	NM_000296	exon13	c.A3111G	p.L1037L	CAGTGCTAGCGTG	.	PASS	Atlas-SNP
NSRP1	84081	hgsc.bcm.edu	37	17	28505174	28505174	+	Missense_Mutation	SNP	A	A	C	rs11544945	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	224	99	198	0	0.441964	0	A|0.966;C|0.034	0.034	strong	.	NSRP1	49	.	NM_032141	exon4	c.A257C	p.K86T	AAAAAAAGGAGGA	.	PASS	Atlas-SNP
TULP3	7289	hgsc.bcm.edu	37	12	3046802	3046802	+	Silent	SNP	A	A	G	rs33973716	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	142	77	121	0	0.542253	0	A|0.796;G|0.204	0.204	strong	.	TULP3	45	.	NM_003324	exon9	c.A930G	p.T310T	GGAAACAAACGTA	.	PASS	Atlas-SNP
NSUN4	387338	hgsc.bcm.edu	37	1	46810670	46810670	+	Silent	SNP	T	T	C	rs17361763	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	111	44	113	0	0.396396	0	T|0.802;C|0.198	0.198	strong	.	NSUN4	26	.	NM_199044	exon2	c.T291C	p.D97D	CAAGGATTTTGTG	.	PASS	Atlas-SNP
SLC35D3	340146	hgsc.bcm.edu	37	6	137245534	137245534	+	Missense_Mutation	SNP	G	G	C	rs150994900	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	108	54	98	0	0.5	0	G|0.983;C|0.017	0.017	strong	.	SLC35D3	33	.	NM_001008783	exon2	c.G951C	p.Q317H	GGCCCAGCCTCGG	.	PASS	Atlas-SNP
RIN2	54453	hgsc.bcm.edu	37	20	19955473	19955473	+	Silent	SNP	C	C	T	rs41306763	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	105	53	61	0	0.504762	0	C|0.990;T|0.010	0.010	strong	.	RIN2	126	.	NM_001242581	exon8	c.C951T	p.A317A	CGGGGCCCTGTGC	.	PASS	Atlas-SNP
GALNT8	26290	hgsc.bcm.edu	37	12	4835923	4835923	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	14	53	0	0.269231	0	.	.	none	.	GALNT8	89	.	NM_017417	exon2	c.A437C	p.K146T	TCCGGAAGTTTGG	.	PASS	Atlas-SNP
OR13C2	392376	hgsc.bcm.edu	37	9	107367841	107367841	+	Missense_Mutation	SNP	A	A	T	rs61745782	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	359	133	351	1	0.370474	0.002849	A|0.026;T|0.974	0.974	strong	OR13C2,NS,carcinoma,-1,1	OR13C2	46	1	NM_001004481	exon1	c.T68A	p.L23H	AACTCAAGTCTTG	.	PASS	Atlas-SNP
LAMA5	3911	hgsc.bcm.edu	37	20	60913127	60913127	+	Silent	SNP	A	A	G	rs8124907	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	119	41	115	0	0.344538	0	A|0.749;G|0.251	0.251	strong	LAMA5,NS,carcinoma,0,3	LAMA5	268	3	NM_005560	exon14	c.T1836C	p.A612A	AGGTCCAGCAAAC	.	PASS	Atlas-SNP
PKD1L1	168507	hgsc.bcm.edu	37	7	47921682	47921682	+	Silent	SNP	A	A	T	rs10951936	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60	23	97	0	0.383333	0	A|0.721;T|0.279	0.279	strong	.	PKD1L1	328	.	NM_138295	exon20	c.T3267A	p.A1089A	GTCCTTAGCTAGG	.	PASS	Atlas-SNP
ZCWPW2	152098	hgsc.bcm.edu	37	3	28533658	28533658	+	Silent	SNP	G	G	A	rs13100556	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	195	68	175	0	0.348718	0	G|0.823;A|0.176	0.176	strong	.	ZCWPW2	49	.	NM_001040432	exon5	c.G651A	p.K217K	GGTCAAGAAAAGG	.	PASS	Atlas-SNP
MUC21	394263	hgsc.bcm.edu	37	6	30954873	30954873	+	Silent	SNP	G	G	A	rs1625781	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	59	43	71	0	0.728814	0	G|0.774;A|0.226	0.226	strong	.	MUC21	98	.	NM_001010909	exon2	c.G921A	p.T307T	CAGTACGACCTCC	.	PASS	Atlas-SNP
ANO7	50636	hgsc.bcm.edu	37	2	242141719	242141719	+	Silent	SNP	C	C	T	rs2074840	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	24	15	29	0	0.625	0	C|0.452;T|0.548	0.548	strong	ANO7,NS,carcinoma,+2,1	ANO7	136	1	NM_001001891	exon8	c.C885T	p.D295D	GCATGACGTGAGC	.	PASS	Atlas-SNP
MUC6	4588	hgsc.bcm.edu	37	11	1017974	1017974	+	Missense_Mutation	SNP	C	C	G	rs200353019	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	346	11	268	3	0.0317919	0.011194	.	.	weak	MUC6_ENST00000421673,colon,carcinoma,0,2	MUC6	408	2	NM_005961	exon31	c.G4827C	p.Q1609H	TGTGGTCTGAGGG	.	scavenged	Atlas-SNP
PTX4	390667	hgsc.bcm.edu	37	16	1538464	1538464	+	Missense_Mutation	SNP	C	C	T	rs2745103	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	147	62	136	0	0.421769	0	C|0.758;T|0.242	0.242	strong	.	PTX4	46	.	NM_001013658	exon1	c.G5A	p.G2E	CCACTCCCCATGA	.	PASS	Atlas-SNP
C1QTNF1	114897	hgsc.bcm.edu	37	17	77043894	77043894	+	Silent	SNP	C	C	T	rs35435268	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	109	30	101	0	0.275229	0	C|0.979;T|0.021	0.021	strong	.	C1QTNF1	62	.	NM_030968	exon4	c.C570T	p.P190P	CGTGCCCGGCCTC	.	PASS	Atlas-SNP
CST1	1469	hgsc.bcm.edu	37	20	23731412	23731412	+	Missense_Mutation	SNP	G	G	A	rs2070856	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	133	74	142	0	0.556391	0	G|0.847;A|0.153	0.153	strong	.	CST1	37	.	NM_001898	exon1	c.C92T	p.P31L	CCACCCGGGATTA	.	PASS	Atlas-SNP
USP8	9101	hgsc.bcm.edu	37	15	50769520	50769520	+	Missense_Mutation	SNP	G	G	A	rs61733869	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	105	54	109	0	0.514286	0	G|0.971;A|0.029	0.029	strong	.	USP8	90	.	NM_001128610	exon10	c.G1042A	p.A348T	AAACCTGCTGCCC	.	PASS	Atlas-SNP
ENTPD6	955	hgsc.bcm.edu	37	20	25193949	25193949	+	Silent	SNP	G	G	A	rs2076561	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	56	25	56	0	0.446429	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
NSUN4	387338	hgsc.bcm.edu	37	1	46806550	46806550	+	Missense_Mutation	SNP	C	C	T	rs41293277	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79	29	94	0	0.367089	0	C|0.790;T|0.210	0.210	strong	.	NSUN4	26	.	NM_199044	exon1	c.C52T	p.L18F	GTGGACCTCGCGA	.	PASS	Atlas-SNP
FAM71F1	84691	hgsc.bcm.edu	37	7	128358891	128358891	+	Silent	SNP	C	C	A	rs745229	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69	35	60	0	0.507246	0	C|0.797;A|0.203	0.203	strong	.	FAM71F1	42	.	NM_032599	exon3	c.C441A	p.L147L	GATTCTCCCATTG	.	PASS	Atlas-SNP
FLNC	2318	hgsc.bcm.edu	37	7	128477547	128477547	+	Silent	SNP	T	T	C	rs2291561	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	23	55	0	0.343284	0	T|0.881;C|0.119	0.119	strong	FLNC,NS,carcinoma,0,1	FLNC	339	1	NM_001127487	exon4	c.T795C	p.G265G	ACCTGGTGCCCCT	.	PASS	Atlas-SNP
SCAF11	9169	hgsc.bcm.edu	37	12	46320944	46320944	+	Missense_Mutation	SNP	C	C	T	rs28930670	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	147	72	155	0	0.489796	0	C|0.978;T|0.022	0.022	strong	.	SCAF11	145	.	NM_004719	exon11	c.G2540A	p.R847H	TGAGAACGGGATT	.	PASS	Atlas-SNP
NOL11	25926	hgsc.bcm.edu	37	17	65739627	65739627	+	Silent	SNP	A	A	G	rs10127	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	186	186	219	0	1	0	A|0.511;G|0.489	0.489	strong	.	NOL11	48	.	NM_015462	exon17	c.A1968G	p.A656A	GGATGCAAATTTT	.	PASS	Atlas-SNP
SLC36A3	285641	hgsc.bcm.edu	37	5	150666933	150666933	+	Silent	SNP	C	C	A	rs375396	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	142	67	129	0	0.471831	0	C|0.776;A|0.224	0.224	strong	.	SLC36A3	54	.	NM_001145017	exon7	c.G705T	p.L235L	GATTATCAGCATG	.	PASS	Atlas-SNP
CCHCR1	54535	hgsc.bcm.edu	37	6	31116502	31116502	+	Missense_Mutation	SNP	C	C	T	rs2027937	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69	5	64	0	0.0724638	0	C|0.937;T|0.063	0.063	strong	.	CCHCR1	68	.	NM_001105564	exon9	c.G1366A	p.A456T	GTGAGGCCACCTG	.	PASS	Atlas-SNP
SLC9A8	23315	hgsc.bcm.edu	37	20	48503306	48503306	+	Silent	SNP	G	G	A	rs73125686	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	105	55	64	0	0.52381	0	G|0.996;A|0.004	0.004	strong	.	SLC9A8	63	.	NM_001260491	exon15	c.G1557A	p.S519S	GGAGTCGGAGCAC	.	PASS	Atlas-SNP
CSMD2	114784	hgsc.bcm.edu	37	1	34071525	34071525	+	Missense_Mutation	SNP	C	C	T	rs1874045	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	75	97	1	1	0.0103093	C|0.479;T|0.521	0.521	strong	CSMD2,brain,glioma,0,1	CSMD2	946	1	NM_052896	exon42	c.G6287A	p.R2096K	TTGGTTCTTTCCA	.	scavenged	Atlas-SNP
OTOR	56914	hgsc.bcm.edu	37	20	16729138	16729138	+	Missense_Mutation	SNP	T	T	C	rs6135876	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	160	78	188	0	0.4875	0	T|0.844;C|0.156	0.156	strong	.	OTOR	22	.	NM_020157	exon1	c.T92C	p.L31P	AGAAGCTCTGTGC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195512439	195512439	+	Silent	SNP	G	G	A	rs112365404	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	148	34	125	0	0.22973	0	G|0.990;A|0.010	0.010	strong	.	MUC4	1505	.	NM_018406	exon2	c.C6012T	p.T2004T	AGTGTCGGTGACC	.	PASS	Atlas-SNP
FANCI	55215	hgsc.bcm.edu	37	15	89838318	89838318	+	Missense_Mutation	SNP	A	A	T	rs35875311	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51	22	57	0	0.431373	0	A|0.931;T|0.069	0.069	strong	.	FANCI	129	.	NM_001113378	exon24	c.A2629T	p.I877L	TGTGACATAACTC	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	78	27	68	0	0.346154	0	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	.	PASS	Atlas-SNP
DSPP	1834	hgsc.bcm.edu	37	4	88537268	88537268	+	Missense_Mutation	SNP	G	G	A	rs202025088	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	121	49	75	0	0.404959	0	.	.	weak	.	DSPP	174	.	NM_014208	exon5	c.G3454A	p.D1152N	AGCAGCGACAGCA	.	PASS	Atlas-SNP
MYO15A	51168	hgsc.bcm.edu	37	17	18057167	18057167	+	Missense_Mutation	SNP	A	A	T	rs712270	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	192	82	162	0	0.427083	0	A|0.723;T|0.277	0.277	strong	MYO15A,NS,carcinoma,0,1	MYO15A	268	1	NM_016239	exon42	c.A8045T	p.Y2682F	ACTTCTACGGCTA	.	PASS	Atlas-SNP
COX10	1352	hgsc.bcm.edu	37	17	13972955	13972955	+	Silent	SNP	C	C	T	rs8076787	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	95	49	83	0	0.515789	0	C|0.957;T|0.043	0.043	strong	.	COX10	36	.	NM_001303	exon1	c.C33T	p.R11R	CTCACGCCTCCTG	.	PASS	Atlas-SNP
CCDC137	339230	hgsc.bcm.edu	37	17	79634774	79634774	+	Missense_Mutation	SNP	A	A	T	rs61742303	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	15	6	28	0	0.4	0	A|0.867;T|0.133	0.133	strong	.	CCDC137	27	.	NM_199287	exon2	c.A150T	p.K50N	GAAGAAAGTGAAC	.	PASS	Atlas-SNP
CASQ2	845	hgsc.bcm.edu	37	1	116243877	116243877	+	Silent	SNP	G	G	A	rs7413162	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	222	100	258	0	0.45045	0	G|0.586;A|0.414	0.414	strong	.	CASQ2	54	.	NM_001232	exon11	c.C1185T	p.D395D	ATCATCGTCATCA	.	PASS	Atlas-SNP
TTLL1	25809	hgsc.bcm.edu	37	22	43455531	43455531	+	Silent	SNP	C	C	T	rs1132079	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	99	49	91	0	0.494949	0	T|0.177;G|0.153	0.177	strong	.	TTLL1	41	.	NM_012263	exon8	c.G750A	p.E250E	GTAGTCCTCCTGG	.	PASS	Atlas-SNP
LRRK2	120892	hgsc.bcm.edu	37	12	40713873	40713873	+	Silent	SNP	A	A	G	rs11176013	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98	47	82	0	0.479592	0	A|0.453;G|0.547	0.547	strong	LRRK2_ENST00000298910,rectum,carcinoma,0,2	LRRK2	763	2	NM_198578	exon34	c.A4911G	p.K1637K	TTCAAAAAAAAGG	.	PASS	Atlas-SNP
RP1L1	94137	hgsc.bcm.edu	37	8	10474042	10474042	+	Missense_Mutation	SNP	T	T	G	rs4388421	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	27	63	0	0.435484	0	T|0.771;G|0.229	0.229	strong	RP1L1,NS,carcinoma,-1,1	RP1L1	453	1	NM_178857	exon3	c.A665C	p.H222P	GCCTCATGCCCGG	.	PASS	Atlas-SNP
FCN2	2220	hgsc.bcm.edu	37	9	137779091	137779091	+	Missense_Mutation	SNP	G	G	T	rs7851696	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100	47	127	0	0.47	0	G|0.858;T|0.142	0.142	strong	.	FCN2	55	.	NM_004108	exon8	c.G772T	p.A258S	AATTGTGCTGTGA	.	PASS	Atlas-SNP
RPRD1B	58490	hgsc.bcm.edu	37	20	36668874	36668874	+	Silent	SNP	G	G	A	rs2273353	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	104	47	116	0	0.451923	0	G|0.747;A|0.253	0.253	strong	RPRD1B,NS,carcinoma,+1,2	RPRD1B	25	2	NM_021215	exon2	c.G189A	p.A63A	TTTAGCGAATGAT	.	PASS	Atlas-SNP
TSC22D2	9819	hgsc.bcm.edu	37	3	150128994	150128994	+	Silent	SNP	T	T	G	rs34647320	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	115	67	91	0	0.582609	0	T|0.866;G|0.134;A|0.000	0.134	strong	.	TSC22D2	42	.	NM_014779	exon1	c.T1857G	p.P619P	GCCGCCTGTTGCA	.	PASS	Atlas-SNP
SRCIN1	80725	hgsc.bcm.edu	37	17	36708225	36708225	+	Missense_Mutation	SNP	C	C	T	rs118010851	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60	30	58	0	0.5	0	C|0.982;T|0.018	0.018	strong	.	SRCIN1	66	.	NM_025248	exon14	c.G2624A	p.S875N	GGCCCGCTCAGCT	.	PASS	Atlas-SNP
MMRN1	22915	hgsc.bcm.edu	37	4	90816294	90816294	+	Missense_Mutation	SNP	A	A	G	rs1442138	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	34	15	39	0	0.441176	0	A|0.914;G|0.086	0.086	strong	.	MMRN1	174	.	NM_007351	exon1	c.A172G	p.T58A	CCAACCACTCGGG	.	PASS	Atlas-SNP
KIAA1432	57589	hgsc.bcm.edu	37	9	5747390	5747390	+	Missense_Mutation	SNP	C	C	A	rs41280731	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	120	73	95	0	0.608333	0	C|0.992;A|0.008	0.008	strong	.	KIAA1432	97	.	NM_001206557	exon12	c.C1337A	p.S446Y	GGAGTTCTTCAAC	.	PASS	Atlas-SNP
MASTL	84930	hgsc.bcm.edu	37	10	27459746	27459746	+	Missense_Mutation	SNP	C	C	G	rs3802526	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68	37	76	0	0.544118	0	C|0.921;G|0.079	0.079	strong	.	MASTL	81	.	NM_032844	exon8	c.C1858G	p.P620A	ACCTCACCAAAAG	.	PASS	Atlas-SNP
LRRC56	115399	hgsc.bcm.edu	37	11	554018	554018	+	Silent	SNP	G	G	A	rs112033363	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	40	99	0	0.45977	0	G|0.939;A|0.061	0.061	strong	.	LRRC56	23	.	NM_198075	exon14	c.G1371A	p.R457R	CCCAAGGCCACGA	.	PASS	Atlas-SNP
HIRA	7290	hgsc.bcm.edu	37	22	19385570	19385570	+	Silent	SNP	T	T	C	rs373432911		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	49	77	0	0.569767	0	.	.	weak	.	HIRA	100	.	NM_003325	exon6	c.A438G	p.L146L	TGAGGCTAGCCAG	.	PASS	Atlas-SNP
HLCS	3141	hgsc.bcm.edu	37	21	38308911	38308911	+	Silent	SNP	G	G	A	rs1065758	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	125	76	113	0	0.608	0	G|0.893;A|0.107	0.107	strong	.	HLCS	64	.	NM_000411	exon5	c.C834T	p.S278S	CACCTCGCTCTGG	.	PASS	Atlas-SNP
NFATC1	4772	hgsc.bcm.edu	37	18	77227476	77227476	+	Silent	SNP	A	A	G	rs25656	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	31	56	0	0.492063	0	A|0.576;G|0.424	0.424	strong	.	NFATC1	105	.	NM_172390	exon8	c.A1986G	p.P662P	CCCGCCATTTCGG	.	PASS	Atlas-SNP
ADAMTS12	81792	hgsc.bcm.edu	37	5	33624430	33624430	+	Silent	SNP	A	A	G	rs61748198	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	253	101	224	0	0.399209	0	A|0.893;G|0.107	0.107	strong	.	ADAMTS12	464	.	NM_030955	exon14	c.T2049C	p.D683D	ATTGGAATCGATC	.	PASS	Atlas-SNP
GRXCR1	389207	hgsc.bcm.edu	37	4	42895423	42895423	+	Missense_Mutation	SNP	C	C	T	rs57655409	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	111	50	116	0	0.45045	0	C|0.877;T|0.123	0.123	strong	.	GRXCR1	78	.	NM_001080476	exon1	c.C140T	p.A47V	AATGTGCCAGTAT	.	PASS	Atlas-SNP
PCDH10	57575	hgsc.bcm.edu	37	4	134072185	134072185	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	39	9	48	0	0.230769	0	.	.	none	.	PCDH10	290	.	NM_032961	exon1	c.C890T	p.A297V	CCCGGGCGCGGGA	.	PASS	Atlas-SNP
SPATA31D1	389763	hgsc.bcm.edu	37	9	84605777	84605777	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	170	84	152	0	0.494118	0	.	.	none	.	.	.	.	NM_001001670	exon4	c.G392A	p.R131Q	TCTGTCGGGTGTG	.	PASS	Atlas-SNP
URGCP	55665	hgsc.bcm.edu	37	7	43916727	43916727	+	Missense_Mutation	SNP	T	T	G	rs2232108	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49	15	104	0	0.306122	0	T|0.515;G|0.485	0.485	strong	.	URGCP	170	.	NM_001077663	exon6	c.A2335C	p.M779L	GTCCCATGAGCAG	.	PASS	Atlas-SNP
IFT74	80173	hgsc.bcm.edu	37	9	27009100	27009100	+	Missense_Mutation	SNP	T	T	C	rs17694549	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	164	61	193	0	0.371951	0	T|0.943;C|0.057	0.057	strong	.	IFT74	46	.	NM_001099222	exon9	c.T670C	p.F224L	ATGTCTTTTGAAA	.	PASS	Atlas-SNP
WDFY4	57705	hgsc.bcm.edu	37	10	50022040	50022040	+	Silent	SNP	G	G	A	rs41283275	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	17	7	26	0	0.411765	0	G|0.855;A|0.145	0.145	strong	.	WDFY4	205	.	NM_020945	exon31	c.G5253A	p.R1751R	GCAGAGGCACCAC	.	PASS	Atlas-SNP
CCDC178	374864	hgsc.bcm.edu	37	18	30825388	30825388	+	Missense_Mutation	SNP	G	G	A	rs146565345	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	22	52	0	0.407407	0	G|0.998;A|0.002	0.002	strong	C18orf34_ENST00000383096,NS,carcinoma,0,2	.	.	2	NM_001105528	exon14	c.C1414T	p.R472W	TTTTCCGTATGCT	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9049149	9049149	+	Missense_Mutation	SNP	G	G	A	rs12461007	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	150	68	120	0	0.453333	0	G|0.783;A|0.217	0.217	strong	.	MUC16	4315	.	NM_024690	exon5	c.C32482T	p.P10828S	GTGCAGGATGCGT	.	PASS	Atlas-SNP
OTUD7B	56957	hgsc.bcm.edu	37	1	149943157	149943157	+	Silent	SNP	G	G	A	rs77015846	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	18	68	0	0.28125	0	G|0.947;A|0.053	0.053	strong	.	OTUD7B	76	.	NM_020205	exon3	c.C108T	p.A36A	GAGGGCGGCATTC	.	PASS	Atlas-SNP
AKNA	80709	hgsc.bcm.edu	37	9	117110046	117110046	+	Missense_Mutation	SNP	C	C	T	rs3748178	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	46	35	70	0	0.76087	0	C|0.891;T|0.109	0.109	strong	.	AKNA	119	.	NM_030767	exon16	c.G3356A	p.R1119Q	GCTGGCCGGCCGC	.	PASS	Atlas-SNP
ZSCAN30	100101467	hgsc.bcm.edu	37	18	32844056	32844056	+	Silent	SNP	G	G	T	rs75902053	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	19	66	0	0.404255	0	G|0.958;T|0.042	0.042	strong	.	ZSCAN30	34	.	NM_001166012	exon3	c.C261A	p.I87I	CTCCAGGATCTGC	.	PASS	Atlas-SNP
OLFML1	283298	hgsc.bcm.edu	37	11	7530985	7530985	+	Missense_Mutation	SNP	G	G	A	rs12803046	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	37	102	0	0.521127	0	G|0.977;A|0.023	0.023	strong	.	OLFML1	54	.	NM_198474	exon3	c.G775A	p.A259T	GGCCGAGCATTGG	.	PASS	Atlas-SNP
RTKN2	219790	hgsc.bcm.edu	37	10	63964653	63964653	+	Silent	SNP	C	C	T	rs41274060	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	43	43	41	0	1	0	C|0.821;T|0.179	0.179	strong	.	RTKN2	68	.	NM_145307	exon10	c.G1149A	p.K383K	CATCCACTTCTGA	.	PASS	Atlas-SNP
CCAR1	55749	hgsc.bcm.edu	37	10	70513614	70513614	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	109	55	122	0	0.504587	0	.	.	none	.	CCAR1	118	.	NM_018237	exon11	c.G1124T	p.S375I	GTCCCAGTTGTGA	.	PASS	Atlas-SNP
TRAPPC10	7109	hgsc.bcm.edu	37	21	45479055	45479055	+	Silent	SNP	C	C	T	rs2838475	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	20	66	0	0.377358	0	C|0.929;T|0.071	0.071	strong	.	TRAPPC10	109	.	NM_003274	exon6	c.C750T	p.D250D	ACTGGACGCCCTC	.	PASS	Atlas-SNP
HPN	3249	hgsc.bcm.edu	37	19	35550878	35550878	+	Silent	SNP	C	C	T	rs45512696	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	29	75	0	0.386667	0	C|0.904;T|0.096	0.096	strong	.	HPN	45	.	NM_182983	exon6	c.C391T	p.L131L	CAGAGGCTGCTGG	.	PASS	Atlas-SNP
LRRIQ3	127255	hgsc.bcm.edu	37	1	74648375	74648375	+	Silent	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83	26	68	0	0.313253	0	.	.	none	.	LRRIQ3	146	.	NM_001105659	exon3	c.T420C	p.Y140Y	ATGTCTATATCCT	.	PASS	Atlas-SNP
ABHD5	51099	hgsc.bcm.edu	37	3	43743773	43743773	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	20	81	0	0.31746	0	.	.	none	ABHD5,NS,carcinoma,-1,1	ABHD5	33	1	NM_016006	exon3	c.A200C	p.K67T	CACTGAAGTTCTC	.	PASS	Atlas-SNP
PRAMEF2	65122	hgsc.bcm.edu	37	1	12921333	12921333	+	Missense_Mutation	SNP	G	G	A	rs56145411	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	272	41	255	0	0.150735	0	G|0.837;A|0.163	0.163	strong	PRAMEF2,NS,carcinoma,+1,1	PRAMEF2	85	1	NM_023014	exon4	c.G1124A	p.C375Y	TGAGCTGCTGCTC	.	PASS	Atlas-SNP
SMC5	23137	hgsc.bcm.edu	37	9	72897440	72897440	+	Missense_Mutation	SNP	T	T	C	rs1180117	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	181	93	211	0	0.513812	0	T|0.778;C|0.222	0.222	strong	.	SMC5	96	.	NM_015110	exon7	c.T922C	p.C308R	GTAACATGTCGAA	.	PASS	Atlas-SNP
SH3GLB2	56904	hgsc.bcm.edu	37	9	131771505	131771505	+	Silent	SNP	C	C	T	rs1129098	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	58	29	70	0	0.5	0	C|0.726;T|0.274	0.274	strong	.	SH3GLB2	32	.	NM_020145	exon10	c.G960A	p.P320P	CTCCCCCGGAGGG	.	PASS	Atlas-SNP
MINOS1	440574	hgsc.bcm.edu	37	1	19950062	19950062	+	Silent	SNP	T	T	C	rs1737428	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	27	37	0	0.574468	0	T|0.661;C|0.339	0.339	strong	.	.	.	.	NM_001032363	exon3	c.T207C	p.H69H	TCTACATGGAAAA	.	PASS	Atlas-SNP
URB1	9875	hgsc.bcm.edu	37	21	33726303	33726303	+	Silent	SNP	C	C	T	rs200555493	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	141	63	95	0	0.446809	0	C|0.998;T|0.002	0.002	weak	.	URB1	176	.	NM_014825	exon18	c.G2355A	p.A785A	GACTACCGCACTG	.	PASS	Atlas-SNP
SLC22A25	387601	hgsc.bcm.edu	37	11	62931484	62931484	+	Missense_Mutation	SNP	T	T	C	rs6591771	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	179	84	192	0	0.469274	0	T|0.486;C|0.514	0.514	strong	.	SLC22A25	87	.	NM_199352	exon9	c.A1456G	p.M486V	TCATCATGAGGGA	.	PASS	Atlas-SNP
NSUN5	55695	hgsc.bcm.edu	37	7	72717933	72717933	+	Silent	SNP	C	C	T	rs61750968	byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	129	69	132	0	0.534884	0	C|0.714;T|0.286	0.286	strong	NSUN5_ENST00000438747,NS,carcinoma,0,2	NSUN5	47	2	NM_148956	exon8	c.G1035A	p.A345A	AGTGAGCGCGTGG	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9056930	9056930	+	Silent	SNP	T	T	G	rs918535	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	95	50	107	0	0.526316	0	T|0.739;G|0.261	0.261	strong	.	MUC16	4315	.	NM_024690	exon3	c.A30516C	p.T10172T	CATGTTTGTCTTC	.	PASS	Atlas-SNP
ZNF417	147687	hgsc.bcm.edu	37	19	58420699	58420699	+	Missense_Mutation	SNP	C	C	A	rs71354064		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	119	57	163	0	0.478992	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
ATP5O	539	hgsc.bcm.edu	37	21	35284683	35284683	+	Silent	SNP	A	A	G	rs78234759	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	19	60	0	0.253333	0	A|0.962;G|0.038;T|0.000	0.038	strong	.	ATP5O	9	.	NM_001697	exon3	c.T108C	p.G36G	TTCAATACCGTAT	.	PASS	Atlas-SNP
GATA6	2627	hgsc.bcm.edu	37	18	19762986	19762986	+	Silent	SNP	A	A	G	rs146949786	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	123	58	114	0	0.471545	0	A|0.996;G|0.004	0.004	strong	.	GATA6	35	.	NM_005257	exon6	c.A1602G	p.T534T	CACAACACAACCT	.	PASS	Atlas-SNP
WDR24	84219	hgsc.bcm.edu	37	16	737269	737269	+	Silent	SNP	C	C	T	rs17850290	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	46	44	46	0	0.956522	0	C|0.902;T|0.098	0.098	strong	.	WDR24	111	.	NM_032259	exon3	c.G807A	p.T269T	GGAGCACGTGGCC	.	PASS	Atlas-SNP
HEATR5B	54497	hgsc.bcm.edu	37	2	37230728	37230728	+	Silent	SNP	T	T	C	rs1007823	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	46	93	0	0.534884	0	C|0.124;T|0.876	0.124	strong	HEATR5B,NS,carcinoma,0,1	HEATR5B	185	1	NM_019024	exon31	c.A5007G	p.V1669V	AGCTCTTACTATC	.	PASS	Atlas-SNP
MEIOB	254528	hgsc.bcm.edu	37	16	1894912	1894912	+	Silent	SNP	C	C	T	rs9806826	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	153	82	212	3	0.535948	0.0141509	C|0.681;T|0.319	0.319	strong	C16orf73_ENST00000412554,NS,carcinoma,-1,2	.	.	2	NM_001163560	exon10	c.G831A	p.T277T	AACATTCGTTTCT	.	scavenged	Atlas-SNP
SVEP1	79987	hgsc.bcm.edu	37	9	113276356	113276356	+	Missense_Mutation	SNP	C	C	G	rs3818764	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	161	81	184	0	0.503106	0	C|0.847;G|0.153	0.153	strong	.	SVEP1	326	.	NM_153366	exon4	c.G995C	p.G332A	GGTGAGCCTTCAG	.	PASS	Atlas-SNP
DDX55	57696	hgsc.bcm.edu	37	12	124104686	124104686	+	Silent	SNP	G	G	A	rs3204541	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	90	43	109	0	0.477778	0	G|0.707;A|0.293	0.293	strong	.	DDX55	51	.	NM_020936	exon14	c.G1802A	p.X601X	ACTGCTGATTCCA	.	PASS	Atlas-SNP
FMN2	56776	hgsc.bcm.edu	37	1	240370952	240370952	+	Missense_Mutation	SNP	C	C	T	rs201741828	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	6	101	0	0.115385	0	C|0.986;G|0.000;T|0.014	0.014	strong	FMN2,NS,carcinoma,+1,2	FMN2	451	2	NM_020066	exon5	c.C2840T	p.P947L	CGCCCCCTCTACC	.	PASS	Atlas-SNP
MTTP	4547	hgsc.bcm.edu	37	4	100510859	100510859	+	Silent	SNP	T	T	C	rs991811	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	45	23	71	0	0.511111	0	T|0.472;C|0.528	0.528	strong	.	MTTP	127	.	NM_000253	exon5	c.T453C	p.G151G	GAGAGGTCTGGCT	.	PASS	Atlas-SNP
MMP8	4317	hgsc.bcm.edu	37	11	102595492	102595492	+	Missense_Mutation	SNP	G	G	A	rs3765620	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	198	198	172	0	1	0	G|0.357;A|0.643	0.643	strong	.	MMP8	68	.	NM_002424	exon1	c.C95T	p.T32I	TGAACAGTTTTTG	.	PASS	Atlas-SNP
BTN3A1	11119	hgsc.bcm.edu	37	6	26413744	26413744	+	Missense_Mutation	SNP	C	C	A	rs4712990	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100	15	87	0	0.15	0	C|0.883;A|0.117	0.117	strong	.	BTN3A1	80	.	NM_007048	exon10	c.C1366A	p.P456T	CCTAAGCCCCCTA	.	PASS	Atlas-SNP
MGAM	8972	hgsc.bcm.edu	37	7	141759274	141759274	+	Silent	SNP	T	T	C	rs77338861		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	151	37	250	0	0.245033	0	C|1.000;|0.000	1.000	weak	.	MGAM	767	.	NM_004668	exon32	c.T3822C	p.D1274D	GCAGGATGTGCAG	.	PASS	Atlas-SNP
OBSL1	23363	hgsc.bcm.edu	37	2	220422905	220422905	+	Splice_Site	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	170	87	214	0	0.511765	0	.	.	none	.	OBSL1	120	.	NM_015311	exon11	c.3502+1G>A	.	CACCCACCAGCCA	.	PASS	Atlas-SNP
C1orf27	54953	hgsc.bcm.edu	37	1	186363119	186363119	+	Missense_Mutation	SNP	C	C	G	rs12084264	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	189	188	193	0	0.994709	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
LRP1B	53353	hgsc.bcm.edu	37	2	141032088	141032088	+	Silent	SNP	C	C	T	rs1386356	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	55	107	0	0.654762	0	C|0.462;T|0.538	0.538	strong	.	LRP1B	1315	.	NM_018557	exon85	c.G13047A	p.T4349T	ATAGCGCGTTGGA	.	PASS	Atlas-SNP
TLE2	7089	hgsc.bcm.edu	37	19	2997897	2997897	+	Silent	SNP	G	G	A	rs11150	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	89	39	133	0	0.438202	0	G|0.801;A|0.199	0.199	strong	.	TLE2	35	.	NM_003260	exon20	c.C2181T	p.I727I	TGTCACGATGTAT	.	PASS	Atlas-SNP
RBAK-LOC389458	0	hgsc.bcm.edu	37	7	5096958	5096958	+	Silent	SNP	T	T	C	rs11975068	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	189	117	145	0	0.619048	0	T|0.756;C|0.244	0.244	strong	RBAK_ENST00000396912,NS,carcinoma,0,1	.	.	1	NM_001204513	exon3	c.T48C	p.D16D	TGTGGATTTCACC	.	PASS	Atlas-SNP
TAF4B	6875	hgsc.bcm.edu	37	18	23866349	23866349	+	Silent	SNP	G	G	A	rs3744961	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	29	56	0	0.453125	0	G|0.879;A|0.121	0.121	strong	.	TAF4B	71	.	NM_005640	exon7	c.G1476A	p.G492G	TGCTGGGACCACA	.	PASS	Atlas-SNP
EXD3	54932	hgsc.bcm.edu	37	9	140243844	140243844	+	Missense_Mutation	SNP	C	C	T	rs28545754	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	43	43	60	0	1	0	C|0.432;T|0.568	0.568	strong	EXD3,NS,carcinoma,0,1	EXD3	86	1	NM_017820	exon15	c.G1634A	p.C545Y	TCCTCGCAGAGCG	.	PASS	Atlas-SNP
KRTAP12-2	353323	hgsc.bcm.edu	37	21	46086488	46086488	+	Missense_Mutation	SNP	C	C	T	rs75799438	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	185	67	194	0	0.362162	0	C|0.963;T|0.037	0.037	strong	.	KRTAP12-2	10	.	NM_181684	exon1	c.G316A	p.V106M	CAGGCACGCACAG	.	PASS	Atlas-SNP
PRKAR1B	5575	hgsc.bcm.edu	37	7	590199	590199	+	Silent	SNP	A	A	G	rs11545042	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	26	14	55	0	0.538462	0	A|0.826;G|0.174	0.174	strong	.	PRKAR1B	32	.	NM_001164760	exon11	c.T1014C	p.T338T	CACGACAGTGGCC	.	PASS	Atlas-SNP
PLEKHA8	84725	hgsc.bcm.edu	37	7	30113706	30113706	+	Silent	SNP	A	A	G	rs11977829	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	201	45	288	0	0.223881	0	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	.	PASS	Atlas-SNP
ALDH7A1	501	hgsc.bcm.edu	37	5	125928395	125928395	+	Silent	SNP	A	A	G	rs60720055	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	96	51	106	0	0.53125	0	A|0.941;G|0.059	0.059	strong	.	ALDH7A1	57	.	NM_001202404	exon3	c.T354C	p.T118T	CTTTACAGTTTCT	.	PASS	Atlas-SNP
ZNF100	163227	hgsc.bcm.edu	37	19	21948570	21948570	+	Missense_Mutation	SNP	T	T	C	rs12974842	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	28	21	25	0	0.75	0	T|0.950;C|0.050	0.050	strong	.	ZNF100	62	.	NM_173531	exon2	c.A22G	p.M8V	GACACATTCCATA	.	PASS	Atlas-SNP
HSPA6	3310	hgsc.bcm.edu	37	1	161496134	161496134	+	Missense_Mutation	SNP	C	C	G	rs753856	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	138	54	191	0	0.391304	0	C|0.914;G|0.086	0.086	strong	.	HSPA6	53	.	NM_002155	exon1	c.C1686G	p.D562E	TAGGGACAAGATT	.	PASS	Atlas-SNP
CTNS	1497	hgsc.bcm.edu	37	17	3559823	3559823	+	Silent	SNP	G	G	A	rs1800528	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	295	290	255	1	0.983051	0.00392157	G|0.853;A|0.147	0.147	strong	.	CTNS	42	.	NM_001031681	exon8	c.G504A	p.T168T	CCTGACGGGCTTC	.	PASS	Atlas-SNP
FBN3	84467	hgsc.bcm.edu	37	19	8197958	8197958	+	Missense_Mutation	SNP	C	C	T	rs36124795	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	24	57	0	0.387097	0	C|0.972;T|0.028	0.028	strong	.	FBN3	300	.	NM_032447	exon13	c.G1624A	p.V542I	CGTTGACGCACAT	.	PASS	Atlas-SNP
PPP1R17	10842	hgsc.bcm.edu	37	7	31746837	31746837	+	Silent	SNP	C	C	T	rs2072409	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	70	15	88	0	0.214286	0	C|0.890;T|0.110	0.110	strong	C7orf16,colon,carcinoma,0,4	.	.	4	NM_006658	exon5	c.C408T	p.D136D	CAGGGACGAGAGA	.	PASS	Atlas-SNP
AMELX	265	hgsc.bcm.edu	37	X	11316742	11316742	+	Silent	SNP	C	C	T	rs2106416	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	47	35	0	0.758065	0	C|0.765;T|0.235	0.235	strong	.	AMELX	31	.	NM_182680	exon6	c.C261T	p.H87H	ACAGCACCCCCCG	.	PASS	Atlas-SNP
UPK3BL	100134938	hgsc.bcm.edu	37	7	102279601	102279601	+	Silent	SNP	G	G	T	rs79054498		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	420	39	469	0	0.0928571	0	G|0.500;T|0.500	0.500	weak	UPK3BL,NS,carcinoma,0,2	UPK3BL	6	2	NM_001114403	exon4	c.C531A	p.T177T	CCACTTGGTTTCA	.	scavenged	Atlas-SNP
NUAK2	81788	hgsc.bcm.edu	37	1	205272722	205272722	+	Silent	SNP	C	C	T	rs41264877	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	31	42	0	0.584906	0	C|0.974;T|0.026	0.026	strong	.	NUAK2	107	.	NM_030952	exon7	c.G1743A	p.E581E	GGGCTCCTCAAGC	.	PASS	Atlas-SNP
ZPLD1	131368	hgsc.bcm.edu	37	3	102171858	102171858	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	118	44	143	0	0.372881	0	.	.	none	.	ZPLD1	82	.	NM_175056	exon3	c.C250A	p.L84M	ACAGATCTGGCAC	.	PASS	Atlas-SNP
CYP2B6	1555	hgsc.bcm.edu	37	19	41512841	41512841	+	Missense_Mutation	SNP	G	G	T	rs56308434		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	143	75	133	0	0.524476	0	.	.	weak	.	CYP2B6	79	.	NM_000767	exon4	c.G516T	p.Q172H	CTTCCAGTCCATT	.	PASS	Atlas-SNP
MAPK8IP3	23162	hgsc.bcm.edu	37	16	1812972	1812972	+	Silent	SNP	G	G	C	rs2294616	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	136	55	159	0	0.404412	0	G|0.835;C|0.165	0.165	strong	.	MAPK8IP3	164	.	NM_015133	exon16	c.G1860C	p.S620S	GATCTCGGCAGGC	.	PASS	Atlas-SNP
MAGEB3	4114	hgsc.bcm.edu	37	X	30254361	30254361	+	Missense_Mutation	SNP	G	G	A	rs2071308	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	77	51	48	0	0.662338	0	G|0.569;A|0.431	0.431	strong	.	MAGEB3	54	.	NM_002365	exon5	c.G320A	p.R107H	AGTCTCGCACAGA	.	PASS	Atlas-SNP
PPP1R1A	5502	hgsc.bcm.edu	37	12	54974803	54974803	+	Silent	SNP	C	C	T	rs8407	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	264	140	210	0	0.530303	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
FOXA2	3170	hgsc.bcm.edu	37	20	22563684	22563684	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68	27	83	0	0.397059	0	.	.	none	.	FOXA2	48	.	NM_021784	exon2	c.G196A	p.A66T	AGCCCGCGCTCAT	.	PASS	Atlas-SNP
PARD3B	117583	hgsc.bcm.edu	37	2	206364737	206364737	+	Silent	SNP	T	T	C	rs10197347	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	70	38	66	0	0.542857	0	T|0.587;C|0.413	0.413	strong	.	PARD3B	314	.	NM_152526	exon20	c.T2976C	p.S992S	GCCATCTGAGTAT	.	PASS	Atlas-SNP
ZNF814	730051	hgsc.bcm.edu	37	19	58386284	58386284	+	Silent	SNP	T	T	C	rs2375155	alternate_allele	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	240	61	358	0	0.254167	0	.	.	alt	ZNF814,NS,carcinoma,0,1	ZNF814	93	1	NM_001144989	exon3	c.A474G	p.A158A	CCTCTTTGCAAAC	.	scavenged	Atlas-SNP
SLC10A1	6554	hgsc.bcm.edu	37	14	70263648	70263648	+	Silent	SNP	C	C	T	rs4646285	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	128	61	112	0	0.476562	0	C|0.920;T|0.080	0.080	strong	.	SLC10A1	32	.	NM_003049	exon1	c.G225A	p.T75T	AAAGGCCGTGAGG	.	PASS	Atlas-SNP
B4GALNT3	283358	hgsc.bcm.edu	37	12	662838	662838	+	Silent	SNP	T	T	C	rs3087639		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	26	50	0	0.553191	0	.	.	weak	.	B4GALNT3	64	.	NM_173593	exon14	c.T1749C	p.P583P	GGCCCCTGGAAGG	.	PASS	Atlas-SNP
CALHM3	119395	hgsc.bcm.edu	37	10	105233301	105233301	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	28	88	0	0.518519	0	.	.	none	.	CALHM3	46	.	NM_001129742	exon3	c.C704T	p.A235V	TCCCGCGCATGCT	.	PASS	Atlas-SNP
PLXNA2	5362	hgsc.bcm.edu	37	1	208391254	208391254	+	Missense_Mutation	SNP	C	C	T	rs2782948	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	41	19	34	0	0.463415	0	C|0.660;T|0.340	0.340	strong	PLXNA2,NS,carcinoma,0,1	PLXNA2	178	1	NM_025179	exon2	c.G14A	p.R5Q	CAGGGCCGCCTCT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195508478	195508478	+	Missense_Mutation	SNP	G	G	C	rs76305071	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	2	61	0	0.030303	0	G|0.990;C|0.010	0.010	strong	MUC4_ENST00000463781,NS,carcinoma,+2,3	MUC4	1505	3	NM_018406	exon2	c.C9973G	p.H3325D	TGGCGTGACCTGT	.	scavenged	Atlas-SNP
KIAA0226	9711	hgsc.bcm.edu	37	3	197427584	197427584	+	Silent	SNP	G	G	A	rs368476866		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	132	63	97	0	0.477273	0	.	.	weak	.	KIAA0226	136	.	NM_014687	exon7	c.C1161T	p.S387S	GAAGCTGGACCTG	.	PASS	Atlas-SNP
MNDA	4332	hgsc.bcm.edu	37	1	158813819	158813819	+	Silent	SNP	A	A	G	rs857870	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93	47	108	0	0.505376	0	A|0.493;G|0.507	0.507	strong	.	MNDA	147	.	NM_002432	exon4	c.A477G	p.P159P	GCCCCCAGGTCCC	.	PASS	Atlas-SNP
TBC1D10C	374403	hgsc.bcm.edu	37	11	67171736	67171736	+	Silent	SNP	C	C	T	rs2514256	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82	13	81	0	0.158537	0	C|0.683;T|0.317	0.317	strong	TBC1D10C,NS,carcinoma,0,1	TBC1D10C	42	1	NM_001256508	exon2	c.C63T	p.S21S	CAGCTCCTTGGGG	.	PASS	Atlas-SNP
ADAMTS7	11173	hgsc.bcm.edu	37	15	79058968	79058968	+	Silent	SNP	T	T	C	rs112827102	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	59	24	68	0	0.40678	0	T|0.935;C|0.065	0.065	strong	.	ADAMTS7	142	.	NM_014272	exon19	c.A3285G	p.T1095T	TGGGGGTGTCCGG	.	PASS	Atlas-SNP
ITIH2	3698	hgsc.bcm.edu	37	10	7759595	7759595	+	Silent	SNP	C	C	T	rs7072478	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44	22	50	0	0.5	0	C|0.819;T|0.181	0.181	strong	ITIH2,NS,carcinoma,0,1	ITIH2	144	1	NM_002216	exon6	c.C474T	p.S158S	GAGCAGCGCTCTT	.	PASS	Atlas-SNP
FMN2	56776	hgsc.bcm.edu	37	1	240371426	240371426	+	Missense_Mutation	SNP	T	T	C	rs200640213	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	42	19	50	4	0.452381	0.08	T|0.940;C|0.060	0.060	strong	FMN2,rectum,carcinoma,0,1	FMN2	451	1	NM_020066	exon5	c.T3314C	p.V1105A	CCGGAGTGGGCAT	.	scavenged	Atlas-SNP
PLA2G2A	5320	hgsc.bcm.edu	37	1	20304926	20304926	+	Silent	SNP	G	G	A	rs4744	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	39	20	39	0	0.512821	0	G|0.860;A|0.140	0.140	strong	PLA2G2A,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	PLA2G2A	14	1	NM_001161729	exon3	c.C132T	p.Y44Y	GCAGCCGTAGAAG	.	PASS	Atlas-SNP
KIAA1211	57482	hgsc.bcm.edu	37	4	57182758	57182758	+	Silent	SNP	C	C	T	rs28559894	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	34	15	40	0	0.441176	0	C|0.728;T|0.272	0.272	strong	KIAA1211,NS,carcinoma,0,1	KIAA1211	178	1	NM_020722	exon8	c.C3090T	p.D1030D	GAGGGACGAGGAG	.	PASS	Atlas-SNP
P2RY2	5029	hgsc.bcm.edu	37	11	72946204	72946204	+	Missense_Mutation	SNP	C	C	T	rs1626154	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	39	47	0	0.735849	0	C|0.873;T|0.127	0.127	strong	.	P2RY2	54	.	NM_176071	exon3	c.C1000T	p.R334C	GCTCGCCGCAGGC	.	PASS	Atlas-SNP
ACVR1	90	hgsc.bcm.edu	37	2	158636910	158636910	+	Silent	SNP	G	G	A	rs2227861	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	59	59	84	0	1	0	G|0.366;A|0.634	0.634	strong	.	ACVR1	52	.	NM_001105	exon4	c.C270T	p.A90A	CTCCACGGCTTGG	.	PASS	Atlas-SNP
ATAD3C	219293	hgsc.bcm.edu	37	1	1403848	1403848	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	172	80	196	0	0.465116	0	.	.	none	.	ATAD3C	23	.	NM_001039211	exon12	c.C1174G	p.Q392E	CACCAGCAGATGA	.	PASS	Atlas-SNP
OR6M1	390261	hgsc.bcm.edu	37	11	123676231	123676231	+	Missense_Mutation	SNP	G	G	T	rs4936845	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	144	119	117	0	0.826389	0	G|0.763;T|0.237	0.237	strong	OR6M1,colon,carcinoma,0,1	OR6M1	60	1	NM_001005325	exon1	c.C827A	p.T276K	ACCACTGTGATGA	.	PASS	Atlas-SNP
CDK5R2	8941	hgsc.bcm.edu	37	2	219824731	219824731	+	Silent	SNP	G	G	C	rs78141300	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	22	12	26	0	0.545455	0	G|0.972;C|0.028	0.028	strong	.	CDK5R2	17	.	NM_003936	exon1	c.G189C	p.A63A	CTCGGCGCTCACC	.	PASS	Atlas-SNP
MCM6	4175	hgsc.bcm.edu	37	2	136602196	136602196	+	Silent	SNP	G	G	A	rs4988270	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	10	48	0	0.185185	0	G|0.997;A|0.003	0.003	strong	.	MCM6	64	.	NM_005915	exon16	c.C2268T	p.I756I	TGATTCGATTTCC	.	PASS	Atlas-SNP
NUP88	4927	hgsc.bcm.edu	37	17	5289580	5289580	+	Silent	SNP	A	A	G	rs11209	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	155	87	185	0	0.56129	0	A|0.526;G|0.474	0.474	strong	.	NUP88	47	.	NM_002532	exon17	c.T2172C	p.H724H	CCTTATATGTTCA	.	PASS	Atlas-SNP
TENM2	57451	hgsc.bcm.edu	37	5	167474474	167474474	+	Missense_Mutation	SNP	A	A	G	rs114898031	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	171	78	179	0	0.45614	0	A|0.990;G|0.010	0.010	strong	ODZ2_ENST00000519204,NS,carcinoma,0,3	.	.	3	NM_001122679	exon6	c.A1229G	p.D410G	CTGCAGATGGGCA	.	PASS	Atlas-SNP
TIMP3	7078	hgsc.bcm.edu	37	22	33253280	33253280	+	Silent	SNP	T	T	C	rs9862	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	183	181	192	0	0.989071	0	T|0.372;C|0.628	0.628	strong	.	TIMP3	31	.	NM_000362	exon3	c.T249C	p.H83H	CATCCATACGGAA	.	PASS	Atlas-SNP
OR10G8	219869	hgsc.bcm.edu	37	11	123901175	123901175	+	Silent	SNP	C	C	A	rs11825515	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	156	120	162	0	0.769231	0	A|0.066;C|0.934;T|0.000	0.066	strong	OR10G8,middle_lobe,carcinoma,+1,2	OR10G8	132	2	NM_001004464	exon1	c.C846A	p.L282L	CCTTCTCAACCCT	.	PASS	Atlas-SNP
ZNF646	9726	hgsc.bcm.edu	37	16	31088347	31088347	+	Silent	SNP	G	G	A	rs749671	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	22	60	0	0.354839	0	G|0.646;A|0.354	0.354	strong	.	ZNF646	133	.	NM_014699	exon2	c.G702A	p.E234E	TGCTGAGGAGGAG	.	PASS	Atlas-SNP
TXNDC11	51061	hgsc.bcm.edu	37	16	11785486	11785486	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	33	46	0	0.532258	0	.	.	none	.	TXNDC11	75	.	NM_015914	exon8	c.C1560T	p.I520I	AGAGTCGATGAAG	.	PASS	Atlas-SNP
TTLL1	25809	hgsc.bcm.edu	37	22	43459846	43459846	+	Silent	SNP	G	G	A	rs1052160	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	108	54	104	0	0.5	0	G|0.794;A|0.206	0.206	strong	.	TTLL1	41	.	NM_012263	exon7	c.C720T	p.L240L	GTTGGTGAGATGA	.	PASS	Atlas-SNP
OR13C2	392376	hgsc.bcm.edu	37	9	107367612	107367612	+	Silent	SNP	C	C	T	rs55706329	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	356	150	364	0	0.421348	0	C|0.652;T|0.348	0.348	strong	.	OR13C2	46	.	NM_001004481	exon1	c.G297A	p.V99V	CATCTGCACTGCA	.	PASS	Atlas-SNP
TEC	7006	hgsc.bcm.edu	37	4	48172266	48172266	+	Silent	SNP	G	G	A	rs2271173	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	173	73	180	0	0.421965	0	G|0.583;A|0.417	0.417	strong	.	TEC	81	.	NM_003215	exon5	c.C453T	p.S151S	CTTACTGCTCTCA	.	PASS	Atlas-SNP
FAM161A	84140	hgsc.bcm.edu	37	2	62069358	62069358	+	Missense_Mutation	SNP	T	T	C	rs11125895	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	107	48	114	0	0.448598	0	T|0.833;C|0.167	0.167	strong	.	FAM161A	200	.	NM_032180	exon2	c.A321G	p.I107M	AGTTTCTATGTGG	.	PASS	Atlas-SNP
DLEC1	9940	hgsc.bcm.edu	37	3	38080952	38080952	+	Missense_Mutation	SNP	T	T	G	rs7625806	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	38	15	79	0	0.394737	0	T|0.555;G|0.445	0.445	strong	DLEC1_ENST00000346219,NS,carcinoma,0,2	DLEC1	278	2	NM_007337	exon1	c.T236G	p.L79R	CTCAGCTGCTTCG	.	PASS	Atlas-SNP
MDN1	23195	hgsc.bcm.edu	37	6	90418331	90418331	+	Silent	SNP	A	A	G	rs55729223	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	70	29	74	0	0.414286	0	A|0.858;G|0.142	0.142	strong	.	MDN1	478	.	NM_014611	exon51	c.T7782C	p.P2594P	ATCCAGAGGGATC	.	PASS	Atlas-SNP
PRRT3	285368	hgsc.bcm.edu	37	3	9989028	9989028	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	17	5	6	0	0.294118	0	.	.	none	.	PRRT3	35	.	NM_207351	exon4	c.C1829T	p.A610V	ACGGCCGCGCCCC	.	PASS	Atlas-SNP
OR51B6	390058	hgsc.bcm.edu	37	11	5372881	5372881	+	Silent	SNP	G	G	A	rs77135024	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	175	68	177	0	0.388571	0	G|0.877;A|0.123	0.123	strong	OR51B6,NS,carcinoma,+1,1	OR51B6	53	1	NM_001004750	exon1	c.G144A	p.R48R	CATCAGGAATGAT	.	PASS	Atlas-SNP
TTYH2	94015	hgsc.bcm.edu	37	17	72240168	72240168	+	Missense_Mutation	SNP	G	G	A	rs35682745	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	32	10	32	0	0.3125	0	G|0.877;A|0.123	0.123	strong	TTYH2,colon,carcinoma,-1,1	TTYH2	63	1	NM_032646	exon6	c.G784A	p.A262T	CTGGCCGCTGATG	.	PASS	Atlas-SNP
BIVM-ERCC5	0	hgsc.bcm.edu	37	13	103514870	103514870	+	Silent	SNP	C	C	T	rs149867583	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	96	2	128	0	0.0208333	0	C|1.000;T|0.000	0.000	strong	ERCC5,NS,carcinoma,+2,1	.	.	1	NM_001204425	exon16	c.C2733T	p.H911H	GGAGCACGTAGCC	.	scavenged	Atlas-SNP
KRT36	8689	hgsc.bcm.edu	37	17	39643340	39643340	+	Missense_Mutation	SNP	T	T	G	rs11657323	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80	79	73	0	0.9875	0	T|0.822;G|0.178	0.178	strong	.	KRT36	52	.	NM_003771	exon6	c.A1070C	p.N357T	TCCACGTTGCTGA	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	112	44	112	0	0.392857	0	T|0.708;C|0.292	0.292	strong	.	.	.	.	NM_183061	exon11	c.A1270G	p.T424A	GTATAGTAACTGC	.	PASS	Atlas-SNP
ODF4	146852	hgsc.bcm.edu	37	17	8243469	8243469	+	Missense_Mutation	SNP	T	T	C	rs12943505	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	70	27	79	0	0.385714	0	T|0.790;C|0.210	0.210	strong	.	ODF4	23	.	NM_153007	exon1	c.T100C	p.W34R	GCAGGATGGGGCA	.	PASS	Atlas-SNP
XIRP2	129446	hgsc.bcm.edu	37	2	168103701	168103701	+	Silent	SNP	A	A	G	rs16853313	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	31	83	0	0.484375	0	A|0.928;G|0.072	0.072	strong	.	XIRP2	914	.	NM_152381	exon9	c.A5799G	p.Q1933Q	AGCACAAAGAAGT	.	PASS	Atlas-SNP
TTC23	64927	hgsc.bcm.edu	37	15	99715352	99715352	+	Silent	SNP	A	A	G	rs2602016	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57	30	76	0	0.526316	0	A|0.168;G|0.832	0.832	strong	.	TTC23	33	.	NM_001040657	exon8	c.T768C	p.L256L	GATGATAAGATGT	.	PASS	Atlas-SNP
LRIT3	345193	hgsc.bcm.edu	37	4	110772711	110772711	+	Silent	SNP	C	C	T	rs17040904	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110	60	91	0	0.545455	0	C|0.972;T|0.028	0.028	strong	.	LRIT3	107	.	NM_198506	exon2	c.C168T	p.P56P	CCTCCCCGTGGAC	.	PASS	Atlas-SNP
TRAK1	22906	hgsc.bcm.edu	37	3	42251321	42251321	+	Missense_Mutation	SNP	C	C	T	rs375255978		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60	24	55	0	0.4	0	.	.	weak	.	TRAK1	188	.	NM_001265608	exon14	c.C1807T	p.P603S	CTGGACCCCCGGC	.	PASS	Atlas-SNP
EP400	57634	hgsc.bcm.edu	37	12	132547090	132547090	+	Silent	SNP	A	A	G	rs7974276	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85	32	68	1	0.376471	0.0147059	A|0.794;G|0.206	0.206	strong	EP400,colon,carcinoma,0,3	EP400	370	3	NM_015409	exon47	c.A8178G	p.Q2726Q	GCAGCAACAACAG	.	scavenged	Atlas-SNP
CYP4A22	284541	hgsc.bcm.edu	37	1	47607785	47607785	+	Missense_Mutation	SNP	G	G	A	rs2056900	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68	38	80	0	0.558824	0	G|0.768;A|0.232	0.232	strong	.	CYP4A22	60	.	NM_001010969	exon4	c.G388A	p.G130S	GGGTACGGCTTGC	.	PASS	Atlas-SNP
SLC6A5	9152	hgsc.bcm.edu	37	11	20648380	20648380	+	Missense_Mutation	SNP	G	G	A	rs1805091	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	33	58	0	0.445946	0	G|0.790;A|0.210	0.210	strong	SLC6A5,caecum,carcinoma,0,1	SLC6A5	151	1	NM_004211	exon8	c.G1387A	p.D463N	CTCACGGATGCCA	.	PASS	Atlas-SNP
VPS13C	54832	hgsc.bcm.edu	37	15	62172907	62172907	+	Silent	SNP	T	T	C	rs12901055	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79	38	75	0	0.481013	0	T|0.946;C|0.054	0.054	strong	VPS13C_ENST00000395896,NS,carcinoma,-2,3	VPS13C	506	3	NM_020821	exon73	c.A9903G	p.Q3301Q	ATCTTGTTGGATT	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	170	135	139	0	0.794118	0	G|0.856;A|0.144	0.144	strong	.	VARS2	60	.	NM_001167734	exon30	c.G3236A	p.R1079Q	ACCTCCGGCAGCT	.	PASS	Atlas-SNP
SF3B14	0	hgsc.bcm.edu	37	2	24290671	24290671	+	Silent	SNP	G	G	A	rs61742149	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	155	66	129	0	0.425806	0	G|0.930;A|0.070	0.070	strong	.	SF3B14	6	.	NM_016047	exon4	c.C339T	p.L113L	CTCCTTGAGAAGC	.	PASS	Atlas-SNP
PCK1	5105	hgsc.bcm.edu	37	20	56137807	56137807	+	Silent	SNP	A	A	G	rs1042523	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	50	49	62	0	0.98	0	A|0.601;G|0.399	0.399	strong	.	PCK1	95	.	NM_002591	exon4	c.A462G	p.S154S	TCTGTCAAAGATC	.	PASS	Atlas-SNP
EPHA2	1969	hgsc.bcm.edu	37	1	16464673	16464673	+	Silent	SNP	G	G	A	rs2230597	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	28	28	37	0	1	0	G|0.649;A|0.351	0.351	strong	.	EPHA2	102	.	NM_004431	exon5	c.C987T	p.P329P	GGCGGAGGGGGGT	.	PASS	Atlas-SNP
FRMD7	90167	hgsc.bcm.edu	37	X	131212512	131212512	+	Silent	SNP	A	A	G	rs5977623	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	107	73	80	0	0.682243	0	A|0.670;0|0.003	.	strong	.	FRMD7	69	.	NM_194277	exon12	c.T1533C	p.I511I	TGCTCTAATTGGG	.	PASS	Atlas-SNP
SPRR1B	6699	hgsc.bcm.edu	37	1	153004853	153004853	+	Missense_Mutation	SNP	C	C	T	rs3795382	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	139	59	170	0	0.42446	0	C|0.497;T|0.503	0.503	strong	SPRR1B,head_neck,carcinoma,0,1	SPRR1B	18	1	NM_003125	exon2	c.C32T	p.T11I	CTTGCACCCCACC	.	PASS	Atlas-SNP
ADAMTS13	11093	hgsc.bcm.edu	37	9	136320665	136320665	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	35	19	47	0	0.542857	0	.	.	none	.	ADAMTS13	113	.	NM_139025	exon25	c.T3508C	p.S1170P	CTCTTCTCCCCGG	.	PASS	Atlas-SNP
AIFM1	9131	hgsc.bcm.edu	37	X	129283520	129283520	+	Silent	SNP	A	A	G	rs1139851	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79	79	54	0	1	0	0|0.004;G|0.504	0.504	strong	.	AIFM1	75	.	NM_001130847	exon3	c.T273C	p.D91D	TTTTTCATCCTCT	.	PASS	Atlas-SNP
MTUS1	57509	hgsc.bcm.edu	37	8	17612639	17612639	+	Silent	SNP	T	T	C	rs209568	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	26	60	0	0.412698	0	T|0.758;C|0.242	0.242	strong	.	MTUS1	144	.	NM_001001924	exon2	c.A678G	p.E226E	AAAGCTTTCTCTA	.	PASS	Atlas-SNP
CD6	923	hgsc.bcm.edu	37	11	60785463	60785463	+	Silent	SNP	C	C	T	rs12417503	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	27	9	26	0	0.333333	0	C|0.875;T|0.125	0.125	strong	CD6_ENST00000313421,NS,carcinoma,+2,2	CD6	122	2	NM_006725	exon11	c.C1815T	p.A605A	GCTGGCCGGCACC	.	scavenged	Atlas-SNP
DAGLA	747	hgsc.bcm.edu	37	11	61511794	61511794	+	Missense_Mutation	SNP	C	C	G	rs117050893	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	50	21	54	0	0.42	0	C|0.994;G|0.006	0.006	strong	.	DAGLA	109	.	NM_006133	exon20	c.C2962G	p.L988V	ATCTCACTCTCGC	.	PASS	Atlas-SNP
WDR93	56964	hgsc.bcm.edu	37	15	90245253	90245253	+	Silent	SNP	C	C	T	rs4316730	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	76	79	0	1	0	C|0.564;T|0.436	0.436	strong	.	WDR93	63	.	NM_020212	exon2	c.C276T	p.T92T	GCCCACCGTCTAC	.	PASS	Atlas-SNP
TP53RK	112858	hgsc.bcm.edu	37	20	45315786	45315786	+	Missense_Mutation	SNP	C	C	T	rs34983477	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79	39	70	0	0.493671	0	C|0.969;T|0.031	0.031	strong	.	TP53RK	13	.	NM_033550	exon2	c.G368A	p.R123Q	TAATCTCGAACAG	.	PASS	Atlas-SNP
PHTF2	57157	hgsc.bcm.edu	37	7	77531113	77531113	+	Silent	SNP	T	T	C	rs78163487	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	199	102	235	0	0.512563	0	T|0.903;C|0.097	0.097	strong	.	PHTF2	104	.	NM_001127359	exon5	c.T219C	p.P73P	AAGTCCTTGGACT	.	PASS	Atlas-SNP
NOP9	161424	hgsc.bcm.edu	37	14	24769663	24769663	+	Silent	SNP	T	T	G	rs11158632	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85	36	77	0	0.423529	0	T|0.838;G|0.162	0.162	strong	.	.	.	.	NM_174913	exon2	c.T297G	p.A99A	CCTAGCTTTGTCC	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	634	123	556	0	0.194006	0	G|0.739;A|0.261	0.261	strong	.	OR4M1	104	.	NM_001005500	exon1	c.G695A	p.G232D	GCTCAGGTGAGAA	.	PASS	Atlas-SNP
MARC2	54996	hgsc.bcm.edu	37	1	220955168	220955168	+	Silent	SNP	A	A	G	rs12030434	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	142	66	164	0	0.464789	0	A|0.974;G|0.026	0.026	strong	.	.	.	.	NM_017898	exon7	c.A933G	p.P311P	GTCTCCACTTTTT	.	PASS	Atlas-SNP
HDC	3067	hgsc.bcm.edu	37	15	50534832	50534832	+	Silent	SNP	A	A	G	rs1549521	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	33	68	0	0.383721	0	A|0.862;G|0.138	0.138	strong	HDC,NS,carcinoma,-2,1	HDC	86	1	NM_002112	exon12	c.T1614C	p.N538N	GAGGCCATTTTCC	.	PASS	Atlas-SNP
ZNF318	24149	hgsc.bcm.edu	37	6	43305520	43305520	+	Silent	SNP	C	C	T	rs35650765	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	142	72	157	0	0.507042	0	C|0.970;T|0.030	0.030	strong	ZNF318,colon,carcinoma,0,1	ZNF318	175	1	NM_014345	exon10	c.G6216A	p.P2072P	ATCTAACGGAAAC	.	PASS	Atlas-SNP
UBOX5	22888	hgsc.bcm.edu	37	20	3102636	3102636	+	Missense_Mutation	SNP	G	G	C	rs148731933	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	27	49	0	0.5	0	G|1.000;C|0.000	0.000	strong	UBOX5,NS,carcinoma,+2,1	UBOX5	47	1	NM_014948	exon3	c.C649G	p.L217V	GAGGCAGGTTCTC	.	PASS	Atlas-SNP
ORC3	23595	hgsc.bcm.edu	37	6	88362943	88362943	+	Silent	SNP	C	C	T	rs2307393	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73	29	47	0	0.39726	0	C|0.945;T|0.055	0.055	strong	.	ORC3	51	.	NM_181837	exon14	c.C1492T	p.L498L	GAGTTCCTGGCCC	.	PASS	Atlas-SNP
OR13C5	138799	hgsc.bcm.edu	37	9	107360826	107360826	+	Missense_Mutation	SNP	A	A	G	rs1851725	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	105	54	129	0	0.514286	0	A|0.634;G|0.366	0.366	strong	.	OR13C5	60	.	NM_001004482	exon1	c.T869C	p.M290T	TTCATCATGGGAG	.	PASS	Atlas-SNP
CD69	969	hgsc.bcm.edu	37	12	9906179	9906179	+	Silent	SNP	G	G	A	rs11052883	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49	22	48	0	0.44898	0	G|0.970;A|0.030	0.030	strong	CD69,NS,carcinoma,-1,1	CD69	23	1	NM_001781	exon5	c.C498T	p.N166N	TGTAACGTTGAAC	.	PASS	Atlas-SNP
SIRPG	55423	hgsc.bcm.edu	37	20	1629906	1629906	+	Silent	SNP	C	C	T	rs6079967	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	286	284	274	0	0.993007	0	C|0.593;T|0.407	0.407	strong	SIRPG,right_upper_lobe,carcinoma,-1,2	SIRPG	61	2	NM_001039508	exon2	c.G222A	p.R74R	TAATTCCCGGCCT	.	PASS	Atlas-SNP
SLC5A9	200010	hgsc.bcm.edu	37	1	48708250	48708250	+	Missense_Mutation	SNP	C	C	T	rs78427303	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85	50	93	0	0.588235	0	C|0.939;T|0.061	0.061	strong	.	SLC5A9	82	.	NM_001135181	exon14	c.C1874T	p.A625V	GTGGAGCGGCAGA	.	PASS	Atlas-SNP
ATP8B2	57198	hgsc.bcm.edu	37	1	154303976	154303976	+	Silent	SNP	T	T	C	rs6702754	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79	37	86	0	0.468354	0	T|0.700;C|0.300	0.300	strong	.	ATP8B2	158	.	NM_020452	exon6	c.T459C	p.N153N	GATCAATGGAATG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195506159	195506159	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	26	19	80	0	0.730769	0	.	.	none	.	MUC4	1505	.	NM_018406	exon2	c.C12292G	p.P4098A	TGAGAGGAAGAGG	.	PASS	Atlas-SNP
C3orf52	79669	hgsc.bcm.edu	37	3	111821747	111821747	+	Missense_Mutation	SNP	A	A	G	rs16859190	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	151	71	132	0	0.470199	0	A|0.895;G|0.105	0.105	strong	.	C3orf52	28	.	NM_001171747	exon3	c.A331G	p.I111V	TTCTTCATCATGC	.	PASS	Atlas-SNP
PLEKHH1	57475	hgsc.bcm.edu	37	14	68024134	68024134	+	Missense_Mutation	SNP	A	A	T	rs3825723	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	29	13	30	0	0.448276	0	A|0.828;T|0.172	0.172	strong	.	PLEKHH1	118	.	NM_020715	exon4	c.A338T	p.Q113L	AGAAGCAGGTAAG	.	PASS	Atlas-SNP
ELMOD3	84173	hgsc.bcm.edu	37	2	85617913	85617913	+	Missense_Mutation	SNP	G	G	T	rs17850709	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68	46	117	0	0.676471	0	G|0.962;T|0.038	0.038	strong	ELMOD3_ENST00000409890,NS,carcinoma,0,1	ELMOD3	53	1	NM_001135022	exon14	c.G974T	p.R325L	GCCCACGGCGGCT	.	PASS	Atlas-SNP
COL18A1	80781	hgsc.bcm.edu	37	21	46876083	46876083	+	Silent	SNP	A	A	G	rs2236451	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	109	39	67	0	0.357798	0	A|0.628;G|0.372	0.372	strong	.	COL18A1	129	.	NM_030582	exon1	c.A639G	p.P213P	ACCACCATCTTCA	.	PASS	Atlas-SNP
ELN	2006	hgsc.bcm.edu	37	7	73470714	73470714	+	Missense_Mutation	SNP	G	G	A	rs2071307	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	129	74	161	0	0.573643	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
WDR43	23160	hgsc.bcm.edu	37	2	29135468	29135468	+	Silent	SNP	C	C	G	rs6715296	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	220	116	194	0	0.527273	0	C|0.293;G|0.707	0.707	strong	.	WDR43	38	.	NM_015131	exon4	c.C498G	p.G166G	GAAAGGCGACAAT	.	PASS	Atlas-SNP
CCDC94	55702	hgsc.bcm.edu	37	19	4251069	4251069	+	Silent	SNP	T	T	C	rs1045750	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98	42	133	0	0.428571	0	T|0.563;C|0.437	0.437	strong	CCDC94,NS,carcinoma,0,1	CCDC94	28	1	NM_018074	exon3	c.T171C	p.N57N	ATTCAATGCTCGG	.	PASS	Atlas-SNP
OTUD3	23252	hgsc.bcm.edu	37	1	20233086	20233086	+	Missense_Mutation	SNP	G	G	A	rs10916668	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	106	58	91	0	0.54717	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
SYNPO2L	79933	hgsc.bcm.edu	37	10	75407290	75407290	+	Missense_Mutation	SNP	G	G	A	rs3812629	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	45	22	26	0	0.488889	0	G|0.841;A|0.159	0.159	strong	SYNPO2L_ENST00000394810,brain,glioma,0,4	SYNPO2L	118	4	NM_001114133	exon4	c.C2120T	p.P707L	ATTGGAGGGGGGG	.	PASS	Atlas-SNP
NLRC5	84166	hgsc.bcm.edu	37	16	57101373	57101373	+	Missense_Mutation	SNP	A	A	G	rs7185320	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	150	78	151	0	0.52	0	A|0.917;G|0.083	0.083	strong	.	NLRC5	186	.	NM_032206	exon34	c.A4397G	p.Q1466R	GGCTGCAGCAGCT	.	PASS	Atlas-SNP
FAM71F2	346653	hgsc.bcm.edu	37	7	128315791	128315791	+	Silent	SNP	C	C	G	rs61738927	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	43	18	42	0	0.418605	0	C|0.679;G|0.321	0.321	strong	.	FAM71F2	19	.	NM_001012454	exon2	c.C243G	p.V81V	CGGGGTCACCTCC	.	PASS	Atlas-SNP
CEP120	153241	hgsc.bcm.edu	37	5	122727026	122727026	+	Silent	SNP	G	G	A	rs6876883	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	43	100	0	0.530864	0	G|0.531;A|0.469	0.469	strong	.	CEP120	72	.	NM_153223	exon8	c.C816T	p.H272H	GCAGAGGTGAATC	.	PASS	Atlas-SNP
SPTA1	6708	hgsc.bcm.edu	37	1	158592935	158592935	+	Silent	SNP	G	G	A	rs3753068	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	209	107	187	0	0.511962	0	G|0.680;A|0.320	0.320	strong	SPTA1,mouth,carcinoma,0,1	SPTA1	720	1	NM_003126	exon43	c.C5958T	p.P1986P	GATCTCGGGAAGT	.	PASS	Atlas-SNP
EGF	1950	hgsc.bcm.edu	37	4	110882051	110882051	+	Silent	SNP	T	T	C	rs11568937	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	159	67	208	0	0.421384	0	T|0.978;C|0.022	0.022	strong	.	EGF	113	.	NM_001963	exon7	c.T1095C	p.H365H	GAATCATGGCTGT	.	PASS	Atlas-SNP
TPRX1	284355	hgsc.bcm.edu	37	19	48305357	48305357	+	Missense_Mutation	SNP	G	G	A	rs77144450	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	36	18	47	0	0.5	0	G|0.965;A|0.035	0.035	strong	.	TPRX1	46	.	NM_198479	exon2	c.C911T	p.P304L	AAAATCGGGGCTA	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	65	30	66	0	0.461538	0	T|0.391;C|0.609	0.609	strong	.	UPK1A	23	.	NM_007000	exon7	c.T770C	p.M257T	ACACCATGCTCTG	.	PASS	Atlas-SNP
WNK1	65125	hgsc.bcm.edu	37	12	993930	993930	+	Silent	SNP	C	C	T	rs7300444	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	193	192	223	0	0.994819	0	C|0.597;T|0.403	0.403	strong	.	WNK1	403	.	NM_001184985	exon19	c.C4740T	p.N1580N	ACCCAACACAGCA	.	PASS	Atlas-SNP
TMCO6	55374	hgsc.bcm.edu	37	5	140021482	140021482	+	Silent	SNP	C	C	T	rs11554680	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	105	47	113	0	0.447619	0	C|0.757;T|0.243	0.243	strong	TMCO6,NS,carcinoma,+1,1	TMCO6	30	1	NM_018502	exon4	c.C342T	p.V114V	CCTGGTCGGGCTC	.	PASS	Atlas-SNP
MEF2D	4209	hgsc.bcm.edu	37	1	156450740	156450740	+	Silent	SNP	G	G	A	rs1925950	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110	109	103	0	0.990909	0	G|0.452;A|0.548	0.548	strong	.	MEF2D	43	.	NM_005920	exon4	c.C282T	p.N94N	GCAGCCGTTGAAG	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	65	30	70	0	0.461538	0	C|0.912;G|0.088	0.088	strong	.	TMF1	77	.	NM_007114	exon10	c.G2392C	p.D798H	GCCTATCAGAAAG	.	PASS	Atlas-SNP
CENPI	2491	hgsc.bcm.edu	37	X	100395663	100395663	+	Silent	SNP	G	G	T	rs2273380	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	134	39	100	0	0.291045	0	G|0.697;0|0.002	.	strong	.	CENPI	70	.	NM_006733	exon15	c.G1479T	p.V493V	TAGTGTGCTTCAG	.	PASS	Atlas-SNP
ESR1	2099	hgsc.bcm.edu	37	6	152129077	152129077	+	Silent	SNP	T	T	C	rs2077647	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	63	88	0	1	0	T|0.538;C|0.462	0.462	strong	.	ESR1	94	.	NM_000125	exon1	c.T30C	p.S10S	AGCATCTGGGATG	.	PASS	Atlas-SNP
PXK	54899	hgsc.bcm.edu	37	3	58395863	58395863	+	Missense_Mutation	SNP	A	A	G	rs56384862	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	32	59	0	0.592593	0	A|0.717;G|0.283	0.283	strong	PXK_ENST00000356151,NS,carcinoma,0,1	PXK	89	1	NM_017771	exon16	c.A1442G	p.K481R	CAGCGAAGTACAG	.	PASS	Atlas-SNP
ZNF385C	201181	hgsc.bcm.edu	37	17	40189830	40189830	+	Silent	SNP	C	C	T	rs60110245	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	42	75	0	0.56	0	C|0.898;T|0.102	0.102	strong	.	ZNF385C	7	.	NM_001242704	exon2	c.G87A	p.P29P	GTCCAGCGGGGGC	.	PASS	Atlas-SNP
RPP38	10557	hgsc.bcm.edu	37	10	15145948	15145948	+	Missense_Mutation	SNP	T	T	C	rs10242	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	28	72	0	0.538462	0	T|0.978;C|0.022	0.022	strong	.	RPP38	26	.	NM_001265601	exon2	c.T635C	p.I212T	ACAGAATTGAAGA	.	PASS	Atlas-SNP
RYR1	6261	hgsc.bcm.edu	37	19	38994910	38994910	+	Silent	SNP	G	G	A	rs2229144	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	113	55	111	0	0.486726	0	G|0.657;A|0.343	0.343	strong	RYR1,NS,carcinoma,0,1	RYR1	708	1	NM_001042723	exon50	c.G7977A	p.T2659T	ACCCACGGGCTGG	.	PASS	Atlas-SNP
NLRP12	91662	hgsc.bcm.edu	37	19	54313944	54313944	+	Missense_Mutation	SNP	A	A	C	rs142063194	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51	27	51	0	0.529412	0	A|0.991;C|0.009	0.009	strong	.	NLRP12	236	.	NM_144687	exon3	c.C969G	p.S323R	GTTAAGAAGCAGC	.	PASS	Atlas-SNP
ADAMTS4	9507	hgsc.bcm.edu	37	1	161168189	161168189	+	Missense_Mutation	SNP	C	C	T	rs34448954	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83	36	63	0	0.433735	0	C|0.946;T|0.054	0.054	strong	ADAMTS4_ENST00000367996,rectum,carcinoma,0,2	ADAMTS4	171	2	NM_005099	exon1	c.G229A	p.A77T	CAGGGGCGCCCGA	.	PASS	Atlas-SNP
LY6D	8581	hgsc.bcm.edu	37	8	143867905	143867905	+	Missense_Mutation	SNP	C	C	T	rs2572925	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	117	60	111	0	0.512821	0	C|0.637;T|0.363	0.363	strong	.	LY6D	10	.	NM_003695	exon1	c.G28A	p.A10T	CCAGGGCTGCAAG	.	PASS	Atlas-SNP
CCDC13	152206	hgsc.bcm.edu	37	3	42787469	42787469	+	Silent	SNP	A	A	G	rs2240859	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55	26	61	0	0.472727	0	A|0.512;G|0.488	0.488	strong	.	CCDC13	71	.	NM_144719	exon7	c.T771C	p.S257S	TGGCGAAGATAGG	.	PASS	Atlas-SNP
RSPH4A	345895	hgsc.bcm.edu	37	6	116938232	116938232	+	Missense_Mutation	SNP	C	C	G	rs13213314	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	156	60	146	0	0.384615	0	C|0.925;G|0.075	0.075	strong	.	RSPH4A	54	.	NM_001161664	exon1	c.C446G	p.T149S	GAAACACCTTTCA	.	PASS	Atlas-SNP
GALR3	8484	hgsc.bcm.edu	37	22	38221141	38221141	+	Silent	SNP	C	C	T	rs117618411	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	27	13	47	0	0.481481	0	C|0.975;T|0.025	0.025	strong	.	GALR3	12	.	NM_003614	exon2	c.C771T	p.C257C	CCTGTGCTTCTGG	.	PASS	Atlas-SNP
SNRNP70	6625	hgsc.bcm.edu	37	19	49611319	49611319	+	Silent	SNP	C	C	T	rs1058882	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	5	5	4	0	1	0	C|0.830;T|0.170	0.170	strong	SNRNP70,NS,carcinoma,0,1	SNRNP70	30	1	NM_003089	exon10	c.C933T	p.G311G	GCGTGGCGGCGGT	.	PASS	Atlas-SNP
CCNG2	901	hgsc.bcm.edu	37	4	78079772	78079772	+	Silent	SNP	G	G	A	rs4150052	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	88	38	104	0	0.431818	0	G|0.914;A|0.086	0.086	strong	.	CCNG2	27	.	NM_004354	exon2	c.G87A	p.E29E	AGAAGAGAGATTC	.	PASS	Atlas-SNP
NKX2-6	137814	hgsc.bcm.edu	37	8	23563908	23563908	+	Silent	SNP	A	A	G	rs61732911	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55	22	54	0	0.4	0	A|0.816;G|0.184	0.184	strong	.	NKX2-6	6	.	NM_001136271	exon1	c.T204C	p.D68D	CGAACCATCCAGC	.	PASS	Atlas-SNP
SNX18	112574	hgsc.bcm.edu	37	5	53815240	53815240	+	Silent	SNP	G	G	C	rs61739378	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	42	12	51	0	0.285714	0	G|0.741;C|0.259	0.259	strong	SNX18,NS,carcinoma,0,1	SNX18	102	1	NM_052870	exon1	c.G1458C	p.S486S	CTTCTCGGTGGGC	.	PASS	Atlas-SNP
PHYHD1	254295	hgsc.bcm.edu	37	9	131689361	131689361	+	Silent	SNP	G	G	A	rs751340	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	146	71	148	0	0.486301	0	G|0.615;A|0.385	0.385	strong	PHYHD1,caecum,carcinoma,+1,2	PHYHD1	29	2	NM_001100877	exon2	c.G78A	p.A26A	GTCTGCGGAAGAG	.	PASS	Atlas-SNP
C1orf127	148345	hgsc.bcm.edu	37	1	11008341	11008341	+	Silent	SNP	G	G	A	rs10864483	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57	27	55	0	0.473684	0	G|0.844;A|0.156	0.156	strong	.	C1orf127	134	.	NM_001170754	exon12	c.C1851T	p.C617C	TCCAGAGCACGTT	.	PASS	Atlas-SNP
TLR8	51311	hgsc.bcm.edu	37	X	12939412	12939412	+	Silent	SNP	C	C	A	rs3747414	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	51	73	0	0.68	0	0|0.006;A|0.430	0.430	strong	.	TLR8	134	.	NM_138636	exon2	c.C2253A	p.I751I	AACAATCAACAAA	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	45	89	0	0.703125	0	A|0.708;G|0.292	0.292	strong	.	NAT8	26	.	NM_003960	exon2	c.T428C	p.F143S	TCCACAAAGAGAT	.	PASS	Atlas-SNP
COL16A1	1307	hgsc.bcm.edu	37	1	32138045	32138045	+	Missense_Mutation	SNP	G	G	A	rs2228553	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	33	69	0	0.5	0	G|0.990;A|0.010	0.010	strong	.	COL16A1	137	.	NM_001856	exon47	c.C3077T	p.P1026L	AATCCCGGAGGAC	.	PASS	Atlas-SNP
MECOM	2122	hgsc.bcm.edu	37	3	168810874	168810874	+	Silent	SNP	C	C	T	rs17466625	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98	39	101	0	0.397959	0	C|0.871;T|0.129	0.129	strong	.	MECOM	216	.	NM_004991	exon14	c.G3036A	p.S1012S	ATGAGGCGACGAT	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1104123	1104123	+	Silent	SNP	C	C	T	rs12270802	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	90	49	114	0	0.544444	0	C|0.894;T|0.106	0.106	strong	MUC2_ENST00000441003,NS,lymphoid_neoplasm,0,1	MUC2	614	1	NM_002457	exon50	c.C8302T	p.L2768L	GTGGTCCTGAGCT	.	PASS	Atlas-SNP
ABCG8	64241	hgsc.bcm.edu	37	2	44102302	44102302	+	Silent	SNP	G	G	A	rs145756111	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98	44	76	0	0.44898	0	G|0.995;A|0.005	0.005	strong	ABCG8,NS,carcinoma,0,2	ABCG8	98	2	NM_022437	exon11	c.G1506A	p.P502P	GCTTCCGGAGCAC	.	PASS	Atlas-SNP
PLXNB3	5365	hgsc.bcm.edu	37	X	153042419	153042419	+	Silent	SNP	G	G	A	rs34966902	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	84	78	0	0.976744	0	G|0.439;A|0.561	0.561	strong	.	PLXNB3	208	.	NM_001163257	exon30	c.G4980A	p.R1660R	CCAGAGGTGCCCC	.	PASS	Atlas-SNP
BCKDK	10295	hgsc.bcm.edu	37	16	31121793	31121793	+	Silent	SNP	G	G	A	rs14235	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98	44	89	0	0.44898	0	G|0.642;A|0.358	0.358	strong	BCKDK_ENST00000394951,rectum,carcinoma,0,2	BCKDK	52	2	NM_005881	exon7	c.G615A	p.T205T	GGCCACGCATCAC	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	63	66	0	0.984375	0	A|0.304;N|0.003	0.304	strong	.	GRHL3	69	.	NM_198174	exon16	c.T1784A	p.M595K	GGAACATGGGTTT	.	PASS	Atlas-SNP
CD276	80381	hgsc.bcm.edu	37	15	73994806	73994806	+	Missense_Mutation	SNP	C	C	T	rs7173448	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	99	51	129	0	0.515152	0	C|0.813;T|0.187	0.187	strong	.	CD276	29	.	NM_025240	exon3	c.C290T	p.P97L	TCTTCCCGGACCT	.	PASS	Atlas-SNP
RNF213	57674	hgsc.bcm.edu	37	17	78319136	78319136	+	Missense_Mutation	SNP	G	G	A	rs9674961	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	114	113	118	0	0.991228	0	G|0.368;A|0.632	0.632	strong	RNF213_ENST00000411702,colon,carcinoma,0,6	RNF213	766	6	NM_001256071	exon29	c.G7001A	p.S2334N	CCATCAGTCACTT	.	PASS	Atlas-SNP
OR4M1	441670	hgsc.bcm.edu	37	14	20248828	20248828	+	Missense_Mutation	SNP	C	C	T	rs2635535	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	538	104	464	0	0.193309	0	C|0.736;T|0.264	0.264	strong	.	OR4M1	104	.	NM_001005500	exon1	c.C347T	p.T116I	TGCTCACAGTGAT	.	PASS	Atlas-SNP
ZNF417	147687	hgsc.bcm.edu	37	19	58420416	58420416	+	Silent	SNP	G	G	A	rs150518835	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80	25	79	0	0.3125	0	G|0.984;A|0.016	0.016	strong	.	ZNF417	44	.	NM_152475	exon3	c.C1230T	p.C410C	TTCCTTGCACTCA	.	PASS	Atlas-SNP
FAM71F1	84691	hgsc.bcm.edu	37	7	128363287	128363287	+	Missense_Mutation	SNP	G	G	A	rs6971091	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44	18	64	0	0.409091	0	G|0.836;A|0.164	0.164	strong	.	FAM71F1	42	.	NM_032599	exon4	c.G724A	p.E242K	CCCAGCGAGAGTC	.	PASS	Atlas-SNP
GLYATL1	92292	hgsc.bcm.edu	37	11	58722296	58722296	+	Silent	SNP	A	A	G	rs140293060	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	194	91	175	0	0.469072	0	A|0.997;G|0.003	0.003	strong	.	GLYATL1	89	.	NM_080661	exon5	c.A333G	p.K111K	CTCCAAAGAGCCT	.	PASS	Atlas-SNP
OR10AD1	121275	hgsc.bcm.edu	37	12	48597053	48597053	+	Missense_Mutation	SNP	A	A	G	rs17122812	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	38	18	33	0	0.473684	0	A|0.830;G|0.170	0.170	strong	OR10AD1,NS,carcinoma,0,1	OR10AD1	24	1	NM_001004134	exon1	c.T23C	p.V8A	TCCGTCACTATGC	.	PASS	Atlas-SNP
TMC2	117532	hgsc.bcm.edu	37	20	2539387	2539387	+	Missense_Mutation	SNP	G	G	A	rs6050063	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	42	77	0	0.518519	0	G|0.349;A|0.651	0.651	strong	.	TMC2	121	.	NM_080751	exon3	c.G368A	p.R123K	CGAGGAGGGAGGA	.	PASS	Atlas-SNP
FAM208A	23272	hgsc.bcm.edu	37	3	56667896	56667896	+	Missense_Mutation	SNP	G	G	T	rs200904014	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	36	97	0	0.537313	0	G|0.999;T|0.001	0.001	strong	.	FAM208A	113	.	NM_001112736	exon18	c.C2923A	p.Q975K	GAAACTGGTAATC	.	PASS	Atlas-SNP
DMP1	1758	hgsc.bcm.edu	37	4	88584160	88584160	+	Silent	SNP	G	G	A	rs2615497	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	99	52	100	0	0.525253	0	G|0.715;A|0.285	0.285	strong	DMP1,caecum,carcinoma,0,1	DMP1	72	1	NM_004407	exon6	c.G1230A	p.E410E	CAGTGAGAGCCTC	.	PASS	Atlas-SNP
OR2L3	391192	hgsc.bcm.edu	37	1	248224754	248224754	+	Silent	SNP	T	T	C	rs76341604		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	165	91	189	0	0.551515	0	.	.	weak	.	OR2L3	97	.	NM_001004687	exon1	c.T771C	p.T257T	CTACACTTATCTA	.	PASS	Atlas-SNP
SIGLEC10	89790	hgsc.bcm.edu	37	19	51917735	51917735	+	Silent	SNP	G	G	A	rs1974821	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73	31	93	1	0.424658	0.0107527	G|0.795;A|0.205	0.205	strong	SIGLEC12_ENST00000439889,NS,carcinoma,0,2	SIGLEC10	112	2	NM_033130	exon9	c.C1650T	p.N550N	CGCTCCGTTGGAG	.	scavenged	Atlas-SNP
ZNF763	284390	hgsc.bcm.edu	37	19	12087921	12087921	+	Silent	SNP	G	G	C	rs376310072	alternate_allele	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	96	9	137	1	0.09375	0.00729927	.	.	alt	ZNF763,NS,carcinoma,+1,2	ZNF763	31	2	NM_001012753	exon2	c.G81C	p.S27S	TATTTCGCAGAGG	.	scavenged	Atlas-SNP
KIAA0947	23379	hgsc.bcm.edu	37	5	5441314	5441314	+	Missense_Mutation	SNP	A	A	G	rs72646675	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	203	93	201	0	0.458128	0	A|0.999;G|0.001	0.001	strong	.	KIAA0947	301	.	NM_015325	exon5	c.A287G	p.K96R	CTTTAAAAGCAGA	.	PASS	Atlas-SNP
ADAM15	8751	hgsc.bcm.edu	37	1	155026871	155026871	+	Silent	SNP	G	G	T	rs11548311	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	27	112	0	0.355263	0	G|0.889;T|0.111	0.111	strong	ADAM15,NS,carcinoma,0,1	ADAM15	92	1	NM_001261464	exon6	c.G531T	p.S177S	TATTTCGCGAATC	.	PASS	Atlas-SNP
OR2L3	391192	hgsc.bcm.edu	37	1	248224578	248224578	+	Missense_Mutation	SNP	T	T	C	rs60743763	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	228	12	357	0	0.0526316	0	T|0.933;C|0.067	0.067	strong	OR2L3,NS,carcinoma,-1,1	OR2L3	97	1	NM_001004687	exon1	c.T595C	p.F199L	ACAGTGTTTTTGA	.	scavenged	Atlas-SNP
COL6A1	1291	hgsc.bcm.edu	37	21	47423389	47423389	+	Missense_Mutation	SNP	G	G	A	rs1053312	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	12	8	22	0	0.666667	0	G|0.703;A|0.297	0.297	strong	.	COL6A1	101	.	NM_001848	exon35	c.G2549A	p.R850H	CCAAGCGCTTCGC	.	PASS	Atlas-SNP
BARX1	56033	hgsc.bcm.edu	37	9	96714491	96714491	+	Silent	SNP	C	C	G	rs11793856	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	31	18	49	0	0.580645	0	C|0.773;G|0.227	0.227	strong	.	BARX1	9	.	NM_021570	exon4	c.G720C	p.P240P	CTCCGCCGGTTTC	.	PASS	Atlas-SNP
ZNF577	84765	hgsc.bcm.edu	37	19	52376507	52376507	+	Missense_Mutation	SNP	T	T	C	rs2288868	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	78	37	64	0	0.474359	0	T|0.520;C|0.480	0.480	strong	.	ZNF577	63	.	NM_032679	exon7	c.A736G	p.K246E	CGCATTTGCTGCA	.	PASS	Atlas-SNP
TSC22D1	8848	hgsc.bcm.edu	37	13	45149973	45149973	+	Missense_Mutation	SNP	G	G	A	rs140514784	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	202	151	128	0	0.747525	0	G|0.999;A|0.001	0.001	strong	.	TSC22D1	88	.	NM_183422	exon1	c.C238T	p.P80S	GAGGCGGAGGCTG	.	PASS	Atlas-SNP
IGSF22	283284	hgsc.bcm.edu	37	11	18728650	18728650	+	Missense_Mutation	SNP	T	T	C	rs2289965	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	37	16	56	0	0.432432	0	T|0.800;C|0.200	0.200	strong	.	IGSF22	211	.	NM_173588	exon21	c.A3391G	p.I1131V	TGATGATGTAGTG	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	45	25	30	0	0.555556	0	A|0.700;G|0.300	0.300	strong	.	TCHP	45	.	NM_001143852	exon3	c.A380G	p.K127R	CAGCCAAAGAAGA	.	PASS	Atlas-SNP
FCHO1	23149	hgsc.bcm.edu	37	19	17886940	17886940	+	Silent	SNP	G	G	A	rs2287854	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44	18	46	0	0.409091	0	G|0.500;A|0.500	0.500	strong	.	FCHO1	69	.	NM_001161358	exon15	c.G1152A	p.A384A	CACCGCGGGCAGC	.	PASS	Atlas-SNP
RBMXL2	27288	hgsc.bcm.edu	37	11	7110363	7110363	+	Silent	SNP	G	G	A	rs4758158	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	124	65	91	0	0.524194	0	G|0.709;A|0.291	0.291	strong	.	RBMXL2	47	.	NM_014469	exon1	c.G12A	p.A4A	TGAAGCGGATCGC	.	PASS	Atlas-SNP
RABEP1	9135	hgsc.bcm.edu	37	17	5284719	5284719	+	Silent	SNP	T	T	C	rs1065482	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	70	31	71	0	0.442857	0	T|0.500;C|0.500	0.500	strong	.	RABEP1	59	.	NM_004703	exon17	c.T2406C	p.N802N	GAAGAATAAAGCT	.	PASS	Atlas-SNP
LIMK2	3985	hgsc.bcm.edu	37	22	31621792	31621792	+	Missense_Mutation	SNP	G	G	A	rs5997917	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	197	84	183	0	0.426396	0	G|0.774;A|0.226	0.226	strong	.	LIMK2	101	.	NM_005569	exon2	c.G103A	p.G35S	TGGCACGGCTCTT	.	PASS	Atlas-SNP
RSAD1	55316	hgsc.bcm.edu	37	17	48559559	48559559	+	Silent	SNP	A	A	G	rs7210579	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	32	90	0	0.450704	0	A|0.693;G|0.307	0.307	strong	RSAD1,colon,carcinoma,0,1	RSAD1	36	1	NM_018346	exon4	c.A582G	p.V194V	GTCTGTAGACTTG	.	PASS	Atlas-SNP
CTCFL	140690	hgsc.bcm.edu	37	20	56090807	56090807	+	Silent	SNP	A	A	G	rs6025601	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	56	24	65	1	0.428571	0.0153846	A|0.717;G|0.283	0.283	strong	CTCFL,bladder,carcinoma,-2,2	CTCFL	97	2	NM_001269044	exon5	c.T1143C	p.D381D	GTAGGTATCTCTG	.	scavenged	Atlas-SNP
NDST3	9348	hgsc.bcm.edu	37	4	119158345	119158345	+	Silent	SNP	C	C	T	rs138955155	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	89	46	83	0	0.516854	0	C|0.990;T|0.010	0.010	strong	.	NDST3	107	.	NM_004784	exon10	c.C2088T	p.D696D	CATTGACCCTTCA	.	PASS	Atlas-SNP
CCDC168	643677	hgsc.bcm.edu	37	13	103400083	103400083	+	Silent	SNP	G	G	A	rs1026158	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	140	104	208	0	0.742857	0	G|0.544;A|0.456	0.456	strong	.	.	.	.	NM_001146197	exon4	c.C2964T	p.S988S	ATCTGTGCTTTGC	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69	31	67	0	0.449275	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
PCF11	51585	hgsc.bcm.edu	37	11	82875359	82875359	+	Silent	SNP	G	G	A	rs7130527	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	78	11	72	0	0.141026	0	G|0.905;A|0.095	0.095	strong	.	PCF11	220	.	NM_015885	exon4	c.G618A	p.Q206Q	AAGGCAGCAGTTA	.	PASS	Atlas-SNP
TET3	200424	hgsc.bcm.edu	37	2	74320089	74320089	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	144	74	202	0	0.513889	0	.	.	none	.	TET3	101	.	NM_144993	exon6	c.C2695T	p.R899X	TACAAGCGACTGG	.	PASS	Atlas-SNP
MYOM3	127294	hgsc.bcm.edu	37	1	24421950	24421950	+	Missense_Mutation	SNP	C	C	G	rs4319261	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93	49	95	0	0.526882	0	C|0.542;G|0.458	0.458	strong	.	MYOM3	131	.	NM_152372	exon8	c.G772C	p.D258H	CTGAATCGAAGCC	.	PASS	Atlas-SNP
POGK	57645	hgsc.bcm.edu	37	1	166818566	166818566	+	Silent	SNP	A	A	G	rs2075946	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44	23	68	0	0.522727	0	A|0.786;G|0.214	0.214	strong	.	POGK	54	.	NM_017542	exon5	c.A750G	p.A250A	GCGGGCATTCCGA	.	PASS	Atlas-SNP
SMCR8	140775	hgsc.bcm.edu	37	17	18221134	18221134	+	Silent	SNP	C	C	T	rs1563631	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68	31	79	0	0.455882	0	C|0.770;T|0.230	0.230	strong	SMCR8,colon,carcinoma,0,1	SMCR8	62	1	NM_144775	exon1	c.C2031T	p.Y677Y	CAGCTACGTGAGC	.	PASS	Atlas-SNP
GP2	2813	hgsc.bcm.edu	37	16	20335325	20335325	+	Silent	SNP	G	G	A	rs12930599	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	78	37	90	0	0.474359	0	G|0.865;A|0.135	0.135	strong	.	GP2	122	.	NM_001007240	exon3	c.C348T	p.D116D	GGGAGCGTCTGTC	.	PASS	Atlas-SNP
CRMP1	1400	hgsc.bcm.edu	37	4	5830296	5830296	+	Missense_Mutation	SNP	C	C	T	rs34611001	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110	41	132	0	0.372727	0	C|0.984;T|0.016	0.016	strong	.	CRMP1	118	.	NM_001014809	exon12	c.G1723A	p.V575I	TGTTGACGTTGAT	.	PASS	Atlas-SNP
SOGA2	23255	hgsc.bcm.edu	37	18	8825096	8825096	+	Silent	SNP	G	G	A	rs113084211	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	99	34	121	0	0.343434	0	G|0.987;A|0.013	0.013	strong	.	.	.	.	NM_015210	exon15	c.G3588A	p.P1196P	CAGCCCGCCTGCC	.	PASS	Atlas-SNP
AGAP6	414189	hgsc.bcm.edu	37	10	51769058	51769058	+	Silent	SNP	G	G	A	rs200123722	byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	112	40	156	0	0.357143	0	G|0.985;A|0.015	0.015	strong	AGAP6,NS,carcinoma,+1,1	AGAP6	53	1	NM_001077665	exon8	c.G1173A	p.P391P	CAACCCGCCCCCC	.	scavenged	Atlas-SNP
PINX1	54984	hgsc.bcm.edu	37	8	10623138	10623138	+	Missense_Mutation	SNP	T	T	A	rs1078543	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	23	69	0	0.425926	0	T|0.831;A|0.169	0.169	strong	PINX1,NS,carcinoma,+2,1	PINX1	38	1	NM_017884	exon7	c.A760T	p.S254C	GCGCGCTCTTCTT	.	PASS	Atlas-SNP
OR6B1	135946	hgsc.bcm.edu	37	7	143701884	143701884	+	Silent	SNP	C	C	T	rs728275	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	89	89	112	0	1	0	C|0.586;T|0.414	0.414	strong	.	OR6B1	60	.	NM_001005281	exon1	c.C795T	p.A265A	CCATGCCTTCAAC	.	PASS	Atlas-SNP
HMCN1	83872	hgsc.bcm.edu	37	1	186026474	186026474	+	Missense_Mutation	SNP	T	T	C	rs12129650	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	33	52	0	0.434211	0	C|0.538;N|0.000	0.538	strong	.	HMCN1	797	.	NM_031935	exon46	c.T7253C	p.I2418T	CTTCCATAACCTG	.	PASS	Atlas-SNP
WNT9B	7484	hgsc.bcm.edu	37	17	44953637	44953637	+	Silent	SNP	G	G	A	rs62071993	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	120	60	106	0	0.5	0	G|0.997;A|0.003	0.003	strong	.	WNT9B	37	.	NM_003396	exon4	c.G627A	p.T209T	GACCACGTGTAAG	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	153	97	106	0	0.633987	0	T|0.954;G|0.046	0.046	strong	.	TRAPPC10	109	.	NM_003274	exon14	c.T1899G	p.I633M	CAGCATTGAGAAA	.	PASS	Atlas-SNP
PAPPA	5069	hgsc.bcm.edu	37	9	119158814	119158814	+	Silent	SNP	T	T	C	rs8456	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98	50	116	0	0.510204	0	C|0.669;N|0.001	0.669	strong	.	PAPPA	243	.	NM_002581	exon22	c.T4803C	p.D1601D	CTGTGATCTACAA	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	121	49	135	0	0.404959	0	G|0.764;A|0.236	0.236	strong	.	CFLAR	37	.	NM_001127184	exon6	c.607-1G>A	.	TCTACAGATGATA	.	PASS	Atlas-SNP
PMPCA	23203	hgsc.bcm.edu	37	9	139306467	139306467	+	Silent	SNP	C	C	T	rs10870144	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	305	161	273	0	0.527869	0	C|0.870;T|0.130	0.130	strong	.	PMPCA	29	.	NM_015160	exon2	c.C90T	p.Y30Y	TGCGTACAGACGG	.	PASS	Atlas-SNP
RSPH1	89765	hgsc.bcm.edu	37	21	43905830	43905830	+	Silent	SNP	G	G	A	rs117797631	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	170	76	112	0	0.447059	0	G|0.992;A|0.008	0.008	strong	.	RSPH1	36	.	NM_080860	exon5	c.C450T	p.A150A	GAGCTCGGCCGTG	.	PASS	Atlas-SNP
PM20D1	148811	hgsc.bcm.edu	37	1	205817018	205817018	+	Missense_Mutation	SNP	T	T	C	rs201477375	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	324	134	358	0	0.41358	0	.	.	weak	.	PM20D1	56	.	NM_152491	exon2	c.A251G	p.H84R	CCTTTATGAATGT	.	PASS	Atlas-SNP
LCP1	3936	hgsc.bcm.edu	37	13	46705068	46705068	+	Silent	SNP	C	C	A	rs11558762	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	145	83	108	0	0.572414	0	T|0.011;G|0.182	.	strong	.	LCP1	69	.	NM_002298	exon15	c.G1632T	p.P544P	AATCTTCGGGTCC	.	PASS	Atlas-SNP
FCGR3A	2214	hgsc.bcm.edu	37	1	161518286	161518286	+	Missense_Mutation	SNP	C	C	T	rs428888	bycluster;byfrequency;by2hit2allele	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	359	37	497	0	0.103064	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
USP42	84132	hgsc.bcm.edu	37	7	6194379	6194379	+	Missense_Mutation	SNP	G	G	C	rs112550268	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	28	20	28	0	0.714286	0	G|0.992;C|0.008	0.008	strong	.	USP42	138	.	NM_032172	exon15	c.G3194C	p.R1065T	ATGACAGGTACGC	.	PASS	Atlas-SNP
HSPA2	3306	hgsc.bcm.edu	37	14	65008251	65008251	+	Silent	SNP	C	C	T	rs1063391	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	71	50	0	1	0	C|0.368;T|0.632	0.632	strong	HSPA2,right_upper_lobe,carcinoma,+1,1	HSPA2	83	1	NM_021979	exon1	c.C684T	p.D228D	CGGCGACACCCAC	.	PASS	Atlas-SNP
SLC5A12	159963	hgsc.bcm.edu	37	11	26692733	26692733	+	Silent	SNP	T	T	C	rs7114378	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	180	86	161	0	0.477778	0	T|0.681;C|0.319	0.319	strong	.	SLC5A12	134	.	NM_178498	exon15	c.A1773G	p.R591R	TTCTCTTCTGAGT	.	PASS	Atlas-SNP
TUBD1	51174	hgsc.bcm.edu	37	17	57963537	57963537	+	Missense_Mutation	SNP	A	A	G	rs1292053	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	103	103	112	0	1	0	A|0.522;G|0.478	0.478	strong	TUBD1,NS,carcinoma,0,1	TUBD1	38	1	NM_016261	exon3	c.T227C	p.M76T	GACAGCATTTGAT	.	PASS	Atlas-SNP
ZNF521	25925	hgsc.bcm.edu	37	18	22807046	22807046	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	125	2	126	0	0.016	0	.	.	none	ZNF521,bladder,carcinoma,0,1	ZNF521	269	1	NM_015461	exon4	c.C836T	p.A279V	AGGGCCGCTCGGT	.	scavenged	Atlas-SNP
NUBP2	10101	hgsc.bcm.edu	37	16	1838037	1838037	+	Silent	SNP	C	C	G	rs2272977	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	41	20	46	0	0.487805	0	C|0.891;G|0.109	0.109	strong	NUBP2,NS,carcinoma,0,1	NUBP2	25	1	NM_012225	exon5	c.C585G	p.T195T	CTTCACCTGCCCA	.	PASS	Atlas-SNP
FMO2	2327	hgsc.bcm.edu	37	1	171168585	171168585	+	Silent	SNP	A	A	G	rs2020861	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	153	153	150	0	1	0	A|0.536;G|0.464	0.464	strong	FMO2,NS,carcinoma,0,2	FMO2	66	2	NM_001460	exon5	c.A585G	p.S195S	AAACTCAGGCTCA	.	PASS	Atlas-SNP
CSAG1	158511	hgsc.bcm.edu	37	X	151909156	151909156	+	Missense_Mutation	SNP	A	A	G	rs2515848	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	404	285	281	0	0.705446	0	A|0.382;G|0.618	0.618	strong	.	CSAG1	27	.	NM_153478	exon5	c.A185G	p.K62R	AACCCAAAAGGGA	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1092954	1092954	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	36	2	45	0	0.0555556	0	.	.	none	MUC2_ENST00000441003,rectum,carcinoma,0,4	MUC2	614	4	NM_002457	exon30	c.G4773A	p.T1591T	CACTACGGTGACC	.	scavenged	Atlas-SNP
ERI2	112479	hgsc.bcm.edu	37	16	20809283	20809283	+	Silent	SNP	C	C	A	rs11648835	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	157	87	151	0	0.55414	0	C|0.817;A|0.183	0.183	strong	.	ERI2	50	.	NM_001142725	exon9	c.G1839T	p.P613P	ATGGTTCGGTCCA	.	PASS	Atlas-SNP
TENM1	10178	hgsc.bcm.edu	37	X	123540315	123540315	+	Silent	SNP	G	G	T	rs960869	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	23	56	0	0.323944	0	G|0.579;0|0.024	.	strong	.	.	.	.	NM_001163278	exon26	c.C5007A	p.T1669T	TGCATTGGTCAGG	.	PASS	Atlas-SNP
ZFYVE1	53349	hgsc.bcm.edu	37	14	73465003	73465003	+	Silent	SNP	A	A	G	rs997667	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	30	14	47	0	0.466667	0	A|0.678;G|0.322	0.322	strong	.	ZFYVE1	67	.	NM_021260	exon3	c.T504C	p.F168F	TCTAATAAAGTCT	.	PASS	Atlas-SNP
TRPM5	29850	hgsc.bcm.edu	37	11	2438963	2438963	+	Missense_Mutation	SNP	C	C	A	rs34350821	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	119	68	125	0	0.571429	0	C|0.925;A|0.075	0.075	strong	.	TRPM5	86	.	NM_014555	exon7	c.G1003T	p.V335L	CTTTCACCAGCGC	.	PASS	Atlas-SNP
DDX51	317781	hgsc.bcm.edu	37	12	132625960	132625960	+	Silent	SNP	G	G	A	rs34067942	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	17	9	18	0	0.529412	0	G|0.961;A|0.039	0.039	strong	.	DDX51	33	.	NM_175066	exon8	c.C1110T	p.I370I	CTCGTCGATAATC	.	PASS	Atlas-SNP
MSH5	4439	hgsc.bcm.edu	37	6	31727897	31727897	+	Silent	SNP	C	C	T	rs3115672	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	66	67	0	0.868421	0	C|0.923;T|0.077	0.077	strong	MSH5_ENST00000375742,bladder,carcinoma,+1,2	MSH5	108	2	NM_025259	exon19	c.C1767T	p.T589T	CCGAACCTTTGTG	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93	49	108	1	0.526882	0.00925926	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	.	scavenged	Atlas-SNP
FAM184B	27146	hgsc.bcm.edu	37	4	17635336	17635336	+	Missense_Mutation	SNP	G	G	A	rs61741403	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	102	47	116	0	0.460784	0	G|0.979;A|0.021	0.021	strong	.	FAM184B	38	.	NM_015688	exon17	c.C3065T	p.S1022F	TCTGTAGACTGGT	.	PASS	Atlas-SNP
HSPG2	3339	hgsc.bcm.edu	37	1	22179451	22179451	+	Silent	SNP	C	C	T	rs34443576	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	38	87	0	0.59375	0	C|0.965;T|0.035	0.035	strong	.	HSPG2	311	.	NM_005529	exon51	c.G6552A	p.T2184T	GTGCCACGTGACC	.	PASS	Atlas-SNP
CEP78	84131	hgsc.bcm.edu	37	9	80879149	80879149	+	Silent	SNP	C	C	T	rs1057650	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	125	56	120	0	0.448	0	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	.	PASS	Atlas-SNP
ACSM1	116285	hgsc.bcm.edu	37	16	20648702	20648702	+	Silent	SNP	G	G	A	rs151328	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	25	64	0	0.462963	0	G|0.685;A|0.315	0.315	strong	.	ACSM1	118	.	NM_052956	exon8	c.C1188T	p.Y396Y	GACGTCGTAGGGT	.	PASS	Atlas-SNP
METTL25	84190	hgsc.bcm.edu	37	12	82780676	82780676	+	Silent	SNP	A	A	G	rs56337649	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	89	52	69	0	0.58427	0	A|0.969;G|0.031	0.031	strong	.	.	.	.	NM_032230	exon2	c.A354G	p.Q118Q	TGTACAAAACTTG	.	PASS	Atlas-SNP
C1orf210	149466	hgsc.bcm.edu	37	1	43748923	43748923	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	392	16	350	0	0.0408163	0	.	.	none	.	C1orf210	9	.	NM_182517	exon2	c.A19C	p.T7P	ACTCACTTTTGTT	.	PASS	Atlas-SNP
CPXCR1	53336	hgsc.bcm.edu	37	X	88009170	88009170	+	Missense_Mutation	SNP	G	G	C	rs41307393	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	112	35	95	0	0.3125	0	G|0.994;C|0.006	0.006	strong	.	CPXCR1	83	.	NM_001184771	exon3	c.G755C	p.G252A	TAAAAGGTTTTGT	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	111	85	93	0	0.765766	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
ANKRD33	341405	hgsc.bcm.edu	37	12	52284620	52284620	+	Missense_Mutation	SNP	C	C	T	rs117498175	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	29	15	30	0	0.517241	0	C|0.978;T|0.022	0.022	strong	.	ANKRD33	33	.	NM_182608	exon5	c.C890T	p.P297L	TTGCCCCGTCTCC	.	PASS	Atlas-SNP
OR2A12	346525	hgsc.bcm.edu	37	7	143792991	143792991	+	Missense_Mutation	SNP	G	G	A	rs34947817	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	29	114	1	0.391892	0.00877193	G|0.844;A|0.156	0.156	strong	OR2A12,colon,carcinoma,+1,4	OR2A12	56	4	NM_001004135	exon1	c.G791A	p.S264N	AGTCAAGCCATTC	.	scavenged	Atlas-SNP
ITGB2	3689	hgsc.bcm.edu	37	21	46330667	46330667	+	Silent	SNP	G	G	A	rs5030667	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	28	80	0	0.378378	0	G|0.975;A|0.025	0.025	strong	.	ITGB2	107	.	NM_000211	exon2	c.C31T	p.L11L	CCACCAGGGCGAG	.	PASS	Atlas-SNP
DSG4	147409	hgsc.bcm.edu	37	18	28956904	28956904	+	Silent	SNP	C	C	T	rs36101975	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94	43	123	1	0.457447	0.00813008	C|0.858;T|0.142	0.142	strong	DSG4,NS,carcinoma,0,1	DSG4	343	1	NM_001134453	exon1	c.C30T	p.C10C	CATTTGCCTTTTG	.	scavenged	Atlas-SNP
ZKSCAN2	342357	hgsc.bcm.edu	37	16	25268368	25268368	+	Silent	SNP	A	A	G	rs4787310	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94	38	80	0	0.404255	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
DGKH	160851	hgsc.bcm.edu	37	13	42764564	42764564	+	Silent	SNP	C	C	G	rs7324235	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94	27	45	0	0.287234	0	C|0.796;G|0.204	0.204	strong	DGKH,caecum,carcinoma,0,1	DGKH	106	1	NM_001204504	exon17	c.C1938G	p.P646P	TCACCCCTGTGAA	.	PASS	Atlas-SNP
MXRA5	25878	hgsc.bcm.edu	37	X	3238167	3238167	+	Silent	SNP	T	T	G	rs1635245	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	126	126	105	0	1	0	T|0.500;G|0.500	0.500	strong	.	MXRA5	815	.	NM_015419	exon5	c.A5559C	p.P1853P	GATTTGTGGCTTT	.	PASS	Atlas-SNP
CEP44	80817	hgsc.bcm.edu	37	4	175237408	175237408	+	Silent	SNP	T	T	C	rs1553669	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	173	173	208	0	1	0	T|0.287;C|0.713	0.713	strong	CEP44,NS,carcinoma,0,1	CEP44	35	1	NM_001040157	exon10	c.T1053C	p.T351T	CTCTACTGTTAAT	.	PASS	Atlas-SNP
PVRL4	81607	hgsc.bcm.edu	37	1	161049509	161049509	+	Missense_Mutation	SNP	G	G	T	rs35434391	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	12	7	22	0	0.583333	0	G|0.929;T|0.071	0.071	strong	.	PVRL4	48	.	NM_030916	exon2	c.C310A	p.P104T	TGCGTGGGGGCGG	.	PASS	Atlas-SNP
PYGB	5834	hgsc.bcm.edu	37	20	25260931	25260931	+	Silent	SNP	A	A	G	rs2227890	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	146	79	132	0	0.541096	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
SAMM50	25813	hgsc.bcm.edu	37	22	44386281	44386281	+	Silent	SNP	C	C	T	rs7587	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	26	91	0	0.42623	0	T|0.178;G|0.125	0.178	strong	.	SAMM50	30	.	NM_015380	exon14	c.C1359T	p.G453G	GACAGGCGACAGG	.	PASS	Atlas-SNP
BPI	671	hgsc.bcm.edu	37	20	36939052	36939052	+	Silent	SNP	G	G	C	rs5743507	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82	38	86	0	0.463415	0	G|0.928;C|0.072	0.072	strong	BPI,caecum,carcinoma,0,1	BPI	67	1	NM_001725	exon4	c.G546C	p.V182V	CAAAGTGGGGTAT	.	PASS	Atlas-SNP
FAM107A	11170	hgsc.bcm.edu	37	3	58552950	58552950	+	Silent	SNP	C	C	T	rs1139701	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	154	82	146	0	0.532468	0	C|0.964;T|0.036	0.036	strong	.	FAM107A	33	.	NM_001076778	exon3	c.G312A	p.Q104Q	CCTCTGCTGCCGT	.	PASS	Atlas-SNP
KRTAP5-5	439915	hgsc.bcm.edu	37	11	1651643	1651643	+	Silent	SNP	C	C	T	rs4752771	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44	8	55	3	0.181818	0.0545455	C|0.691;T|0.309	0.309	strong	KRTAP5-5,NS,carcinoma,0,1	KRTAP5-5	86	1	NM_001001480	exon1	c.C573T	p.P191P	TAAGCCCTACTGC	.	scavenged	Atlas-SNP
GRM1	2911	hgsc.bcm.edu	37	6	146755560	146755560	+	Silent	SNP	T	T	G	rs1047006	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	37	11	119	0	0.297297	0	T|0.746;G|0.254	0.254	strong	GRM1,colon,carcinoma,0,2	GRM1	419	2	NM_000838	exon9	c.T3213G	p.P1071P	GCCACCTCCGCAG	.	PASS	Atlas-SNP
PIGG	54872	hgsc.bcm.edu	37	4	509850	509850	+	Silent	SNP	T	T	C	rs11726338	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80	27	86	0	0.3375	0	T|0.972;C|0.028	0.028	strong	.	PIGG	86	.	NM_017733	exon6	c.T990C	p.S330S	AGACAGTGTAGGG	.	PASS	Atlas-SNP
EPPK1	83481	hgsc.bcm.edu	37	8	144945535	144945535	+	Silent	SNP	G	G	A	rs73715515	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60	22	62	0	0.366667	0	G|0.977;A|0.023	0.023	strong	.	EPPK1	199	.	NM_031308	exon1	c.C1887T	p.A629A	GCATCGGGCCTCA	.	PASS	Atlas-SNP
F13A1	2162	hgsc.bcm.edu	37	6	6174866	6174866	+	Missense_Mutation	SNP	G	G	A	rs5982	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	264	222	258	0	0.840909	0	G|0.798;A|0.202	0.202	strong	F13A1,NS,malignant_melanoma,-1,2	F13A1	135	2	NM_000129	exon12	c.C1694T	p.P565L	GCCTTCGGGACCC	.	PASS	Atlas-SNP
PFKM	5213	hgsc.bcm.edu	37	12	48527186	48527186	+	Silent	SNP	C	C	T	rs1049392	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	248	123	153	0	0.495968	0	C|0.804;T|0.196	0.196	strong	.	PFKM	117	.	NM_001166686	exon8	c.C729T	p.T243T	TGGCACCGATATG	.	PASS	Atlas-SNP
DOCK10	55619	hgsc.bcm.edu	37	2	225672460	225672460	+	Silent	SNP	G	G	A	rs12328236	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	32	89	0	0.432432	0	G|0.827;A|0.173	0.173	strong	DOCK10,colon,carcinoma,0,1	DOCK10	308	1	NM_014689	exon33	c.C3627T	p.Y1209Y	CATGCCGTACAGG	.	PASS	Atlas-SNP
KRTAP16-1	100505753	hgsc.bcm.edu	37	17	39465449	39465449	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	18	91	0	0.253521	0	.	.	none	.	KRTAP16-1	12	.	NM_001146182	exon1	c.C57T	p.C19C	AGTGGAGCAGAGA	.	PASS	Atlas-SNP
YTHDF1	54915	hgsc.bcm.edu	37	20	61834092	61834092	+	Silent	SNP	G	G	A	rs41282994	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	33	49	0	0.532258	0	G|0.930;A|0.070	0.070	strong	.	YTHDF1	66	.	NM_017798	exon4	c.C1200T	p.D400D	GATGTCGTCCTCA	.	PASS	Atlas-SNP
VOPP1	81552	hgsc.bcm.edu	37	7	55540707	55540707	+	Silent	SNP	G	G	A	rs815957	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	196	186	190	0	0.94898	0	G|0.651;A|0.348	0.348	strong	.	VOPP1	14	.	NM_030796	exon5	c.C360T	p.T120T	TGGGTCGGTGTAA	.	PASS	Atlas-SNP
GJD2	57369	hgsc.bcm.edu	37	15	35045276	35045276	+	Silent	SNP	G	G	A	rs35174018	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	174	85	136	0	0.488506	0	G|0.933;A|0.067	0.067	strong	.	GJD2	49	.	NM_020660	exon2	c.C369T	p.S123S	TCCTATGGACTCA	.	PASS	Atlas-SNP
TMEM17	200728	hgsc.bcm.edu	37	2	62733253	62733253	+	Silent	SNP	C	C	T	rs11676567	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49	48	61	0	0.979592	0	C|0.598;T|0.402	0.402	strong	TMEM17,NS,carcinoma,0,1	TMEM17	19	1	NM_198276	exon1	c.G12A	p.P4P	CGGATCCGGCAGC	.	PASS	Atlas-SNP
MUC6	4588	hgsc.bcm.edu	37	11	1017566	1017566	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	477	20	338	7	0.0419287	0.0207101	.	.	none	MUC6_ENST00000421673,NS,carcinoma,-2,2	MUC6	408	2	NM_005961	exon31	c.C5235T	p.T1745T	TGTAGAGGTTTTG	.	scavenged	Atlas-SNP
RAP1GAP2	23108	hgsc.bcm.edu	37	17	2929392	2929392	+	Silent	SNP	G	G	A	rs55904912	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	204	89	217	0	0.436274	0	G|0.579;A|0.421	0.421	strong	RAP1GAP2_ENST00000254695,NS,carcinoma,0,2	RAP1GAP2	90	2	NM_015085	exon20	c.G1842A	p.P614P	CTCTCCGGAAATC	.	PASS	Atlas-SNP
CLCN6	1185	hgsc.bcm.edu	37	1	11897082	11897082	+	Silent	SNP	C	C	T	rs41275500	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44	20	40	0	0.454545	0	C|0.954;T|0.046	0.046	strong	.	CLCN6	77	.	NM_001286	exon19	c.C2007T	p.G669G	GGCTGGCGAGCAG	.	PASS	Atlas-SNP
ATP13A2	23400	hgsc.bcm.edu	37	1	17314942	17314942	+	Silent	SNP	G	G	A	rs9435662	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	124	69	116	0	0.556452	0	G|0.606;A|0.394	0.394	strong	.	ATP13A2	85	.	NM_022089	exon24	c.C2637T	p.G879G	ATTGGCGCCGTCT	.	PASS	Atlas-SNP
NUCB1	4924	hgsc.bcm.edu	37	19	49407660	49407660	+	Silent	SNP	G	G	A	rs1058483	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	77	32	68	0	0.415584	0	G|0.903;A|0.097	0.097	strong	NUCB1,NS,carcinoma,+1,1	NUCB1	44	1	NM_006184	exon3	c.G192A	p.T64T	GGAGACGGATGGG	.	PASS	Atlas-SNP
ZHX3	23051	hgsc.bcm.edu	37	20	39832628	39832628	+	Missense_Mutation	SNP	T	T	C	rs17265513	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	88	44	88	0	0.5	0	T|0.891;C|0.109	0.109	strong	.	ZHX3	78	.	NM_015035	exon3	c.A929G	p.N310S	GCTGCATTGTACG	.	PASS	Atlas-SNP
TRIM22	10346	hgsc.bcm.edu	37	11	5718517	5718517	+	Missense_Mutation	SNP	G	G	A	rs7935564	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	89	40	75	0	0.449438	0	G|0.528;A|0.472	0.472	strong	.	TRIM22	66	.	NM_001199573	exon3	c.G463A	p.D155N	AAGGAGGATCAAG	.	PASS	Atlas-SNP
TRIM26	7726	hgsc.bcm.edu	37	6	30166266	30166266	+	Silent	SNP	C	C	T	rs2523721	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	47	62	0	0.734375	0	C|0.765;T|0.235	0.235	strong	.	TRIM26	74	.	NM_001242783	exon4	c.G474A	p.R158R	TCTGTCCCTCCTT	.	PASS	Atlas-SNP
KRT14	3861	hgsc.bcm.edu	37	17	39742898	39742898	+	Silent	SNP	G	G	A	rs11551758	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	26	17	23	0	0.653846	0	G|0.461;A|0.539	0.539	strong	KRT14,NS,carcinoma,0,4	KRT14	65	4	NM_000526	exon1	c.C189T	p.C63C	CAGCCCGCAGGCT	.	PASS	Atlas-SNP
RP1L1	94137	hgsc.bcm.edu	37	8	10480679	10480679	+	Silent	SNP	C	C	T	rs80059299	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	50	25	40	0	0.5	0	C|0.987;T|0.013	0.013	strong	.	RP1L1	453	.	NM_178857	exon2	c.G33A	p.P11P	GTGGCTCGGGGCC	.	PASS	Atlas-SNP
MYH4	4622	hgsc.bcm.edu	37	17	10355371	10355371	+	Missense_Mutation	SNP	C	C	T	rs11651295	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85	43	108	0	0.505882	0	C|0.616;T|0.384	0.384	strong	.	MYH4	349	.	NM_017533	exon27	c.G3625A	p.E1209K	TCTGCTCCCCAAG	.	PASS	Atlas-SNP
TMEM132A	54972	hgsc.bcm.edu	37	11	60699230	60699230	+	Silent	SNP	G	G	A	rs2285733	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110	50	105	0	0.454545	0	G|0.973;A|0.027	0.027	strong	.	TMEM132A	135	.	NM_017870	exon6	c.G1089A	p.A363A	CGTAGCGGTCACT	.	PASS	Atlas-SNP
MARCH8	220972	hgsc.bcm.edu	37	10	45953767	45953767	+	Missense_Mutation	SNP	A	A	G	rs7908745	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	33	82	0	0.434211	0	A|0.697;G|0.303	0.303	strong	.	MARCH8	29	.	NM_001002266	exon7	c.T796C	p.Y266H	TTCCATATCCATG	.	PASS	Atlas-SNP
HSPA4	3308	hgsc.bcm.edu	37	5	132437531	132437531	+	Silent	SNP	C	C	T	rs1131809	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	133	133	135	0	1	0	C|0.802;T|0.198	0.198	strong	.	HSPA4	68	.	NM_002154	exon17	c.C2118T	p.I706I	ACAGATCCAACAG	.	PASS	Atlas-SNP
ATP2A3	489	hgsc.bcm.edu	37	17	3844787	3844787	+	Silent	SNP	C	C	G	rs1800912	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80	36	70	0	0.45	0	C|0.787;G|0.213	0.213	strong	ATP2A3,NS,carcinoma,-2,1	ATP2A3	148	1	NM_174956	exon13	c.G1707C	p.A569A	TGGGGGCGCGTCC	.	PASS	Atlas-SNP
SETD6	79918	hgsc.bcm.edu	37	16	58552921	58552921	+	Silent	SNP	G	G	A	rs3607	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	14	14	32	0	1	0	G|0.344;A|0.656	0.656	strong	.	SETD6	27	.	NM_001160305	exon8	c.G1410A	p.E470E	GTTGGAGCTGACA	.	PASS	Atlas-SNP
FCGR2A	2212	hgsc.bcm.edu	37	1	161487863	161487863	+	Silent	SNP	C	C	T	rs143182858	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	226	102	256	1	0.451327	0.00390625	C|0.901;T|0.099	0.099	strong	.	FCGR2A	38	.	NM_001136219	exon7	c.C879T	p.P293P	GAACCCCAGGGCA	.	PASS	Atlas-SNP
KPRP	448834	hgsc.bcm.edu	37	1	152732106	152732106	+	Missense_Mutation	SNP	A	A	T	rs17612167	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	108	60	127	0	0.555556	0	A|0.835;T|0.165	0.165	strong	.	KPRP	152	.	NM_001025231	exon2	c.A42T	p.Q14H	GCTCCAACAGTGC	.	PASS	Atlas-SNP
MED8	112950	hgsc.bcm.edu	37	1	43851797	43851797	+	Silent	SNP	G	G	A	rs11541153	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	29	65	0	0.54717	0	G|0.958;A|0.042	0.042	strong	.	MED8	38	.	NM_201542	exon6	c.C594T	p.G198G	ACTGCTGCCTGAA	.	PASS	Atlas-SNP
CCT6A	908	hgsc.bcm.edu	37	7	56126360	56126360	+	Silent	SNP	T	T	C	rs2230197	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	144	143	210	0	0.993056	0	T|0.335;C|0.665	0.665	strong	.	CCT6A	44	.	NM_001762	exon8	c.T933C	p.V311V	CATAGTTGCTCTG	.	PASS	Atlas-SNP
RAPGEF5	9771	hgsc.bcm.edu	37	7	22202117	22202117	+	Silent	SNP	G	G	A	rs12592	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	45	45	82	0	1	0	G|0.404;A|0.596	0.596	strong	.	RAPGEF5	96	.	NM_012294	exon13	c.C867T	p.D289D	CGGAACGTCTGAG	.	PASS	Atlas-SNP
KBTBD13	390594	hgsc.bcm.edu	37	15	65369395	65369395	+	Missense_Mutation	SNP	C	C	T	rs2919358	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	5	5	3	0	1	0	C|0.451;T|0.549	0.549	strong	.	KBTBD13	9	.	NM_001101362	exon1	c.C242T	p.A81V	TGCAGGCCGTGGA	.	PASS	Atlas-SNP
FAM211A	388341	hgsc.bcm.edu	37	17	16347325	16347325	+	Missense_Mutation	SNP	T	T	C	rs61745139	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	56	24	55	0	0.428571	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
SLCO1C1	53919	hgsc.bcm.edu	37	12	20903757	20903757	+	Silent	SNP	T	T	C	rs10841611	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	120	65	146	0	0.541667	0	T|0.496;C|0.504	0.504	strong	.	SLCO1C1	216	.	NM_001145946	exon15	c.T1947C	p.H649H	ATCTCATTGCTAC	.	PASS	Atlas-SNP
DEAF1	10522	hgsc.bcm.edu	37	11	654043	654043	+	Silent	SNP	G	G	A	rs10902188	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	37	21	29	0	0.567568	0	G|0.911;A|0.089	0.089	strong	.	DEAF1	47	.	NM_021008	exon11	c.C1512T	p.C504C	GTTAACGCAGGAC	.	PASS	Atlas-SNP
MGAT5B	146664	hgsc.bcm.edu	37	17	74928758	74928758	+	Silent	SNP	C	C	T	rs79286496	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	135	73	155	0	0.540741	0	C|0.825;T|0.175	0.175	strong	.	MGAT5B	98	.	NM_198955	exon10	c.C1356T	p.F452F	GGGCTTCGTGTCC	.	PASS	Atlas-SNP
CYP2S1	29785	hgsc.bcm.edu	37	19	41703793	41703793	+	Silent	SNP	G	G	A	rs57266494	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	22	46	0	0.423077	0	G|0.975;A|0.025	0.025	strong	.	CYP2S1	47	.	NM_030622	exon3	c.G453A	p.A151A	CCAGGCGGAGGCC	.	PASS	Atlas-SNP
HLX	3142	hgsc.bcm.edu	37	1	221057662	221057662	+	Silent	SNP	G	G	A	rs3738182	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	135	64	119	0	0.474074	0	G|0.810;A|0.190	0.190	strong	.	HLX	67	.	NM_021958	exon4	c.G1083A	p.E361E	TGGCGAGCAGGAC	.	PASS	Atlas-SNP
SGK1	6446	hgsc.bcm.edu	37	6	134495725	134495725	+	Splice_Site	SNP	C	C	G	rs186450029	by1000genomes;alternate_allele	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	41	11	67	0	0.268293	0	C|1.000;T|0.000	.	alt	SGK1_ENST00000528577,NS,lymphoid_neoplasm,0,4	SGK1	387	4	NM_005627	exon3	c.77-1G>C	.	TGAAAGCTGTGGA	.	PASS	Atlas-SNP
KRT74	121391	hgsc.bcm.edu	37	12	52966428	52966428	+	Missense_Mutation	SNP	G	G	C	rs11170177	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	113	49	109	0	0.433628	0	G|0.933;C|0.067	0.067	strong	.	KRT74	67	.	NM_175053	exon2	c.C495G	p.N165K	AACCTGGTTCTGC	.	PASS	Atlas-SNP
COL2A1	1280	hgsc.bcm.edu	37	12	48376291	48376291	+	Silent	SNP	G	G	A	rs2276454	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	71	87	0	0.959459	0	G|0.590;A|0.410	0.410	strong	.	COL2A1	368	.	NM_001844	exon34	c.C2295T	p.G765G	CCTGTCGCCTTTG	.	PASS	Atlas-SNP
IGSF3	3321	hgsc.bcm.edu	37	1	117158745	117158745	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	263	13	235	1	0.0494297	0.00425532	.	.	none	IGSF3,extremity,malignant_melanoma,0,1	IGSF3	294	1	NM_001542	exon3	c.T378G	p.D126E	TTGCTTATCAGTG	.	scavenged	Atlas-SNP
ZNF7	7553	hgsc.bcm.edu	37	8	146068322	146068322	+	Silent	SNP	C	C	T	rs9004	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51	24	42	0	0.470588	0	C|0.716;T|0.284	0.284	strong	.	ZNF7	62	.	NM_003416	exon5	c.C1830T	p.Y610Y	GTTTTACGAATAT	.	PASS	Atlas-SNP
OTOGL	283310	hgsc.bcm.edu	37	12	80761411	80761411	+	Missense_Mutation	SNP	G	G	T	rs11114416	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	30	69	0	0.483871	0	G|0.827;T|0.173	0.173	strong	C12orf64,NS,carcinoma,-1,1	OTOGL	235	1	NM_173591	exon53	c.G6375T	p.L2125F	GTATTTGGAAGAA	.	PASS	Atlas-SNP
TMEM99	147184	hgsc.bcm.edu	37	17	38991032	38991032	+	Silent	SNP	T	T	A	rs6694	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	179	178	159	0	0.994413	0	T|0.426;A|0.574	0.574	strong	.	TMEM99	21	.	NM_001195386	exon3	c.T264A	p.G88G	TTGCGGTCATCGG	.	PASS	Atlas-SNP
SAPCD2	89958	hgsc.bcm.edu	37	9	139959231	139959231	+	Silent	SNP	G	G	A	rs140919217	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	112	59	114	0	0.526786	0	G|0.995;A|0.005	0.005	strong	.	.	.	.	NM_178448	exon6	c.C1065T	p.T355T	CTTCTCGGTCACC	.	PASS	Atlas-SNP
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32629161	32629161	+	Silent	SNP	A	A	G	rs35457576	byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	45	19	5	5	0.422222	1	A|0.389;G|0.611	0.611	strong	HLA-DQB1,NS,carcinoma,0,1	HLA-DQB1	15	1	NM_002123	exon4	c.T735C	p.L245L	CAGCCCAAGGAAG	.	scavenged	Atlas-SNP
C5orf52	100190949	hgsc.bcm.edu	37	5	157098756	157098756	+	Missense_Mutation	SNP	G	G	T	rs11740603	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	135	71	207	0	0.525926	0	G|0.814;T|0.186	0.186	strong	.	C5orf52	17	.	NM_001145132	exon1	c.G134T	p.R45L	GCCGCCGCCCAGA	.	PASS	Atlas-SNP
CCDC146	57639	hgsc.bcm.edu	37	7	76871113	76871113	+	Silent	SNP	A	A	G	rs17230060	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	242	93	234	0	0.384298	0	A|0.896;G|0.104	0.104	strong	CCDC146,NS,carcinoma,0,1	CCDC146	87	1	NM_020879	exon4	c.A345G	p.A115A	AGAAGCATTCTCC	.	PASS	Atlas-SNP
PLCG2	5336	hgsc.bcm.edu	37	16	81819768	81819768	+	Silent	SNP	T	T	C	rs1143685	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	38	71	0	0.535211	0	T|0.273;C|0.727	0.727	strong	PLCG2_ENST00000359376,NS,carcinoma,+2,2	PLCG2	276	2	NM_002661	exon2	c.T174C	p.A58A	GACCGCTGACAAG	.	PASS	Atlas-SNP
DNAH8	1769	hgsc.bcm.edu	37	6	38746176	38746176	+	Missense_Mutation	SNP	G	G	A	rs61748601	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	41	99	0	0.640625	0	G|0.880;A|0.120	0.120	strong	.	DNAH8	1239	.	NM_001206927	exon14	c.G1975A	p.A659T	ATACAGGCATTTA	.	PASS	Atlas-SNP
SSTR4	6754	hgsc.bcm.edu	37	20	23017082	23017082	+	Missense_Mutation	SNP	T	T	C	rs2567608	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	77	38	102	0	0.493506	0	T|0.474;C|0.526	0.526	strong	SSTR4,colon,carcinoma,0,1	SSTR4	83	1	NM_001052	exon1	c.T962C	p.F321S	GCCGATTCTTCCA	.	PASS	Atlas-SNP
GPR133	283383	hgsc.bcm.edu	37	12	131590404	131590404	+	Silent	SNP	G	G	A	rs4759544	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	14	9	18	0	0.642857	0	G|0.798;A|0.202	0.202	strong	.	GPR133	136	.	NM_198827	exon17	c.G1881A	p.P627P	CGAGCCGGGCACG	.	PASS	Atlas-SNP
DMBT1	1755	hgsc.bcm.edu	37	10	124345721	124345721	+	Silent	SNP	G	G	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93	49	76	0	0.526882	0	.	.	none	.	DMBT1	677	.	NM_007329	exon16	c.G1605T	p.L535L	GCAGCTGGGCTGT	.	PASS	Atlas-SNP
TLE3	7090	hgsc.bcm.edu	37	15	70346923	70346923	+	Silent	SNP	C	C	T	rs2228178	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68	38	69	0	0.558824	0	C|0.629;T|0.371	0.371	strong	TLE3,bladder,carcinoma,-1,1	TLE3	104	1	NM_005078	exon16	c.G1689A	p.S563S	CGTGGGCGAGGCC	.	PASS	Atlas-SNP
MBP	4155	hgsc.bcm.edu	37	18	74701984	74701984	+	Silent	SNP	G	G	A	rs470797	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	81	80	0	1	0	A|0.185;C|0.000;G|0.815;T|0.000	0.185	strong	MBP,colon,carcinoma,0,2	MBP	45	2	NM_001025101	exon5	c.C609T	p.Y203Y	GGAGCCGTAGTGA	.	PASS	Atlas-SNP
ABCC4	10257	hgsc.bcm.edu	37	13	95859035	95859035	+	Missense_Mutation	SNP	C	C	A	rs2274407	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	38	14	35	0	0.368421	0	A|0.118;C|0.882	0.118	strong	.	ABCC4	248	.	NM_005845	exon8	c.G912T	p.K304N	CTCCTTCCTGAAA	.	PASS	Atlas-SNP
VCAN	1462	hgsc.bcm.edu	37	5	82833391	82833391	+	Silent	SNP	A	A	G	rs16900528	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72	30	62	0	0.416667	0	A|0.942;G|0.058	0.058	strong	.	VCAN	498	.	NM_004385	exon8	c.A4569G	p.T1523T	AGTCACAGAGAGA	.	PASS	Atlas-SNP
PDGFA	5154	hgsc.bcm.edu	37	7	552046	552046	+	Silent	SNP	A	A	G	rs1129401	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	151	151	78	0	1	0	A|0.769;G|0.231	0.231	strong	.	PDGFA	34	.	NM_002607	exon3	c.T207C	p.H69H	AGTGGCATGGACC	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	118	46	114	0	0.38983	0	G|0.347;T|0.653	0.653	strong	.	KRTAP10-9	24	.	NM_198690	exon1	c.G837T	p.P279P	CCGCCCGGCCTGC	.	PASS	Atlas-SNP
WNK2	65268	hgsc.bcm.edu	37	9	95993215	95993215	+	Silent	SNP	C	C	T	rs34976687	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79	47	71	0	0.594937	0	C|0.953;T|0.047	0.047	strong	.	WNK2	277	.	NM_006648	exon3	c.C900T	p.S300S	CCGCAGCTGGTGC	.	PASS	Atlas-SNP
OR4L1	122742	hgsc.bcm.edu	37	14	20529043	20529043	+	Silent	SNP	C	C	G	rs1959628	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	99	45	86	0	0.454545	0	C|0.638;G|0.362	0.362	strong	.	OR4L1	98	.	NM_001004717	exon1	c.C840G	p.P280P	CACACCCTTACTG	.	PASS	Atlas-SNP
ARRDC2	27106	hgsc.bcm.edu	37	19	18121454	18121454	+	Silent	SNP	G	G	C	rs147293119	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48	25	34	0	0.520833	0	G|0.998;C|0.002	0.002	strong	.	ARRDC2	60	.	NM_015683	exon7	c.G1086C	p.P362P	GCTTCCGCAGGAC	.	PASS	Atlas-SNP
CCDC27	148870	hgsc.bcm.edu	37	1	3669201	3669201	+	Silent	SNP	A	A	G	rs10797410	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	99	35	123	0	0.353535	0	A|0.502;G|0.498	0.498	strong	.	CCDC27	79	.	NM_152492	exon1	c.A156G	p.P52P	CAGCCCATCTCAG	.	PASS	Atlas-SNP
PCLO	27445	hgsc.bcm.edu	37	7	82785097	82785097	+	Missense_Mutation	SNP	T	T	C	rs61741659	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	147	68	195	0	0.462585	0	T|0.813;C|0.187	0.187	strong	.	PCLO	1506	.	NM_014510	exon2	c.A860G	p.D287G	ACTATGTCTGCCT	.	PASS	Atlas-SNP
C14orf159	80017	hgsc.bcm.edu	37	14	91636532	91636532	+	Missense_Mutation	SNP	C	C	T	rs4900072	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	29	17	33	0	0.586207	0	C|0.773;T|0.227	0.227	strong	.	C14orf159	57	.	NM_001102368	exon5	c.C443T	p.A148V	GCCAGGCGGGTGC	.	PASS	Atlas-SNP
DNLZ	728489	hgsc.bcm.edu	37	9	139256495	139256495	+	Missense_Mutation	SNP	G	G	T	rs3812553	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	33	72	0	0.540984	0	G|0.956;T|0.044	0.044	strong	.	DNLZ	8	.	NM_001080849	exon3	c.C506A	p.P169H	CTGGGGGGACCCT	.	PASS	Atlas-SNP
NCOR1	9611	hgsc.bcm.edu	37	17	15950400	15950400	+	Missense_Mutation	SNP	C	C	T	rs61753149	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	150	70	127	0	0.466667	0	C|0.993;T|0.007	0.007	strong	.	NCOR1	240	.	NM_006311	exon42	c.G6544A	p.A2182T	AGCGGGCATCATT	.	PASS	Atlas-SNP
RNF43	54894	hgsc.bcm.edu	37	17	56492800	56492800	+	Missense_Mutation	SNP	T	T	C	rs3744093	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	58	27	66	0	0.465517	0	T|0.651;C|0.349	0.349	strong	.	RNF43	157	.	NM_017763	exon2	c.A139G	p.I47V	TGATAATAGCTTT	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	145	61	155	0	0.42069	0	A|0.386;G|0.614	0.614	strong	.	ADAMTSL3	290	.	NM_207517	exon6	c.A437G	p.H146R	AGGGGCATTACTA	.	PASS	Atlas-SNP
RSPO3	84870	hgsc.bcm.edu	37	6	127476516	127476516	+	Silent	SNP	G	G	A	rs1892172	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	142	68	131	0	0.478873	0	G|0.455;A|0.545	0.545	strong	RSPO3,rectum,carcinoma,0,1	RSPO3	32	1	NM_032784	exon4	c.G567A	p.L189L	TAACCTGTGTCCC	.	PASS	Atlas-SNP
ALDH3B2	222	hgsc.bcm.edu	37	11	67430698	67430698	+	Silent	SNP	G	G	A	rs3741172	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69	59	63	0	0.855072	0	G|0.917;A|0.083	0.083	strong	.	ALDH3B2	46	.	NM_001031615	exon10	c.C1146T	p.C382C	GAGGGTGCAGCTC	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	164	164	166	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
IGFLR1	79713	hgsc.bcm.edu	37	19	36230767	36230767	+	Missense_Mutation	SNP	A	A	G	rs34562867	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	70	34	53	0	0.485714	0	T|0.000;G|0.091;A|0.909	0.091	strong	.	IGFLR1	28	.	NM_024660	exon4	c.T565C	p.W189R	TGGGCCAGCAGAG	.	PASS	Atlas-SNP
RBMXL1	494115	hgsc.bcm.edu	37	1	89448608	89448608	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	168	10	203	5	0.0595238	0.0246305	.	.	none	CCBL2,caecum,carcinoma,+1,1	.	.	1	NM_001162536	exon3	c.C902T	p.P301L	GATGGCGGGGGCC	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	56	29	51	0	0.517857	0	C|0.836;T|0.164	0.164	strong	.	CCDC27	79	.	NM_152492	exon7	c.C1058T	p.T353M	AGGACACGGGTGC	.	PASS	Atlas-SNP
TTLL3	26140	hgsc.bcm.edu	37	3	9874914	9874914	+	Nonsense_Mutation	SNP	C	C	T	rs115917139	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	37	82	0	0.606557	0	C|0.975;T|0.025	0.025	strong	.	TTLL3	51	.	NM_001025930	exon11	c.C2110T	p.R704X	ACCCAGCGAGGCT	.	PASS	Atlas-SNP
ZNF587B	100293516	hgsc.bcm.edu	37	19	58352806	58352806	+	Missense_Mutation	SNP	T	T	C	rs35313547	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	59	25	57	0	0.423729	0	T|0.866;C|0.134	0.134	strong	.	.	.	.	NM_001204818	exon3	c.T764C	p.V255A	AATATGTTAGCTT	.	PASS	Atlas-SNP
CEACAM19	56971	hgsc.bcm.edu	37	19	45176028	45176028	+	Silent	SNP	C	C	T	rs35695969	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	130	62	144	0	0.476923	0	C|0.959;T|0.041	0.041	strong	.	CEACAM19	27	.	NM_001127893	exon2	c.C216T	p.Y72Y	GACGTACGGAGGC	.	PASS	Atlas-SNP
STH	246744	hgsc.bcm.edu	37	17	44076665	44076665	+	Missense_Mutation	SNP	A	A	G	rs62063857	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	124	123	96	0	0.991935	0	A|0.159;C|0.093	.	strong	STH,rectum,carcinoma,+1,1	STH	14	1	NM_001007532	exon1	c.A20G	p.Q7R	GAGGCCAAGTCTC	.	PASS	Atlas-SNP
ANO3	63982	hgsc.bcm.edu	37	11	26621117	26621117	+	Silent	SNP	A	A	C	rs11604868	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	197	80	232	0	0.406091	0	A|0.835;C|0.165	0.165	strong	.	ANO3	145	.	NM_031418	exon17	c.A1692C	p.A564A	CACTGCAGTGTTT	.	PASS	Atlas-SNP
KIF16B	55614	hgsc.bcm.edu	37	20	16359650	16359650	+	Silent	SNP	C	C	T	rs8116503	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	170	80	208	0	0.470588	0	C|0.793;T|0.207	0.207	strong	.	KIF16B	305	.	NM_001199865	exon19	c.G2997A	p.K999K	CTGCTGCTTCTCT	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	223	126	178	0	0.565022	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
MRPL10	124995	hgsc.bcm.edu	37	17	45904420	45904420	+	Missense_Mutation	SNP	C	C	T	rs11538868	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	118	54	109	0	0.457627	0	C|0.761;T|0.239	0.239	strong	.	MRPL10	24	.	NM_148887	exon4	c.G403A	p.V135I	GGAAGACCTTCAT	.	PASS	Atlas-SNP
ABCC2	1244	hgsc.bcm.edu	37	10	101563815	101563815	+	Missense_Mutation	SNP	G	G	A	rs2273697	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	204	121	145	0	0.593137	0	A|0.183;C|0.005	0.183	strong	ABCC2,NS,adenoma,0,1	ABCC2	160	1	NM_000392	exon10	c.G1249A	p.V417I	TACACCGTTGGAG	.	PASS	Atlas-SNP
GPR149	344758	hgsc.bcm.edu	37	3	154146922	154146922	+	Silent	SNP	A	A	G	rs34792862	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	32	32	59	0	1	0	A|0.841;G|0.159	0.159	strong	.	GPR149	134	.	NM_001038705	exon1	c.T483C	p.S161S	CAGCAGACTGGCT	.	PASS	Atlas-SNP
HCN1	348980	hgsc.bcm.edu	37	5	45396654	45396654	+	Silent	SNP	G	G	A	rs369683016		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	157	43	157	0	0.273885	0	.	.	weak	.	HCN1	298	.	NM_021072	exon4	c.C1170T	p.V390V	ATGGCCGACAAAC	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93	47	101	0	0.505376	0	C|0.780;T|0.220	0.220	strong	.	TMEM173	19	.	NM_198282	exon7	c.G878A	p.R293Q	AGTGTCCGGCAGA	.	PASS	Atlas-SNP
CCDC50	152137	hgsc.bcm.edu	37	3	191093310	191093310	+	Missense_Mutation	SNP	A	A	G	rs4677728	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60	32	72	0	0.533333	0	A|0.502;G|0.498	0.498	strong	.	CCDC50	39	.	NM_178335	exon6	c.A908G	p.K303R	ACAGAAAAAGGAG	.	PASS	Atlas-SNP
WDR55	54853	hgsc.bcm.edu	37	5	140048544	140048544	+	Missense_Mutation	SNP	C	C	T	rs2286394	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	40	79	0	0.540541	0	C|0.806;T|0.194	0.194	strong	.	WDR55	27	.	NM_017706	exon5	c.C629T	p.S210F	CTCAGTCTGGGGA	.	PASS	Atlas-SNP
DPYSL3	1809	hgsc.bcm.edu	37	5	146780273	146780273	+	Silent	SNP	G	G	A	rs10515587	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	122	55	111	1	0.45082	0.00900901	G|0.890;A|0.110	0.110	strong	DPYSL3,NS,carcinoma,-1,1	DPYSL3	58	1	NM_001197294	exon10	c.C1434T	p.V478V	CCAGATGACAGAC	.	scavenged	Atlas-SNP
MXRA5	25878	hgsc.bcm.edu	37	X	3238733	3238733	+	Missense_Mutation	SNP	G	G	A	rs1974522	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	86	94	0	1	0	0|0.015;A|0.441;C|0.000;G|0.544;N|0.000	0.441	strong	.	MXRA5	815	.	NM_015419	exon5	c.C4993T	p.P1665S	ATCTTGGAGTTGT	.	PASS	Atlas-SNP
PSG1	5669	hgsc.bcm.edu	37	19	43383680	43383680	+	Silent	SNP	G	G	T	rs1141653	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	17	10	16	0	0.588235	0	G|0.775;T|0.225	0.225	strong	.	PSG1	196	.	NM_001184826	exon1	c.C54A	p.L18L	GAGCAGGAGCCCC	.	PASS	Atlas-SNP
KIAA1199	57214	hgsc.bcm.edu	37	15	81212521	81212521	+	Silent	SNP	T	T	C	rs2271160	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	84	129	0	1	0	T|0.844;C|0.156	0.156	strong	KIAA1199,NS,carcinoma,0,1	KIAA1199	118	1	NM_018689	exon14	c.T1884C	p.C628C	CCACTGTCTTGGC	.	PASS	Atlas-SNP
ZNF638	27332	hgsc.bcm.edu	37	2	71633275	71633275	+	Silent	SNP	T	T	C	rs3732233	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73	72	100	0	0.986301	0	T|0.560;C|0.440	0.440	strong	.	ZNF638	179	.	NM_014497	exon19	c.T3018C	p.I1006I	TACAATTTATGAT	.	PASS	Atlas-SNP
KCNC4	3749	hgsc.bcm.edu	37	1	110766185	110766185	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	42	110	0	0.518519	0	.	.	none	.	KCNC4	113	.	NM_001039574	exon2	c.C1278T	p.G426G	CATTGGCTTCTGG	.	PASS	Atlas-SNP
C9orf84	158401	hgsc.bcm.edu	37	9	114468966	114468966	+	Missense_Mutation	SNP	A	A	C	rs7036568	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93	46	91	0	0.494624	0	A|0.750;C|0.250	0.250	strong	C9orf84_ENST00000374287,colon,carcinoma,0,2	C9orf84	207	2	NM_173521	exon18	c.T2427G	p.N809K	TGAGAAATTACTC	.	PASS	Atlas-SNP
ADCK4	79934	hgsc.bcm.edu	37	19	41209477	41209477	+	Silent	SNP	C	C	T	rs11538385	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	78	44	91	1	0.564103	0.010989	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
HCLS1	3059	hgsc.bcm.edu	37	3	121351338	121351338	+	Missense_Mutation	SNP	C	C	T	rs2070180	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	35	53	0	0.546875	0	C|0.798;T|0.202	0.202	strong	.	HCLS1	78	.	NM_005335	exon12	c.G1081A	p.E361K	CTGCTTCGTACAC	.	PASS	Atlas-SNP
ST14	6768	hgsc.bcm.edu	37	11	130068491	130068491	+	Silent	SNP	G	G	C	rs11827924	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	168	37	153	0	0.220238	0	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	.	PASS	Atlas-SNP
PABPC3	5042	hgsc.bcm.edu	37	13	25670627	25670627	+	Silent	SNP	A	A	G	rs369126872	alternate_allele	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	151	85	137	0	0.562914	0	.	.	alt	.	PABPC3	129	.	NM_030979	exon1	c.A291G	p.G97G	AAGTGGAGTGGGC	.	PASS	Atlas-SNP
KCNS1	3787	hgsc.bcm.edu	37	20	43723627	43723627	+	Missense_Mutation	SNP	T	T	C	rs734784	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	35	74	0	0.546875	0	T|0.555;C|0.445	0.445	strong	KCNS1,NS,carcinoma,0,1	KCNS1	30	1	NM_002251	exon5	c.A1465G	p.I489V	CATCAATGCTGCT	.	PASS	Atlas-SNP
SPHKAP	80309	hgsc.bcm.edu	37	2	228886457	228886457	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	143	4	127	0	0.027972	0	.	.	none	SPHKAP_ENST00000392056,NS,malignant_melanoma,0,2	SPHKAP	750	2	NM_030623	exon6	c.G667A	p.E223K	TTTCCTCCTCCAA	.	scavenged	Atlas-SNP
SERPINB6	5269	hgsc.bcm.edu	37	6	2955802	2955802	+	Missense_Mutation	SNP	T	T	C	rs2295769	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	51	78	0	0.761194	0	C|0.227;N|0.000	0.227	strong	.	SERPINB6	31	.	NM_001271823	exon3	c.A325G	p.M109V	TGGCCATCCTAAG	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	65	25	66	0	0.384615	0	T|0.785;C|0.215	0.215	strong	.	C1orf85	41	.	NM_001256608	exon4	c.A667G	p.I223V	CTCCAATCAGGGC	.	PASS	Atlas-SNP
RNF43	54894	hgsc.bcm.edu	37	17	56448297	56448297	+	Missense_Mutation	SNP	C	C	T	rs2257205	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	28	64	0	0.424242	0	C|0.838;T|0.162	0.162	strong	.	RNF43	157	.	NM_017763	exon3	c.G350A	p.R117H	CAGGGGCGGGGGG	.	PASS	Atlas-SNP
COX18	285521	hgsc.bcm.edu	37	4	73930552	73930552	+	Silent	SNP	G	G	A	rs3762883	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	153	80	187	0	0.522876	0	G|0.650;C|0.000;A|0.350	0.350	strong	.	COX18	20	.	NM_173827	exon4	c.C663T	p.P221P	GGAGTCGGGTGCA	.	PASS	Atlas-SNP
OR13J1	392309	hgsc.bcm.edu	37	9	35870225	35870225	+	Silent	SNP	G	G	A	rs72727089	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	103	58	100	0	0.563107	0	G|0.779;A|0.221	0.221	strong	.	OR13J1	37	.	NM_001004487	exon1	c.C174T	p.P58P	GTACACGGGCGTG	.	PASS	Atlas-SNP
TET2	54790	hgsc.bcm.edu	37	4	106196951	106196951	+	Missense_Mutation	SNP	A	A	G	rs2454206	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51	31	60	0	0.607843	0	A|0.768;G|0.232	0.232	strong	.	TET2	1762	.	NM_001127208	exon11	c.A5284G	p.I1762V	TCTCACATAATCC	.	PASS	Atlas-SNP
FCGR3B	2215	hgsc.bcm.edu	37	1	161599693	161599693	+	Missense_Mutation	SNP	T	T	C	rs76714703	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	101	96	80	0	0.950495	0	T|0.338;C|0.662	0.662	strong	.	FCGR3B	35	.	NM_001244753	exon3	c.A302G	p.N101S	ATGAGGTTCTCAT	.	PASS	Atlas-SNP
CDSN	1041	hgsc.bcm.edu	37	6	31084048	31084048	+	Silent	SNP	A	A	G	rs3094216	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	107	83	74	0	0.775701	0	A|0.790;G|0.210	0.210	strong	.	CDSN	48	.	NM_001264	exon2	c.T1344C	p.C448C	GCTGCCACAAGGC	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	173	62	119	0	0.358382	0	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
NPY	4852	hgsc.bcm.edu	37	7	24325009	24325009	+	Silent	SNP	G	G	A	rs5573	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	37	11	41	0	0.297297	0	A|0.483;C|0.000;G|0.517;T|0.000	0.483	strong	NPY,colon,carcinoma,0,1	NPY	25	1	NM_000905	exon2	c.G150A	p.S50S	CTACTCGGCGCTG	.	PASS	Atlas-SNP
VWA3B	200403	hgsc.bcm.edu	37	2	98709684	98709684	+	Silent	SNP	T	T	C	rs298917	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	182	92	178	0	0.505495	0	T|0.871;C|0.129	0.129	strong	.	VWA3B	138	.	NM_144992	exon2	c.T129C	p.H43H	ACTGCATGGGCTT	.	PASS	Atlas-SNP
ALG1	56052	hgsc.bcm.edu	37	16	5128857	5128857	+	Silent	SNP	G	G	C	rs12921879	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	161	60	150	0	0.372671	0	G|0.949;C|0.051	0.051	strong	.	ALG1	35	.	NM_019109	exon7	c.G840C	p.L280L	CCTGCTGGTCAGC	.	PASS	Atlas-SNP
SNAPC4	6621	hgsc.bcm.edu	37	9	139270876	139270876	+	Missense_Mutation	SNP	G	G	A	rs3812561	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	34	74	0	0.395349	0	G|0.949;A|0.051	0.051	strong	.	SNAPC4	82	.	NM_003086	exon22	c.C4342T	p.P1448S	CGTCAGGGTCATT	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	129	64	104	1	0.496124	0.00961538	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
DGKQ	1609	hgsc.bcm.edu	37	4	956309	956309	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57	6	72	0	0.105263	0	.	.	none	.	DGKQ	29	.	NM_001347	exon18	c.G2128A	p.V710M	TGAGCACGGCGTC	.	PASS	Atlas-SNP
CCDC168	643677	hgsc.bcm.edu	37	13	103388764	103388764	+	Silent	SNP	T	T	C	rs113711522	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	290	206	385	0	0.710345	0	T|0.996;C|0.004	0.004	strong	.	.	.	.	NM_001146197	exon4	c.A14283G	p.V4761V	TGTTTGTACTCTG	.	PASS	Atlas-SNP
GRID2IP	392862	hgsc.bcm.edu	37	7	6591008	6591008	+	Silent	SNP	C	C	T	rs73059373	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	29	19	40	0	0.655172	0	C|0.859;T|0.141	0.141	strong	GRID2IP_ENST00000457091,NS,carcinoma,0,2	GRID2IP	82	2	NM_001145118	exon1	c.G60A	p.R20R	ACCTAGCCGGAAG	.	PASS	Atlas-SNP
PIDD	55367	hgsc.bcm.edu	37	11	802379	802379	+	Missense_Mutation	SNP	T	T	C	rs10902221	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91	90	90	1	0.989011	0.0111111	T|0.588;C|0.412	0.412	strong	PIDD_ENST00000347755,NS,carcinoma,-1,1	PIDD	76	1	NM_145887	exon6	c.A992G	p.Q331R	CAGCCTTGAGGGG	.	scavenged	Atlas-SNP
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32551915	32551915	+	Missense_Mutation	SNP	A	A	G	rs17424145	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	13	6	34	0	0.461538	0	A|0.941;G|0.059	0.059	strong	.	HLA-DRB1	41	.	NM_002124	exon2	c.T341C	p.V114A	TCCACAACCCCGT	.	PASS	Atlas-SNP
ZNF280D	54816	hgsc.bcm.edu	37	15	56959028	56959028	+	Missense_Mutation	SNP	C	C	T	rs28620278	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	229	95	245	0	0.414847	0	C|0.495;T|0.505	0.505	strong	.	ZNF280D	82	.	NM_017661	exon15	c.G1702A	p.V568I	ATTTGACTGTATT	.	PASS	Atlas-SNP
MAVS	57506	hgsc.bcm.edu	37	20	3844929	3844929	+	Missense_Mutation	SNP	C	C	T	rs45437096	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	41	84	0	0.471264	0	C|0.888;T|0.112	0.112	strong	.	MAVS	34	.	NM_020746	exon6	c.C652T	p.R218C	CCATCCCGTGGGC	.	PASS	Atlas-SNP
C17orf102	400591	hgsc.bcm.edu	37	17	32906008	32906008	+	Missense_Mutation	SNP	C	C	G	rs58529418	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	39	13	64	0	0.333333	0	C|0.876;G|0.124	0.124	strong	.	C17orf102	24	.	NM_207454	exon1	c.G292C	p.G98R	AGCCCCCGCGGCC	.	PASS	Atlas-SNP
ZNF860	344787	hgsc.bcm.edu	37	3	32031622	32031622	+	Missense_Mutation	SNP	T	T	C	rs13087612	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	131	128	216	0	0.977099	0	T|0.621;C|0.379	0.379	strong	ZNF860_ENST00000360311,NS,carcinoma,0,2	ZNF860	96	2	NM_001137674	exon2	c.T1051C	p.F351L	AAGGCTTTCAGGC	.	PASS	Atlas-SNP
PDE1C	5137	hgsc.bcm.edu	37	7	32209459	32209459	+	Silent	SNP	C	C	T	rs977626	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	19	150	0	0.22619	0	C|0.476;N|0.002	.	strong	.	PDE1C	465	.	NM_001191058	exon3	c.G246A	p.E82E	TAGGATCTCCTCT	.	PASS	Atlas-SNP
GTF3C2	2976	hgsc.bcm.edu	37	2	27550967	27550967	+	Silent	SNP	A	A	G	rs1049817	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	39	85	0	0.527027	0	A|0.544;G|0.456	0.456	strong	.	GTF3C2	73	.	NM_001521	exon18	c.T2346C	p.H782H	AGCCTTAGGAGGG	.	PASS	Atlas-SNP
IRF1	3659	hgsc.bcm.edu	37	5	131825088	131825088	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48	19	69	0	0.395833	0	.	.	none	.	IRF1	26	.	NM_002198	exon2	c.A83C	p.N28T	ACTTTATTAATCC	.	PASS	Atlas-SNP
PRSS3	5646	hgsc.bcm.edu	37	9	33796673	33796673	+	Missense_Mutation	SNP	G	G	A	rs76740888	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	116	16	129	0	0.137931	0	.	.	weak	.	PRSS3	79	.	NM_007343	exon2	c.G244A	p.V82I	AAGATTGTTGGGG	.	PASS	Atlas-SNP
CDHR1	92211	hgsc.bcm.edu	37	10	85978939	85978939	+	Silent	SNP	G	G	A	rs4244947	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	46	88	0	0.621622	0	G|0.460;A|0.540	0.540	strong	.	CDHR1	122	.	NM_001171971	exon17	c.G2145A	p.L715L	GGGTCTGTTCTTG	.	PASS	Atlas-SNP
FSIP1	161835	hgsc.bcm.edu	37	15	40005772	40005772	+	Missense_Mutation	SNP	C	C	T	rs937961	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	90	40	117	0	0.444444	0	C|0.882;T|0.118	0.118	strong	.	FSIP1	53	.	NM_152597	exon10	c.G1061A	p.R354H	CCATCACGGTCAG	.	PASS	Atlas-SNP
PRRC2A	7916	hgsc.bcm.edu	37	6	31604591	31604591	+	Missense_Mutation	SNP	C	C	T	rs10885	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	40	36	0	0.655738	0	C|0.836;T|0.164	0.164	strong	.	PRRC2A	152	.	NM_004638	exon28	c.C6016T	p.P2006S	CCACCTCCCCTTT	.	PASS	Atlas-SNP
PPA2	27068	hgsc.bcm.edu	37	4	106395181	106395181	+	Silent	SNP	G	G	A	rs4699179	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	23	23	11	0	1	0	G|0.892;A|0.108	0.108	strong	.	PPA2	23	.	NM_176866	exon1	c.C27T	p.R9R	ACCCGTGCGCAGC	.	PASS	Atlas-SNP
HDAC10	83933	hgsc.bcm.edu	37	22	50687178	50687178	+	Silent	SNP	C	C	T	rs41283469	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49	22	58	0	0.44898	0	C|0.974;T|0.026	0.026	strong	HDAC10,NS,carcinoma,-1,1	HDAC10	29	1	NM_032019	exon10	c.G819A	p.G273G	CATTTGCCCCTGG	.	PASS	Atlas-SNP
HLA-C	3107	hgsc.bcm.edu	37	6	31239518	31239518	+	Silent	SNP	C	C	T	rs1050420	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	136	22	153	0	0.161765	0	C|0.581;T|0.419	0.419	strong	.	HLA-C	92	.	NM_002117	exon2	c.G201A	p.P67P	CCCTCTCGGACTC	.	PASS	Atlas-SNP
GET4	51608	hgsc.bcm.edu	37	7	925717	925717	+	Silent	SNP	G	G	A	rs11543222	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98	29	76	0	0.295918	0	G|0.878;A|0.122	0.122	strong	.	GET4	17	.	NM_015949	exon2	c.G180A	p.T60T	GCACACGGAGGCC	.	PASS	Atlas-SNP
LAMC2	3918	hgsc.bcm.edu	37	1	183201970	183201970	+	Missense_Mutation	SNP	G	G	C	rs2296303	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51	23	60	0	0.45098	0	G|0.841;C|0.159	0.159	strong	.	LAMC2	113	.	NM_005562	exon14	c.G2198C	p.S733T	CAGAAAGTGAAGC	.	PASS	Atlas-SNP
CDH23	64072	hgsc.bcm.edu	37	10	73537978	73537978	+	Silent	SNP	C	C	T	rs10762480	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	38	95	0	0.436782	0	C|0.824;T|0.176	0.176	strong	CDH23,NS,carcinoma,0,1	CDH23	365	1	NM_022124	exon38	c.C5100T	p.Y1700Y	GGACTACGAGATC	.	PASS	Atlas-SNP
HSPG2	3339	hgsc.bcm.edu	37	1	22168845	22168845	+	Missense_Mutation	SNP	A	A	T	rs2229489	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	41	68	0	0.546667	0	A|0.957;T|0.043	0.043	strong	HSPG2,NS,carcinoma,0,1	HSPG2	311	1	NM_005529	exon68	c.T8939A	p.L2980H	GAGACGAGGTGGA	.	PASS	Atlas-SNP
NUDT1	4521	hgsc.bcm.edu	37	7	2290522	2290522	+	Silent	SNP	C	C	T	rs1799832	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91	52	68	0	0.571429	0	C|0.841;T|0.159	0.159	strong	.	NUDT1	22	.	NM_198949	exon5	c.C426T	p.D142D	GCCCGACGACAGC	.	PASS	Atlas-SNP
PLEKHG7	440107	hgsc.bcm.edu	37	12	93139348	93139348	+	Missense_Mutation	SNP	A	A	G	rs17790310	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	29	69	0	0.537037	0	A|0.966;G|0.034	0.034	strong	.	PLEKHG7	38	.	NM_001004330	exon5	c.A296G	p.D99G	GAGATGACTTTGG	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	152	67	160	0	0.440789	0	T|0.530;C|0.470	0.470	strong	.	CCDC27	79	.	NM_152492	exon5	c.T800C	p.M267T	TGAAGATGCAGCT	.	PASS	Atlas-SNP
SH3BP2	6452	hgsc.bcm.edu	37	4	2831383	2831383	+	Silent	SNP	T	T	G	rs231399	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	59	30	72	0	0.508475	0	T|0.554;G|0.446	0.446	strong	SH3BP2,NS,carcinoma,0,1	SH3BP2	43	1	NM_001145856	exon8	c.T921G	p.A307A	CCTGGCTGCTGAG	.	PASS	Atlas-SNP
METTL13	51603	hgsc.bcm.edu	37	1	171755182	171755182	+	Missense_Mutation	SNP	G	G	A	rs2232819	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	109	64	93	0	0.587156	0	G|0.869;A|0.131	0.131	strong	METTL13,NS,carcinoma,0,1	METTL13	67	1	NM_015935	exon3	c.G1077A	p.M359I	AGTCATGGAGCTG	.	PASS	Atlas-SNP
ITPKB	3707	hgsc.bcm.edu	37	1	226923264	226923264	+	Silent	SNP	G	G	A	rs708775	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	142	65	172	0	0.457746	0	G|0.716;A|0.284	0.284	strong	ITPKB_ENST00000429204,NS,carcinoma,0,1	ITPKB	158	1	NM_002221	exon2	c.C1896T	p.A632A	CAGGAAGGCTGAG	.	PASS	Atlas-SNP
CRMP1	1400	hgsc.bcm.edu	37	4	5830393	5830393	+	Silent	SNP	C	C	T	rs61746000	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	31	112	0	0.413333	0	C|0.918;T|0.082	0.082	strong	CRMP1,NS,carcinoma,-1,1	CRMP1	118	1	NM_001014809	exon12	c.G1626A	p.A542A	CTCCACCGCCTGC	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	107	107	99	0	1	0	A|0.647;G|0.353	0.353	strong	.	FAM135A	181	.	NM_001162529	exon14	c.A3725G	p.D1242G	AAGAGGATGGTTC	.	PASS	Atlas-SNP
KRT28	162605	hgsc.bcm.edu	37	17	38955991	38955991	+	Missense_Mutation	SNP	C	C	T	rs7209228	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	31	31	46	0	1	0	C|0.859;T|0.141	0.141	strong	.	KRT28	65	.	NM_181535	exon1	c.G155A	p.G52D	CCCAAGCCCCCTC	.	PASS	Atlas-SNP
ADCY1	107	hgsc.bcm.edu	37	7	45753324	45753324	+	Silent	SNP	G	G	A	rs2293106	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	36	26	60	0	0.722222	0	G|0.797;A|0.203	0.203	strong	.	ADCY1	187	.	NM_021116	exon20	c.G3090A	p.R1030R	GAGAAGGTGCCCC	.	PASS	Atlas-SNP
FAM186B	84070	hgsc.bcm.edu	37	12	49993678	49993678	+	Missense_Mutation	SNP	C	C	T	rs52824916	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	128	61	131	0	0.476562	0	C|0.886;T|0.114	0.114	strong	.	FAM186B	72	.	NM_032130	exon4	c.G1745A	p.R582Q	TGGGTCCGGCTTG	.	PASS	Atlas-SNP
OR5P2	120065	hgsc.bcm.edu	37	11	7818190	7818190	+	Silent	SNP	C	C	T	rs73406607	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	27	27	36	0	1	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
POLRMT	5442	hgsc.bcm.edu	37	19	621063	621063	+	Silent	SNP	A	A	G	rs76890343	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	28	53	0	0.459016	0	A|0.839;G|0.161	0.161	strong	.	POLRMT	91	.	NM_005035	exon10	c.T2635C	p.L879L	CCGTCAAGGGTTG	.	PASS	Atlas-SNP
TMEM150B	284417	hgsc.bcm.edu	37	19	55824332	55824332	+	Missense_Mutation	SNP	T	T	G	rs7246479	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	130	65	151	0	0.5	0	T|0.444;G|0.556	0.556	strong	TMEM150B,NS,carcinoma,0,2	TMEM150B	19	2	NM_001085488	exon8	c.A597C	p.L199F	AACGGCTAAGAGA	.	PASS	Atlas-SNP
MYH11	4629	hgsc.bcm.edu	37	16	15839034	15839034	+	Silent	SNP	G	G	A	rs1050113	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	28	52	0	0.595745	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
KLHL38	340359	hgsc.bcm.edu	37	8	124663895	124663895	+	Silent	SNP	G	G	A	rs16898689	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49	23	49	0	0.469388	0	G|0.857;A|0.143	0.143	strong	.	KLHL38	81	.	NM_001081675	exon1	c.C1272T	p.P424P	GACTGCGGGGTGG	.	PASS	Atlas-SNP
ARSG	22901	hgsc.bcm.edu	37	17	66364804	66364804	+	Missense_Mutation	SNP	T	T	C	rs1558878	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100	45	108	0	0.45	0	T|0.602;C|0.398	0.398	strong	.	ARSG	55	.	NM_001267727	exon7	c.T820C	p.W274R	GGGCTCTGGGAGA	.	PASS	Atlas-SNP
SPPL2C	162540	hgsc.bcm.edu	37	17	43923683	43923683	+	Missense_Mutation	SNP	A	A	G	rs12185268	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94	94	88	0	1	0	A|0.853;G|0.147	0.147	strong	.	.	.	.	NM_175882	exon1	c.A1411G	p.I471V	CGTCAGATCTACT	.	PASS	Atlas-SNP
CAMTA1	23261	hgsc.bcm.edu	37	1	7723588	7723588	+	Silent	SNP	C	C	T	rs3737906	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	92	49	111	0	0.532609	0	C|0.901;T|0.099	0.099	strong	.	CAMTA1	226	.	NM_015215	exon9	c.C981T	p.N327N	GAGGAACGGCAAG	.	PASS	Atlas-SNP
WDR93	56964	hgsc.bcm.edu	37	15	90246336	90246336	+	Silent	SNP	A	A	G	rs16974175	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	150	149	145	0	0.993333	0	A|0.575;G|0.425	0.425	strong	.	WDR93	63	.	NM_020212	exon3	c.A459G	p.L153L	AGATTTAGGGAAT	.	PASS	Atlas-SNP
TMEM63A	9725	hgsc.bcm.edu	37	1	226046974	226046974	+	Silent	SNP	T	T	C	rs2292561	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	193	91	147	0	0.471503	0	T|0.916;C|0.084	0.084	strong	.	TMEM63A	75	.	NM_014698	exon15	c.A1299G	p.L433L	GAAAAATAGCCCC	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1281932	1281932	+	Silent	SNP	C	C	T	rs61734215	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	106	49	137	0	0.462264	0	C|0.992;T|0.008	0.008	strong	.	MUC5B	473	.	NM_002458	exon48	c.C17043T	p.C5681C	CTTCTGCGAGGGC	.	PASS	Atlas-SNP
MAPT	4137	hgsc.bcm.edu	37	17	44073889	44073889	+	Silent	SNP	A	A	G	rs1052553	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	89	88	151	0	0.988764	0	A|0.865;G|0.135	0.135	strong	MAPT_ENST00000344290,NS,carcinoma,0,2	MAPT	135	2	NM_001123066	exon11	c.A1686G	p.A562A	GGTGGCAGTGGTC	.	PASS	Atlas-SNP
PHYHD1	254295	hgsc.bcm.edu	37	9	131702891	131702891	+	Missense_Mutation	SNP	A	A	G	rs2273866	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	34	72	0	0.62963	0	A|0.643;G|0.357	0.357	strong	PHYHD1,NS,carcinoma,0,1	PHYHD1	29	1	NM_174933	exon10	c.A578G	p.E193G	GTCAAGAAGGATG	.	PASS	Atlas-SNP
SYNJ2	8871	hgsc.bcm.edu	37	6	158517308	158517308	+	Missense_Mutation	SNP	A	A	G	rs2502601	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55	54	67	0	0.981818	0	A|0.464;G|0.536	0.536	strong	SYNJ2,colon,carcinoma,0,1	SYNJ2	111	1	NM_003898	exon27	c.A4403G	p.E1468G	ATCATGAACACAA	.	PASS	Atlas-SNP
C9orf152	401546	hgsc.bcm.edu	37	9	112963702	112963702	+	Silent	SNP	G	G	A	rs4978888	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	17	9	23	0	0.529412	0	G|0.786;A|0.214	0.214	strong	.	C9orf152	20	.	NM_001012993	exon2	c.C246T	p.N82N	CTCCTTGTTAATC	.	PASS	Atlas-SNP
LOXHD1	125336	hgsc.bcm.edu	37	18	44181227	44181227	+	Missense_Mutation	SNP	C	C	T	rs10163657	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	58	24	49	0	0.413793	0	C|0.945;T|0.055	0.055	strong	.	LOXHD1	367	.	NM_144612	exon8	c.G1087A	p.V363I	GCCCGACGGAGAC	.	PASS	Atlas-SNP
DBC1	1620	hgsc.bcm.edu	37	9	122001000	122001000	+	Silent	SNP	G	G	A	rs2274157	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	103	102	130	0	0.990291	0	A|0.392;C|0.004	0.392	strong	DBC1,NS,carcinoma,0,1	DBC1	194	1	NM_014618	exon5	c.C618T	p.S206S	GTCATAGCTGTTA	.	PASS	Atlas-SNP
IFNGR2	3460	hgsc.bcm.edu	37	21	34787312	34787312	+	Missense_Mutation	SNP	A	A	G	rs9808753	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	118	32	67	0	0.271186	0	A|0.793;G|0.207	0.207	strong	.	IFNGR2	30	.	NM_005534	exon2	c.A191G	p.Q64R	TCTACCAAGTGCA	.	PASS	Atlas-SNP
OR13D1	286365	hgsc.bcm.edu	37	9	107456933	107456933	+	Silent	SNP	C	C	T	rs12347076	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	121	56	164	0	0.46281	0	C|0.771;T|0.229	0.229	strong	.	OR13D1	42	.	NM_001004484	exon1	c.C231T	p.L77L	CCTCCTCATTATC	.	PASS	Atlas-SNP
LZTS2	84445	hgsc.bcm.edu	37	10	102766574	102766574	+	Silent	SNP	A	A	G	rs807024	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	39	29	49	0	0.74359	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
ENPP3	5169	hgsc.bcm.edu	37	6	132068060	132068060	+	Silent	SNP	A	A	G	rs145544747	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	36	42	0	0.545455	0	A|0.994;G|0.006	0.006	strong	.	ENPP3	117	.	NM_005021	exon25	c.A2592G	p.L864L	GCAACTAAAGACA	.	PASS	Atlas-SNP
FAM71F2	346653	hgsc.bcm.edu	37	7	128323034	128323034	+	Missense_Mutation	SNP	A	A	G	rs1109552	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68	32	68	0	0.470588	0	A|0.674;G|0.326	0.326	strong	.	FAM71F2	19	.	NM_001012454	exon5	c.A751G	p.I251V	ACTGCCATTGAAA	.	PASS	Atlas-SNP
SACS	26278	hgsc.bcm.edu	37	13	23905711	23905711	+	Silent	SNP	A	A	G	rs2737699	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	109	66	113	0	0.605505	0	G|0.232;N|0.000	0.232	strong	.	SACS	871	.	NM_014363	exon10	c.T12304C	p.L4102L	TTGCCAATGCTAA	.	PASS	Atlas-SNP
GAREM	64762	hgsc.bcm.edu	37	18	29867504	29867504	+	Silent	SNP	T	T	C	rs16962977	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	116	60	135	0	0.517241	0	T|0.907;C|0.093	0.093	strong	.	.	.	.	NM_022751	exon4	c.A1056G	p.E352E	GCATTCTTCATTC	.	PASS	Atlas-SNP
ZFP64	55734	hgsc.bcm.edu	37	20	50803444	50803444	+	Silent	SNP	C	C	T	rs36027430	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	185	88	191	0	0.475676	0	C|0.865;T|0.135	0.135	strong	.	ZFP64	240	.	NM_018197	exon2	c.G213A	p.S71S	TTCCTCCGATACA	.	PASS	Atlas-SNP
LILRB5	10990	hgsc.bcm.edu	37	19	54754778	54754778	+	Missense_Mutation	SNP	G	G	A	rs150660840	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	151	6	84	0	0.0397351	0	G|0.994;A|0.006	0.006	strong	LILRB5,NS,carcinoid-endocrine_tumour,+1,1	LILRB5	176	1	NM_001081442	exon13	c.C1648T	p.P550S	CCTGGGGGGCTTC	.	scavenged	Atlas-SNP
MTRR	4552	hgsc.bcm.edu	37	5	7873566	7873566	+	Silent	SNP	C	C	G	rs41282641	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80	37	94	0	0.4625	0	C|0.997;G|0.003	0.003	strong	.	MTRR	74	.	NM_024010	exon3	c.C291G	p.R97R	AGCCCGCAAGTTT	.	PASS	Atlas-SNP
RYR1	6261	hgsc.bcm.edu	37	19	38990345	38990345	+	Silent	SNP	C	C	T	rs2229147	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	27	20	31	0	0.740741	0	C|0.893;T|0.107	0.107	strong	.	RYR1	708	.	NM_001042723	exon44	c.C7098T	p.P2366P	CGGACCCGCCCTG	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	118	118	107	0	1	0	C|0.609;G|0.000;T|0.391	0.609	strong	CAND2_ENST00000456430,NS,carcinoma,0,2	CAND2	138	2	NM_001162499	exon10	c.T1597C	p.S533P	GCTGACTCTTTCT	.	PASS	Atlas-SNP
PROKR1	10887	hgsc.bcm.edu	37	2	68882661	68882661	+	Missense_Mutation	SNP	A	A	G	rs34715748	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	41	25	79	0	0.609756	0	A|0.960;G|0.040	0.040	strong	PROKR1,NS,carcinoma,0,1	PROKR1	69	1	NM_138964	exon2	c.A1135G	p.I379V	AAGACAATTGGGA	.	PASS	Atlas-SNP
EPHX2	2053	hgsc.bcm.edu	37	8	27358505	27358505	+	Missense_Mutation	SNP	A	A	G	rs41507953	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	59	29	53	0	0.491525	0	A|0.878;G|0.122	0.122	strong	.	EPHX2	57	.	NM_001979	exon2	c.A164G	p.K55R	TTATGAAAGGAGA	.	PASS	Atlas-SNP
SEPT4	5414	hgsc.bcm.edu	37	17	56598439	56598439	+	Silent	SNP	T	T	C	rs1057068	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	176	83	207	0	0.471591	0	T|0.629;C|0.371	0.371	strong	.	SEPT4	48	.	NM_001256782	exon11	c.A1242G	p.T414T	CTCCCGTGTCACA	.	PASS	Atlas-SNP
TMEM2	23670	hgsc.bcm.edu	37	9	74354983	74354983	+	Silent	SNP	A	A	G	rs25691	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60	32	51	0	0.533333	0	A|0.937;G|0.063	0.063	strong	.	TMEM2	112	.	NM_001135820	exon5	c.T1200C	p.I400I	ACCTTCAATCCAT	.	PASS	Atlas-SNP
UBXN2B	137886	hgsc.bcm.edu	37	8	59329438	59329438	+	Silent	SNP	A	A	G	rs13277646	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	27	27	40	0	1	0	A|0.746;G|0.254	0.254	strong	.	UBXN2B	36	.	NM_001077619	exon2	c.A114G	p.E38E	AGATGAAGTGAAG	.	PASS	Atlas-SNP
SDCCAG3	10807	hgsc.bcm.edu	37	9	139301960	139301960	+	Silent	SNP	G	G	A	rs3812580	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	59	26	50	0	0.440678	0	G|0.918;A|0.082	0.082	strong	.	SDCCAG3	41	.	NM_001039707	exon5	c.C456T	p.T152T	CCCGCCGGTTTGG	.	PASS	Atlas-SNP
LTB	4050	hgsc.bcm.edu	37	6	31549599	31549599	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	46	70	0	0.547619	0	.	.	none	.	LTB	19	.	NM_002341	exon2	c.A200G	p.Q67R	AGTCCTTGCTGGG	.	PASS	Atlas-SNP
PDE6C	5146	hgsc.bcm.edu	37	10	95372734	95372734	+	Silent	SNP	G	G	A	rs1131978	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	31	13	31	0	0.419355	0	A|0.180;G|0.820;T|0.000	0.180	strong	.	PDE6C	97	.	NM_006204	exon1	c.G252A	p.L84L	GGCCCTGCAGAGG	.	PASS	Atlas-SNP
BTG1	694	hgsc.bcm.edu	37	12	92539223	92539223	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	151	48	140	0	0.317881	0	.	.	none	.	BTG1	30	.	NM_001731	exon1	c.G89A	p.G30E	GTGAGCCCCTTGG	.	PASS	Atlas-SNP
CREB3	10488	hgsc.bcm.edu	37	9	35733116	35733116	+	Missense_Mutation	SNP	C	C	T	rs200166825	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	250	135	263	0	0.54	0	C|0.999;T|0.001	0.001	weak	.	CREB3	24	.	NM_006368	exon2	c.C253T	p.R85W	CTCCCACGGGAAA	.	PASS	Atlas-SNP
STX17	55014	hgsc.bcm.edu	37	9	102677589	102677589	+	Missense_Mutation	SNP	T	T	C	rs41305451	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	70	30	52	0	0.428571	0	T|0.945;C|0.055	0.055	strong	.	STX17	17	.	NM_017919	exon2	c.T68C	p.I23T	TTAAGATAGTAAT	.	PASS	Atlas-SNP
TENM2	57451	hgsc.bcm.edu	37	5	167674472	167674472	+	Silent	SNP	G	G	A	rs17070023	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	117	59	117	0	0.504274	0	G|0.910;A|0.090	0.090	strong	ODZ2_ENST00000519204,NS,carcinoma,+1,6	.	.	6	NM_001122679	exon27	c.G6501A	p.T2167T	GATGACGGTGCAA	.	PASS	Atlas-SNP
GNG2	54331	hgsc.bcm.edu	37	14	52433339	52433339	+	Silent	SNP	C	C	T	rs61740049	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	127	58	116	0	0.456693	0	C|0.993;T|0.007	0.007	strong	.	GNG2	12	.	NM_053064	exon4	c.C150T	p.L50L	CCCCCTCCTGACC	.	PASS	Atlas-SNP
HELZ2	85441	hgsc.bcm.edu	37	20	62196253	62196253	+	Missense_Mutation	SNP	C	C	A	rs310631	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	40	104	0	0.465116	0	T|0.004;G|0.003	.	strong	.	.	.	.	NM_001037335	exon9	c.G3922T	p.V1308L	GGGGCACCCTCAA	.	PASS	Atlas-SNP
CCDC88B	283234	hgsc.bcm.edu	37	11	64110668	64110668	+	Silent	SNP	G	G	A	rs574835	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	24	12	25	0	0.5	0	G|0.738;A|0.262	0.262	strong	.	CCDC88B	89	.	NM_032251	exon11	c.G1080A	p.S360S	GCTCTCGGGGGTG	.	PASS	Atlas-SNP
POM121L2	94026	hgsc.bcm.edu	37	6	27278838	27278838	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	135	32	157	0	0.237037	0	.	.	none	.	POM121L2	61	.	NM_033482	exon1	c.A1112C	p.N371T	TCTGTGTTGACCT	.	PASS	Atlas-SNP
PHF15	23338	hgsc.bcm.edu	37	5	133901934	133901934	+	Silent	SNP	C	C	T	rs148155246	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	43	114	0	0.511905	0	C|0.997;T|0.003	0.003	strong	.	PHF15	60	.	NM_015288	exon9	c.C1098T	p.D366D	CAGTGACGGGGGC	.	PASS	Atlas-SNP
ISG20	3669	hgsc.bcm.edu	37	15	89182736	89182736	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	16	58	0	0.25	0	.	.	none	.	ISG20	17	.	NM_002201	exon2	c.G139A	p.G47R	CCTGAGGGAGAGA	.	PASS	Atlas-SNP
STK10	6793	hgsc.bcm.edu	37	5	171533629	171533629	+	Silent	SNP	A	A	G	rs2306963	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85	37	104	0	0.435294	0	A|0.272;G|0.728	0.728	strong	.	STK10	100	.	NM_005990	exon6	c.T783C	p.S261S	CCACTTAGAGGGC	.	PASS	Atlas-SNP
NRXN1	9378	hgsc.bcm.edu	37	2	51255307	51255307	+	Silent	SNP	G	G	T	rs55640811	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	38	22	37	0	0.578947	0	.	.	weak	.	NRXN1	1118	.	NM_004801	exon2	c.C105A	p.G35G	CTCGGCGCCCGGA	.	PASS	Atlas-SNP
SPRR2F	6705	hgsc.bcm.edu	37	1	153085152	153085152	+	Missense_Mutation	SNP	C	C	T	rs79214550		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	8	53	0	0.125	0	.	.	weak	SPRR2F,caecum,carcinoma,+2,1	SPRR2F	12	1	NM_001014450	exon2	c.G58A	p.A20T	TTGGCGCGGGGCA	.	scavenged	Atlas-SNP
SPAG1	6674	hgsc.bcm.edu	37	8	101253184	101253184	+	Silent	SNP	G	G	A	rs1788190	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85	41	92	0	0.482353	0	G|0.707;A|0.293	0.293	strong	.	SPAG1	80	.	NM_003114	exon19	c.G2715A	p.S905S	CCTTTCGGACACA	.	PASS	Atlas-SNP
VASN	114990	hgsc.bcm.edu	37	16	4431373	4431373	+	Silent	SNP	G	G	C	rs740374	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	24	15	27	0	0.625	0	G|0.986;C|0.014	0.014	strong	.	VASN	21	.	NM_138440	exon2	c.G495C	p.P165P	GCCCCCGCTGCGC	.	PASS	Atlas-SNP
HAPLN1	1404	hgsc.bcm.edu	37	5	82940273	82940273	+	Silent	SNP	C	C	G	rs2242128	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	143	69	144	0	0.482517	0	C|0.272;G|0.728	0.728	strong	.	HAPLN1	79	.	NM_001884	exon4	c.G684C	p.G228G	GTTCTGCCCCCCA	.	PASS	Atlas-SNP
PTK2B	2185	hgsc.bcm.edu	37	8	27293865	27293865	+	Silent	SNP	C	C	T	rs7005936	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	236	124	262	0	0.525424	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
MOV10	4343	hgsc.bcm.edu	37	1	113236681	113236681	+	Silent	SNP	C	C	T	rs3748656	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	117	53	124	0	0.452991	0	C|0.752;T|0.248	0.248	strong	MOV10,NS,carcinoma,+1,1	MOV10	74	1	NM_020963	exon8	c.C1182T	p.G394G	ACGGGGCGACCAC	.	PASS	Atlas-SNP
KIAA1804	0	hgsc.bcm.edu	37	1	233514975	233514975	+	Missense_Mutation	SNP	G	G	T	rs3795374	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	34	17	39	1	0.5	0.025641	G|0.774;T|0.226	0.226	strong	KIAA1804,NS,carcinoma,0,1	KIAA1804	129	1	NM_032435	exon9	c.G2223T	p.E741D	CAGAGAGCTTCAT	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94	46	95	0	0.489362	0	G|0.933;A|0.067	0.067	strong	.	TM7SF3	41	.	NM_016551	exon6	c.C743T	p.P248L	TGTCCCGGGAGGG	.	PASS	Atlas-SNP
RTN3	10313	hgsc.bcm.edu	37	11	63487033	63487033	+	Silent	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	21	87	0	0.244186	0	.	.	none	.	RTN3	104	.	NM_001265589	exon3	c.T1059C	p.D353D	GACCGATAAATCT	.	PASS	Atlas-SNP
PBX1	5087	hgsc.bcm.edu	37	1	164761924	164761924	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51	13	58	0	0.254902	0	.	.	none	.	PBX1	60	.	NM_001204963	exon3	c.A459C	p.K153N	AGCCAAACTCTCA	.	PASS	Atlas-SNP
OR10H5	284433	hgsc.bcm.edu	37	19	15905639	15905639	+	Silent	SNP	C	C	T	rs3746151	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	134	61	140	0	0.455224	0	C|0.841;T|0.159	0.159	strong	.	OR10H5	49	.	NM_001004466	exon1	c.C781T	p.L261L	ATTTACCTGAAGC	.	PASS	Atlas-SNP
KIAA1614	57710	hgsc.bcm.edu	37	1	180905694	180905694	+	Silent	SNP	C	C	T	rs3795503	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	88	42	97	0	0.477273	0	C|0.696;T|0.304	0.304	strong	.	KIAA1614	75	.	NM_020950	exon5	c.C2649T	p.N883N	CAACAACAGCGCA	.	PASS	Atlas-SNP
PREX2	80243	hgsc.bcm.edu	37	8	69017584	69017584	+	Missense_Mutation	SNP	G	G	T	rs35559159	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	92	52	82	0	0.565217	0	G|0.990;T|0.010	0.010	strong	.	PREX2	614	.	NM_025170	exon24	c.G2927T	p.R976M	CAGAGAGGGCCCC	.	PASS	Atlas-SNP
CCDC34	91057	hgsc.bcm.edu	37	11	27362359	27362359	+	Missense_Mutation	SNP	T	T	G	rs17244028	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	203	203	261	0	1	0	T|0.772;G|0.228	0.228	strong	.	CCDC34	48	.	NM_030771	exon5	c.A791C	p.E264A	TGTATTTCAGCTT	.	PASS	Atlas-SNP
RPTOR	57521	hgsc.bcm.edu	37	17	78865546	78865546	+	Silent	SNP	T	T	C	rs2289764	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	27	74	0	0.442623	0	T|0.634;C|0.366	0.366	strong	.	RPTOR	122	.	NM_020761	exon18	c.T2010C	p.L670L	TCATCTTGTGGTT	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228525008	228525008	+	Missense_Mutation	SNP	G	G	A	rs3795809	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	164	65	196	0	0.396341	0	G|0.913;A|0.087	0.087	strong	OBSCN_ENST00000570156,caecum,carcinoma,0,3	OBSCN	2142	3	NM_001271223	exon77	c.G19595A	p.R6532H	CCCCCCGCCATGG	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	196	33	186	0	0.168367	0	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	.	PASS	Atlas-SNP
PADI2	11240	hgsc.bcm.edu	37	1	17419024	17419024	+	Silent	SNP	G	G	A	rs11203297	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	22	49	0	0.468085	0	G|0.800;A|0.200	0.200	strong	PADI2,NS,carcinoma,-2,1	PADI2	72	1	NM_007365	exon6	c.C534T	p.L178L	GTCCTTGAGATCT	.	PASS	Atlas-SNP
HAVCR1	26762	hgsc.bcm.edu	37	5	156482296	156482296	+	Missense_Mutation	SNP	C	C	G	rs56084311	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	133	71	112	0	0.533835	0	C|0.992;G|0.008	0.008	strong	HAVCR1,NS,carcinoma,+1,1	HAVCR1	84	1	NM_001099414	exon3	c.G295C	p.D99H	CACTGTCAGACAC	.	PASS	Atlas-SNP
PCDH19	57526	hgsc.bcm.edu	37	X	99662459	99662459	+	Silent	SNP	G	G	A	rs56277715	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51	30	38	0	0.588235	0	G|0.993;A|0.007	0.007	strong	.	PCDH19	269	.	NM_001184880	exon1	c.C1137T	p.G379G	ATTGAGGCCTGAG	.	PASS	Atlas-SNP
NLRP5	126206	hgsc.bcm.edu	37	19	56549518	56549518	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	133	24	127	0	0.180451	0	.	.	none	.	NLRP5	217	.	NM_153447	exon10	c.A2743G	p.S915G	CCTCTCAGTGATG	.	PASS	Atlas-SNP
CASP5	838	hgsc.bcm.edu	37	11	104869708	104869708	+	Missense_Mutation	SNP	G	G	C	rs523104	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	139	15	117	0	0.107914	0	G|0.508;C|0.492	0.492	strong	CASP5_ENST00000393141,NS,carcinoma,0,2	CASP5	213	2	NM_001136112	exon7	c.C1039G	p.L347V	AGATGAGTGCCAA	.	PASS	Atlas-SNP
HOXC4	3221	hgsc.bcm.edu	37	12	54448106	54448106	+	Missense_Mutation	SNP	A	A	G	rs75256744	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	109	49	103	0	0.449541	0	A|0.880;G|0.120	0.120	strong	.	HOXC4	29	.	NM_014620	exon3	c.A400G	p.I134V	CAACCCATAGTCT	.	PASS	Atlas-SNP
C9orf156	51531	hgsc.bcm.edu	37	9	100675816	100675816	+	Silent	SNP	A	A	G	rs1127703	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	19	54	0	0.404255	0	A|0.790;G|0.210	0.210	strong	.	C9orf156	35	.	NM_016481	exon3	c.T276C	p.N92N	ATGACCATTTTTG	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	45	146	0	0.517241	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
PNMAL1	55228	hgsc.bcm.edu	37	19	46974233	46974233	+	Silent	SNP	G	G	A	rs3826851	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	65	25	57	0	0.384615	0	A|0.247;C|0.000;G|0.753	0.247	strong	.	PNMAL1	87	.	NM_018215	exon2	c.C60T	p.D20D	GTGGATGTCCACT	.	PASS	Atlas-SNP
TFEB	7942	hgsc.bcm.edu	37	6	41652514	41652514	+	Silent	SNP	C	C	T	rs2073158	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	135	28	121	0	0.207407	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
EPHX2	2053	hgsc.bcm.edu	37	8	27394366	27394366	+	Silent	SNP	C	C	T	rs13439459	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93	52	103	0	0.55914	0	C|0.918;T|0.082	0.082	strong	.	EPHX2	57	.	NM_001979	exon13	c.C1236T	p.S412S	AGCAAGCGATGAG	.	PASS	Atlas-SNP
ITIH6	347365	hgsc.bcm.edu	37	X	54783779	54783779	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94	7	55	0	0.0744681	0	.	.	none	.	.	.	.	NM_198510	exon8	c.A2728G	p.S910G	TGGAACTTGAGAT	.	PASS	Atlas-SNP
LAMB2	3913	hgsc.bcm.edu	37	3	49162583	49162583	+	Missense_Mutation	SNP	C	C	T	rs35713889	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	112	57	101	0	0.508929	0	C|0.959;T|0.041	0.041	strong	.	LAMB2	156	.	NM_002292	exon20	c.G2740A	p.G914R	GGTCCCCGTGGAA	.	PASS	Atlas-SNP
CWH43	80157	hgsc.bcm.edu	37	4	48988450	48988450	+	Missense_Mutation	SNP	C	C	A	rs3747690	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	50	29	77	0	0.58	0	C|0.691;A|0.309	0.309	strong	.	CWH43	101	.	NM_025087	exon1	c.C4A	p.P2T	GCGATGCCCTCGC	.	PASS	Atlas-SNP
NLRP11	204801	hgsc.bcm.edu	37	19	56329334	56329334	+	Silent	SNP	G	G	C	rs8113630	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	148	66	186	0	0.445946	0	G|0.900;C|0.100	0.100	strong	.	NLRP11	139	.	NM_145007	exon4	c.C207G	p.L69L	GCTGAAGAGCATA	.	PASS	Atlas-SNP
FBXW10	10517	hgsc.bcm.edu	37	17	18682505	18682505	+	Missense_Mutation	SNP	T	T	C	rs117160613	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	195	5	185	1	0.025641	0.00540541	T|0.778;C|0.222	0.222	strong	FBXW10,NS,carcinoma,0,2	FBXW10	82	2	NM_001267585	exon14	c.T3053C	p.V1018A	GAAAAGTCAGCAA	.	scavenged	Atlas-SNP
CELSR2	1952	hgsc.bcm.edu	37	1	109810544	109810544	+	Silent	SNP	C	C	A	rs2281894	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	125	68	115	0	0.544	0	C|0.824;A|0.176	0.176	strong	.	CELSR2	228	.	NM_001408	exon17	c.C6180A	p.R2060R	CCTGCGCAACGCC	.	PASS	Atlas-SNP
PRAMEF1	65121	hgsc.bcm.edu	37	1	12855898	12855898	+	Missense_Mutation	SNP	C	C	T	rs76032448	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	233	59	86	1	0.253219	0.0116279	C|0.986;T|0.014	0.014	strong	PRAMEF1,NS,carcinoma,+1,2	PRAMEF1	78	2	NM_023013	exon4	c.C1178T	p.A393V	TTGACGCCCTGAA	.	scavenged	Atlas-SNP
MAP3K1	4214	hgsc.bcm.edu	37	5	56178615	56178615	+	Silent	SNP	A	A	C	rs55912465	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	28	55	0	0.595745	0	A|0.993;C|0.007	0.007	strong	.	MAP3K1	355	.	NM_005921	exon14	c.A3588C	p.S1196S	AATGTCAGCGTCT	.	PASS	Atlas-SNP
DOCK10	55619	hgsc.bcm.edu	37	2	225709926	225709926	+	Silent	SNP	A	A	G	rs7577271	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	38	89	0	0.452381	0	A|0.820;G|0.180	0.180	strong	.	DOCK10	308	.	NM_014689	exon21	c.T2475C	p.S825S	CTTTCCACTTGCA	.	PASS	Atlas-SNP
EGFLAM	133584	hgsc.bcm.edu	37	5	38370537	38370537	+	Missense_Mutation	SNP	T	T	C	rs1465567	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	70	40	76	0	0.571429	0	T|0.741;C|0.259	0.259	strong	EGFLAM,NS,carcinoma,0,1	EGFLAM	302	1	NM_001205301	exon6	c.T685C	p.W229R	CGCAGCTGGCCCA	.	PASS	Atlas-SNP
NRG3	10718	hgsc.bcm.edu	37	10	84745256	84745256	+	Silent	SNP	C	C	T	rs2295933	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	35	13	55	0	0.371429	0	C|0.606;T|0.394	0.394	strong	.	NRG3	301	.	NM_001010848	exon9	c.C1986T	p.S662S	TGCAAGCGAAAAC	.	PASS	Atlas-SNP
ARHGEF10L	55160	hgsc.bcm.edu	37	1	17914122	17914122	+	Missense_Mutation	SNP	G	G	A	rs35497285	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	32	9	39	0	0.28125	0	G|0.929;A|0.071	0.071	strong	.	ARHGEF10L	219	.	NM_018125	exon3	c.G205A	p.D69N	CACTTGGACTCCA	.	PASS	Atlas-SNP
MROH2B	133558	hgsc.bcm.edu	37	5	40998235	40998235	+	Silent	SNP	C	C	T	rs722575	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	78	32	76	0	0.410256	0	C|0.702;T|0.298	0.298	strong	HEATR7B2,NS,carcinoma,-2,2	.	.	2	NM_173489	exon42	c.G4677A	p.P1559P	AATACACGGATCT	.	PASS	Atlas-SNP
CTAGE1	64693	hgsc.bcm.edu	37	18	19996805	19996805	+	Missense_Mutation	SNP	T	T	C	rs12961009	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	97	62	88	0	0.639175	0	T|0.976;C|0.024	0.024	strong	.	CTAGE1	146	.	NM_172241	exon1	c.A970G	p.I324V	TTTTAATATGCTC	.	PASS	Atlas-SNP
BTG2	7832	hgsc.bcm.edu	37	1	203274835	203274835	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110	31	124	0	0.281818	0	.	.	none	.	BTG2	16	.	NM_006763	exon1	c.G101A	p.R34K	AGCAGAGGCTTAA	.	PASS	Atlas-SNP
IL32	9235	hgsc.bcm.edu	37	16	3119304	3119304	+	Missense_Mutation	SNP	A	A	G	rs2981599	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	157	66	76	1	0.420382	0.0131579	.	.	weak	IL32,NS,carcinoma,+1,2	IL32	32	2	NM_004221	exon7	c.A515G	p.D172G	GGGGGGACAAGGA	.	scavenged	Atlas-SNP
RNF123	63891	hgsc.bcm.edu	37	3	49728870	49728870	+	Missense_Mutation	SNP	A	A	G	rs145883512	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	108	48	129	0	0.444444	0	A|0.995;G|0.005	0.005	strong	.	RNF123	100	.	NM_022064	exon3	c.A95G	p.E32G	TGCAGGAGAAGCT	.	PASS	Atlas-SNP
SGK1	6446	hgsc.bcm.edu	37	6	134495155	134495155	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	12	76	1	0.196721	0.0131579	.	.	none	SGK1_ENST00000528577,NS,lymphoid_neoplasm,-2,5	SGK1	387	5	NM_001143676	exon5	c.C501T	p.N167N	AGAAGGGTTGGCA	.	scavenged	Atlas-SNP
CADPS2	93664	hgsc.bcm.edu	37	7	122078414	122078414	+	Silent	SNP	T	T	G	rs2074589	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	157	78	195	0	0.496815	0	T|0.713;G|0.287	0.287	strong	.	CADPS2	116	.	NM_001167940	exon17	c.A2457C	p.T819T	ATATTCTGTGAGT	.	PASS	Atlas-SNP
RAP1GAP	5909	hgsc.bcm.edu	37	1	21943820	21943820	+	Silent	SNP	G	G	A	rs2275360	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	106	47	101	0	0.443396	0	G|0.715;A|0.285	0.285	strong	.	RAP1GAP	119	.	NM_001145658	exon7	c.C462T	p.Y154Y	CTTCCGGTAGATG	.	PASS	Atlas-SNP
FAM65B	9750	hgsc.bcm.edu	37	6	24839461	24839461	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	118	38	120	0	0.322034	0	.	.	none	.	FAM65B	134	.	NM_014722	exon15	c.A1960C	p.S654R	TGAGACTTAAACT	.	PASS	Atlas-SNP
FOXM1	2305	hgsc.bcm.edu	37	12	2968169	2968169	+	Missense_Mutation	SNP	A	A	G	rs3742076	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	25	6	33	0	0.24	0	A|0.714;G|0.286	0.286	strong	FOXM1,NS,carcinoma,0,2	FOXM1	62	2	NM_202002	exon10	c.T2041C	p.S681P	CCTGGGAGGTTTG	.	PASS	Atlas-SNP
WLS	79971	hgsc.bcm.edu	37	1	68614320	68614320	+	Silent	SNP	G	G	A	rs17130529	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	24	69	0	0.444444	0	G|0.937;A|0.063	0.063	strong	.	WLS	97	.	NM_024911	exon7	c.C996T	p.I332I	CCCTGCGATGTGG	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	137	137	144	0	1	0	A|0.770;G|0.230	0.230	strong	.	.	.	.	NM_014283	exon14	c.A1368G	p.E456E	GGAAGAATATGAA	.	PASS	Atlas-SNP
RSU1	6251	hgsc.bcm.edu	37	10	16796919	16796919	+	Silent	SNP	C	C	A	rs1049632	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	35	84	0	0.466667	0	C|0.598;A|0.402	0.402	strong	.	RSU1	31	.	NM_012425	exon5	c.G351T	p.T117T	GTTGTACGTCAAG	.	PASS	Atlas-SNP
UHRF2	115426	hgsc.bcm.edu	37	9	6413498	6413498	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	70	13	73	0	0.185714	0	.	.	none	.	UHRF2	50	.	NM_152896	exon1	c.T8A	p.I3K	TGTGGATACAGGT	.	PASS	Atlas-SNP
CX3CR1	1524	hgsc.bcm.edu	37	3	39307162	39307162	+	Missense_Mutation	SNP	G	G	A	rs3732378	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	124	44	117	0	0.354839	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
STPG2	285555	hgsc.bcm.edu	37	4	99027137	99027137	+	Silent	SNP	T	T	C	rs2865979	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	114	47	106	0	0.412281	0	T|0.607;C|0.393	0.393	strong	.	.	.	.	NM_174952	exon5	c.A579G	p.L193L	TTCATATAGTCGT	.	PASS	Atlas-SNP
TCOF1	6949	hgsc.bcm.edu	37	5	149772280	149772280	+	Missense_Mutation	SNP	C	C	G	rs1136103	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	45	24	34	0	0.533333	0	C|0.855;G|0.145	0.145	strong	.	TCOF1	154	.	NM_001135243	exon22	c.C3527G	p.P1176R	CCACCCCCTCCAG	.	PASS	Atlas-SNP
OPA1	4976	hgsc.bcm.edu	37	3	193332566	193332566	+	Silent	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	158	8	155	0	0.0506329	0	.	.	none	.	OPA1	79	.	NM_130832	exon2	c.A87G	p.P29P	TTTACCACTACAA	.	PASS	Atlas-SNP
FBXO25	26260	hgsc.bcm.edu	37	8	363192	363192	+	Missense_Mutation	SNP	G	G	A	rs10090550	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	136	56	162	0	0.411765	0	G|0.481;A|0.519	0.519	strong	.	FBXO25	25	.	NM_183420	exon2	c.G113A	p.R38H	ATAACCGTTGTAA	.	PASS	Atlas-SNP
MAPT	4137	hgsc.bcm.edu	37	17	44061023	44061023	+	Missense_Mutation	SNP	G	G	A	rs62063786	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	97	95	93	0	0.979381	0	A|0.118;C|0.246	0.118	strong	.	MAPT	135	.	NM_001123066	exon6	c.G853A	p.D285N	GAGCCCGACGGGC	.	PASS	Atlas-SNP
THAP9	79725	hgsc.bcm.edu	37	4	83838262	83838262	+	Missense_Mutation	SNP	G	G	T	rs897945	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	108	108	102	0	1	0	G|0.624;T|0.375	0.375	strong	THAP9,colon,carcinoma,+2,1	THAP9	65	1	NM_024672	exon5	c.G897T	p.L299F	CAGTTTGCAGGGG	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	40	65	0	0.634921	0	G|0.373;C|0.627	0.627	strong	.	DUSP27	235	.	NM_001080426	exon5	c.G795C	p.E265D	CAATGAGGGCTTC	.	PASS	Atlas-SNP
RYR2	6262	hgsc.bcm.edu	37	1	237841390	237841390	+	Missense_Mutation	SNP	A	A	G	rs34967813	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100	40	88	0	0.4	0	A|0.827;G|0.173	0.173	strong	.	RYR2	1273	.	NM_001035	exon61	c.A8873G	p.Q2958R	ATGAACAAGAAAT	.	PASS	Atlas-SNP
GPR112	139378	hgsc.bcm.edu	37	X	135430803	135430803	+	Silent	SNP	C	C	G	rs111880833	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	106	28	73	0	0.264151	0	C|0.978;G|0.022	0.022	strong	.	GPR112	459	.	NM_153834	exon6	c.C4938G	p.L1646L	CTTTCTCTCTCCA	.	PASS	Atlas-SNP
OR13F1	138805	hgsc.bcm.edu	37	9	107267244	107267244	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	114	2	137	0	0.0175439	0	.	.	none	OR13F1,rectum,carcinoma,+1,2	OR13F1	75	2	NM_001004485	exon1	c.G701A	p.R234Q	AAGGTCGAAGTAA	.	scavenged	Atlas-SNP
SERHL2	253190	hgsc.bcm.edu	37	22	42970032	42970032	+	Missense_Mutation	SNP	T	T	C	rs52818842	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	374	157	345	2	0.419786	0.0057971	.	.	weak	SERHL2,NS,carcinoma,0,1	SERHL2	23	1	NM_014509	exon12	c.T916C	p.C306R	TTACAGTGCACAC	.	scavenged	Atlas-SNP
SLC5A9	200010	hgsc.bcm.edu	37	1	48708228	48708228	+	Nonsense_Mutation	SNP	G	G	T	rs850763	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	101	35	110	0	0.346535	0	G|0.867;T|0.133	0.133	strong	.	SLC5A9	82	.	NM_001135181	exon14	c.G1852T	p.E618X	GCCGGGGAGTGCC	.	PASS	Atlas-SNP
PITPNA	5306	hgsc.bcm.edu	37	17	1456318	1456318	+	Silent	SNP	G	G	A	rs2230463	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	26	55	0	0.412698	0	G|0.940;C|0.000;A|0.060	0.060	strong	.	PITPNA	14	.	NM_006224	exon3	c.C177T	p.H59H	GATCTTGTGTGTG	.	PASS	Atlas-SNP
KIAA1211	57482	hgsc.bcm.edu	37	4	57181995	57181995	+	Missense_Mutation	SNP	C	C	T	rs3796547	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44	17	51	0	0.386364	0	C|0.728;T|0.272	0.272	strong	KIAA1211,NS,carcinoma,0,1	KIAA1211	178	1	NM_020722	exon8	c.C2327T	p.S776L	AGAAGTCGGAGAT	.	PASS	Atlas-SNP
PMFBP1	83449	hgsc.bcm.edu	37	16	72184629	72184629	+	Missense_Mutation	SNP	C	C	T	rs217180	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85	35	87	0	0.411765	0	C|0.923;T|0.077	0.077	strong	.	PMFBP1	101	.	NM_031293	exon5	c.G514A	p.A172T	GAGAGGCGATCTT	.	PASS	Atlas-SNP
OR2F2	135948	hgsc.bcm.edu	37	7	143633157	143633157	+	Missense_Mutation	SNP	T	T	C	rs13235235	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110	49	88	0	0.445455	0	T|0.805;C|0.195	0.195	strong	.	OR2F2	63	.	NM_001004685	exon1	c.T832C	p.Y278H	GTCTTCTATGCCA	.	PASS	Atlas-SNP
STK40	83931	hgsc.bcm.edu	37	1	36807481	36807481	+	Missense_Mutation	SNP	C	C	T	rs3795498	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	163	76	220	0	0.466258	0	C|0.795;T|0.205	0.205	strong	SgK495,NS,lymphoid_neoplasm,0,2	STK40	53	2	NM_032017	exon12	c.G1183A	p.A395T	TCCGGGCGTCATG	.	PASS	Atlas-SNP
F7	2155	hgsc.bcm.edu	37	13	113770068	113770068	+	Silent	SNP	C	C	T	rs6042	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	50	79	0	0.78125	0	C|0.876;T|0.124	0.124	strong	F7,NS,carcinoma,0,1	F7	49	1	NM_000131	exon6	c.C525T	p.H175H	GTGCCACGAGGGG	.	PASS	Atlas-SNP
INADL	10207	hgsc.bcm.edu	37	1	62253483	62253483	+	Missense_Mutation	SNP	G	G	A	rs3762321	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	56	20	68	0	0.357143	0	G|0.916;A|0.084	0.084	strong	.	INADL	179	.	NM_176877	exon8	c.G907A	p.G303R	GTGCAGGGAATGA	.	PASS	Atlas-SNP
RPS6KB2	6199	hgsc.bcm.edu	37	11	67202156	67202156	+	Missense_Mutation	SNP	C	C	T	rs13859	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	77	75	83	0	0.974026	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
ZIM2	23619	hgsc.bcm.edu	37	19	57293394	57293394	+	Silent	SNP	A	A	G	rs2286751	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	60	83	0	0.983607	0	A|0.252;G|0.748	0.748	strong	.	ZIM2	511	.	NM_015363	exon9	c.T573C	p.S191S	AAGGGAACTAAGT	.	PASS	Atlas-SNP
CAPG	822	hgsc.bcm.edu	37	2	85622059	85622059	+	Missense_Mutation	SNP	T	T	C	rs6886	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	126	91	151	0	0.722222	0	T|0.353;C|0.647	0.647	strong	.	CAPG	32	.	NM_001256139	exon10	c.A1004G	p.H335R	CTCTCATGGCCCT	.	PASS	Atlas-SNP
PRC1	9055	hgsc.bcm.edu	37	15	91525048	91525048	+	Missense_Mutation	SNP	C	C	G	rs142416384	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	186	92	189	0	0.494624	0	C|0.992;G|0.008	0.008	strong	.	PRC1	51	.	NM_199413	exon4	c.G431C	p.S144T	GAGGCACTGTCAA	.	PASS	Atlas-SNP
ZNF667	63934	hgsc.bcm.edu	37	19	56953585	56953585	+	Missense_Mutation	SNP	T	T	C	rs3760849	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	113	47	120	0	0.415929	0	T|0.426;C|0.574	0.574	strong	.	ZNF667	95	.	NM_022103	exon5	c.A779G	p.K260R	AAGGCTTTTCCGC	.	PASS	Atlas-SNP
F7	2155	hgsc.bcm.edu	37	13	113773159	113773159	+	Missense_Mutation	SNP	G	G	A	rs6046	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85	61	121	0	0.717647	0	T|0.001;G|0.877;C|0.007;A|0.115	0.115	strong	.	F7	49	.	NM_000131	exon9	c.G1238A	p.R413Q	ACTACCGGGGCAC	.	PASS	Atlas-SNP
LAMC2	3918	hgsc.bcm.edu	37	1	183184616	183184616	+	Silent	SNP	C	C	T	rs2274980	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	155	70	112	0	0.451613	0	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	.	PASS	Atlas-SNP
PCF11	51585	hgsc.bcm.edu	37	11	82880341	82880341	+	Silent	SNP	G	G	A	rs12284052	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	193	33	167	0	0.170984	0	G|0.783;A|0.217	0.217	strong	.	PCF11	220	.	NM_015885	exon8	c.G2964A	p.Q988Q	TGGTCAGCCAGGG	.	PASS	Atlas-SNP
SGK223	0	hgsc.bcm.edu	37	8	8234192	8234192	+	Missense_Mutation	SNP	G	G	C	rs4840953	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	37	17	26	0	0.459459	0	G|0.602;C|0.398	0.398	strong	.	.	.	.	NM_001080826	exon2	c.C1727G	p.S576C	CCGCCAGAGCTCC	.	PASS	Atlas-SNP
VWF	7450	hgsc.bcm.edu	37	12	6153514	6153514	+	Silent	SNP	A	A	G	rs1063857	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	31	106	0	0.418919	0	A|0.615;G|0.385	0.385	strong	.	VWF	338	.	NM_000552	exon18	c.T2385C	p.Y795Y	CAGGTCATAGTTC	.	PASS	Atlas-SNP
GATA5	140628	hgsc.bcm.edu	37	20	61048549	61048549	+	Silent	SNP	G	G	A	rs41305803	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	138	71	111	0	0.514493	0	G|0.568;A|0.432	0.432	strong	.	GATA5	22	.	NM_080473	exon3	c.C609T	p.D203D	GGTGCCGTCTCGG	.	PASS	Atlas-SNP
PCF11	51585	hgsc.bcm.edu	37	11	82879825	82879825	+	Silent	SNP	G	G	A	rs75717911	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	134	113	109	0	0.843284	0	G|0.995;A|0.005	0.005	strong	.	PCF11	220	.	NM_015885	exon8	c.G2448A	p.G816G	AGGTGGGTGTCCT	.	PASS	Atlas-SNP
RYR1	6261	hgsc.bcm.edu	37	19	38993547	38993547	+	Silent	SNP	C	C	T	rs2229142	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	36	14	27	0	0.388889	0	C|0.834;T|0.166	0.166	strong	RYR1,NS,carcinoma,0,1	RYR1	708	1	NM_001042723	exon49	c.C7863T	p.H2621H	GCAGCACCTGTTG	.	PASS	Atlas-SNP
C2CD3	26005	hgsc.bcm.edu	37	11	73796917	73796917	+	Missense_Mutation	SNP	C	C	T	rs826058	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	68	82	0	0.809524	0	C|0.635;T|0.365	0.365	strong	C2CD3_ENST00000334126,NS,adenoma,0,2	C2CD3	288	2	NM_015531	exon21	c.G3656A	p.R1219Q	GGTTCCCGTTCAG	.	PASS	Atlas-SNP
FAM214A	56204	hgsc.bcm.edu	37	15	52901283	52901283	+	Missense_Mutation	SNP	T	T	C	rs61731670	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72	25	54	0	0.347222	0	T|0.697;C|0.303	0.303	strong	.	.	.	.	NM_019600	exon6	c.A1828G	p.T610A	AGGAAGTTGATAA	.	PASS	Atlas-SNP
FKRP	79147	hgsc.bcm.edu	37	19	47258842	47258842	+	Silent	SNP	C	C	T	rs2287717	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93	49	95	0	0.526882	0	C|0.859;T|0.141	0.141	strong	.	FKRP	16	.	NM_024301	exon4	c.C135T	p.A45A	TGCTGCCGGCCCC	.	PASS	Atlas-SNP
C10orf71	118461	hgsc.bcm.edu	37	10	50534862	50534862	+	Silent	SNP	T	T	C	rs12411843	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51	29	48	0	0.568627	0	T|0.690;C|0.310	0.310	strong	.	C10orf71	179	.	NM_001135196	exon3	c.T4272C	p.D1424D	CACTGATGACCTA	.	PASS	Atlas-SNP
EFNA3	1944	hgsc.bcm.edu	37	1	155058663	155058663	+	Missense_Mutation	SNP	G	G	A	rs17723260	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	226	113	215	0	0.5	0	G|0.911;A|0.089	0.089	strong	EFNA3,colon,carcinoma,0,1	EFNA3	15	1	NM_004952	exon4	c.G568A	p.V190M	CCCAATGTGAAGA	.	PASS	Atlas-SNP
OR2L3	391192	hgsc.bcm.edu	37	1	248224099	248224099	+	Missense_Mutation	SNP	T	T	C	rs79225254	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	271	108	265	0	0.398524	0	.	.	weak	.	OR2L3	97	.	NM_001004687	exon1	c.T116C	p.I39T	CTCTAATTGGAAA	.	PASS	Atlas-SNP
SQSTM1	8878	hgsc.bcm.edu	37	5	179263542	179263542	+	Silent	SNP	C	C	T	rs374985304		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	70	30	81	0	0.428571	0	.	.	weak	SQSTM1,NS,carcinoma,0,1	SQSTM1	30	1	NM_003900	exon8	c.C1272T	p.I424I	TGACATCGGAGCG	.	PASS	Atlas-SNP
MYO1C	4641	hgsc.bcm.edu	37	17	1382889	1382889	+	Silent	SNP	G	G	A	rs146685153		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	123	57	138	0	0.463415	0	G|1.000;A|0.000	0.000	weak	.	MYO1C	57	.	NM_001080779	exon8	c.C1017T	p.T339T	CACCCTGGTCAGA	.	PASS	Atlas-SNP
SDHA	6389	hgsc.bcm.edu	37	5	236617	236617	+	Silent	SNP	G	G	T	rs200223188	byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	236	7	215	3	0.029661	0.0139535	A|0.002;G|0.988;T|0.011	0.011	strong	SDHA,NS,carcinoma,0,1	SDHA	80	1	NM_004168	exon10	c.G1335T	p.S445S	TGCCTCGGTACAT	.	scavenged	Atlas-SNP
HTATSF1	27336	hgsc.bcm.edu	37	X	135593629	135593629	+	Silent	SNP	C	C	T	rs3027849	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	31	20	18	0	0.645161	0	C|0.902;0|0.017	.	strong	.	HTATSF1	66	.	NM_001163280	exon10	c.C1725T	p.D575D	TTTGGACGAGGAA	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	121	47	132	0	0.38843	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
RCN3	57333	hgsc.bcm.edu	37	19	50046437	50046437	+	Silent	SNP	C	C	T	rs1129459	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	125	58	130	0	0.464	0	C|0.895;T|0.105	0.105	strong	.	RCN3	28	.	NM_020650	exon7	c.C954T	p.G318G	CTATGGCGAGGAC	.	PASS	Atlas-SNP
DHX58	79132	hgsc.bcm.edu	37	17	40257163	40257163	+	Missense_Mutation	SNP	T	T	C	rs2074158	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51	51	58	0	1	0	T|0.647;C|0.353	0.353	strong	.	DHX58	39	.	NM_024119	exon10	c.A1274G	p.Q425R	AACTTCTGGATCA	.	PASS	Atlas-SNP
GNL1	2794	hgsc.bcm.edu	37	6	30515043	30515043	+	Silent	SNP	T	T	C	rs3130247	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	90	76	86	0	0.844444	0	T|0.939;C|0.061	0.061	strong	.	GNL1	47	.	NM_005275	exon10	c.A1287G	p.A429A	GATCCCTGCCAGA	.	PASS	Atlas-SNP
FGFBP2	83888	hgsc.bcm.edu	37	4	15964485	15964485	+	Missense_Mutation	SNP	G	G	A	rs758329	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	9	5	22	0	0.555556	0	G|0.606;A|0.394	0.394	strong	FGFBP2,colon,carcinoma,0,2	FGFBP2	22	2	NM_031950	exon1	c.C268T	p.P90S	AGTAAGGTTTGGG	.	PASS	Atlas-SNP
CABP5	56344	hgsc.bcm.edu	37	19	48543923	48543923	+	Silent	SNP	C	C	A	rs12982629	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100	46	86	0	0.46	0	C|0.798;A|0.202	0.202	strong	.	CABP5	28	.	NM_019855	exon3	c.G177T	p.T59T	ACCCATCGTCCTC	.	PASS	Atlas-SNP
CNGB1	1258	hgsc.bcm.edu	37	16	57950057	57950057	+	Silent	SNP	G	G	A	rs376270	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98	98	139	0	1	0	A|0.342;C|0.004;G|0.647;N|0.000;T|0.007	0.342	strong	.	CNGB1	105	.	NM_001297	exon22	c.C2193T	p.N731N	CAGGTAGTTATTT	.	PASS	Atlas-SNP
DZANK1	55184	hgsc.bcm.edu	37	20	18445963	18445963	+	Silent	SNP	A	A	G	rs6035051	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51	22	41	0	0.431373	0	A|0.419;G|0.581	0.581	strong	DZANK1,caecum,carcinoma,+1,1	DZANK1	65	1	NM_001099407	exon2	c.T40C	p.L14L	CTCGTAATGGTAT	.	PASS	Atlas-SNP
BTN3A1	11119	hgsc.bcm.edu	37	6	26405835	26405835	+	Missense_Mutation	SNP	G	G	A	rs56161420	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	155	36	154	0	0.232258	0	G|0.835;A|0.165	0.165	strong	BTN3A1_ENST00000476549,NS,carcinoma,0,4	BTN3A1	80	4	NM_007048	exon2	c.G44A	p.R15H	ACTTTCGTGTCTG	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91	91	89	0	1	0	C|0.805;T|0.195	0.195	strong	.	FKBP15	128	.	NM_015258	exon4	c.G316A	p.A106T	CTCTGGCTGTGTG	.	PASS	Atlas-SNP
COMMD5	28991	hgsc.bcm.edu	37	8	146076708	146076708	+	Missense_Mutation	SNP	C	C	T	rs1209879	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	169	87	163	0	0.514793	0	T|0.254;G|0.001	0.254	strong	.	COMMD5	18	.	NM_001081004	exon2	c.G16A	p.A6T	TTGCAGCCCCCAC	.	PASS	Atlas-SNP
METTL12	751071	hgsc.bcm.edu	37	11	62434173	62434173	+	Missense_Mutation	SNP	G	G	A	rs11231181	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	43	25	75	0	0.581395	0	G|0.803;A|0.197	0.197	strong	.	METTL12	11	.	NM_001043229	exon3	c.G373A	p.G125S	GGCCCAGGCCAAA	.	PASS	Atlas-SNP
NDC80	10403	hgsc.bcm.edu	37	18	2616457	2616457	+	Missense_Mutation	SNP	G	G	C	rs9051	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	169	84	198	0	0.497041	0	G|0.806;C|0.194	0.194	strong	.	NDC80	62	.	NM_006101	exon17	c.G1813C	p.A605P	CAGATTGCTAAAG	.	PASS	Atlas-SNP
MARVELD3	91862	hgsc.bcm.edu	37	16	71660310	71660310	+	Missense_Mutation	SNP	G	G	A	rs4788821	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	32	18	46	0	0.5625	0	G|0.561;A|0.439	0.439	strong	.	MARVELD3	63	.	NM_001017967	exon1	c.G178A	p.E60K	GACCCGGAGAGAG	.	PASS	Atlas-SNP
PAPL	0	hgsc.bcm.edu	37	19	39589189	39589189	+	Silent	SNP	C	C	T	rs55878600	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	28	12	31	0	0.428571	0	C|0.796;T|0.204	0.204	strong	.	.	.	.	NM_001004318	exon3	c.C213T	p.P71P	CCTGCCCCTCCGC	.	PASS	Atlas-SNP
CEL	1056	hgsc.bcm.edu	37	9	135947034	135947034	+	Silent	SNP	G	G	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	37	18	27	3	0.486486	0.111111	.	.	none	CEL,NS,carcinoma,+2,2	CEL	71	2	NM_001807	exon11	c.G2154C	p.P718P	CGTGCCGCCCACG	.	scavenged	Atlas-SNP
KCNS3	3790	hgsc.bcm.edu	37	2	18113508	18113508	+	Silent	SNP	G	G	A	rs3747516	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94	40	90	0	0.425532	0	G|0.744;A|0.256	0.256	strong	.	KCNS3	85	.	NM_002252	exon3	c.G1233A	p.K411K	TTCCAAGTACTAC	.	PASS	Atlas-SNP
OR1S1	219959	hgsc.bcm.edu	37	11	57982896	57982896	+	Missense_Mutation	SNP	G	G	T	rs2903566	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94	94	92	0	1	0	G|0.565;T|0.435	0.435	strong	.	OR1S1	139	.	NM_001004458	exon1	c.G680T	p.S227I	CACTCAGCTTCTT	.	PASS	Atlas-SNP
KLK3	354	hgsc.bcm.edu	37	19	51361315	51361315	+	Silent	SNP	C	C	T	rs12946	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	42	21	43	0	0.5	0	C|0.890;T|0.110	0.110	strong	.	KLK3	76	.	NM_001030047	exon3	c.C237T	p.S79S	GCACAGCCTGTTT	.	PASS	Atlas-SNP
SPATA17	128153	hgsc.bcm.edu	37	1	217915324	217915324	+	Silent	SNP	C	C	T	rs34347452	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	40	18	37	0	0.45	0	C|0.870;T|0.130	0.130	strong	.	SPATA17	59	.	NM_138796	exon6	c.C403T	p.L135L	AAGGCACTGGAGG	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	129	59	146	0	0.457364	0	C|0.631;T|0.368	0.368	strong	.	MEP1B	54	.	NM_005925	exon14	c.C2084T	p.P695L	TGACTCCGCAAAA	.	PASS	Atlas-SNP
ALMS1	7840	hgsc.bcm.edu	37	2	73651967	73651967	+	Missense_Mutation	SNP	C	C	T	rs3813227	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	130	80	211	0	0.615385	0	C|0.661;T|0.339	0.339	strong	.	ALMS1	384	.	NM_015120	exon5	c.C1174T	p.R392C	GCTGCTCGTTCAT	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	210	110	159	1	0.52381	0.00628931	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	.	scavenged	Atlas-SNP
PTPRQ	374462	hgsc.bcm.edu	37	12	80865948	80865948	+	Silent	SNP	A	A	G	rs61729291	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	116	53	120	0	0.456897	0	A|0.969;G|0.031	0.031	strong	.	PTPRQ	119	.	NM_001145026	exon5	c.A588G	p.T196T	ATTTACAATGTAT	.	PASS	Atlas-SNP
RBBP6	5930	hgsc.bcm.edu	37	16	24583406	24583406	+	Silent	SNP	A	A	G	rs7593	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	107	106	108	0	0.990654	0	A|0.650;G|0.350	0.350	strong	.	RBBP6	158	.	NM_006910	exon18	c.A5019G	p.A1673A	GAAAGCAAAAGAG	.	PASS	Atlas-SNP
WBSCR28	135886	hgsc.bcm.edu	37	7	73279361	73279361	+	Silent	SNP	C	C	T	rs61742124	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	155	75	176	0	0.483871	0	C|0.789;T|0.211	0.211	strong	.	WBSCR28	24	.	NM_182504	exon2	c.C111T	p.L37L	CCTGCTCCTCAAG	.	PASS	Atlas-SNP
LEPR	3953	hgsc.bcm.edu	37	1	66058513	66058513	+	Missense_Mutation	SNP	A	A	G	rs1137101	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	118	45	139	0	0.381356	0	A|0.463;G|0.537	0.537	strong	.	LEPR	284	.	NM_001003680	exon6	c.A668G	p.Q223R	TTTTCCAGTCACC	.	PASS	Atlas-SNP
LAMA4	3910	hgsc.bcm.edu	37	6	112522852	112522852	+	Missense_Mutation	SNP	G	G	A	rs11757455	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49	22	53	0	0.44898	0	G|0.961;A|0.039	0.039	strong	.	LAMA4	227	.	NM_001105206	exon5	c.C460T	p.R154W	TGCACCGAACAGC	.	PASS	Atlas-SNP
STARD13	90627	hgsc.bcm.edu	37	13	33700374	33700374	+	Silent	SNP	T	T	G	rs1980781	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48	23	51	0	0.479167	0	T|0.780;G|0.220	0.220	strong	.	STARD13	100	.	NM_178006	exon7	c.A1926C	p.S642S	TGGAACTGACCTA	.	PASS	Atlas-SNP
IGSF22	283284	hgsc.bcm.edu	37	11	18743180	18743180	+	Missense_Mutation	SNP	C	C	G	rs10832975	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	111	111	105	2	1	0.0190476	C|0.636;G|0.364	0.364	strong	IGSF22_ENST00000513874,NS,carcinoma,0,2	IGSF22	211	2	NM_173588	exon4	c.G280C	p.A94P	GTTTGGCGTTCCC	.	scavenged	Atlas-SNP
EVA1A	84141	hgsc.bcm.edu	37	2	75720372	75720372	+	Missense_Mutation	SNP	C	C	T	rs11126472	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	58	10	101	0	0.172414	0	C|0.948;T|0.052	0.052	strong	.	.	.	.	NM_032181	exon4	c.G449A	p.R150H	TAGTAGCGATTCA	.	PASS	Atlas-SNP
SYNE1	23345	hgsc.bcm.edu	37	6	152532702	152532702	+	Missense_Mutation	SNP	T	T	C	rs35763277	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55	34	64	0	0.618182	0	T|0.988;C|0.012	0.012	strong	.	SYNE1	3227	.	NM_182961	exon124	c.A22516G	p.S7506G	GACGACTGAACAT	.	PASS	Atlas-SNP
ZBTB21	49854	hgsc.bcm.edu	37	21	43412705	43412705	+	Silent	SNP	A	A	G	rs61751943	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	105	42	82	0	0.4	0	A|0.931;G|0.069	0.069	strong	.	.	.	.	NM_001098402	exon3	c.T1500C	p.N500N	GTGCTCATTCACC	.	PASS	Atlas-SNP
SEH1L	81929	hgsc.bcm.edu	37	18	12984144	12984144	+	Missense_Mutation	SNP	C	C	A	rs6505776	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	164	163	180	0	0.993902	0	C|0.252;A|0.748	0.748	strong	.	SEH1L	33	.	NM_001013437	exon8	c.C1025A	p.T342N	GTTCAACTATTCC	.	PASS	Atlas-SNP
TANC1	85461	hgsc.bcm.edu	37	2	159954175	159954175	+	Missense_Mutation	SNP	C	C	T	rs34588551	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	18	92	0	0.285714	0	C|0.753;T|0.247	0.247	strong	.	TANC1	157	.	NM_033394	exon4	c.C88T	p.P30S	ACTTCTCCAGTCC	.	PASS	Atlas-SNP
PIWIL4	143689	hgsc.bcm.edu	37	11	94337220	94337220	+	Silent	SNP	C	C	T	rs593690	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	88	17	65	0	0.193182	0	C|0.455;T|0.545	0.545	strong	.	PIWIL4	70	.	NM_152431	exon13	c.C1636T	p.L546L	GTTCAGCTGGTAA	.	PASS	Atlas-SNP
KCNH2	3757	hgsc.bcm.edu	37	7	150649531	150649531	+	Silent	SNP	G	G	A	rs1805120	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	27	58	0	0.409091	0	G|0.708;A|0.292	0.292	strong	.	KCNH2	157	.	NM_000238	exon6	c.C1539T	p.F513F	AGAGCCGAAGATG	.	PASS	Atlas-SNP
CMPK2	129607	hgsc.bcm.edu	37	2	6990020	6990020	+	Silent	SNP	C	C	T	rs10495545	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	21	64	0	0.344262	0	C|0.876;N|0.001	.	strong	.	CMPK2	30	.	NM_207315	exon5	c.G1311A	p.T437T	TAATACCGTCTGC	.	PASS	Atlas-SNP
MMP24	10893	hgsc.bcm.edu	37	20	33855126	33855126	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	97	4	85	0	0.0412371	0	.	.	none	.	MMP24	35	.	NM_006690	exon6	c.C1098T	p.L366L	GCCCCTCGGGGAC	.	PASS	Atlas-SNP
RASGRF1	5923	hgsc.bcm.edu	37	15	79277511	79277511	+	Silent	SNP	A	A	G	rs2230518	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	106	46	112	0	0.433962	0	T|0.132;G|0.239;C|0.053;N|0.000;A|0.576	0.239	strong	.	RASGRF1	168	.	NM_002891	exon24	c.T3300C	p.N1100N	GTCCTCATTGCGG	.	PASS	Atlas-SNP
POM121L12	285877	hgsc.bcm.edu	37	7	53103571	53103571	+	Silent	SNP	G	G	A	rs11238248	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	23	22	45	0	0.956522	0	G|0.585;A|0.415	0.415	strong	.	POM121L12	146	.	NM_182595	exon1	c.G207A	p.G69G	GTGGGGGCGCCCG	.	PASS	Atlas-SNP
HHIPL2	79802	hgsc.bcm.edu	37	1	222713503	222713503	+	Silent	SNP	C	C	G	rs3748664	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	65	65	81	0	1	0	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	.	PASS	Atlas-SNP
OR2T12	127064	hgsc.bcm.edu	37	1	248458051	248458051	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	267	5	267	0	0.0187266	0	.	.	none	OR2T12,NS,carcinoma,0,1	OR2T12	113	1	NM_001004692	exon1	c.C830G	p.T277S	AACATAGTATAGA	.	scavenged	Atlas-SNP
SOCS6	9306	hgsc.bcm.edu	37	18	67992684	67992684	+	Silent	SNP	C	C	T	rs1047657	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	200	92	190	0	0.46	0	C|0.900;T|0.100	0.100	strong	SOCS6,NS,carcinoma,+2,2	SOCS6	54	2	NM_004232	exon2	c.C780T	p.R260R	AGGGCGCGCTTTC	.	PASS	Atlas-SNP
H2BFM	286436	hgsc.bcm.edu	37	X	103294760	103294760	+	Nonsense_Mutation	SNP	C	C	T	rs2301384	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	114	74	69	0	0.649123	0	C|0.676;T|0.324	0.324	strong	.	H2BFM	25	.	NM_001164416	exon1	c.C217T	p.Q73X	GTTCACCAGGGCC	.	PASS	Atlas-SNP
C4orf17	84103	hgsc.bcm.edu	37	4	100443720	100443720	+	Missense_Mutation	SNP	G	G	A	rs13143848	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110	49	107	0	0.445455	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
IQGAP3	128239	hgsc.bcm.edu	37	1	156526387	156526387	+	Missense_Mutation	SNP	C	C	G	rs11264498	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	90	90	124	1	1	0.00806452	C|0.513;G|0.487	0.487	strong	.	IQGAP3	146	.	NM_178229	exon12	c.G1228C	p.V410L	GGTACACTGGAGG	.	PASS	Atlas-SNP
TSPYL5	85453	hgsc.bcm.edu	37	8	98289329	98289329	+	Silent	SNP	G	G	A	rs34070970	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	34	23	31	0	0.676471	0	G|0.953;A|0.047	0.047	strong	.	TSPYL5	48	.	NM_033512	exon1	c.C744T	p.I248I	GCCCGGGATATTT	.	PASS	Atlas-SNP
ACTG1	71	hgsc.bcm.edu	37	17	79478007	79478007	+	Silent	SNP	G	G	A	rs1135989	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94	94	72	0	1	0	G|0.711;A|0.289	0.289	strong	.	ACTG1	55	.	NM_001614	exon5	c.C930T	p.A310A	CCTGTCGGCAATG	.	PASS	Atlas-SNP
CCDC168	643677	hgsc.bcm.edu	37	13	103397387	103397387	+	Missense_Mutation	SNP	T	T	G	rs7339187	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	58	21	71	0	0.362069	0	T|0.916;G|0.084	0.084	strong	.	.	.	.	NM_001146197	exon4	c.A5660C	p.Q1887P	CCATTTTGGGTCT	.	PASS	Atlas-SNP
PCBP3	54039	hgsc.bcm.edu	37	21	47329352	47329352	+	Silent	SNP	T	T	C	rs2277812	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	79	44	0	0.975309	0	T|0.204;C|0.796	0.796	strong	.	PCBP3	82	.	NM_001130141	exon6	c.T423C	p.C141C	CCAGTGTGGGTCC	.	PASS	Atlas-SNP
DNHD1	144132	hgsc.bcm.edu	37	11	6541225	6541225	+	Missense_Mutation	SNP	C	C	G	rs11603869	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	56	21	79	0	0.375	0	C|0.836;G|0.164	0.164	strong	.	DNHD1	198	.	NM_173589	exon8	c.C1678G	p.Q560E	TCATCACAGCTGG	.	PASS	Atlas-SNP
CERK	64781	hgsc.bcm.edu	37	22	47116905	47116905	+	Silent	SNP	G	G	A	rs12166204	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	37	85	0	0.440476	0	G|0.891;A|0.109	0.109	strong	.	CERK	40	.	NM_022766	exon2	c.C150T	p.C50C	CACAGAGCAGGCA	.	PASS	Atlas-SNP
OCA2	4948	hgsc.bcm.edu	37	15	28211921	28211921	+	Silent	SNP	G	G	A	rs1800411	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	114	113	115	0	0.991228	0	G|0.543;A|0.457	0.457	strong	OCA2,NS,carcinoma,-2,1	OCA2	173	1	NM_000275	exon15	c.C1551T	p.C517C	AACAAGGCAAATC	.	PASS	Atlas-SNP
SPTLC3	55304	hgsc.bcm.edu	37	20	13071816	13071816	+	Silent	SNP	C	C	T	rs6109692	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	157	87	138	0	0.55414	0	C|0.913;T|0.087	0.087	strong	.	SPTLC3	78	.	NM_018327	exon5	c.C693T	p.F231F	GGGATTCGCAACT	.	PASS	Atlas-SNP
CCDC66	285331	hgsc.bcm.edu	37	3	56628031	56628031	+	Missense_Mutation	SNP	G	G	A	rs7637449	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	113	113	124	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
TACC2	10579	hgsc.bcm.edu	37	10	123847355	123847355	+	Silent	SNP	G	G	A	rs10788237	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	42	20	33	0	0.47619	0	G|0.767;A|0.233	0.233	strong	TACC2,colon,carcinoma,0,1	TACC2	271	1	NM_206862	exon4	c.G5340A	p.G1780G	GCCAGGGCCTGAG	.	PASS	Atlas-SNP
FLAD1	80308	hgsc.bcm.edu	37	1	154956487	154956487	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	103	31	102	0	0.300971	0	.	.	none	.	FLAD1	52	.	NM_025207	exon1	c.C317A	p.S106Y	AACTTTCTCCGGG	.	PASS	Atlas-SNP
COL13A1	1305	hgsc.bcm.edu	37	10	71678058	71678058	+	Silent	SNP	C	C	G	rs2274181	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	34	13	40	0	0.382353	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
TRPV1	7442	hgsc.bcm.edu	37	17	3495374	3495374	+	Missense_Mutation	SNP	G	G	A	rs222749	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79	33	43	0	0.417722	0	G|0.903;A|0.097	0.097	strong	.	TRPV1	99	.	NM_018727	exon2	c.C271T	p.P91S	CGGTGGGGCCGTC	.	PASS	Atlas-SNP
C3orf17	25871	hgsc.bcm.edu	37	3	112724619	112724619	+	Missense_Mutation	SNP	A	A	G	rs7628368	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	116	65	129	0	0.560345	0	A|0.949;G|0.051	0.051	strong	C3orf17,lymph_node,lymphoid_neoplasm,0,1	C3orf17	37	1	NM_015412	exon9	c.T1468C	p.S490P	AGTGTGAGAGTCT	.	PASS	Atlas-SNP
C15orf41	84529	hgsc.bcm.edu	37	15	36946303	36946303	+	Missense_Mutation	SNP	C	C	G	rs3784678	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110	53	118	0	0.481818	0	C|0.492;G|0.508	0.508	strong	.	C15orf41	24	.	NM_001130010	exon4	c.C217G	p.L73V	AGGTACCTGAATG	.	PASS	Atlas-SNP
TTLL12	23170	hgsc.bcm.edu	37	22	43576904	43576904	+	Silent	SNP	G	G	A	rs2071723	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94	44	103	1	0.468085	0.00970874	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	.	scavenged	Atlas-SNP
TNFRSF25	8718	hgsc.bcm.edu	37	1	6524688	6524688	+	Silent	SNP	T	T	C	rs3170675	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	46	73	0	0.605263	0	T|0.965;C|0.035	0.035	strong	.	TNFRSF25	22	.	NM_148966	exon4	c.A387G	p.Q129Q	GACACATTGGCTG	.	PASS	Atlas-SNP
CTSB	1508	hgsc.bcm.edu	37	8	11710888	11710888	+	Missense_Mutation	SNP	G	G	C	rs12338	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	46	28	48	0	0.608696	0	G|0.625;C|0.375	0.375	strong	.	CTSB	24	.	NM_147780	exon4	c.C76G	p.L26V	CCGACAGGGGATG	.	PASS	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	160	81	127	0	0.50625	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
KCNA1	3736	hgsc.bcm.edu	37	12	5021984	5021984	+	Silent	SNP	T	T	A	rs4766309	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	42	42	48	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
OR2T34	127068	hgsc.bcm.edu	37	1	248737319	248737319	+	Missense_Mutation	SNP	G	G	A	rs77940099	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	314	87	229	1	0.27707	0.00436681	G|0.841;A|0.159	0.159	strong	OR2T34,NS,carcinoma,0,1	OR2T34	72	1	NM_001001821	exon1	c.C740T	p.S247F	TGGGAGGAGCAGG	.	scavenged	Atlas-SNP
ABCG8	64241	hgsc.bcm.edu	37	2	44104925	44104925	+	Missense_Mutation	SNP	T	T	C	rs6544718	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	164	161	139	1	0.981707	0.00719424	C|0.867;T|0.133	0.867	strong	.	ABCG8	98	.	NM_022437	exon13	c.T1895C	p.V632A	TCAGTGTCATGGA	.	PASS	Atlas-SNP
TRIM45	80263	hgsc.bcm.edu	37	1	117659283	117659283	+	Missense_Mutation	SNP	C	C	T	rs61758105	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73	40	80	0	0.547945	0	C|0.989;T|0.011	0.011	strong	.	TRIM45	55	.	NM_025188	exon3	c.G1307A	p.G436E	TTGTCTCCTCCCC	.	PASS	Atlas-SNP
KIAA1804	0	hgsc.bcm.edu	37	1	233515071	233515071	+	Silent	SNP	C	C	T	rs963982	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	59	21	65	0	0.355932	0	C|0.775;T|0.225	0.225	strong	.	KIAA1804	129	.	NM_032435	exon9	c.C2319T	p.S773S	CAGAAGCGCCAGT	.	PASS	Atlas-SNP
MTNR1A	4543	hgsc.bcm.edu	37	4	187455399	187455399	+	Missense_Mutation	SNP	C	C	T	rs28383653	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69	33	71	0	0.478261	0	C|0.988;T|0.012	0.012	strong	.	MTNR1A	46	.	NM_005958	exon2	c.G497A	p.G166E	AGAGTCCCTGCAC	.	PASS	Atlas-SNP
MOB3C	148932	hgsc.bcm.edu	37	1	47080741	47080741	+	Missense_Mutation	SNP	C	C	T	rs12029680	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	123	40	130	0	0.325203	0	C|0.666;T|0.334	0.334	strong	.	MOB3C	1	.	NM_145279	exon1	c.G8A	p.R3H	TTTCTGCGCTTCA	.	PASS	Atlas-SNP
SLC4A4	8671	hgsc.bcm.edu	37	4	72433545	72433545	+	Missense_Mutation	SNP	A	A	C	rs1062677	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	166	86	172	0	0.518072	0	A|0.847;C|0.153	0.153	strong	.	SLC4A4	269	.	NM_001134742	exon25	c.A3220C	p.I1074L	ATTAGAATAGAAC	.	PASS	Atlas-SNP
DKKL1	27120	hgsc.bcm.edu	37	19	49878196	49878196	+	Missense_Mutation	SNP	G	G	A	rs2288481	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	37	22	35	0	0.594595	0	G|0.767;A|0.233	0.233	strong	.	DKKL1	23	.	NM_014419	exon5	c.G640A	p.E214K	GTCCTAGAAGAGG	.	PASS	Atlas-SNP
RBM19	9904	hgsc.bcm.edu	37	12	114377835	114377835	+	Missense_Mutation	SNP	A	A	G	rs2290788	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	19	67	0	0.306452	0	A|0.832;G|0.168	0.168	strong	.	RBM19	117	.	NM_001146699	exon15	c.T1868C	p.I623T	GCAGTGATTCCGC	.	PASS	Atlas-SNP
YAE1D1	57002	hgsc.bcm.edu	37	7	39610177	39610177	+	Missense_Mutation	SNP	A	A	G	rs6947660	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	46	82	0	0.978723	0	A|0.858;G|0.142	0.142	strong	.	YAE1D1	2	.	NM_020192	exon2	c.A202G	p.K68E	TATAAGAAAGGTG	.	PASS	Atlas-SNP
REST	5978	hgsc.bcm.edu	37	4	57798189	57798189	+	Silent	SNP	G	G	A	rs2227901	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	131	57	121	0	0.435115	0	G|0.791;A|0.209	0.209	strong	.	REST	104	.	NM_001193508	exon4	c.G3165A	p.A1055A	CAAAGCGGCTAAG	.	PASS	Atlas-SNP
TEC	7006	hgsc.bcm.edu	37	4	48147309	48147309	+	Silent	SNP	T	T	C	rs17574371	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	88	46	101	0	0.522727	0	T|0.704;C|0.296	0.296	strong	.	TEC	81	.	NM_003215	exon14	c.A1257G	p.K419K	TGTCAGTTTCCTG	.	PASS	Atlas-SNP
CD101	9398	hgsc.bcm.edu	37	1	117560929	117560929	+	Silent	SNP	C	C	A	rs3736907	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	127	67	117	0	0.527559	0	C|0.812;N|0.000	.	strong	.	CD101	95	.	NM_001256109	exon6	c.C1764A	p.I588I	TCACATCTTCCAC	.	PASS	Atlas-SNP
SPATA13	221178	hgsc.bcm.edu	37	13	24797169	24797169	+	Silent	SNP	G	G	A	rs369711697		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	42	73	0	0.518519	0	.	.	weak	SPATA13_ENST00000382108,NS,carcinoma,+1,2	SPATA13	92	2	NM_001166271	exon2	c.G102A	p.S34S	AGGCTCGGACCTG	.	PASS	Atlas-SNP
MCEE	84693	hgsc.bcm.edu	37	2	71351487	71351487	+	Missense_Mutation	SNP	G	G	A	rs11541017	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	75	117	0	0.986842	0	G|0.753;A|0.247	0.247	strong	MCEE,colon,carcinoma,0,2	MCEE	19	2	NM_032601	exon2	c.C227T	p.A76V	GGGACCGCTTCAC	.	PASS	Atlas-SNP
ARHGEF28	64283	hgsc.bcm.edu	37	5	73163965	73163965	+	Missense_Mutation	SNP	C	C	A	rs2973558	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	128	62	114	0	0.484375	0	C|0.764;A|0.236	0.236	strong	.	.	.	.	NM_001080479	exon20	c.C2338A	p.H780N	AGTGACCATAACA	.	PASS	Atlas-SNP
SPANXE	171489	hgsc.bcm.edu	37	X	140785739	140785739	+	Missense_Mutation	SNP	A	A	C	rs149295712	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	576	76	371	0	0.131944	0	.	.	weak	.	.	.	.	NM_145665	exon2	c.T177G	p.F59L	TCTTTTAAAGTTC	.	PASS	Atlas-SNP
PREX1	57580	hgsc.bcm.edu	37	20	47261017	47261017	+	Silent	SNP	T	T	C	rs6066802	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	31	59	0	0.508197	0	T|0.728;C|0.272	0.272	strong	PREX1,NS,carcinoma,0,1	PREX1	441	1	NM_020820	exon27	c.A3531G	p.R1177R	CGAGTCTCGATTG	.	PASS	Atlas-SNP
STAB1	23166	hgsc.bcm.edu	37	3	52537109	52537109	+	Silent	SNP	G	G	A	rs112337417	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	97	54	101	0	0.556701	0	G|0.970;A|0.030	0.030	strong	.	STAB1	178	.	NM_015136	exon7	c.G678A	p.Q226Q	ACAGCAGGGCAGT	.	PASS	Atlas-SNP
UBN1	29855	hgsc.bcm.edu	37	16	4930100	4930100	+	Silent	SNP	C	C	T	rs1876359	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	113	58	110	0	0.513274	0	C|0.650;T|0.350	0.350	strong	.	UBN1	88	.	NM_001079514	exon18	c.C3372T	p.H1124H	GCTTCACGGGAAA	.	PASS	Atlas-SNP
ORC4	5000	hgsc.bcm.edu	37	2	148716428	148716428	+	Missense_Mutation	SNP	T	T	C	rs2307394	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	147	147	227	0	1	0	T|0.653;C|0.346	0.346	strong	.	ORC4	40	.	NM_002552	exon5	c.A233G	p.N78S	GCATGATTTATTA	.	PASS	Atlas-SNP
SHPK	23729	hgsc.bcm.edu	37	17	3526637	3526637	+	Missense_Mutation	SNP	C	C	T	rs150857	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	99	41	93	0	0.414141	0	C|0.763;T|0.237	0.237	strong	.	SHPK	34	.	NM_013276	exon4	c.G643A	p.E215K	ACGTCTCTACGTT	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228504591	228504591	+	Missense_Mutation	SNP	C	C	A	rs61825301	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	31	42	0	0.596154	0	C|0.841;A|0.159	0.159	strong	.	OBSCN	2142	.	NM_001271223	exon62	c.C16338A	p.H5446Q	TCACCACGCCCTA	.	PASS	Atlas-SNP
CRYBA1	1411	hgsc.bcm.edu	37	17	27580756	27580756	+	Silent	SNP	C	C	T	rs1047790	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	70	70	64	0	1	0	C|0.756;T|0.244	0.244	strong	.	CRYBA1	15	.	NM_005208	exon5	c.C456T	p.G152G	CATGGGCTGGTTC	.	PASS	Atlas-SNP
TEX101	83639	hgsc.bcm.edu	37	19	43920612	43920612	+	Missense_Mutation	SNP	G	G	T	rs35033974	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	127	66	111	0	0.519685	0	G|0.921;T|0.079	0.079	strong	.	TEX101	28	.	NM_031451	exon7	c.G350T	p.G117V	CTCCCGGCCTGAT	.	PASS	Atlas-SNP
KIAA1430	57587	hgsc.bcm.edu	37	4	186097045	186097045	+	Silent	SNP	C	C	T	rs6855305	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	157	78	177	0	0.496815	0	C|0.502;N|0.000	.	strong	.	KIAA1430	55	.	NM_020827	exon3	c.G1215A	p.P405P	GCTTCCCGGCTTT	.	PASS	Atlas-SNP
RMDN2	151393	hgsc.bcm.edu	37	2	38178406	38178406	+	Silent	SNP	A	A	G	rs4670799	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	33	33	27	0	1	0	A|0.638;G|0.362	0.362	strong	.	.	.	.	NM_144713	exon2	c.A48G	p.R16R	CCAACGATGTTCT	.	PASS	Atlas-SNP
FAM69C	125704	hgsc.bcm.edu	37	18	72103782	72103782	+	Missense_Mutation	SNP	T	T	C	rs2278154	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	38	12	31	0	0.315789	0	T|0.666;C|0.334	0.334	strong	.	FAM69C	45	.	NM_001044369	exon4	c.A1214G	p.Q405R	AGGAGTTGGCGAA	.	PASS	Atlas-SNP
SLC26A7	115111	hgsc.bcm.edu	37	8	92330561	92330561	+	Silent	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	10	101	0	0.116279	0	.	.	none	.	SLC26A7	207	.	NM_134266	exon5	c.T595C	p.L199L	TATCTCTTGGGAA	.	PASS	Atlas-SNP
ERLIN1	10613	hgsc.bcm.edu	37	10	101912064	101912064	+	Missense_Mutation	SNP	T	T	C	rs2862954	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	199	91	218	0	0.457286	0	A|0.005;C|0.270	0.270	strong	.	.	.	.	NM_006459	exon11	c.A871G	p.I291V	AAGCAATGGCCTG	.	PASS	Atlas-SNP
SYNC	81493	hgsc.bcm.edu	37	1	33160644	33160644	+	Missense_Mutation	SNP	T	T	G	rs3795424	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69	34	61	0	0.492754	0	T|0.959;G|0.041	0.041	strong	.	SYNC	36	.	NM_001161708	exon2	c.A1055C	p.E352A	TTCCTCTCTAGGA	.	PASS	Atlas-SNP
DNAJC13	23317	hgsc.bcm.edu	37	3	132221139	132221139	+	Missense_Mutation	SNP	C	C	T	rs55825559	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	115	59	125	0	0.513043	0	C|0.981;T|0.019	0.019	strong	.	DNAJC13	253	.	NM_015268	exon40	c.C4543T	p.P1515S	AGTATTCCCCGCG	.	PASS	Atlas-SNP
TAS2R50	259296	hgsc.bcm.edu	37	12	11138852	11138852	+	Missense_Mutation	SNP	C	C	T	rs1376251	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69	30	96	0	0.434783	0	C|0.687;A|0.002	.	strong	.	TAS2R50	37	.	NM_176890	exon1	c.G608A	p.C203Y	TGTTTACACAGAG	.	PASS	Atlas-SNP
CCDC50	152137	hgsc.bcm.edu	37	3	191075902	191075902	+	Silent	SNP	C	C	T	rs11542549	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110	56	124	0	0.509091	0	C|0.584;A|0.042	.	strong	.	CCDC50	39	.	NM_174908	exon3	c.C228T	p.R76R	GAAGCGCTACAAA	.	PASS	Atlas-SNP
SOCS5	9655	hgsc.bcm.edu	37	2	46986416	46986416	+	Silent	SNP	A	A	G	rs6738426	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	217	101	212	0	0.465438	0	A|0.715;G|0.285	0.285	strong	.	SOCS5	62	.	NM_144949	exon2	c.A747G	p.T249T	TGATACATTTGAT	.	PASS	Atlas-SNP
ETV3L	440695	hgsc.bcm.edu	37	1	157067699	157067699	+	Missense_Mutation	SNP	T	T	C	rs61736984	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	34	53	0	0.641509	0	T|0.957;C|0.043	0.043	strong	.	ETV3L	73	.	NM_001004341	exon4	c.A568G	p.T190A	CAGAGGTCTCTGG	.	PASS	Atlas-SNP
AGBL1	123624	hgsc.bcm.edu	37	15	86838497	86838497	+	Silent	SNP	C	C	T	rs9630451	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	39	56	0	0.722222	0	C|0.819;T|0.181	0.181	strong	.	AGBL1	151	.	NM_152336	exon16	c.C2094T	p.D698D	TCTTGACATCCTG	.	PASS	Atlas-SNP
CNGA4	1262	hgsc.bcm.edu	37	11	6262715	6262715	+	Silent	SNP	G	G	A	rs7129498	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	49	79	0	0.569767	0	G|0.774;A|0.226	0.226	strong	.	CNGA4	96	.	NM_001037329	exon5	c.G972A	p.Q324Q	CTTACAGCACTTG	.	PASS	Atlas-SNP
PDE4DIP	9659	hgsc.bcm.edu	37	1	145021150	145021150	+	Missense_Mutation	SNP	T	T	C	rs11538401	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	216	28	202	1	0.12963	0.00495049	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	.	scavenged	Atlas-SNP
SERPINA9	327657	hgsc.bcm.edu	37	14	94933640	94933640	+	Missense_Mutation	SNP	A	A	T	rs28583900	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	115	53	102	0	0.46087	0	A|0.681;T|0.319	0.319	strong	.	SERPINA9	105	.	NM_175739	exon3	c.T762A	p.H254Q	GGGGACATGCACA	.	PASS	Atlas-SNP
ADAMTS2	9509	hgsc.bcm.edu	37	5	178634672	178634672	+	Missense_Mutation	SNP	C	C	T	rs398829	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	40	63	0	0.645161	0	C|0.635;T|0.365	0.365	strong	.	ADAMTS2	190	.	NM_021599	exon4	c.G733A	p.V245I	CTAGGACGCCCAG	.	PASS	Atlas-SNP
C9orf84	158401	hgsc.bcm.edu	37	9	114476748	114476748	+	Missense_Mutation	SNP	T	T	A	rs11791445	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	171	74	206	0	0.432749	0	T|0.809;A|0.191	0.191	strong	C9orf84_ENST00000374287,NS,adenoma,0,2	C9orf84	207	2	NM_173521	exon15	c.A2200T	p.M734L	TTTGCATCCAACT	.	PASS	Atlas-SNP
PGM2	55276	hgsc.bcm.edu	37	4	37857342	37857342	+	Silent	SNP	G	G	C	rs11554509	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	122	48	108	0	0.393443	0	G|0.826;C|0.174	0.174	strong	.	PGM2	45	.	NM_018290	exon13	c.G1716C	p.L572L	AGAGCTGTGTGCC	.	PASS	Atlas-SNP
ICAM3	3385	hgsc.bcm.edu	37	19	10444603	10444603	+	Missense_Mutation	SNP	C	C	G	rs2230399	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	229	98	216	0	0.427948	0	C|0.889;G|0.111	0.111	strong	ICAM3,NS,adenoma,0,1	ICAM3	29	1	NM_002162	exon7	c.G1574C	p.S525T	TAGGTGCTCTCCT	.	PASS	Atlas-SNP
DND1	373863	hgsc.bcm.edu	37	5	140052331	140052331	+	Silent	SNP	G	G	T	rs200268202	byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	17	8	15	1	0.470588	0.0666667	G|0.952;T|0.047	0.047	strong	DND1,NS,carcinoma,0,1	DND1	15	1	NM_194249	exon3	c.C303A	p.A101A	GGCATAGGCGAAG	.	scavenged	Atlas-SNP
RNF207	388591	hgsc.bcm.edu	37	1	6279370	6279370	+	Missense_Mutation	SNP	G	G	C	rs846111	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	207	115	187	1	0.555556	0.00534759	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
CD97	976	hgsc.bcm.edu	37	19	14512489	14512489	+	Missense_Mutation	SNP	G	G	A	rs2230748	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69	28	61	0	0.405797	0	G|0.848;A|0.152	0.152	strong	.	CD97	86	.	NM_078481	exon11	c.G1100A	p.R367Q	AGGAGCGGGGGGA	.	PASS	Atlas-SNP
ZNF668	79759	hgsc.bcm.edu	37	16	31075175	31075175	+	Silent	SNP	G	G	A	rs2303223	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	36	65	0	0.486486	0	G|0.657;A|0.343	0.343	strong	ZNF668,NS,carcinoma,-2,1	ZNF668	121	1	NM_001172669	exon3	c.C675T	p.G225G	GGCTTTGCCGCAA	.	PASS	Atlas-SNP
ZNF417	147687	hgsc.bcm.edu	37	19	58421128	58421128	+	Missense_Mutation	SNP	C	C	T	rs3826671	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	518	211	325	2	0.407336	0.00615385	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
SBF1	6305	hgsc.bcm.edu	37	22	50898026	50898026	+	Silent	SNP	G	G	A	rs58335489	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	37	18	54	0	0.486486	0	G|0.848;A|0.152	0.152	strong	.	SBF1	211	.	NM_002972	exon27	c.C3561T	p.Y1187Y	CTGGCGGTAGCAG	.	PASS	Atlas-SNP
ASXL3	80816	hgsc.bcm.edu	37	18	31326554	31326554	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	20	7	21	0	0.35	0	.	.	none	ASXL3_ENST00000269197,NS,carcinoma,-1,1	ASXL3	405	1	NM_030632	exon12	c.C6742T	p.R2248X	GTTGTACGATAAG	.	PASS	Atlas-SNP
DNMT3A	1788	hgsc.bcm.edu	37	2	25469502	25469502	+	Silent	SNP	C	C	T	rs2276598	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	33	75	0	0.532258	0	C|0.792;T|0.208	0.208	strong	.	DNMT3A	1807	.	NM_175629	exon10	c.G1266A	p.L422L	TGGCTCCAGGCCC	.	PASS	Atlas-SNP
MDC1	9656	hgsc.bcm.edu	37	6	30680916	30680916	+	Missense_Mutation	SNP	C	C	T	rs9262152	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	177	31	151	0	0.175141	0	C|0.897;T|0.103	0.103	strong	.	MDC1	218	.	NM_014641	exon5	c.G803A	p.R268K	TTGTCCCTCTCCT	.	PASS	Atlas-SNP
HNRNPCL1	343069	hgsc.bcm.edu	37	1	12907385	12907385	+	Missense_Mutation	SNP	G	G	A	rs150590256	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	213	8	132	12	0.0375587	0.0909091	.	.	weak	HNRNPCL1,NS,carcinoma,0,1	HNRNPCL1	68	1	NM_001013631	exon2	c.C758T	p.P253L	TCCAGTGGGTCCC	.	scavenged	Atlas-SNP
SLC12A3	6559	hgsc.bcm.edu	37	16	56904075	56904075	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80	4	90	0	0.05	0	.	.	none	.	SLC12A3	99	.	NM_001126108	exon5	c.C669T	p.F223F	CATTTTCGCTTTC	.	PASS	Atlas-SNP
RRP12	23223	hgsc.bcm.edu	37	10	99125949	99125949	+	Missense_Mutation	SNP	C	C	T	rs2275580	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	42	42	38	0	1	0	C|0.553;T|0.447	0.447	strong	.	RRP12	97	.	NM_015179	exon29	c.G3433A	p.G1145S	TGAAGCCGTGGTC	.	PASS	Atlas-SNP
ZNF366	167465	hgsc.bcm.edu	37	5	71757267	71757267	+	Silent	SNP	C	C	T	rs78980395	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	31	52	0	0.596154	0	C|0.950;T|0.050	0.050	strong	.	ZNF366	108	.	NM_152625	exon2	c.G57A	p.V19V	CTTCTTCACAGCC	.	PASS	Atlas-SNP
PTPRN2	5799	hgsc.bcm.edu	37	7	157396697	157396697	+	Silent	SNP	G	G	A	rs17853260	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100	37	101	0	0.37	0	G|0.779;A|0.221	0.221	strong	PTPRN2,NS,carcinoma,0,1	PTPRN2	243	1	NM_002847	exon16	c.C2415T	p.P805P	TACGATGGGGCTA	.	PASS	Atlas-SNP
VSIG10	54621	hgsc.bcm.edu	37	12	118520170	118520170	+	Silent	SNP	G	G	A	rs7488309	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68	26	99	0	0.382353	0	G|0.506;A|0.494	0.494	strong	VSIG10,colon,carcinoma,0,1	VSIG10	41	1	NM_019086	exon3	c.C426T	p.Y142Y	GGCTGCGTAGAGG	.	PASS	Atlas-SNP
INPP5B	3633	hgsc.bcm.edu	37	1	38343863	38343863	+	Silent	SNP	G	G	A	rs141357169	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	92	37	118	0	0.402174	0	G|0.997;A|0.003	0.003	strong	.	INPP5B	76	.	NM_005540	exon16	c.C1674T	p.I558I	TACCCCGATGTCA	.	PASS	Atlas-SNP
C2orf49	79074	hgsc.bcm.edu	37	2	105954140	105954140	+	Silent	SNP	G	G	A	rs55772482	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	30	66	0	0.483871	0	G|0.927;A|0.073	0.073	strong	C2orf49,NS,carcinoma,+2,1	C2orf49	19	1	NM_024093	exon1	c.G96A	p.E32E	TCTGGAGCAGGTT	.	PASS	Atlas-SNP
TMEM63C	57156	hgsc.bcm.edu	37	14	77708804	77708804	+	Silent	SNP	C	C	T	rs61731611	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	107	35	107	0	0.327103	0	C|0.813;T|0.187	0.187	strong	.	TMEM63C	77	.	NM_020431	exon14	c.C1179T	p.D393D	CAAAGACATTATT	.	PASS	Atlas-SNP
SH3YL1	26751	hgsc.bcm.edu	37	2	224919	224919	+	Silent	SNP	A	A	G	rs2290911	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	243	119	270	0	0.489712	0	A|0.752;G|0.248	0.248	strong	.	SH3YL1	49	.	NM_015677	exon9	c.T783C	p.S261S	TCTGTTACCTGCC	.	PASS	Atlas-SNP
BRD4	23476	hgsc.bcm.edu	37	19	15349962	15349962	+	Silent	SNP	G	G	A	rs118000160	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	104	55	116	0	0.528846	0	G|0.997;A|0.003	0.003	strong	.	BRD4	172	.	NM_058243	exon18	c.C3690T	p.A1230A	CCGAGCGGCGCGG	.	PASS	Atlas-SNP
TELO2	9894	hgsc.bcm.edu	37	16	1559838	1559838	+	Silent	SNP	T	T	C	rs3180228	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	20	9	28	0	0.45	0	T|0.598;C|0.402	0.402	strong	.	TELO2	44	.	NM_016111	exon21	c.T2415C	p.A805A	CGTGGCTGAGAAA	.	PASS	Atlas-SNP
UBE2J1	51465	hgsc.bcm.edu	37	6	90039670	90039670	+	Missense_Mutation	SNP	G	G	C	rs10502	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	41	90	0	0.476744	0	G|0.396;C|0.604	0.604	strong	.	UBE2J1	28	.	NM_016021	exon8	c.C685G	p.L229V	TCTGGAGTCCGTA	.	PASS	Atlas-SNP
DEPDC5	9681	hgsc.bcm.edu	37	22	32217539	32217539	+	Missense_Mutation	SNP	C	C	T	rs16989528	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	41	99	0	0.476744	0	C|0.967;T|0.033	0.033	strong	.	DEPDC5	266	.	NM_001136029	exon22	c.C1922T	p.A641V	ATATGGCGGAGCT	.	PASS	Atlas-SNP
UPK1A	11045	hgsc.bcm.edu	37	19	36159368	36159368	+	Missense_Mutation	SNP	T	T	G	rs2267586	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	90	53	89	2	0.588889	0.0224719	T|0.893;G|0.107	0.107	strong	UPK1A,NS,carcinoma,0,1	UPK1A	23	1	NM_007000	exon2	c.T97G	p.S33A	GGCCTGTCCCTGT	.	scavenged	Atlas-SNP
OR2F2	135948	hgsc.bcm.edu	37	7	143632833	143632833	+	Missense_Mutation	SNP	A	A	G	rs13229174	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	181	104	226	0	0.574586	0	A|0.871;G|0.129	0.129	strong	.	OR2F2	63	.	NM_001004685	exon1	c.A508G	p.T170A	ATGTGCACTAACA	.	PASS	Atlas-SNP
ANKLE2	23141	hgsc.bcm.edu	37	12	133306503	133306503	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	223	5	184	0	0.0224215	0	.	.	none	ANKLE2,NS,carcinoma,+1,1	ANKLE2	76	1	NM_015114	exon11	c.T2245C	p.S749P	TCTTGGAAACGCT	.	scavenged	Atlas-SNP
CDHR3	222256	hgsc.bcm.edu	37	7	105662690	105662690	+	Silent	SNP	T	T	C	rs10258293	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	252	122	328	0	0.484127	0	T|0.839;C|0.161	0.161	strong	.	CDHR3	153	.	NM_152750	exon14	c.T1872C	p.N624N	TTCCAATGTCACA	.	PASS	Atlas-SNP
SPTBN1	6711	hgsc.bcm.edu	37	2	54886347	54886347	+	Silent	SNP	G	G	A	rs1052820	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85	44	77	0	0.517647	0	G|0.724;A|0.276	0.276	strong	SPTBN1,NS,carcinoma,0,1	SPTBN1	378	1	NM_003128	exon31	c.G6300A	p.P2100P	GCGGCCGCCTTCT	.	PASS	Atlas-SNP
DHRS7C	201140	hgsc.bcm.edu	37	17	9676148	9676148	+	Silent	SNP	C	C	T	rs2280489	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	24	23	26	0	0.958333	0	T|0.103;C|0.897	0.103	strong	.	DHRS7C	34	.	NM_001220493	exon5	c.G666A	p.P222P	GAAAGTCGGGCTC	.	PASS	Atlas-SNP
OR56A1	120796	hgsc.bcm.edu	37	11	6048056	6048056	+	Silent	SNP	T	T	C	rs11040335	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68	33	101	0	0.485294	0	T|0.695;C|0.305	0.305	strong	.	OR56A1	73	.	NM_001001917	exon1	c.A879G	p.A293A	GTTCAATGCAGGA	.	PASS	Atlas-SNP
LTF	4057	hgsc.bcm.edu	37	3	46488854	46488854	+	Silent	SNP	T	T	C	rs2239692	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	90	47	104	0	0.522222	0	T|0.845;C|0.155	0.155	strong	.	LTF	98	.	NM_002343	exon10	c.A1248G	p.G416G	CACATATCCTCCA	.	PASS	Atlas-SNP
MFRP	83552	hgsc.bcm.edu	37	11	119216279	119216279	+	Silent	SNP	G	G	A	rs36015759	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	58	10	31	0	0.172414	0	G|0.781;A|0.219	0.219	strong	.	MFRP	63	.	NM_031433	exon5	c.C492T	p.Y164Y	GGGGGGGTAAGGG	.	PASS	Atlas-SNP
ZNF419	79744	hgsc.bcm.edu	37	19	58002964	58002964	+	Silent	SNP	G	G	C	rs8108040	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	128	123	168	1	0.960938	0.00595238	G|0.730;C|0.270	0.270	strong	.	ZNF419	134	.	NM_001098494	exon3	c.G201C	p.L67L	CTCTCTGGGTAAG	.	PASS	Atlas-SNP
SLC25A29	123096	hgsc.bcm.edu	37	14	100759046	100759046	+	Silent	SNP	C	C	A	rs3825555	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	41	41	25	0	1	0	C|0.465;A|0.535	0.535	strong	SLC25A29,NS,carcinoma,0,1	SLC25A29	14	1	NM_001039355	exon4	c.G486T	p.T162T	GCTGGGCGTCTCA	.	PASS	Atlas-SNP
IFT172	26160	hgsc.bcm.edu	37	2	27676287	27676287	+	Silent	SNP	A	A	T	rs56076827	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73	30	71	0	0.410959	0	A|0.641;T|0.359	0.359	strong	.	IFT172	119	.	NM_015662	exon35	c.T3915A	p.S1305S	GTTTCCAGAGTCT	.	PASS	Atlas-SNP
RHBDD3	25807	hgsc.bcm.edu	37	22	29659960	29659960	+	Silent	SNP	C	C	T	rs879580	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	25	65	0	0.462963	0	C|0.814;T|0.186	0.186	strong	.	RHBDD3	17	.	NM_012265	exon4	c.G396A	p.E132E	GTGTCCCTCCCCA	.	PASS	Atlas-SNP
PTBP1	5725	hgsc.bcm.edu	37	19	804642	804642	+	Silent	SNP	C	C	T	rs3170451	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	39	24	53	1	0.615385	0.0188679	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	.	scavenged	Atlas-SNP
CRYBA1	1411	hgsc.bcm.edu	37	17	27576202	27576202	+	Missense_Mutation	SNP	C	C	T	rs142631461	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	34	64	0	0.641509	0	C|0.983;T|0.017	0.017	strong	.	CRYBA1	15	.	NM_005208	exon2	c.C74T	p.P25L	CTACGCCGGGGTC	.	PASS	Atlas-SNP
PPP1R15A	23645	hgsc.bcm.edu	37	19	49379182	49379182	+	Silent	SNP	G	G	C	rs527	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	88	38	70	0	0.431818	0	G|0.646;C|0.354	0.354	strong	.	PPP1R15A	48	.	NM_014330	exon3	c.G1977C	p.S659S	CCGCTCGTCTGCT	.	PASS	Atlas-SNP
ACSF3	197322	hgsc.bcm.edu	37	16	89199651	89199651	+	Silent	SNP	G	G	A	rs12447947	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	28	66	0	0.528302	0	G|0.746;A|0.254	0.254	strong	.	ACSF3	40	.	NM_174917	exon8	c.G1347A	p.L449L	CACCCTGGATGGC	.	PASS	Atlas-SNP
ATF1	466	hgsc.bcm.edu	37	12	51203371	51203371	+	Silent	SNP	C	C	T	rs1129406	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	105	53	84	0	0.504762	0	C|0.586;T|0.414	0.414	strong	.	ATF1	32	.	NM_005171	exon4	c.C327T	p.Y109Y	ACAGTACAGTATG	.	PASS	Atlas-SNP
AHCTF1	25909	hgsc.bcm.edu	37	1	247021085	247021085	+	Silent	SNP	G	G	C	rs41308162	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	237	234	228	0	0.987342	0	G|0.826;C|0.174	0.174	strong	AHCTF1,NS,carcinoma,0,1	AHCTF1	187	1	NM_015446	exon30	c.C4191G	p.L1397L	AACTAAGAGATCC	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9047305	9047305	+	Silent	SNP	G	G	A	rs10415818	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	45	70	0	0.608108	0	G|0.797;A|0.203	0.203	strong	.	MUC16	4315	.	NM_024690	exon5	c.C34326T	p.H11442H	ACTTGTGTGTGTC	.	PASS	Atlas-SNP
NPTXR	23467	hgsc.bcm.edu	37	22	39222598	39222598	+	Silent	SNP	G	G	A	rs56034166	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	27	99	0	0.435484	0	G|0.979;A|0.021	0.021	strong	.	NPTXR	34	.	NM_014293	exon3	c.C1005T	p.G335G	GGGGGTGCCCTGG	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	22	66	0	0.354839	0	T|0.150;G|0.006	0.150	strong	.	ADAMTSL3	290	.	NM_207517	exon30	c.C4979T	p.T1660I	ACTGCACAGACAC	.	PASS	Atlas-SNP
ZBTB42	100128927	hgsc.bcm.edu	37	14	105267934	105267934	+	Missense_Mutation	SNP	G	G	A	rs34284721	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	115	63	108	0	0.547826	0	G|0.930;A|0.070	0.070	strong	.	ZBTB42	10	.	NM_001137601	exon2	c.G400A	p.A134T	CCTGGGGCAGAAC	.	PASS	Atlas-SNP
RNF26	79102	hgsc.bcm.edu	37	11	119206375	119206375	+	Silent	SNP	G	G	A	rs2511841	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	196	196	175	0	1	0	G|0.315;A|0.685	0.685	strong	.	RNF26	23	.	NM_032015	exon1	c.G543A	p.T181T	GATGACGGACGTA	.	PASS	Atlas-SNP
CHPF2	54480	hgsc.bcm.edu	37	7	150934975	150934975	+	Silent	SNP	C	C	G	rs2487154	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60	60	65	0	1	0	C|0.595;G|0.405	0.405	strong	.	CHPF2	52	.	NM_019015	exon4	c.C1527G	p.A509A	CGAGGCCTTTGCA	.	PASS	Atlas-SNP
ASAH1	427	hgsc.bcm.edu	37	8	17928811	17928811	+	Missense_Mutation	SNP	C	C	T	rs1071645	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	36	36	47	0	1	0	T|0.339;G|0.122	0.339	strong	.	ASAH1	71	.	NM_001127505	exon4	c.G283A	p.V95M	ATACCACTGGTGC	.	PASS	Atlas-SNP
MORC4	79710	hgsc.bcm.edu	37	X	106200202	106200202	+	Missense_Mutation	SNP	G	G	A	rs6622126	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	128	36	105	0	0.28125	0	0|0.012;A|0.648	0.648	strong	.	MORC4	155	.	NM_001085354	exon12	c.C1418T	p.T473I	TCATCAGTGAGTT	.	PASS	Atlas-SNP
FIGNL1	63979	hgsc.bcm.edu	37	7	50514577	50514577	+	Missense_Mutation	SNP	C	C	T	rs10235371	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	42	104	0	0.666667	0	C|0.920;T|0.080	0.080	strong	.	FIGNL1	73	.	NM_001042762	exon4	c.G409A	p.V137M	TTACCACTGATGC	.	PASS	Atlas-SNP
CIITA	4261	hgsc.bcm.edu	37	16	11000862	11000862	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	41	19	33	0	0.463415	0	.	.	none	.	CIITA	92	.	NM_000246	exon11	c.G1513T	p.E505X	GAGCTGGAAGCGC	.	PASS	Atlas-SNP
THUMPD3	25917	hgsc.bcm.edu	37	3	9425911	9425911	+	Silent	SNP	G	G	A	rs1129170	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	65	65	66	0	1	0	G|0.425;A|0.575	0.575	strong	.	THUMPD3	46	.	NM_001114092	exon9	c.G1251A	p.K417K	CAAGAAGAGAAAC	.	PASS	Atlas-SNP
MPHOSPH6	10200	hgsc.bcm.edu	37	16	82203742	82203742	+	Silent	SNP	T	T	C	rs1134847	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68	26	119	0	0.382353	0	T|0.362;G|0.000;C|0.638;A|0.000	0.638	strong	MPHOSPH6,rectum,carcinoma,0,1	MPHOSPH6	16	1	NM_005792	exon1	c.A39G	p.L13L	GCGCAGTAGATTC	.	PASS	Atlas-SNP
MYO1C	4641	hgsc.bcm.edu	37	17	1387472	1387472	+	Silent	SNP	C	C	T	rs11538156	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	40	20	37	0	0.5	0	T|0.112;G|0.000;C|0.888	0.112	strong	.	MYO1C	57	.	NM_001080779	exon2	c.G201A	p.L67L	CCGCCGCAGGTTC	.	PASS	Atlas-SNP
KIF19	124602	hgsc.bcm.edu	37	17	72350362	72350362	+	Silent	SNP	G	G	A	rs72852235	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	32	18	25	0	0.5625	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
MAP3K1	4214	hgsc.bcm.edu	37	5	56168712	56168712	+	Silent	SNP	C	C	T	rs2229882	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83	49	101	0	0.590361	0	C|0.953;T|0.047	0.047	strong	.	MAP3K1	355	.	NM_005921	exon9	c.C1566T	p.T522T	GCAAACCGTACAG	.	PASS	Atlas-SNP
ABHD15	116236	hgsc.bcm.edu	37	17	27889986	27889986	+	Missense_Mutation	SNP	T	T	C	rs542939	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	77	76	72	0	0.987013	0	T|0.268;C|0.732	0.732	strong	.	ABHD15	18	.	NM_198147	exon2	c.A1000G	p.T334A	AGTAGGTATCCCA	.	PASS	Atlas-SNP
OR5B17	219965	hgsc.bcm.edu	37	11	58125620	58125620	+	Missense_Mutation	SNP	T	T	C	rs4127353	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	46	41	0	0.978723	0	T|0.312;C|0.688	0.688	strong	OR5B17,NS,adenoma,0,1	OR5B17	64	1	NM_001005489	exon1	c.A923G	p.Y308C	AGAGAATATTTTG	.	PASS	Atlas-SNP
CCDC168	643677	hgsc.bcm.edu	37	13	103386940	103386940	+	Silent	SNP	C	C	T	rs367699341		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93	30	155	0	0.322581	0	.	.	weak	.	.	.	.	NM_001146197	exon4	c.G16107A	p.E5369E	GTTCCTCTCTTCT	.	PASS	Atlas-SNP
CCDC168	643677	hgsc.bcm.edu	37	13	103392562	103392562	+	Missense_Mutation	SNP	C	C	A	rs12585626	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	34	9	50	0	0.264706	0	C|0.905;A|0.095	0.095	strong	.	.	.	.	NM_001146197	exon4	c.G10485T	p.M3495I	TGATTTCATTCCT	.	PASS	Atlas-SNP
DCST2	127579	hgsc.bcm.edu	37	1	155004092	155004092	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	165	78	161	0	0.472727	0	.	.	none	.	DCST2	80	.	NM_144622	exon4	c.G697A	p.V233M	TGAGCACGTAACA	.	PASS	Atlas-SNP
ZNF451	26036	hgsc.bcm.edu	37	6	56966040	56966040	+	Silent	SNP	T	T	C	rs188982073	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	28	56	0	0.528302	0	T|0.999;C|0.001	0.001	strong	.	ZNF451	181	.	NM_001257273	exon4	c.T826C	p.L276L	GTGACATTACAAT	.	PASS	Atlas-SNP
MAFG	4097	hgsc.bcm.edu	37	17	79880565	79880565	+	Silent	SNP	G	G	A	rs61752690	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	12	7	14	0	0.583333	0	A|0.002;G|0.998	0.002	strong	.	MAFG	9	.	NM_032711	exon3	c.C405T	p.A135A	CAGGCCGGCGGCA	.	PASS	Atlas-SNP
AIRE	326	hgsc.bcm.edu	37	21	45709906	45709906	+	Missense_Mutation	SNP	C	C	G	rs1800520	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	151	84	116	0	0.556291	0	C|0.804;G|0.196	0.196	strong	.	AIRE	61	.	NM_000383	exon7	c.C834G	p.S278R	GGGCAGCGTTCCC	.	PASS	Atlas-SNP
R3HDM1	23518	hgsc.bcm.edu	37	2	136467080	136467080	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	206	87	253	0	0.42233	0	.	.	none	.	R3HDM1	84	.	NM_015361	exon21	c.A2432T	p.Q811L	GTTCCCAGCAGCT	.	PASS	Atlas-SNP
ABP1	26	hgsc.bcm.edu	37	7	150555915	150555915	+	Silent	SNP	A	A	G	rs10893	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	106	41	111	0	0.386792	0	A|0.571;G|0.429	0.429	strong	.	ABP1	92	.	NM_001091	exon3	c.A1635G	p.P545P	GAGCCCAAGACAC	.	PASS	Atlas-SNP
AMPD1	270	hgsc.bcm.edu	37	1	115231254	115231254	+	Missense_Mutation	SNP	G	G	A	rs61752479	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	188	97	185	0	0.515957	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
NMT1	4836	hgsc.bcm.edu	37	17	43171154	43171154	+	Silent	SNP	C	C	T	rs1132898	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60	31	70	0	0.516667	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
FCGBP	8857	hgsc.bcm.edu	37	19	40389657	40389657	+	Missense_Mutation	SNP	T	T	G	rs3746010	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	226	19	430	7	0.0840708	0.0162791	T|0.250;G|0.750	0.750	weak	FCGBP,rectum,carcinoma,0,1	FCGBP	416	1	NM_003890	exon18	c.A8525C	p.N2842T	CCTTTGTTGACGC	.	scavenged	Atlas-SNP
PADI3	51702	hgsc.bcm.edu	37	1	17601165	17601165	+	Silent	SNP	C	C	T	rs11585357	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94	46	82	0	0.489362	0	C|0.902;T|0.098	0.098	strong	PADI3,colon,carcinoma,+2,1	PADI3	81	1	NM_016233	exon11	c.C1191T	p.R397R	ACCACGCGACAGG	.	PASS	Atlas-SNP
FGL1	2267	hgsc.bcm.edu	37	8	17731876	17731876	+	Silent	SNP	A	A	G	rs34871936	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	102	45	115	0	0.441176	0	A|0.990;G|0.010	0.010	strong	.	FGL1	31	.	NM_201553	exon5	c.T399C	p.F133F	CCTGTTAAAGTTT	.	PASS	Atlas-SNP
PDGFC	56034	hgsc.bcm.edu	37	4	157684248	157684248	+	Silent	SNP	T	T	C	rs3815861	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	31	78	1	0.43662	0.0128205	A|0.000;C|0.171;T|0.829	0.171	strong	PDGFC,NS,carcinoma,0,1	PDGFC	46	1	NM_016205	exon6	c.A1032G	p.G344G	CTATCCTCCTGTG	.	scavenged	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9069792	9069792	+	Missense_Mutation	SNP	G	G	A	rs1862458	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	125	50	116	0	0.4	0	G|0.798;A|0.202	0.202	strong	.	MUC16	4315	.	NM_024690	exon3	c.C17654T	p.S5885F	TCCCAGGAAGCTG	.	PASS	Atlas-SNP
NRP1	8829	hgsc.bcm.edu	37	10	33510768	33510768	+	Silent	SNP	G	G	A	rs2229934	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	95	44	97	0	0.463158	0	G|0.724;A|0.276	0.276	strong	.	NRP1	126	.	NM_001244973	exon8	c.C1161T	p.P387P	ATCTGTGGGGTTG	.	PASS	Atlas-SNP
RNF123	63891	hgsc.bcm.edu	37	3	49751585	49751585	+	Silent	SNP	C	C	T	rs2291542	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	27	62	0	0.442623	0	C|0.736;T|0.264	0.264	strong	RNF123,caecum,carcinoma,0,1	RNF123	100	1	NM_022064	exon31	c.C2988T	p.D996D	TGAGGACGCCAAT	.	PASS	Atlas-SNP
LMBRD2	92255	hgsc.bcm.edu	37	5	36142648	36142648	+	Silent	SNP	A	A	G	rs12658867	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	27	13	37	0	0.481481	0	A|0.736;G|0.264	0.264	strong	LMBRD2,NS,carcinoma,0,1	LMBRD2	89	1	NM_001007527	exon3	c.T228C	p.N76N	GTTGCTATTCTCA	.	PASS	Atlas-SNP
OR2L13	284521	hgsc.bcm.edu	37	1	248262731	248262731	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	179	2	185	1	0.0111732	0.00540541	.	.	none	OR2L13_ENST00000366478,NS,carcinoma,0,2	OR2L13	261	2	NM_175911	exon3	c.C54T	p.P18P	GCTTCCCCCAAAT	.	scavenged	Atlas-SNP
DPF1	8193	hgsc.bcm.edu	37	19	38702950	38702950	+	Silent	SNP	G	G	A	rs11547760	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80	38	57	0	0.475	0	G|0.929;A|0.071	0.071	strong	.	DPF1	54	.	NM_001135155	exon11	c.C1144T	p.L382L	GACTCAGGCAGTA	.	PASS	Atlas-SNP
STK17A	9263	hgsc.bcm.edu	37	7	43647879	43647879	+	Silent	SNP	C	C	T	rs11555026	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	40	59	0	0.634921	0	C|0.858;T|0.142	0.142	strong	.	STK17A	31	.	NM_004760	exon3	c.C444T	p.D148D	CTTTGACCAGTGT	.	PASS	Atlas-SNP
MARC2	54996	hgsc.bcm.edu	37	1	220936372	220936372	+	Missense_Mutation	SNP	G	G	A	rs3795535	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85	45	99	0	0.529412	0	G|0.977;A|0.023	0.023	strong	MOSC2,NS,carcinoma,-2,1	.	.	1	NM_017898	exon4	c.G730A	p.G244S	GTGACCGGCTGTG	.	PASS	Atlas-SNP
FREM2	341640	hgsc.bcm.edu	37	13	39264690	39264690	+	Missense_Mutation	SNP	T	T	C	rs2496425	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	114	31	89	0	0.27193	0	T|0.546;C|0.454	0.454	strong	FREM2,colon,carcinoma,0,1	FREM2	385	1	NM_207361	exon1	c.T3209C	p.F1070S	AAATCTTTGTAGG	.	PASS	Atlas-SNP
DTHD1	401124	hgsc.bcm.edu	37	4	36345377	36345377	+	Silent	SNP	G	G	A	rs2270880	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	25	64	0	0.403226	0	G|0.895;A|0.105	0.105	strong	.	DTHD1	63	.	NM_001170700	exon9	c.G2277A	p.E759E	AGAAGAGCTCAAA	.	PASS	Atlas-SNP
FBXO34	55030	hgsc.bcm.edu	37	14	55818517	55818517	+	Missense_Mutation	SNP	T	T	A	rs1045002	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	192	188	184	0	0.979167	0	A|0.366;N|0.000	0.366	strong	FBXO34,NS,carcinoma,0,1	FBXO34	61	1	NM_017943	exon2	c.T1409A	p.I470N	CTTCCATTTTAAA	.	PASS	Atlas-SNP
PTBP1	5725	hgsc.bcm.edu	37	19	808742	808742	+	Silent	SNP	G	G	T	rs1135908	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	149	68	163	0	0.456376	0	G|0.864;T|0.136	0.136	strong	.	PTBP1	43	.	NM_002819	exon13	c.G1443T	p.T481T	GGCCACGCTGCAC	.	PASS	Atlas-SNP
GNGT1	2792	hgsc.bcm.edu	37	7	93540153	93540153	+	Missense_Mutation	SNP	G	G	A	rs17243826	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	101	39	97	0	0.386139	0	A|0.023;C|0.029;G|0.948	0.023	strong	.	GNGT1	12	.	NM_021955	exon3	c.G148A	p.E50K	TCTGGCGAGGATC	.	PASS	Atlas-SNP
LPA	4018	hgsc.bcm.edu	37	6	161006172	161006172	+	Missense_Mutation	SNP	T	T	G	rs41272110	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	104	52	105	0	0.5	0	T|0.898;G|0.102	0.102	strong	.	LPA	237	.	NM_005577	exon27	c.A4195C	p.T1399P	AGAGTGTGCCTCG	.	PASS	Atlas-SNP
OGFR	11054	hgsc.bcm.edu	37	20	61444600	61444600	+	Missense_Mutation	SNP	C	C	A	rs6122313	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	8	4	15	0	0.5	0	C|0.918;A|0.082	0.082	strong	OGFR,extremity,malignant_melanoma,0,1	OGFR	63	1	NM_007346	exon7	c.C1633A	p.R545S	GGCCCCCGCCCAG	.	scavenged	Atlas-SNP
SETBP1	26040	hgsc.bcm.edu	37	18	42532693	42532693	+	Missense_Mutation	SNP	C	C	A	rs1064204	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98	41	85	0	0.418367	0	C|0.892;A|0.108	0.108	strong	.	SETBP1	577	.	NM_015559	exon4	c.C3388A	p.P1130T	ATGCAGCCTTCTC	.	PASS	Atlas-SNP
UIMC1	51720	hgsc.bcm.edu	37	5	176382995	176382995	+	Missense_Mutation	SNP	G	G	A	rs3733876	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	200	110	195	0	0.55	0	G|0.879;A|0.121	0.121	strong	.	UIMC1	55	.	NM_016290	exon8	c.C1304T	p.P435L	CTCTCTGGCATAA	.	PASS	Atlas-SNP
GABRD	2563	hgsc.bcm.edu	37	1	1960674	1960674	+	Silent	SNP	C	C	T	rs28408173	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	97	53	124	0	0.546392	0	C|0.874;T|0.126	0.126	strong	.	GABRD	49	.	NM_000815	exon7	c.C816T	p.S272S	GATCAGCCAGGCG	.	PASS	Atlas-SNP
TTLL3	26140	hgsc.bcm.edu	37	3	9870857	9870857	+	Silent	SNP	G	G	A	rs2290303	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	105	104	104	1	0.990476	0.00961538	G|0.623;A|0.377	0.377	strong	.	TTLL3	51	.	NM_001025930	exon10	c.G1761A	p.Q587Q	CGTGCAGTGTCGG	.	PASS	Atlas-SNP
FABP2	2169	hgsc.bcm.edu	37	4	120240238	120240238	+	Silent	SNP	T	T	C	rs1511025	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	163	86	174	0	0.527607	0	T|0.654;C|0.346	0.346	strong	FABP2,NS,carcinoma,-1,1	FABP2	21	1	NM_000134	exon4	c.A357G	p.V119V	TTCATATACATAA	.	PASS	Atlas-SNP
PRR5L	79899	hgsc.bcm.edu	37	11	36458997	36458997	+	Missense_Mutation	SNP	A	A	G	rs62621409	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60	24	85	0	0.4	0	A|0.972;G|0.028	0.028	strong	.	PRR5L	35	.	NM_024841	exon7	c.A415G	p.T139A	CTCCCTACCCTGC	.	PASS	Atlas-SNP
ANKS1B	56899	hgsc.bcm.edu	37	12	99837570	99837570	+	Missense_Mutation	SNP	C	C	T	rs148678454	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	107	47	126	0	0.439252	0	C|0.986;T|0.014	0.014	strong	.	ANKS1B	180	.	NM_152788	exon11	c.G1456A	p.A486T	TAACTGCTACCTC	.	PASS	Atlas-SNP
AIPL1	23746	hgsc.bcm.edu	37	17	6330068	6330068	+	Silent	SNP	T	T	C	rs2292546	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	28	61	0	0.451613	0	T|0.262;C|0.738	0.738	strong	AIPL1,NS,carcinoma,0,1	AIPL1	34	1	NM_014336	exon5	c.A651G	p.P217P	CTCCCATGGCTTC	.	PASS	Atlas-SNP
POLR1A	25885	hgsc.bcm.edu	37	2	86259443	86259443	+	Silent	SNP	C	C	T	rs2276626	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	69	116	0	0.932432	0	T|0.595;C|0.405;A|0.000	0.595	strong	POLR1A,NS,carcinoma,0,1	POLR1A	137	1	NM_015425	exon29	c.G4224A	p.G1408G	GGCGTCCCCCTCC	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1280238	1280238	+	Missense_Mutation	SNP	G	G	A	rs55856616	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51	23	57	0	0.45098	0	G|0.961;A|0.039	0.039	strong	.	MUC5B	473	.	NM_002458	exon44	c.G16660A	p.D5554N	ACCCAGGACCCAA	.	PASS	Atlas-SNP
TULP3	7289	hgsc.bcm.edu	37	12	3042634	3042634	+	Silent	SNP	C	C	T	rs145294361	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	101	44	102	0	0.435644	0	C|0.996;T|0.004	0.004	strong	.	TULP3	45	.	NM_003324	exon7	c.C747T	p.Y249Y	CAACTACCTTATC	.	PASS	Atlas-SNP
LRRC19	64922	hgsc.bcm.edu	37	9	26995787	26995787	+	Missense_Mutation	SNP	G	G	A	rs41272237	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	38	74	0	0.575758	0	G|0.949;A|0.051	0.051	strong	.	LRRC19	24	.	NM_022901	exon5	c.C845T	p.T282M	GAAGTCGTCAGTA	.	PASS	Atlas-SNP
TTC21A	199223	hgsc.bcm.edu	37	3	39161464	39161464	+	Missense_Mutation	SNP	G	G	A	rs1274971	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	147	58	155	0	0.394558	0	G|0.552;A|0.448	0.448	strong	.	TTC21A	96	.	NM_145755	exon8	c.G877A	p.E293K	GAACCCGAAAATC	.	PASS	Atlas-SNP
SLC22A5	6584	hgsc.bcm.edu	37	5	131705949	131705949	+	Silent	SNP	T	T	C	rs61742215	byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68	35	83	0	0.514706	0	T|0.732;C|0.268	0.268	strong	.	SLC22A5	34	.	NM_003060	exon1	c.T285C	p.L95L	GGCGCTTGGGCTG	.	PASS	Atlas-SNP
CEACAM5	1048	hgsc.bcm.edu	37	19	42213772	42213772	+	Missense_Mutation	SNP	A	A	G	rs12971352	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	175	109	170	0	0.622857	0	A|0.810;G|0.190	0.190	strong	.	CEACAM5	84	.	NM_004363	exon2	c.A238G	p.I80V	CAAATTATAGGAT	.	PASS	Atlas-SNP
DMGDH	29958	hgsc.bcm.edu	37	5	78328560	78328560	+	Silent	SNP	G	G	A	rs1805072	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	29	59	0	0.460317	0	G|0.796;A|0.204	0.204	strong	.	DMGDH	88	.	NM_013391	exon9	c.C1467T	p.G489G	CTCCCAGCCAGCA	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	42	101	1	0.5	0.00990099	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	.	scavenged	Atlas-SNP
NEK10	152110	hgsc.bcm.edu	37	3	27332820	27332820	+	Missense_Mutation	SNP	A	A	G	rs10510592	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	239	119	249	0	0.497908	0	A|0.824;G|0.176	0.176	strong	.	NEK10	271	.	NM_199347	exon19	c.T1538C	p.L513S	TATTTCAAAGGAG	.	PASS	Atlas-SNP
GIT1	28964	hgsc.bcm.edu	37	17	27904711	27904711	+	Silent	SNP	G	G	A	rs11080105	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	113	59	95	0	0.522124	0	G|0.638;A|0.362	0.362	strong	.	GIT1	84	.	NM_001085454	exon11	c.C960T	p.A320A	GGGCACGGCACTG	.	PASS	Atlas-SNP
ATXN1	6310	hgsc.bcm.edu	37	6	16327903	16327903	+	Missense_Mutation	SNP	C	C	A	rs3817753	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	6	38	3	0.12766	0.0789474	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	.	scavenged	Atlas-SNP
IRF1	3659	hgsc.bcm.edu	37	5	131825083	131825083	+	Splice_Site	SNP	C	C	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49	21	66	0	0.428571	0	.	.	none	.	IRF1	26	.	NM_002198	exon3	c.87+1G>T	.	CACTCACTTTATT	.	PASS	Atlas-SNP
SLC4A11	83959	hgsc.bcm.edu	37	20	3214581	3214581	+	Silent	SNP	C	C	T	rs3803956	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	61	50	0	1	0	C|0.820;T|0.180	0.180	strong	.	SLC4A11	188	.	NM_001174090	exon6	c.G720A	p.S240S	GAGCCACGACTGC	.	PASS	Atlas-SNP
FLRT1	23769	hgsc.bcm.edu	37	11	63884474	63884474	+	Silent	SNP	C	C	T	rs3751121	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	29	102	0	0.391892	0	C|0.950;T|0.050	0.050	strong	.	FLRT1	46	.	NM_013280	exon2	c.C735T	p.S245S	CTTCAGCCGCCTA	.	PASS	Atlas-SNP
BACE1	23621	hgsc.bcm.edu	37	11	117163824	117163824	+	Silent	SNP	C	C	G	rs638405	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	142	115	124	0	0.809859	0	C|0.533;G|0.467	0.467	strong	.	BACE1	33	.	NM_012104	exon5	c.G786C	p.V262V	AATGATCACCTCA	.	PASS	Atlas-SNP
SLC39A3	29985	hgsc.bcm.edu	37	19	2733250	2733250	+	Silent	SNP	C	C	T	rs61736898	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	15	9	21	0	0.6	0	C|0.879;T|0.121	0.121	strong	.	SLC39A3	20	.	NM_144564	exon3	c.G444A	p.V148V	GGGCTCCACGTAC	.	PASS	Atlas-SNP
SGIP1	84251	hgsc.bcm.edu	37	1	67148009	67148009	+	Silent	SNP	G	G	A	rs61798708	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	106	45	109	0	0.424528	0	G|0.994;A|0.006	0.006	strong	.	SGIP1	272	.	NM_032291	exon15	c.G1272A	p.S424S	GGTTTCGTCCCCC	.	PASS	Atlas-SNP
NCOA3	8202	hgsc.bcm.edu	37	20	46279839	46279839	+	Silent	SNP	G	G	A	rs2664555		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	46	5	36	0	0.108696	0	.	.	weak	NCOA3,rectum,carcinoma,0,1	NCOA3	156	1	NM_181659	exon20	c.G3765A	p.Q1255Q	GCAACAGCAGCAG	.	PASS	Atlas-SNP
VWA5B2	90113	hgsc.bcm.edu	37	3	183958706	183958706	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60	15	79	0	0.25	0	.	.	none	.	VWA5B2	47	.	NM_138345	exon16	c.G2868A	p.V956V	GCAGGTGTGCAGC	.	PASS	Atlas-SNP
PREX1	57580	hgsc.bcm.edu	37	20	47269233	47269233	+	Missense_Mutation	SNP	C	C	G	rs41283558	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	50	27	58	0	0.54	0	C|0.852;G|0.148	0.148	strong	PREX1_ENST00000396220,colon,carcinoma,0,2	PREX1	441	2	NM_020820	exon21	c.G2358C	p.Q786H	GATCCACTGGTAC	.	PASS	Atlas-SNP
IMMT	10989	hgsc.bcm.edu	37	2	86389119	86389119	+	Silent	SNP	G	G	A	rs370662846		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	169	4	267	0	0.0236686	0	.	.	weak	IMMT,NS,carcinoma,-1,1	IMMT	65	1	NM_006839	exon8	c.C876T	p.A292A	GGCATCGGCAGCT	.	scavenged	Atlas-SNP
RBBP8NL	140893	hgsc.bcm.edu	37	20	60986019	60986019	+	Missense_Mutation	SNP	A	A	C	rs2236200	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	119	54	128	0	0.453782	0	A|0.827;C|0.173	0.173	strong	C20orf151,NS,carcinoma,0,1	.	.	1	NM_080833	exon14	c.T1910G	p.L637R	GCTGTCAGTTTCC	.	PASS	Atlas-SNP
NEU4	129807	hgsc.bcm.edu	37	2	242757411	242757411	+	Silent	SNP	C	C	T	rs36111671	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	88	48	109	0	0.545455	0	C|0.817;T|0.183	0.183	strong	.	NEU4	39	.	NM_001167599	exon4	c.C531T	p.G177G	CCACGGCGTGCAG	.	PASS	Atlas-SNP
USH1C	10083	hgsc.bcm.edu	37	11	17552707	17552707	+	Silent	SNP	C	C	A	rs41282942	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	36	65	0	0.48	0	C|0.998;A|0.002	0.002	strong	.	USH1C	157	.	NM_005709	exon4	c.G381T	p.G127G	CTGGAGCCCGACG	.	PASS	Atlas-SNP
ALS2CR11	151254	hgsc.bcm.edu	37	2	202430584	202430584	+	Missense_Mutation	SNP	G	G	A	rs73991652	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	27	73	0	0.409091	0	G|0.948;A|0.052	0.052	strong	.	ALS2CR11	194	.	NM_001168217	exon9	c.C845T	p.T282I	TGTGGTGTAATAA	.	PASS	Atlas-SNP
MAVS	57506	hgsc.bcm.edu	37	20	3838441	3838441	+	Missense_Mutation	SNP	C	C	G	rs17857295	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	54	94	0	0.62069	0	C|0.764;G|0.236	0.236	strong	.	MAVS	34	.	NM_020746	exon3	c.C277G	p.Q93E	GTCTACCAGAGCT	.	PASS	Atlas-SNP
EPG5	57724	hgsc.bcm.edu	37	18	43481075	43481075	+	Missense_Mutation	SNP	G	G	A	rs1893523	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	27	12	38	0	0.444444	0	G|0.748;A|0.252	0.252	strong	EPG5,NS,carcinoma,-1,1	EPG5	199	1	NM_020964	exon26	c.C4532T	p.A1511V	TGCAGAGCAAGGG	.	PASS	Atlas-SNP
HOXA10	3206	hgsc.bcm.edu	37	7	27211548	27211548	+	Silent	SNP	C	C	T	rs34957925	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	123	32	166	0	0.260163	0	C|0.959;T|0.041	0.041	strong	.	HOXA10	55	.	NM_018951	exon2	c.G1203A	p.R401R	GAGCTCCCGGATC	.	PASS	Atlas-SNP
AMBRA1	55626	hgsc.bcm.edu	37	11	46456444	46456444	+	Silent	SNP	G	G	A	rs61999319	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	176	101	161	0	0.573864	0	G|0.985;A|0.015	0.015	strong	.	AMBRA1	201	.	NM_001267782	exon15	c.C2785T	p.L929L	GGGCCAGGGAGTA	.	PASS	Atlas-SNP
TGIF1	7050	hgsc.bcm.edu	37	18	3457607	3457607	+	Missense_Mutation	SNP	C	C	T	rs2229333	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	150	77	140	0	0.513333	0	C|0.942;G|0.000;T|0.057	0.057	strong	.	TGIF1	41	.	NM_170695	exon3	c.C875T	p.P292L	CATCCCCGGGATC	.	PASS	Atlas-SNP
FIBCD1	84929	hgsc.bcm.edu	37	9	133787225	133787225	+	Silent	SNP	A	A	G	rs6597650	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73	32	127	0	0.438356	0	A|0.442;G|0.558	0.558	strong	.	FIBCD1	34	.	NM_001145106	exon6	c.T900C	p.D300D	GTACGCATCCCAG	.	PASS	Atlas-SNP
EPHX1	2052	hgsc.bcm.edu	37	1	226019653	226019653	+	Silent	SNP	G	G	A	rs1131873	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	19	42	0	0.404255	0	G|0.831;A|0.169	0.169	strong	.	EPHX1	57	.	NM_001136018	exon3	c.G357A	p.K119K	GACTAAGATTGAA	.	PASS	Atlas-SNP
UQCRH	7388	hgsc.bcm.edu	37	1	46774783	46774783	+	Missense_Mutation	SNP	A	A	G	rs41292543	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	163	76	140	0	0.466258	0	A|0.926;G|0.074	0.074	strong	.	UQCRH	4	.	NM_006004	exon2	c.A65G	p.E22G	AAGAGGAAGAGGA	.	PASS	Atlas-SNP
ULK1	8408	hgsc.bcm.edu	37	12	132401566	132401566	+	Missense_Mutation	SNP	C	C	T	rs11546871	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	170	93	164	0	0.547059	0	C|0.780;T|0.220	0.220	strong	ULK1,NS,carcinoma,0,2	ULK1	92	2	NM_003565	exon21	c.C2141T	p.P714L	CGGACCCGGGCAG	.	PASS	Atlas-SNP
PCDHB8	56128	hgsc.bcm.edu	37	5	140558580	140558580	+	Missense_Mutation	SNP	C	C	T	rs7700833	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	297	71	239	0	0.239057	0	C|0.932;T|0.068	0.068	strong	.	PCDHB8	199	.	NM_019120	exon1	c.C965T	p.A322V	TCGAGGCGAGAGA	.	PASS	Atlas-SNP
GYPB	2994	hgsc.bcm.edu	37	4	144922436	144922436	+	Missense_Mutation	SNP	T	T	G	rs79488525		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	414	68	384	2	0.164251	0.00520833	.	.	weak	GYPB_ENST00000502664,NS,carcinoma,0,3	GYPB	17	3	NM_002100	exon2	c.A38C	p.E13A	ACAATTTCTGTAT	.	scavenged	Atlas-SNP
H1FNT	341567	hgsc.bcm.edu	37	12	48723595	48723595	+	Missense_Mutation	SNP	G	G	A	rs1471997	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	42	27	53	0	0.642857	0	G|0.832;A|0.168	0.168	strong	.	H1FNT	30	.	NM_181788	exon1	c.G521A	p.R174Q	GGAGACGGAACGC	.	PASS	Atlas-SNP
USHBP1	83878	hgsc.bcm.edu	37	19	17361064	17361064	+	Silent	SNP	C	C	T	rs10415471	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	70	26	56	0	0.371429	0	C|0.828;T|0.172	0.172	strong	.	USHBP1	85	.	NM_031941	exon13	c.G2082A	p.P694P	GGGAGGCGGGAGG	.	PASS	Atlas-SNP
SLC37A2	219855	hgsc.bcm.edu	37	11	124947396	124947396	+	Missense_Mutation	SNP	A	A	G	rs55752830	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	102	79	86	0	0.77451	0	A|0.619;G|0.381	0.381	strong	.	SLC37A2	105	.	NM_001145290	exon4	c.A286G	p.I96V	TTCCTCATCGCCT	.	PASS	Atlas-SNP
KIF19	124602	hgsc.bcm.edu	37	17	72351406	72351406	+	Silent	SNP	C	C	T	rs2271536	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	28	11	26	0	0.392857	0	C|0.650;T|0.350	0.350	strong	.	KIF19	102	.	NM_153209	exon20	c.C2952T	p.H984H	GCCCCACGGCACA	.	PASS	Atlas-SNP
EVPL	2125	hgsc.bcm.edu	37	17	74003525	74003525	+	Missense_Mutation	SNP	C	C	T	rs141706835	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	33	68	0	0.5	0	C|1.000;T|0.000	0.000	weak	EVPL,colon,carcinoma,0,1	EVPL	155	1	NM_001988	exon22	c.G5761A	p.V1921I	TCTGGACGGCCTC	.	PASS	Atlas-SNP
PPA2	27068	hgsc.bcm.edu	37	4	106317429	106317429	+	Missense_Mutation	SNP	C	C	G	rs13787	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	126	126	230	0	1	0	C|0.611;G|0.389	0.389	strong	.	PPA2	23	.	NM_176869	exon9	c.G846C	p.K282N	ATTACACTTCTTC	.	PASS	Atlas-SNP
SLC4A7	9497	hgsc.bcm.edu	37	3	27473066	27473066	+	Silent	SNP	A	A	G	rs13077400	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100	49	107	0	0.49	0	A|0.800;G|0.200	0.200	strong	.	SLC4A7	119	.	NM_003615	exon7	c.T846C	p.L282L	ATGACCAAGAAGA	.	PASS	Atlas-SNP
COL2A1	1280	hgsc.bcm.edu	37	12	48381394	48381394	+	Silent	SNP	G	G	A	rs150865922	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	28	12	30	0	0.428571	0	G|0.997;A|0.003	0.003	strong	.	COL2A1	368	.	NM_001844	exon19	c.C1221T	p.S407S	ACTTACGGAGGCA	.	PASS	Atlas-SNP
BTN3A2	11118	hgsc.bcm.edu	37	6	26370605	26370605	+	Silent	SNP	T	T	C	rs9379860	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94	23	89	0	0.244681	0	T|0.614;C|0.386	0.386	strong	.	BTN3A2	44	.	NM_001197246	exon3	c.T489C	p.H163H	GATCCATCTGGAG	.	PASS	Atlas-SNP
MYPOP	339344	hgsc.bcm.edu	37	19	46394322	46394322	+	Silent	SNP	G	G	A	rs114387602	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	37	16	47	0	0.432432	0	G|0.923;A|0.077	0.077	strong	.	MYPOP	23	.	NM_001012643	exon3	c.C759T	p.L253L	GGCCGAGAGCGTG	.	PASS	Atlas-SNP
PPL	5493	hgsc.bcm.edu	37	16	4935146	4935146	+	Silent	SNP	C	C	T	rs1049206	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80	43	90	0	0.5375	0	C|0.673;T|0.327	0.327	strong	PPL,NS,carcinoma,0,1	PPL	168	1	NM_002705	exon22	c.G3510A	p.V1170V	CTCCTGCACCACC	.	PASS	Atlas-SNP
GRIN3A	116443	hgsc.bcm.edu	37	9	104433347	104433347	+	Silent	SNP	G	G	A	rs13284303	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100	49	109	0	0.49	0	G|0.871;A|0.129	0.129	strong	.	GRIN3A	186	.	NM_133445	exon3	c.C1347T	p.I449I	TACTCTGATGGAA	.	PASS	Atlas-SNP
KIAA0556	23247	hgsc.bcm.edu	37	16	27720201	27720201	+	Missense_Mutation	SNP	C	C	T	rs12930355	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85	47	61	1	0.552941	0.0163934	C|0.898;T|0.102	0.102	strong	KIAA0556_ENST00000261588,caecum,carcinoma,-1,3	KIAA0556	348	3	NM_015202	exon13	c.C1565T	p.T522M	CAGCCACGCCTGG	.	scavenged	Atlas-SNP
BCAN	63827	hgsc.bcm.edu	37	1	156616814	156616814	+	Missense_Mutation	SNP	C	C	G	rs115373136	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	22	62	0	0.468085	0	C|0.989;G|0.011	0.011	strong	.	BCAN	174	.	NM_198427	exon3	c.C313G	p.R105G	GCCTACCGGTTCC	.	PASS	Atlas-SNP
OASL	8638	hgsc.bcm.edu	37	12	121471337	121471337	+	Silent	SNP	G	G	A	rs3213545	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79	77	97	0	0.974684	0	G|0.722;A|0.278	0.278	strong	.	OASL	49	.	NM_198213	exon2	c.C408T	p.L136L	GAAGACGAGAGCA	.	PASS	Atlas-SNP
INPP5E	56623	hgsc.bcm.edu	37	9	139327034	139327034	+	Silent	SNP	A	A	G	rs10870194	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	26	12	33	0	0.461538	0	A|0.612;G|0.388	0.388	strong	.	INPP5E	18	.	NM_019892	exon6	c.T1284C	p.G428G	CCCGTCACCTGCT	.	PASS	Atlas-SNP
HSPA6	3310	hgsc.bcm.edu	37	1	161495040	161495040	+	Missense_Mutation	SNP	C	C	T	rs63749092	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	229	99	246	0	0.432314	0	C|0.897;T|0.103	0.103	strong	.	HSPA6	53	.	NM_002155	exon1	c.C592T	p.L198F	AACGTGCTCATTT	.	PASS	Atlas-SNP
CTDP1	9150	hgsc.bcm.edu	37	18	77473127	77473127	+	Missense_Mutation	SNP	C	C	T	rs2279103	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	89	51	102	0	0.573034	0	C|0.885;T|0.115	0.115	strong	.	CTDP1	67	.	NM_004715	exon7	c.C1019T	p.T340M	CTCAGACGAGAAA	.	PASS	Atlas-SNP
CARD11	84433	hgsc.bcm.edu	37	7	2984153	2984153	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	25	45	0	0.396825	0	.	.	none	CARD11,colon,carcinoma,+1,4	CARD11	339	4	NM_032415	exon5	c.G377A	p.G126D	GTGAGGCCCTCGT	.	PASS	Atlas-SNP
SYNE1	23345	hgsc.bcm.edu	37	6	152668211	152668211	+	Missense_Mutation	SNP	A	A	G	rs111449472	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	104	42	116	0	0.403846	0	A|0.990;G|0.010	0.010	strong	.	SYNE1	3227	.	NM_182961	exon73	c.T12061C	p.C4021R	TGCTGCAGATCGC	.	PASS	Atlas-SNP
TRPM1	4308	hgsc.bcm.edu	37	15	31329944	31329944	+	Silent	SNP	G	G	A	rs12911350	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	142	71	109	0	0.5	0	G|0.909;A|0.091	0.091	strong	.	TRPM1	183	.	NM_001252020	exon19	c.C2592T	p.N864N	GGGCGCGTTATAG	.	PASS	Atlas-SNP
FHAD1	114827	hgsc.bcm.edu	37	1	15679393	15679393	+	Silent	SNP	G	G	A	rs35368057	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85	33	86	0	0.388235	0	G|0.991;A|0.009	0.009	strong	.	FHAD1	78	.	NM_052929	exon19	c.G2409A	p.A803A	CATTGCGTACGAG	.	PASS	Atlas-SNP
ABCF2	10061	hgsc.bcm.edu	37	7	150916228	150916228	+	Silent	SNP	G	G	A	rs6949587	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80	80	109	0	1	0	G|0.611;A|0.389	0.389	strong	.	ABCF2	54	.	NM_007189	exon8	c.C939T	p.Y313Y	CTTCACGTACTGA	.	PASS	Atlas-SNP
RYR1	6261	hgsc.bcm.edu	37	19	39061258	39061258	+	Silent	SNP	C	C	G	rs35959206	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	116	57	118	0	0.491379	0	C|0.960;G|0.040	0.040	strong	.	RYR1	708	.	NM_000540	exon94	c.C13671G	p.S4557S	CCTGTCCCGGAAC	.	PASS	Atlas-SNP
HELZ	9931	hgsc.bcm.edu	37	17	65212042	65212042	+	Missense_Mutation	SNP	C	C	T	rs8080100	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	340	141	365	0	0.414706	0	C|0.831;T|0.169	0.169	strong	.	HELZ	160	.	NM_014877	exon5	c.G220A	p.V74M	CTTGCACATAATT	.	PASS	Atlas-SNP
ALPK1	80216	hgsc.bcm.edu	37	4	113353358	113353358	+	Silent	SNP	G	G	A	rs35129721	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100	3	115	0	0.03	0	G|0.994;A|0.006	0.006	strong	ALPK1,caecum,carcinoma,+1,1	ALPK1	125	1	NM_001102406	exon11	c.G2655A	p.A885A	GAGGGCGGAGACC	.	scavenged	Atlas-SNP
FDFT1	2222	hgsc.bcm.edu	37	8	11660362	11660362	+	Silent	SNP	T	T	C	rs1047643	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69	32	63	0	0.463768	0	T|0.802;C|0.198	0.198	strong	.	FDFT1	25	.	NM_004462	exon1	c.T21C	p.L7L	ATGCCTTGGCCAC	.	PASS	Atlas-SNP
HIST1H2AK	8330	hgsc.bcm.edu	37	6	27805865	27805865	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	128	50	121	0	0.390625	0	.	.	none	.	HIST1H2AK	28	.	NM_003510	exon1	c.C253T	p.Q85X	CCAGCTGCAAGTG	.	PASS	Atlas-SNP
NPNT	255743	hgsc.bcm.edu	37	4	106859549	106859549	+	Missense_Mutation	SNP	G	G	C	rs35132891	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	35	22	30	0	0.628571	0	G|0.658;C|0.342	0.342	strong	.	NPNT	69	.	NM_001184691	exon6	c.G567C	p.Q189H	CCTGCAGCTGGCT	.	PASS	Atlas-SNP
ASGR1	432	hgsc.bcm.edu	37	17	7080316	7080316	+	Silent	SNP	C	C	T	rs55714927	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	14	81	0	0.222222	0	C|0.844;T|0.156	0.156	strong	.	ASGR1	20	.	NM_001671	exon4	c.G267A	p.K89K	CAAGCCCTTGACC	.	PASS	Atlas-SNP
GPSM3	63940	hgsc.bcm.edu	37	6	32159956	32159956	+	Silent	SNP	T	T	C	rs3134605	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51	36	60	0	0.705882	0	T|0.814;C|0.186	0.186	strong	GPSM3,colon,carcinoma,0,1	GPSM3	9	1	NM_022107	exon6	c.A114G	p.P38P	AGGGGATGGAGGA	.	PASS	Atlas-SNP
OR10R2	343406	hgsc.bcm.edu	37	1	158450192	158450192	+	Silent	SNP	C	C	T	rs61741711	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	218	91	207	0	0.417431	0	C|0.926;T|0.074	0.074	strong	OR10R2,NS,carcinoma,+1,1	OR10R2	81	1	NM_001004472	exon1	c.C525T	p.A175A	CTTGGCCTCTCTT	.	PASS	Atlas-SNP
COL12A1	1303	hgsc.bcm.edu	37	6	75848181	75848181	+	Missense_Mutation	SNP	A	A	G	rs240736	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	96	58	106	0	0.604167	0	A|0.734;G|0.266	0.266	strong	.	COL12A1	385	.	NM_004370	exon29	c.T5213C	p.I1738T	CTGCCAATCAGGT	.	PASS	Atlas-SNP
PGPEP1L	145814	hgsc.bcm.edu	37	15	99511873	99511873	+	Missense_Mutation	SNP	G	G	A	rs2715423	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57	31	67	1	0.54386	0.0149254	G|0.846;A|0.154	0.154	strong	PGPEP1L,NS,carcinoma,-1,2	PGPEP1L	26	2	NM_001102612	exon5	c.C425T	p.A142V	AGTGCCGCGCAGC	.	scavenged	Atlas-SNP
CSMD1	64478	hgsc.bcm.edu	37	8	2807783	2807783	+	Silent	SNP	G	G	A	rs35043129	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	116	52	136	0	0.448276	0	G|0.836;A|0.164	0.164	strong	.	CSMD1	1469	.	NM_033225	exon67	c.C10284T	p.F3428F	ATTTTCGAACTTG	.	PASS	Atlas-SNP
THBS1	7057	hgsc.bcm.edu	37	15	39880277	39880277	+	Silent	SNP	G	G	A	rs35275624	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	125	69	156	0	0.552	0	A|0.072;G|0.928;T|0.000	0.072	strong	.	THBS1	106	.	NM_003246	exon9	c.G1329A	p.P443P	GTCCCCGTGGTCA	.	PASS	Atlas-SNP
CCDC168	643677	hgsc.bcm.edu	37	13	103394613	103394613	+	Missense_Mutation	SNP	T	T	G	rs9585986	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	64	143	0	1	0	T|0.304;G|0.696	0.696	strong	.	.	.	.	NM_001146197	exon4	c.A8434C	p.T2812P	AAACTGTTATTCT	.	PASS	Atlas-SNP
FYCO1	79443	hgsc.bcm.edu	37	3	46009487	46009487	+	Missense_Mutation	SNP	G	G	A	rs33910087	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	125	60	103	0	0.48	0	G|0.916;A|0.084	0.084	strong	.	FYCO1	115	.	NM_024513	exon8	c.C1339T	p.R447C	CCAGGCGCTCCAG	.	PASS	Atlas-SNP
VNN1	8876	hgsc.bcm.edu	37	6	133015271	133015271	+	Missense_Mutation	SNP	T	T	C	rs2272996	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	189	98	176	0	0.518519	0	T|0.736;C|0.264	0.264	strong	.	VNN1	69	.	NM_004666	exon3	c.A392G	p.N131S	ATAGAGTTGTTCT	.	PASS	Atlas-SNP
SLC7A1	6541	hgsc.bcm.edu	37	13	30107067	30107067	+	Silent	SNP	G	G	C	rs2277451	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	117	58	112	1	0.495726	0.00892857	G|0.860;C|0.140	0.140	strong	SLC7A1,NS,carcinoma,0,1	SLC7A1	64	1	NM_003045	exon4	c.C423G	p.G141G	GGGTCTGCCTATC	.	scavenged	Atlas-SNP
EPHB1	2047	hgsc.bcm.edu	37	3	134670524	134670524	+	Silent	SNP	C	C	T	rs7644369	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	185	181	184	1	0.978378	0.00543478	C|0.559;T|0.441	0.441	strong	.	EPHB1	519	.	NM_004441	exon3	c.C435T	p.S145S	TGAGAGCTTCTCC	.	PASS	Atlas-SNP
SLC6A11	6538	hgsc.bcm.edu	37	3	10960057	10960057	+	Missense_Mutation	SNP	G	G	A	rs376135284		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100	42	111	0	0.42	0	.	.	weak	.	SLC6A11	87	.	NM_014229	exon8	c.G1039A	p.V347M	AGCTTCGTGGCTG	.	PASS	Atlas-SNP
SCN9A	6335	hgsc.bcm.edu	37	2	167144995	167144995	+	Silent	SNP	T	T	C	rs13402180	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55	36	89	0	0.654545	0	C|0.338;T|0.662	0.338	strong	.	SCN9A	296	.	NM_002977	exon10	c.A1266G	p.E422E	TTGAAATTCTAAT	.	PASS	Atlas-SNP
WDR65	149465	hgsc.bcm.edu	37	1	43680952	43680952	+	Silent	SNP	C	C	T	rs74422853	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	113	61	123	0	0.539823	0	C|0.989;T|0.011	0.011	strong	.	WDR65	76	.	NM_001195831	exon12	c.C1956T	p.F652F	TCAGTTCCTGCTG	.	PASS	Atlas-SNP
CATSPERD	257062	hgsc.bcm.edu	37	19	5772950	5772950	+	Missense_Mutation	SNP	G	G	A	rs61180947	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	29	63	0	0.453125	0	G|0.749;A|0.251	0.251	strong	.	.	.	.	NM_152784	exon20	c.G1915A	p.G639R	GAATTCGGGGGGC	.	PASS	Atlas-SNP
TLE6	79816	hgsc.bcm.edu	37	19	2994921	2994921	+	Silent	SNP	G	G	A	rs34551565	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48	24	48	0	0.5	0	G|0.736;A|0.264	0.264	strong	.	TLE6	68	.	NM_001143986	exon17	c.G1638A	p.T546T	AGTCACGTGCTGT	.	PASS	Atlas-SNP
C14orf182	283551	hgsc.bcm.edu	37	14	50472405	50472405	+	Missense_Mutation	SNP	G	G	A	rs6572635	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	165	82	188	0	0.49697	0	G|0.739;A|0.261	0.261	strong	C14orf182,bladder,carcinoma,+1,1	C14orf182	8	1	NM_001012706	exon1	c.C113T	p.P38L	CCTCTCGGTTCGT	.	PASS	Atlas-SNP
FREM1	158326	hgsc.bcm.edu	37	9	14740229	14740229	+	Silent	SNP	G	G	A	rs187325866	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	32	42	0	0.5	0	G|0.999;A|0.001	0.001	strong	.	FREM1	261	.	NM_144966	exon37	c.C6258T	p.Y2086Y	GCCCAGGTATCTA	.	PASS	Atlas-SNP
RBM19	9904	hgsc.bcm.edu	37	12	114383651	114383651	+	Silent	SNP	C	C	T	rs12321179	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	95	45	107	0	0.473684	0	C|0.823;T|0.177	0.177	strong	RBM19,NS,carcinoma,0,1	RBM19	117	1	NM_001146699	exon13	c.G1608A	p.K536K	TTGACTCTTGGTG	.	PASS	Atlas-SNP
SPTBN5	51332	hgsc.bcm.edu	37	15	42145936	42145936	+	Missense_Mutation	SNP	G	G	C	rs1197660	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	23	23	54	0	1	0	G|0.736;C|0.264	0.264	strong	.	SPTBN5	171	.	NM_016642	exon58	c.C9719G	p.A3240G	CGGCAGGCCTCCG	.	PASS	Atlas-SNP
TM4SF19	116211	hgsc.bcm.edu	37	3	196054439	196054439	+	Missense_Mutation	SNP	T	T	G	rs6785339	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94	48	92	0	0.510638	0	T|0.414;G|0.586	0.586	strong	TM4SF19,NS,carcinoma,0,1	TM4SF19	21	1	NM_001204897	exon2	c.A23C	p.Q8P	CTTGCCTGCGTGC	.	PASS	Atlas-SNP
GRIN3A	116443	hgsc.bcm.edu	37	9	104449294	104449294	+	Silent	SNP	G	G	A	rs33945236	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	143	59	110	1	0.412587	0.00909091	G|0.865;A|0.135	0.135	strong	GRIN3A,colon,carcinoma,0,1	GRIN3A	186	1	NM_133445	exon2	c.C888T	p.N296N	GGTGATGTTGATG	.	scavenged	Atlas-SNP
CAPRIN2	65981	hgsc.bcm.edu	37	12	30881884	30881884	+	Missense_Mutation	SNP	G	G	A	rs374198235	alternate_allele	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	155	92	161	0	0.593548	0	.	.	alt	.	CAPRIN2	109	.	NM_023925	exon8	c.C1480T	p.P494S	GCTTTGGTGTCTC	.	PASS	Atlas-SNP
BEND3	57673	hgsc.bcm.edu	37	6	107391396	107391396	+	Silent	SNP	G	G	A	rs3814073	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	65	29	68	0	0.446154	0	G|0.783;A|0.217	0.217	strong	.	BEND3	70	.	NM_001080450	exon5	c.C999T	p.N333N	GAAGTCGTTCAGC	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	121	120	116	0	0.991736	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
OR6K3	391114	hgsc.bcm.edu	37	1	158687163	158687163	+	Missense_Mutation	SNP	G	G	A	rs28568406	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85	50	95	0	0.588235	0	G|0.585;A|0.415	0.415	strong	.	OR6K3	101	.	NM_001005327	exon1	c.C743T	p.P248L	AATATCGGGAAGA	.	PASS	Atlas-SNP
LCP2	3937	hgsc.bcm.edu	37	5	169693858	169693858	+	Silent	SNP	G	G	A	rs56262228	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	179	84	202	0	0.469274	0	G|0.960;A|0.040	0.040	strong	.	LCP2	133	.	NM_005565	exon10	c.C726T	p.P242P	ATCTAGGGGAGGT	.	PASS	Atlas-SNP
CAD	790	hgsc.bcm.edu	37	2	27460968	27460968	+	Silent	SNP	A	A	G	rs1141313	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	144	84	108	0	0.583333	0	A|0.568;G|0.432	0.432	strong	CAD,NS,carcinoma,+1,1	CAD	199	1	NM_004341	exon30	c.A4773G	p.A1591A	TCACGCAGAGCAG	.	PASS	Atlas-SNP
DNAH8	1769	hgsc.bcm.edu	37	6	38729511	38729511	+	Missense_Mutation	SNP	T	T	C	rs61748600	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	157	129	149	0	0.821656	0	T|0.879;C|0.121	0.121	strong	.	DNAH8	1239	.	NM_001206927	exon11	c.T1549C	p.Y517H	AAAGCATATATTA	.	PASS	Atlas-SNP
COL16A1	1307	hgsc.bcm.edu	37	1	32127953	32127953	+	Silent	SNP	G	G	A	rs2271928	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94	48	101	0	0.510638	0	G|0.511;A|0.489	0.489	strong	.	COL16A1	137	.	NM_001856	exon58	c.C3663T	p.D1221D	CTTGCCGTCCTTC	.	PASS	Atlas-SNP
TM4SF4	7104	hgsc.bcm.edu	37	3	149192676	149192676	+	Silent	SNP	G	G	A	rs12488126	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	46	79	0	0.528736	0	G|0.791;A|0.209	0.209	strong	.	TM4SF4	27	.	NM_004617	exon1	c.G12A	p.G4G	CACTGGGGGCTGT	.	PASS	Atlas-SNP
ZNF414	84330	hgsc.bcm.edu	37	19	8576390	8576390	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	103	57	100	0	0.553398	0	.	.	none	.	ZNF414	25	.	NM_032370	exon6	c.G905A	p.G302D	GAGCCGCCCTGGG	.	PASS	Atlas-SNP
CAB39L	81617	hgsc.bcm.edu	37	13	49951142	49951142	+	Silent	SNP	T	T	C	rs8002829	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	160	94	125	0	0.5875	0	T|0.457;C|0.543	0.543	strong	.	CAB39L	35	.	NM_030925	exon3	c.A237G	p.L79L	TGTCACTAGCAGG	.	PASS	Atlas-SNP
ANO4	121601	hgsc.bcm.edu	37	12	101520689	101520689	+	Silent	SNP	A	A	G	rs1055734	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	214	92	201	1	0.429907	0.00497512	A|0.860;G|0.140	0.140	strong	ANO4,NS,carcinoma,+1,1	ANO4	183	1	NM_178826	exon26	c.A2604G	p.S868S	CATTTCATATCTG	.	scavenged	Atlas-SNP
WFIKKN1	117166	hgsc.bcm.edu	37	16	681284	681284	+	Silent	SNP	C	C	T	rs8062289	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	17	8	39	0	0.470588	0	C|0.799;T|0.201	0.201	strong	WFIKKN1,rectum,carcinoma,0,2	WFIKKN1	30	2	NM_053284	exon1	c.C31T	p.L11L	CCGCTCCTGCTCC	.	scavenged	Atlas-SNP
ZNF646	9726	hgsc.bcm.edu	37	16	31088625	31088625	+	Missense_Mutation	SNP	A	A	G	rs749670	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	33	16	31	0	0.484848	0	A|0.653;G|0.347	0.347	strong	.	ZNF646	133	.	NM_014699	exon2	c.A980G	p.E327G	GGGAGGAGAAAGG	.	PASS	Atlas-SNP
TCP11L1	55346	hgsc.bcm.edu	37	11	33079580	33079580	+	Missense_Mutation	SNP	A	A	G	rs2273549	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80	36	72	0	0.45	0	A|0.857;G|0.143	0.143	strong	.	TCP11L1	40	.	NM_001145541	exon5	c.A533G	p.K178R	TTTCCAAGCTGGC	.	PASS	Atlas-SNP
IL17REL	400935	hgsc.bcm.edu	37	22	50435480	50435480	+	Missense_Mutation	SNP	A	A	G	rs5771069	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	251	121	274	1	0.482072	0.00364964	A|0.431;G|0.569	0.569	strong	.	IL17REL	21	.	NM_001001694	exon14	c.T998C	p.L333P	GGCAAAAGCAGGG	.	PASS	Atlas-SNP
BAZ1A	11177	hgsc.bcm.edu	37	14	35222732	35222732	+	Silent	SNP	C	C	T	rs61754296	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	117	66	76	0	0.564103	0	C|0.895;T|0.105	0.105	strong	BAZ1A,NS,carcinoma,0,2	BAZ1A	128	2	NM_013448	exon27	c.G4653A	p.A1551A	CTTTTTCGCAGCC	.	PASS	Atlas-SNP
SH3D21	79729	hgsc.bcm.edu	37	1	36773405	36773405	+	Silent	SNP	T	T	G	rs35343437	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	133	70	135	0	0.526316	0	T|0.555;G|0.445	0.445	strong	.	SH3D21	73	.	NM_001162530	exon6	c.T471G	p.P157P	CAGCCCTGGTCCC	.	PASS	Atlas-SNP
MOB3C	148932	hgsc.bcm.edu	37	1	47080679	47080679	+	Nonsense_Mutation	SNP	G	G	A	rs6671527	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	101	41	134	0	0.405941	0	G|0.438;A|0.562	0.562	strong	.	MOB3C	1	.	NM_145279	exon1	c.C70T	p.R24X	CTCTTCGACTTCT	.	PASS	Atlas-SNP
ABCD4	5826	hgsc.bcm.edu	37	14	74759059	74759059	+	Missense_Mutation	SNP	G	G	C	rs35073715	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	39	24	25	0	0.615385	0	G|0.982;C|0.018	0.018	strong	.	ABCD4	54	.	NM_005050	exon11	c.C1049G	p.T350R	AGAAGCGTCTCCC	.	PASS	Atlas-SNP
HTT	3064	hgsc.bcm.edu	37	4	3213832	3213832	+	Silent	SNP	G	G	A	rs362336	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	35	17	47	0	0.485714	0	G|0.718;A|0.282	0.282	strong	.	HTT	221	.	NM_002111	exon48	c.G6591A	p.E2197E	TGCAGAGCCGGCG	.	PASS	Atlas-SNP
C5orf52	100190949	hgsc.bcm.edu	37	5	157106968	157106968	+	Silent	SNP	C	C	T	rs6892478	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	112	54	130	0	0.482143	0	C|0.837;G|0.000;T|0.162	0.162	strong	.	C5orf52	17	.	NM_001145132	exon3	c.C441T	p.S147S	GAACAGCAACCGG	.	PASS	Atlas-SNP
MYOM1	8736	hgsc.bcm.edu	37	18	3173964	3173964	+	Silent	SNP	G	G	A	rs2230163	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	33	55	0	0.52381	0	T|0.130;G|0.427;C|0.268;A|0.175	0.175	strong	.	MYOM1	192	.	NM_003803	exon8	c.C1146T	p.H382H	CCCAGCGTGGAAG	.	PASS	Atlas-SNP
SEMA4D	10507	hgsc.bcm.edu	37	9	91978397	91978397	+	Missense_Mutation	SNP	C	C	T	rs13295305	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	32	59	0	0.432432	0	C|0.880;T|0.120	0.120	strong	.	SEMA4D	81	.	NM_001142287	exon20	c.G2138A	p.R713K	ACAGCCCTCCAGG	.	PASS	Atlas-SNP
CCDC88B	283234	hgsc.bcm.edu	37	11	64124515	64124515	+	Silent	SNP	T	T	C	rs612448	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	95	55	93	1	0.578947	0.0107527	T|0.706;C|0.294	0.294	strong	CCDC88B_ENST00000359902,NS,carcinoma,-1,1	CCDC88B	89	1	NM_032251	exon27	c.T4380C	p.P1460P	AGGCCCTGAGGTA	.	scavenged	Atlas-SNP
ALKBH3	221120	hgsc.bcm.edu	37	11	43913604	43913604	+	Silent	SNP	G	G	A	rs16937692	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	127	62	110	0	0.488189	0	G|0.961;A|0.039	0.039	strong	.	ALKBH3	33	.	NM_139178	exon7	c.G384A	p.Q128Q	TTATCAGCAACCA	.	PASS	Atlas-SNP
RNF175	285533	hgsc.bcm.edu	37	4	154644537	154644537	+	Missense_Mutation	SNP	T	T	C	rs10517577	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98	62	62	0	0.632653	0	T|0.917;C|0.083	0.083	strong	.	RNF175	40	.	NM_173662	exon5	c.A475G	p.M159V	TAAACATGATCGC	.	PASS	Atlas-SNP
ATP10A	57194	hgsc.bcm.edu	37	15	25926179	25926179	+	Missense_Mutation	SNP	C	C	T	rs2076744	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100	45	94	0	0.45	0	C|0.734;T|0.266	0.266	strong	ATP10A,colon,carcinoma,0,1	ATP10A	270	1	NM_024490	exon18	c.G3535A	p.A1179T	GGAAGGCGGCGTC	.	PASS	Atlas-SNP
AOC3	8639	hgsc.bcm.edu	37	17	41004637	41004637	+	Missense_Mutation	SNP	G	G	A	rs33986943	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	262	120	212	0	0.458015	0	G|0.930;A|0.070	0.070	strong	.	AOC3	88	.	NM_003734	exon1	c.G1277A	p.R426H	CAATACGTGATGC	.	PASS	Atlas-SNP
PDE1C	5137	hgsc.bcm.edu	37	7	32338337	32338337	+	Missense_Mutation	SNP	G	G	A	rs215607	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	25	25	28	0	1	0	G|0.214;A|0.786	0.786	strong	.	PDE1C	465	.	NM_001191058	exon1	c.C11T	p.A4V	TTGCCGGCGTCCG	.	PASS	Atlas-SNP
ZNF682	91120	hgsc.bcm.edu	37	19	20133876	20133876	+	Missense_Mutation	SNP	G	G	A	rs201103446	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	89	3	84	0	0.0337079	0	.	.	weak	ZNF682,NS,carcinoma,0,2	ZNF682	51	2	NM_033196	exon3	c.C163T	p.R55C	CCAGACGGCTAAT	.	scavenged	Atlas-SNP
RSF1	51773	hgsc.bcm.edu	37	11	77378388	77378388	+	Silent	SNP	T	T	C	rs4945197	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	109	93	104	0	0.853211	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
ALG10B	144245	hgsc.bcm.edu	37	12	38715000	38715000	+	Silent	SNP	A	A	G	rs35518352	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	115	115	143	0	1	0	A|0.664;G|0.336	0.336	strong	ALG10B,colon,carcinoma,0,1	ALG10B	58	1	NM_001013620	exon3	c.A1407G	p.Q469Q	CATTCAAAGGTTT	.	PASS	Atlas-SNP
DACT1	51339	hgsc.bcm.edu	37	14	59113721	59113721	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	30	13	50	0	0.433333	0	.	.	none	.	DACT1	119	.	NM_016651	exon4	c.C2380G	p.Q794E	CCCATTCAAACGG	.	PASS	Atlas-SNP
BTBD2	55643	hgsc.bcm.edu	37	19	1997363	1997363	+	Silent	SNP	A	A	G	rs1610045	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	40	20	63	0	0.5	0	A|0.571;G|0.429	0.429	strong	.	BTBD2	31	.	NM_017797	exon2	c.T507C	p.A169A	GAAGGCAGCGGGT	.	PASS	Atlas-SNP
AFF3	3899	hgsc.bcm.edu	37	2	100210642	100210642	+	Missense_Mutation	SNP	T	T	C	rs1047265	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	166	76	210	0	0.457831	0	T|0.848;C|0.152	0.152	strong	.	AFF3	164	.	NM_001025108	exon14	c.A1556G	p.N519S	TACTGATTGCTCT	.	PASS	Atlas-SNP
C9orf24	84688	hgsc.bcm.edu	37	9	34397545	34397545	+	Silent	SNP	A	A	G	rs11790577	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85	44	90	0	0.517647	0	A|0.552;G|0.448	0.448	strong	.	C9orf24	15	.	NM_032596	exon1	c.T87C	p.Y29Y	GTCCTTATAGACC	.	PASS	Atlas-SNP
COL5A3	50509	hgsc.bcm.edu	37	19	10114759	10114759	+	Silent	SNP	C	C	T	rs76321360	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	104	64	108	0	0.615385	0	C|0.959;G|0.000;T|0.041	0.041	strong	.	COL5A3	243	.	NM_015719	exon5	c.G657A	p.R219R	GAGGTACCGCTCA	.	PASS	Atlas-SNP
FAM22G	441457	hgsc.bcm.edu	37	9	99701002	99701002	+	Silent	SNP	C	C	T	rs76993010		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	360	124	315	0	0.344444	0	T|1.000;|0.000	1.000	weak	.	FAM22G	66	.	NM_001170741	exon7	c.C1797T	p.L599L	GGGTCTCCCTGGA	.	PASS	Atlas-SNP
SETBP1	26040	hgsc.bcm.edu	37	18	42532606	42532606	+	Missense_Mutation	SNP	G	G	A	rs3744825	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	125	62	96	0	0.496	0	G|0.874;A|0.126	0.126	strong	SETBP1,NS,carcinoma,0,1	SETBP1	577	1	NM_015559	exon4	c.G3301A	p.V1101I	TCCCACGTAAAGA	.	PASS	Atlas-SNP
DAO	1610	hgsc.bcm.edu	37	12	109293183	109293183	+	Missense_Mutation	SNP	T	T	G	rs113854555	alternate_allele	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	14	33	0	0.269231	0	T|0.500;C|0.500	.	alt	.	DAO	58	.	NM_001917	exon10	c.T844G	p.F282V	ACTGGCTTCCGGC	.	PASS	Atlas-SNP
ANKRD44	91526	hgsc.bcm.edu	37	2	197872574	197872574	+	Missense_Mutation	SNP	C	C	T	rs61752170	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	126	62	96	0	0.492063	0	C|0.991;T|0.009	0.009	strong	.	ANKRD44	281	.	NM_001195144	exon20	c.G2086A	p.V696I	TGTCTACGTTGGC	.	PASS	Atlas-SNP
TTC40	54777	hgsc.bcm.edu	37	10	134664628	134664628	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	43	12	43	0	0.27907	0	.	.	none	.	TTC40	100	.	NM_001200049	exon40	c.T5756C	p.V1919A	AGGCCGACGGAAG	.	PASS	Atlas-SNP
KRTAP9-2	83899	hgsc.bcm.edu	37	17	39383027	39383027	+	Missense_Mutation	SNP	G	G	T	rs71371478	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	40	11	43	2	0.275	0.0465116	G|0.997;T|0.003	0.003	strong	KRTAP9-2,extremity,malignant_melanoma,0,1	KRTAP9-2	24	1	NM_031961	exon1	c.G121T	p.A41S	CAGCCCGCCTGCT	.	scavenged	Atlas-SNP
TNS3	64759	hgsc.bcm.edu	37	7	47343083	47343083	+	Silent	SNP	C	C	T	rs3807589	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	59	17	63	0	0.288136	0	C|0.907;T|0.093	0.093	strong	.	TNS3	140	.	NM_022748	exon22	c.G2922A	p.E974E	GGAGAACTCAGCG	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9060059	9060059	+	Missense_Mutation	SNP	A	A	C	rs12977368	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	117	46	155	0	0.393162	0	A|0.794;C|0.206	0.206	strong	.	MUC16	4315	.	NM_024690	exon3	c.T27387G	p.D9129E	TGGCACATCTCCA	.	PASS	Atlas-SNP
USP17L7	392197	hgsc.bcm.edu	37	8	11990038	11990038	+	Missense_Mutation	SNP	G	G	A	rs9694759	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	153	38	153	0	0.248366	0	G|0.911;A|0.089	0.089	strong	.	.	.	.	NM_001256869	exon1	c.C1481T	p.P494L	TCTGTCGGTTTCG	.	PASS	Atlas-SNP
ALDH3A1	218	hgsc.bcm.edu	37	17	19646690	19646690	+	Silent	SNP	C	C	T	rs138392076	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	112	3	97	0	0.0267857	0	A|0.000;C|1.000;T|0.000	0.000	strong	ALDH3A1,NS,carcinoma,-1,1	ALDH3A1	40	1	NM_001135168	exon2	c.G249A	p.A83A	CTCATCCGCGGCC	.	scavenged	Atlas-SNP
PROSER2	254427	hgsc.bcm.edu	37	10	11911764	11911764	+	Missense_Mutation	SNP	G	G	A	rs117789748	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	25	16	22	0	0.64	0	G|0.943;A|0.057	0.057	strong	.	.	.	.	NM_153256	exon4	c.G667A	p.G223R	CGGCCCGGGGAGT	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9071834	9071834	+	Silent	SNP	G	G	C	rs17000803	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	112	47	118	1	0.419643	0.00847458	G|0.792;C|0.208	0.208	strong	MUC16_ENST00000397910,NS,carcinoma,-1,3	MUC16	4315	3	NM_024690	exon3	c.C15612G	p.P5204P	GTCCGTGGGAAAG	.	scavenged	Atlas-SNP
DNAH3	55567	hgsc.bcm.edu	37	16	20966273	20966273	+	Missense_Mutation	SNP	G	G	A	rs12924551	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	131	66	118	0	0.503817	0	G|0.926;A|0.074	0.074	strong	DNAH3_ENST00000261383,NS,carcinoma,+1,4	DNAH3	1142	4	NM_017539	exon55	c.C10933T	p.R3645C	AGGAGCGCAACAG	.	PASS	Atlas-SNP
RSPH1	89765	hgsc.bcm.edu	37	21	43896143	43896143	+	Missense_Mutation	SNP	C	C	T	rs117385282	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	30	68	0	0.357143	0	C|0.869;T|0.131	0.131	strong	RSPH1,NS,carcinoma,0,1	RSPH1	36	1	NM_080860	exon8	c.G742A	p.G248R	CCTCCCCGGGTTC	.	PASS	Atlas-SNP
ABHD12B	145447	hgsc.bcm.edu	37	14	51368610	51368610	+	Missense_Mutation	SNP	A	A	G	rs28564871	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	49	92	0	0.604938	0	A|0.765;G|0.235	0.235	strong	ABHD12B_ENST00000337334,colon,carcinoma,-1,5	ABHD12B	53	5	NM_001206673	exon10	c.A844G	p.I282V	AAAATAATCTTTC	.	PASS	Atlas-SNP
FAM21C	253725	hgsc.bcm.edu	37	10	46254783	46254783	+	Silent	SNP	A	A	G	rs61856727	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	158	28	361	0	0.177215	0	A|0.375;G|0.625	0.625	strong	FAM21C,caecum,carcinoma,0,1	FAM21C	68	1	NM_015262	exon17	c.A1569G	p.K523K	CAGCAAAAATCTC	.	scavenged	Atlas-SNP
KIAA1033	23325	hgsc.bcm.edu	37	12	105550565	105550565	+	Silent	SNP	C	C	T	rs35149056	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	38	71	0	0.44186	0	C|0.946;T|0.054	0.054	strong	.	KIAA1033	83	.	NM_015275	exon27	c.C2820T	p.A940A	CAATGCCATTAGG	.	PASS	Atlas-SNP
TIAM2	26230	hgsc.bcm.edu	37	6	155575639	155575639	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	175	94	144	0	0.537143	0	.	.	none	TIAM2,NS,carcinoma,+1,1	TIAM2	161	1	NM_012454	exon25	c.C4400T	p.P1467L	AATTACCACTGGA	.	PASS	Atlas-SNP
OR2W5	441932	hgsc.bcm.edu	37	1	247654498	247654498	+	Silent	SNP	G	G	A	rs61070846	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	182	73	196	0	0.401099	0	G|0.820;A|0.180	0.180	strong	.	OR2W5	97	.	NM_001004698	exon1	c.G69A	p.L23L	TGGACTGGAGAAA	.	PASS	Atlas-SNP
CPSF3L	54973	hgsc.bcm.edu	37	1	1247494	1247494	+	Silent	SNP	T	T	C	rs12103	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	27	27	74	0	1	0	T|0.554;C|0.446	0.446	strong	.	CPSF3L	33	.	NM_001256456	exon18	c.A1659G	p.P553P	GCCGTCTGGGAGG	.	PASS	Atlas-SNP
PARP16	54956	hgsc.bcm.edu	37	15	65553246	65553246	+	Silent	SNP	C	C	T	rs2304896	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	136	136	171	0	1	0	C|0.729;T|0.271	0.271	strong	.	PARP16	23	.	NM_017851	exon5	c.G810A	p.V270V	TGAATACACCAGG	.	PASS	Atlas-SNP
CFHR3	10878	hgsc.bcm.edu	37	1	196759347	196759347	+	Silent	SNP	A	A	T	rs379049		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	222	21	246	0	0.0945946	0	.	.	weak	CFHR3,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	CFHR3	52	1	NM_021023	exon5	c.A786T	p.P262P	ACCACCAAGATGC	.	scavenged	Atlas-SNP
SPRR1A	6698	hgsc.bcm.edu	37	1	152957887	152957887	+	Missense_Mutation	SNP	G	G	A	rs1611764	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	39	79	0	0.52	0	G|0.417;A|0.583	0.583	strong	.	SPRR1A	17	.	NM_001199828	exon2	c.G181A	p.V61I	CCCAAGGTTCCAG	.	PASS	Atlas-SNP
CCDC137	339230	hgsc.bcm.edu	37	17	79634813	79634813	+	Silent	SNP	T	T	C	rs11546632	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	17	7	25	0	0.411765	0	T|0.868;C|0.132	0.132	strong	.	CCDC137	27	.	NM_199287	exon2	c.T189C	p.I63I	GGAGATTCCTTTC	.	PASS	Atlas-SNP
CEL	1056	hgsc.bcm.edu	37	9	135947032	135947032	+	Missense_Mutation	SNP	C	C	A	rs201411101		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	33	11	23	0	0.333333	0	.	.	weak	CEL,NS,carcinoma,0,2	CEL	71	2	NM_001807	exon11	c.C2152A	p.P718T	CCCGTGCCGCCCA	.	scavenged	Atlas-SNP
RAPGEF3	10411	hgsc.bcm.edu	37	12	48143315	48143315	+	Missense_Mutation	SNP	A	A	G	rs145878042	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	14	5	20	0	0.357143	0	A|0.993;G|0.007	0.007	strong	.	RAPGEF3	98	.	NM_001098531	exon10	c.T899C	p.L300P	GTCACCAGCCCCT	.	PASS	Atlas-SNP
ABCC2	1244	hgsc.bcm.edu	37	10	101604207	101604207	+	Silent	SNP	C	C	T	rs3740066	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	37	16	47	0	0.432432	0	C|0.678;T|0.322	0.322	strong	ABCC2,NS,carcinoma,0,1	ABCC2	160	1	NM_000392	exon28	c.C3972T	p.I1324I	TGACATCGGTAGC	.	PASS	Atlas-SNP
SERPINB2	5055	hgsc.bcm.edu	37	18	61570470	61570470	+	Silent	SNP	T	T	G	rs6102	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	155	56	182	0	0.36129	0	T|0.779;G|0.221	0.221	strong	SERPINB2,NS,carcinoma,0,1	SERPINB2	63	1	NM_002575	exon8	c.T1179G	p.P393P	TCATCCTTTTCTT	.	PASS	Atlas-SNP
ABCA13	154664	hgsc.bcm.edu	37	7	48312674	48312674	+	Silent	SNP	G	G	A	rs1358066	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	30	29	77	1	0.966667	0.012987	G|0.441;A|0.559	0.559	strong	ABCA13_ENST00000435803,NS,carcinoma,0,2	ABCA13	1192	2	NM_152701	exon17	c.G3411A	p.V1137V	CAGTGTGTTCAAC	.	scavenged	Atlas-SNP
ALPP	250	hgsc.bcm.edu	37	2	233243981	233243981	+	Missense_Mutation	SNP	A	A	T	rs13026692	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	155	73	143	0	0.470968	0	A|0.675;T|0.325	0.325	strong	ALPP,NS,carcinoma,0,1	ALPP	53	1	NM_001632	exon3	c.A265T	p.I89L	CCTGAGATACCCC	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	103	31	80	0	0.300971	0	G|0.655;0|0.003	.	strong	.	CA5B	23	.	NM_007220	exon8	c.G918A	p.A306A	ACAAGCGAAACCC	.	PASS	Atlas-SNP
NLRP2	55655	hgsc.bcm.edu	37	19	55512137	55512137	+	Silent	SNP	C	C	A	rs12768	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	50	26	73	0	0.52	0	T|0.004;G|0.004	.	strong	.	NLRP2	161	.	NM_017852	exon13	c.C3060A	p.I1020I	GAAAATCGATGAC	.	PASS	Atlas-SNP
SYPL2	284612	hgsc.bcm.edu	37	1	110019439	110019439	+	Missense_Mutation	SNP	A	A	G	rs62623713	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82	36	70	0	0.439024	0	A|0.962;G|0.038	0.038	strong	SYPL2,NS,carcinoma,-1,1	SYPL2	41	1	NM_001040709	exon4	c.A296G	p.E99G	ATGAAGAGTCCAG	.	PASS	Atlas-SNP
KLK3	354	hgsc.bcm.edu	37	19	51359503	51359503	+	Silent	SNP	A	A	G	rs1135766	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	78	78	86	0	1	0	A|0.599;C|0.019	.	strong	KLK3_ENST00000360617,colon,carcinoma,0,2	KLK3	76	2	NM_001030050	exon2	c.A54G	p.A18A	TGCTGCACCCCTC	.	PASS	Atlas-SNP
FBXO39	162517	hgsc.bcm.edu	37	17	6683215	6683215	+	Missense_Mutation	SNP	C	C	T	rs4796555	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	39	77	0	0.52	0	C|0.730;N|0.000	.	strong	.	FBXO39	50	.	NM_153230	exon2	c.C28T	p.P10S	ATCCAGCCCCAAG	.	PASS	Atlas-SNP
FBF1	85302	hgsc.bcm.edu	37	17	73922941	73922941	+	Missense_Mutation	SNP	T	T	C	rs2305913	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	138	138	114	0	1	0	T|0.549;C|0.451	0.451	strong	.	FBF1	48	.	NM_001080542	exon9	c.A451G	p.R151G	GTCCTCTCAATGG	.	PASS	Atlas-SNP
ZFHX3	463	hgsc.bcm.edu	37	16	72993622	72993622	+	Silent	SNP	C	C	T	rs62053190	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98	42	98	0	0.428571	0	C|0.941;T|0.059	0.059	strong	ZFHX3,NS,carcinoma,0,2	ZFHX3	404	2	NM_006885	exon2	c.G423A	p.A141A	AATGTACGCGGAG	.	PASS	Atlas-SNP
CELA2A	63036	hgsc.bcm.edu	37	1	15789297	15789297	+	Silent	SNP	A	A	C	rs55772743		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	169	168	131	1	0.994083	0.00763359	.	.	weak	CELA2A,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	CELA2A	32	1	NM_033440	exon4	c.A297C	p.A99A	GCTGGCAGTCAGT	.	PASS	Atlas-SNP
OCEL1	79629	hgsc.bcm.edu	37	19	17337928	17337928	+	Silent	SNP	C	C	T	rs1045201	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	17	72	0	0.361702	0	C|0.914;T|0.086	0.086	strong	OCEL1,colon,carcinoma,0,1	OCEL1	20	1	NM_024578	exon3	c.C372T	p.A124A	CCAGGCCCTCCTG	.	PASS	Atlas-SNP
ULK4	54986	hgsc.bcm.edu	37	3	41756965	41756965	+	Missense_Mutation	SNP	C	C	T	rs61744388	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	36	64	0	0.537313	0	C|0.772;T|0.228	0.228	strong	.	ULK4	150	.	NM_017886	exon24	c.G2551A	p.V851I	GCACTACAGGCAT	.	PASS	Atlas-SNP
SNAPC4	6621	hgsc.bcm.edu	37	9	139272058	139272058	+	Silent	SNP	A	A	G	rs10781507	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68	67	64	0	0.985294	0	A|0.635;G|0.365	0.365	strong	SNAPC4,NS,lymphoid_neoplasm,0,1	SNAPC4	82	1	NM_003086	exon21	c.T4221C	p.S1407S	CAGCTCACTCAGG	.	PASS	Atlas-SNP
C10orf120	399814	hgsc.bcm.edu	37	10	124459139	124459139	+	Silent	SNP	T	T	C	rs11813597	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	112	59	100	0	0.526786	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
SPAG1	6674	hgsc.bcm.edu	37	8	101252680	101252680	+	Missense_Mutation	SNP	T	T	C	rs6511	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	33	13	42	0	0.393939	0	T|0.369;C|0.631	0.631	strong	SPAG1,pharynx,carcinoma,-1,2	SPAG1	80	2	NM_003114	exon18	c.T2330C	p.M777T	TCTCCATGGGATG	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	97	55	87	0	0.56701	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
CADM3	57863	hgsc.bcm.edu	37	1	159169641	159169641	+	Silent	SNP	T	T	C	rs862999	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	104	44	84	0	0.423077	0	T|0.188;C|0.812	0.812	strong	.	CADM3	118	.	NM_021189	exon9	c.T1155C	p.L385L	CTTCCTTGGCCAC	.	PASS	Atlas-SNP
DMKN	93099	hgsc.bcm.edu	37	19	36002393	36002393	+	Missense_Mutation	SNP	C	C	T	rs11667007	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	37	32	55	0	0.864865	0	C|0.691;T|0.309	0.309	strong	.	DMKN	116	.	NM_001126058	exon5	c.G838A	p.G280S	TGCTGCCGCCACT	.	PASS	Atlas-SNP
FER1L6	654463	hgsc.bcm.edu	37	8	125061895	125061895	+	Silent	SNP	G	G	A	rs4870887	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	161	83	145	0	0.515528	0	G|0.501;A|0.498	0.498	strong	FER1L6,colon,carcinoma,+2,2	FER1L6	268	2	NM_001039112	exon22	c.G2772A	p.K924K	TGTGAAGCTGGCT	.	PASS	Atlas-SNP
AFP	174	hgsc.bcm.edu	37	4	74318177	74318177	+	Silent	SNP	T	T	C	rs35920062	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	187	101	162	0	0.540107	0	T|0.955;C|0.045	0.045	strong	.	AFP	60	.	NM_001134	exon12	c.T1488C	p.G496G	CCCTGGTGTTGGC	.	PASS	Atlas-SNP
KANSL1	284058	hgsc.bcm.edu	37	17	44159849	44159849	+	Silent	SNP	T	T	C	rs17576165	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	119	118	107	0	0.991597	0	T|0.854;C|0.146	0.146	strong	.	.	.	.	NM_001193466	exon4	c.A1491G	p.P497P	ACTAAGTGGAAGA	.	PASS	Atlas-SNP
SYNE1	23345	hgsc.bcm.edu	37	6	152660451	152660451	+	Silent	SNP	G	G	A	rs71575926	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	28	55	0	0.538462	0	G|0.895;A|0.105	0.105	strong	.	SYNE1	3227	.	NM_182961	exon75	c.C12276T	p.L4092L	GCAAAGGAGATCT	.	PASS	Atlas-SNP
ADAMTS5	11096	hgsc.bcm.edu	37	21	28338298	28338298	+	Missense_Mutation	SNP	C	C	G	rs457947	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93	53	104	0	0.569892	0	C|0.834;G|0.166	0.166	strong	.	ADAMTS5	184	.	NM_007038	exon1	c.G413C	p.G138A	GGACTACCGTCCA	.	PASS	Atlas-SNP
XDH	7498	hgsc.bcm.edu	37	2	31590917	31590917	+	Missense_Mutation	SNP	T	T	C	rs17011368	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	157	79	163	0	0.503185	0	T|0.942;C|0.058	0.058	strong	.	XDH	191	.	NM_000379	exon20	c.A2107G	p.I703V	TCTTTATAGCATC	.	PASS	Atlas-SNP
GRIK2	2898	hgsc.bcm.edu	37	6	102266322	102266322	+	Silent	SNP	C	C	G	rs34747916	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	188	88	201	0	0.468085	0	C|0.954;G|0.046	0.046	strong	GRIK2_ENST00000421544,mucosal,malignant_melanoma,+2,3	GRIK2	487	3	NM_021956	exon9	c.C1281G	p.S427S	AGATTCCTTATCC	.	PASS	Atlas-SNP
SLC25A10	1468	hgsc.bcm.edu	37	17	79682051	79682051	+	Silent	SNP	C	C	T	rs3204270	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	153	69	123	0	0.45098	0	C|0.937;G|0.000;T|0.062	0.062	strong	SLC25A10,NS,carcinoma,0,2	SLC25A10	24	2	NM_001270888	exon2	c.C162T	p.T54T	GCGTACCGACGGC	.	PASS	Atlas-SNP
SLC9C1	285335	hgsc.bcm.edu	37	3	111901099	111901099	+	Missense_Mutation	SNP	T	T	C	rs74840030	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	107	55	108	0	0.514019	0	T|0.962;C|0.038	0.038	strong	.	.	.	.	NM_183061	exon21	c.A2530G	p.M844V	TGGCCATGATTAA	.	PASS	Atlas-SNP
MCF2L	23263	hgsc.bcm.edu	37	13	113720476	113720476	+	Silent	SNP	C	C	T	rs2297192	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	28	8	40	0	0.285714	0	C|0.846;T|0.154	0.154	strong	.	MCF2L	182	.	NM_001112732	exon8	c.C873T	p.T291T	GGCCACCGTGCAG	.	PASS	Atlas-SNP
BTBD8	284697	hgsc.bcm.edu	37	1	92568089	92568089	+	Missense_Mutation	SNP	A	A	G	rs17131602	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	145	66	188	0	0.455172	0	A|0.986;G|0.014	0.014	strong	BTBD8,colon,carcinoma,0,4	BTBD8	32	4	NM_183242	exon3	c.A407G	p.K136R	GGAAAAAGATAAT	.	PASS	Atlas-SNP
PMS2	5395	hgsc.bcm.edu	37	7	6018231	6018231	+	Silent	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	396	212	325	0	0.535354	0	.	.	none	.	PMS2	88	.	NM_000535	exon13	c.A2271G	p.E757E	ACCATTTTCATCG	.	PASS	Atlas-SNP
RINL	126432	hgsc.bcm.edu	37	19	39360597	39360597	+	Missense_Mutation	SNP	C	C	T	rs113728915	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	50	23	45	0	0.46	0	C|0.924;T|0.076	0.076	strong	RINL,NS,carcinoma,0,1	RINL	32	1	NM_001195833	exon9	c.G1328A	p.R443Q	TCGCCTCGAGCCA	.	PASS	Atlas-SNP
ALDH3B2	222	hgsc.bcm.edu	37	11	67432799	67432799	+	Silent	SNP	G	G	A	rs80147122	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	232	5	218	2	0.0215517	0.00917431	.	.	strong	ALDH3B2,NS,haematopoietic_neoplasm,0,2	ALDH3B2	46	2	NM_001031615	exon7	c.C663T	p.R221R	GGCCACGCGGCTG	.	scavenged	Atlas-SNP
SAMD12	401474	hgsc.bcm.edu	37	8	119391866	119391866	+	Silent	SNP	G	G	A	rs12171673	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	246	123	220	0	0.5	0	G|0.884;A|0.116	0.116	strong	.	SAMD12	24	.	NM_207506	exon4	c.C396T	p.H132H	TAAGATGTGCTGC	.	PASS	Atlas-SNP
IP6K3	117283	hgsc.bcm.edu	37	6	33694659	33694659	+	Silent	SNP	G	G	A	rs34252064	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	112	18	72	0	0.160714	0	G|0.901;A|0.099	0.099	strong	.	IP6K3	52	.	NM_001142883	exon5	c.C438T	p.S146S	GGGCTCGGACCTC	.	PASS	Atlas-SNP
F13A1	2162	hgsc.bcm.edu	37	6	6152137	6152137	+	Missense_Mutation	SNP	C	C	G	rs5988	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48	13	51	0	0.270833	0	C|0.786;G|0.214	0.214	strong	.	F13A1	135	.	NM_000129	exon14	c.G1954C	p.E652Q	TAAACTCAACTGT	.	PASS	Atlas-SNP
CD207	50489	hgsc.bcm.edu	37	2	71058835	71058835	+	Missense_Mutation	SNP	A	A	G	rs741326	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	37	22	77	0	0.594595	0	A|0.465;G|0.535	0.535	strong	CD207,NS,carcinoma,-1,1	CD207	47	1	NM_015717	exon5	c.T833C	p.V278A	TACCTCACACTTT	.	PASS	Atlas-SNP
TMEM150A	129303	hgsc.bcm.edu	37	2	85826721	85826721	+	Silent	SNP	G	G	A	rs11891495	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	180	52	180	0	0.288889	0	G|0.810;A|0.190	0.190	strong	.	TMEM150A	15	.	NM_001031738	exon7	c.C501T	p.T167T	CGGGGCGGTGGCC	.	PASS	Atlas-SNP
SVEP1	79987	hgsc.bcm.edu	37	9	113169126	113169126	+	Silent	SNP	G	G	A	rs2281937	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	13	63	0	0.245283	0	G|0.723;A|0.277	0.277	strong	.	SVEP1	326	.	NM_153366	exon38	c.C8754T	p.H2918H	GCCCTCGTGACAG	.	PASS	Atlas-SNP
RBM19	9904	hgsc.bcm.edu	37	12	114377885	114377885	+	Silent	SNP	G	G	C	rs2290790	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	41	80	0	0.66129	0	G|0.761;C|0.239	0.239	strong	.	RBM19	117	.	NM_001146699	exon15	c.C1818G	p.T606T	GCCGAAGGTCTCC	.	PASS	Atlas-SNP
TRIB3	57761	hgsc.bcm.edu	37	20	377226	377226	+	Silent	SNP	C	C	T	rs6115830	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	90	49	66	0	0.544444	0	C|0.572;T|0.428	0.428	strong	.	TRIB3	50	.	NM_021158	exon4	c.C969T	p.A323A	CTTAGCCCCAACC	.	PASS	Atlas-SNP
C14orf159	80017	hgsc.bcm.edu	37	14	91636395	91636395	+	Silent	SNP	C	C	T	rs4900071	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	70	45	73	0	0.642857	0	C|0.767;T|0.233	0.233	strong	C14orf159,NS,carcinoma,0,1	C14orf159	57	1	NM_001102366	exon7	c.C306T	p.G102G	CACCGGCAGCCTG	.	PASS	Atlas-SNP
COX10	1352	hgsc.bcm.edu	37	17	13980058	13980058	+	Missense_Mutation	SNP	A	A	T	rs2230351	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60	31	50	0	0.516667	0	A|0.940;T|0.060	0.060	strong	.	COX10	36	.	NM_001303	exon3	c.A184T	p.T62S	TATGTCACACAGC	.	PASS	Atlas-SNP
NPPA	4878	hgsc.bcm.edu	37	1	11907648	11907648	+	Missense_Mutation	SNP	C	C	T	rs5063	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	108	52	108	0	0.481481	0	C|0.943;T|0.057	0.057	strong	.	NPPA	14	.	NM_006172	exon1	c.G94A	p.V32M	TGGACACGGCATT	.	PASS	Atlas-SNP
XRCC6	2547	hgsc.bcm.edu	37	22	42059768	42059768	+	Silent	SNP	G	G	T	rs56558005		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	151	74	141	0	0.490066	0	.	.	weak	.	XRCC6	64	.	NM_001469	exon13	c.G1779T	p.G593G	GAGTGGGCTGAAG	.	PASS	Atlas-SNP
NOP56	10528	hgsc.bcm.edu	37	20	2638882	2638882	+	Missense_Mutation	SNP	T	T	C	rs5856	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	30	75	0	0.4	0	T|0.673;C|0.327	0.327	strong	.	NOP56	73	.	NM_006392	exon12	c.T1727C	p.V576A	AGGCGGTTGGCAA	.	PASS	Atlas-SNP
TAS2R46	259292	hgsc.bcm.edu	37	12	11214145	11214145	+	Nonsense_Mutation	SNP	C	C	T	rs2708381	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	194	104	226	0	0.536082	0	C|0.785;T|0.215	0.215	strong	.	TAS2R46	43	.	NM_176887	exon1	c.G749A	p.W250X	AAACTCCAAACTG	.	PASS	Atlas-SNP
PRC1	9055	hgsc.bcm.edu	37	15	91525197	91525197	+	Silent	SNP	C	C	T	rs2301826	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	134	68	160	1	0.507463	0.00625	C|0.592;T|0.408	0.408	strong	PRC1,NS,carcinoma,-1,1	PRC1	51	1	NM_199413	exon4	c.G282A	p.T94T	GATGGTCGTCTCT	.	scavenged	Atlas-SNP
ZNF134	7693	hgsc.bcm.edu	37	19	58131576	58131576	+	Missense_Mutation	SNP	T	T	C	rs10414451	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80	37	80	0	0.4625	0	T|0.913;C|0.087	0.087	strong	.	ZNF134	34	.	NM_003435	exon3	c.T89C	p.I30T	AGAGCATTTCTAT	.	PASS	Atlas-SNP
MLPH	79083	hgsc.bcm.edu	37	2	238427251	238427251	+	Missense_Mutation	SNP	G	G	A	rs3751107	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	120	67	127	0	0.558333	0	G|0.795;A|0.205	0.205	strong	.	MLPH	41	.	NM_001042467	exon5	c.G515A	p.G172D	AACCTGGCTCAGA	.	PASS	Atlas-SNP
DDX58	23586	hgsc.bcm.edu	37	9	32526146	32526146	+	Missense_Mutation	SNP	G	G	A	rs10813831	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83	49	92	0	0.590361	0	G|0.788;A|0.212	0.212	strong	.	DDX58	82	.	NM_014314	exon1	c.C19T	p.R7C	GGCTGCGTCGCTG	.	PASS	Atlas-SNP
PRX	57716	hgsc.bcm.edu	37	19	40901604	40901604	+	Silent	SNP	A	A	G	rs268672	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	50	23	45	0	0.46	0	A|0.457;G|0.543	0.543	strong	.	PRX	151	.	NM_181882	exon7	c.T2655C	p.P885P	CACCTCAGGGCCC	.	PASS	Atlas-SNP
POLD4	57804	hgsc.bcm.edu	37	11	67120530	67120530	+	Missense_Mutation	SNP	C	C	G	rs28364240	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	23	53	0	0.310811	0	G|0.015;C|0.985;A|0.000	0.015	strong	.	POLD4	9	.	NM_021173	exon2	c.G116C	p.R39P	TCGTCGCGGGGCT	.	PASS	Atlas-SNP
SGK1	6446	hgsc.bcm.edu	37	6	134495709	134495709	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	40	8	70	0	0.2	0	.	.	none	SGK1_ENST00000367858,NS,lymphoid_neoplasm,-1,2	SGK1	387	2	NM_001143676	exon4	c.G377A	p.R126K	ATCCTCCTCTGCT	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	95	54	103	0	0.568421	0	C|0.830;G|0.170	0.170	strong	.	SV2C	97	.	NM_014979	exon9	c.C1445G	p.T482S	ATTTCACTATTAA	.	PASS	Atlas-SNP
PARP4	143	hgsc.bcm.edu	37	13	25052393	25052393	+	Missense_Mutation	SNP	G	G	T	rs79107024	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	121	34	84	0	0.280992	0	G|0.874;T|0.126	0.126	strong	.	PARP4	142	.	NM_006437	exon13	c.C1470A	p.H490Q	TCCCGGGTGTGAG	.	PASS	Atlas-SNP
VWA8	23078	hgsc.bcm.edu	37	13	42465713	42465713	+	Missense_Mutation	SNP	C	C	T	rs9562362	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	54	53	0	0.642857	0	C|0.775;T|0.225	0.225	strong	.	.	.	.	NM_015058	exon5	c.G494A	p.R165H	GCTGCACGAACTG	.	PASS	Atlas-SNP
GGA3	23163	hgsc.bcm.edu	37	17	73237124	73237124	+	Missense_Mutation	SNP	T	T	C	rs146877619	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	102	49	89	0	0.480392	0	T|0.998;C|0.002	0.002	strong	.	GGA3	54	.	NM_138619	exon11	c.A961G	p.S321G	GGTTACTGCACTG	.	PASS	Atlas-SNP
GABRE	2564	hgsc.bcm.edu	37	X	151138179	151138179	+	Missense_Mutation	SNP	A	A	C	rs1139916	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100	100	111	0	1	0	A|0.369;C|0.631	0.631	strong	.	GABRE	141	.	NM_004961	exon3	c.T304G	p.S102A	TGACGGAGATCTC	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	27	50	0	0.5	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
SPRR1A	6698	hgsc.bcm.edu	37	1	152957832	152957832	+	Missense_Mutation	SNP	C	C	A	rs1611762	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83	38	76	0	0.457831	0	C|0.457;A|0.543	0.543	strong	.	SPRR1A	17	.	NM_001199828	exon2	c.C126A	p.H42Q	CTGCCACCCCAAG	.	PASS	Atlas-SNP
BTD	686	hgsc.bcm.edu	37	3	15686611	15686611	+	Silent	SNP	C	C	T	rs372039874		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	131	64	117	0	0.48855	0	.	.	weak	.	BTD	49	.	NM_000060	exon4	c.C1248T	p.H416H	TCTCCACGTCTGT	.	PASS	Atlas-SNP
SORCS1	114815	hgsc.bcm.edu	37	10	108434858	108434858	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	25	66	0	0.337838	0	.	.	none	.	SORCS1	534	.	NM_001206572	exon14	c.T1889G	p.L630R	ACAAAAAGTGGAA	.	PASS	Atlas-SNP
USP42	84132	hgsc.bcm.edu	37	7	6194383	6194383	+	Silent	SNP	C	C	T	rs73058659	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	27	7	27	0	0.259259	0	C|0.929;T|0.071	0.071	strong	USP42_ENST00000306177,NS,carcinoma,0,2	USP42	138	2	NM_032172	exon15	c.C3198T	p.Y1066Y	CAGGTACGCCCTG	.	PASS	Atlas-SNP
AAMDC	28971	hgsc.bcm.edu	37	11	77553638	77553638	+	Silent	SNP	T	T	C	rs585721	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	73	68	0	0.901235	0	T|0.588;C|0.412	0.412	strong	C11orf67,NS,carcinoma,0,1	.	.	1	NM_024684	exon2	c.T96C	p.G32G	AGGGGGTAGTCGG	.	PASS	Atlas-SNP
HNRNPCL1	343069	hgsc.bcm.edu	37	1	12907263	12907263	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	130	30	126	0	0.230769	0	.	.	none	.	HNRNPCL1	68	.	NM_001013631	exon2	c.T880A	p.X294K	GTGCTTAAGAGTC	.	PASS	Atlas-SNP
TMC1	117531	hgsc.bcm.edu	37	9	75315438	75315438	+	Missense_Mutation	SNP	G	G	A	rs1796993	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	38	17	47	0	0.447368	0	G|0.761;A|0.239	0.239	strong	.	TMC1	87	.	NM_138691	exon8	c.G241A	p.E81K	AGAGAAGAAGAAG	.	PASS	Atlas-SNP
MS4A15	219995	hgsc.bcm.edu	37	11	60531264	60531264	+	Missense_Mutation	SNP	A	A	G	rs12363342	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	43	52	0	0.565789	0	A|0.709;G|0.291	0.291	strong	.	MS4A15	37	.	NM_001098835	exon2	c.A58G	p.S20G	AACGCCAGTGGCC	.	PASS	Atlas-SNP
JAG1	182	hgsc.bcm.edu	37	20	10625804	10625804	+	Silent	SNP	T	T	G	rs1801140	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	38	126	0	0.5	0	T|0.921;G|0.079	0.079	strong	.	JAG1	213	.	NM_000214	exon17	c.A2214C	p.T738T	ACAGGTTGTTCCT	.	PASS	Atlas-SNP
RTL1	388015	hgsc.bcm.edu	37	14	101348584	101348584	+	Missense_Mutation	SNP	C	C	G	rs11623267	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	46	19	36	0	0.413043	0	C|0.751;G|0.249	0.249	strong	RTL1,NS,carcinoma,0,1	RTL1	120	1	NM_001134888	exon1	c.G2542C	p.E848Q	GCTCCTCGACTCC	.	PASS	Atlas-SNP
KRT7	3855	hgsc.bcm.edu	37	12	52636919	52636919	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	40	8	37	0	0.2	0	.	.	none	.	KRT7	48	.	NM_005556	exon6	c.C982T	p.Q328X	AAGAACCAGGTGG	.	PASS	Atlas-SNP
CCM2	83605	hgsc.bcm.edu	37	7	45113170	45113170	+	Silent	SNP	G	G	A	rs2289367	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	28	18	59	0	0.642857	0	G|0.779;A|0.221	0.221	strong	CCM2,NS,carcinoma,0,1	CCM2	42	1	NM_001029835	exon8	c.G978A	p.T326T	GCTGACGGTAGGC	.	PASS	Atlas-SNP
DPY19L2	283417	hgsc.bcm.edu	37	12	63954300	63954300	+	Missense_Mutation	SNP	C	C	T	rs12314553	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	66	132	0	1	0	C|0.836;T|0.164	0.164	strong	.	DPY19L2	97	.	NM_173812	exon22	c.G2269A	p.V757I	AGTTAACCTTTAA	.	PASS	Atlas-SNP
ARID5B	84159	hgsc.bcm.edu	37	10	63829539	63829539	+	Silent	SNP	C	C	T	rs76296217	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	41	21	55	0	0.512195	0	C|0.954;T|0.046	0.046	strong	.	ARID5B	125	.	NM_032199	exon8	c.C1182T	p.T394T	TTGTACCCGCAGA	.	PASS	Atlas-SNP
CSPG4	1464	hgsc.bcm.edu	37	15	75982085	75982085	+	Missense_Mutation	SNP	C	C	T	rs79463888	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	131	12	116	0	0.0916031	0	C|0.878;T|0.122	0.122	strong	CSPG4,NS,haematopoietic_neoplasm,0,1	CSPG4	175	1	NM_001897	exon3	c.G1321A	p.E441K	CCCCCTCGGCCAC	.	PASS	Atlas-SNP
OR5A2	219981	hgsc.bcm.edu	37	11	59190120	59190120	+	Missense_Mutation	SNP	A	A	G	rs17153691	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	56	29	78	0	0.517857	0	A|0.965;G|0.035	0.035	strong	.	OR5A2	35	.	NM_001001954	exon1	c.T307C	p.F103L	AGACAAAGTACTG	.	PASS	Atlas-SNP
EN2	2020	hgsc.bcm.edu	37	7	155255332	155255332	+	Silent	SNP	T	T	C	rs2361689	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	32	19	51	0	0.59375	0	T|0.630;C|0.370	0.370	strong	.	EN2	14	.	NM_001427	exon2	c.T952C	p.L318L	CAGGGCTTGTACA	.	PASS	Atlas-SNP
CCDC65	85478	hgsc.bcm.edu	37	12	49314994	49314994	+	Missense_Mutation	SNP	A	A	G	rs4760600	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	31	60	0	0.508197	0	A|0.679;G|0.321	0.321	strong	.	CCDC65	41	.	NM_033124	exon8	c.A1223G	p.Y408C	AAAGGTACAACAA	.	PASS	Atlas-SNP
ERCC6	2074	hgsc.bcm.edu	37	10	50678717	50678717	+	Missense_Mutation	SNP	T	T	C	rs2228526	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	104	48	115	0	0.461538	0	T|0.824;C|0.176	0.176	strong	.	ERCC6	162	.	NM_000124	exon18	c.A3289G	p.M1097V	TACTCATGTGAGG	.	PASS	Atlas-SNP
ITGA9	3680	hgsc.bcm.edu	37	3	37536056	37536056	+	Silent	SNP	C	C	T	rs2507941	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	288	126	291	0	0.4375	0	C|0.959;T|0.041	0.041	strong	.	ITGA9	98	.	NM_002207	exon5	c.C609T	p.T203T	CTTCACCGAGGTG	.	PASS	Atlas-SNP
MRPL17	63875	hgsc.bcm.edu	37	11	6703569	6703569	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	113	3	138	0	0.0265487	0	.	.	none	MRPL17,NS,carcinoma,-1,1	MRPL17	11	1	NM_022061	exon3	c.G308A	p.G103D	GTGTAGCCCCCAG	.	scavenged	Atlas-SNP
GATM	2628	hgsc.bcm.edu	37	15	45660421	45660421	+	Silent	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	23	98	0	0.425926	0	.	.	none	.	GATM	34	.	NM_001482	exon4	c.T522C	p.V174V	GCCCACAACTATC	.	PASS	Atlas-SNP
ALG6	29929	hgsc.bcm.edu	37	1	63872032	63872032	+	Missense_Mutation	SNP	T	T	C	rs35383149	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	102	49	108	0	0.480392	0	T|0.974;C|0.026	0.026	strong	.	ALG6	33	.	NM_013339	exon6	c.T391C	p.Y131H	GTTTTGTACTGTT	.	PASS	Atlas-SNP
SFTPA1	653509	hgsc.bcm.edu	37	10	81373562	81373562	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	299	115	306	0	0.384615	0	.	.	none	.	SFTPA1	23	.	NM_001093770	exon6	c.C485G	p.T162S	CCATCACTTTTGA	.	PASS	Atlas-SNP
ADAM30	11085	hgsc.bcm.edu	37	1	120436751	120436751	+	Missense_Mutation	SNP	T	T	C	rs35273427	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	248	114	266	0	0.459677	0	T|0.878;C|0.122	0.122	strong	.	ADAM30	88	.	NM_021794	exon1	c.A2209G	p.T737A	TTTTTGTTTTAGA	.	PASS	Atlas-SNP
RNF145	153830	hgsc.bcm.edu	37	5	158603839	158603839	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	172	8	178	0	0.0465116	0	.	.	none	RNF145,NS,carcinoma,0,4	RNF145	110	4	NM_001199380	exon5	c.T512C	p.M171T	GTTTTCATGACAC	.	scavenged	Atlas-SNP
RILPL1	353116	hgsc.bcm.edu	37	12	124017850	124017850	+	Silent	SNP	G	G	C	rs28492040	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	27	17	39	0	0.62963	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
CMYA5	202333	hgsc.bcm.edu	37	5	79029594	79029594	+	Missense_Mutation	SNP	T	T	C	rs1019762	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72	46	88	0	0.638889	0	T|0.888;C|0.112	0.112	strong	.	CMYA5	643	.	NM_153610	exon2	c.T5006C	p.L1669S	CTGTTTTAGAAAA	.	PASS	Atlas-SNP
OTC	5009	hgsc.bcm.edu	37	X	38226603	38226603	+	Missense_Mutation	SNP	A	A	G	rs1800321	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	162	116	120	0	0.716049	0	A|0.721;0|0.027	.	strong	.	OTC	60	.	NM_000531	exon2	c.A137G	p.K46R	CTCTAAAAAACTT	.	PASS	Atlas-SNP
MYH10	4628	hgsc.bcm.edu	37	17	8402769	8402769	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	154	50	160	0	0.324675	0	.	.	none	.	MYH10	148	.	NM_001256012	exon30	c.A3770C	p.K1257T	CCCTGCTTGTTCT	.	PASS	Atlas-SNP
ZNF23	7571	hgsc.bcm.edu	37	16	71483497	71483497	+	Missense_Mutation	SNP	C	C	G	rs72795864	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	24	92	0	0.338028	0	A|0.000;C|0.878;G|0.122	0.122	strong	.	ZNF23	65	.	NM_145911	exon6	c.G431C	p.G144A	CCCAATCCTGTAC	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9049396	9049396	+	Silent	SNP	C	C	G	rs10425044	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	152	69	179	0	0.453947	0	C|0.781;G|0.219	0.219	strong	.	MUC16	4315	.	NM_024690	exon5	c.G32235C	p.G10745G	GTCTGTCCCAGAA	.	PASS	Atlas-SNP
APOA4	337	hgsc.bcm.edu	37	11	116691675	116691675	+	Missense_Mutation	SNP	T	T	A	rs675	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	180	23	158	0	0.127778	0	A|0.142;T|0.858	0.142	strong	.	APOA4	51	.	NM_000482	exon3	c.A1099T	p.T367S	AGAGAGTCTTGTC	.	PASS	Atlas-SNP
CD69	969	hgsc.bcm.edu	37	12	9906146	9906146	+	Silent	SNP	T	T	C	rs117419783	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	65	37	75	0	0.569231	0	T|0.994;C|0.006	0.006	strong	CD69,colon,carcinoma,0,1	CD69	23	1	NM_001781	exon5	c.A531G	p.K177K	TGTGTTTTTCAGA	.	PASS	Atlas-SNP
MBD1	4152	hgsc.bcm.edu	37	18	47800179	47800179	+	Missense_Mutation	SNP	G	G	C	rs125555	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	37	37	46	0	1	0	G|0.819;C|0.181	0.181	strong	.	MBD1	228	.	NM_001204137	exon13	c.C1276G	p.P426A	AAGGTGGGGGCGA	.	PASS	Atlas-SNP
CYP2C19	1557	hgsc.bcm.edu	37	10	96541616	96541616	+	Silent	SNP	G	G	A	rs4244285	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	36	87	0	0.444444	0	A|0.170;G|0.830	0.170	strong	.	CYP2C19	88	.	NM_000769	exon5	c.G681A	p.P227P	TTTCCCGGGAACC	.	PASS	Atlas-SNP
NCAPG	64151	hgsc.bcm.edu	37	4	17812796	17812796	+	Silent	SNP	C	C	T	rs16895792	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	36	21	38	0	0.583333	0	C|0.950;T|0.050	0.050	strong	.	NCAPG	76	.	NM_022346	exon1	c.C96T	p.S32S	GCTGAGCCGCACC	.	PASS	Atlas-SNP
HLA-C	3107	hgsc.bcm.edu	37	6	31239544	31239544	+	Silent	SNP	G	G	T	rs281860356	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	109	19	105	2	0.174312	0.0190476	.	.	weak	HLA-C_ENST00000383329,colon,carcinoma,0,2	HLA-C	92	2	NM_002117	exon2	c.C175A	p.R59R	CGAACCGCACGAA	.	scavenged	Atlas-SNP
FBXL7	23194	hgsc.bcm.edu	37	5	15937010	15937010	+	Silent	SNP	C	C	T	rs61748187	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98	51	94	0	0.520408	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
CCDC87	55231	hgsc.bcm.edu	37	11	66358126	66358126	+	Silent	SNP	C	C	T	rs486584	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85	84	77	0	0.988235	0	C|0.597;T|0.402	0.402	strong	.	CCDC87	83	.	NM_018219	exon1	c.G2361A	p.L787L	CTCCTCCAGGAGG	.	PASS	Atlas-SNP
SLC2A9	56606	hgsc.bcm.edu	37	4	9998476	9998476	+	Silent	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	203	60	216	0	0.295566	0	.	.	none	.	SLC2A9	158	.	NM_020041	exon3	c.T339C	p.T113T	GGACACAGTCACA	.	PASS	Atlas-SNP
EPHA7	2045	hgsc.bcm.edu	37	6	94067981	94067981	+	Silent	SNP	C	C	T	rs164544	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	42	81	0	0.552632	0	C|0.322;T|0.678	0.678	strong	.	EPHA7	251	.	NM_004440	exon4	c.G981A	p.A327A	TGTGCACGCAACG	.	PASS	Atlas-SNP
PHLDB2	90102	hgsc.bcm.edu	37	3	111688578	111688578	+	Silent	SNP	C	C	T	rs774854	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51	29	58	0	0.568627	0	C|0.808;T|0.192	0.192	strong	.	PHLDB2	449	.	NM_001134439	exon16	c.C3357T	p.D1119D	GGAAGACTTTGAT	.	PASS	Atlas-SNP
KDELR3	11015	hgsc.bcm.edu	37	22	38877461	38877461	+	Missense_Mutation	SNP	T	T	G	rs12004	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	118	118	171	0	1	0	A|0.004;C|0.002	.	strong	.	KDELR3	39	.	NM_016657	exon4	c.T596G	p.V199G	TGTATGTGACCAA	.	PASS	Atlas-SNP
PAPLN	89932	hgsc.bcm.edu	37	14	73718474	73718474	+	Missense_Mutation	SNP	G	G	T	rs141960540	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	146	76	122	0	0.520548	0	G|0.998;T|0.002	0.002	strong	.	PAPLN	180	.	NM_173462	exon8	c.G692T	p.G231V	AGCGGGGTGCTGA	.	PASS	Atlas-SNP
TPPP2	122664	hgsc.bcm.edu	37	14	21500121	21500121	+	Missense_Mutation	SNP	G	G	T	rs9624	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93	51	103	0	0.548387	0	G|0.882;T|0.118	0.118	strong	.	TPPP2	22	.	NM_173846	exon4	c.G398T	p.R133L	AGGAGCGCTTTGA	.	PASS	Atlas-SNP
COQ5	84274	hgsc.bcm.edu	37	12	120966921	120966921	+	Silent	SNP	A	A	G	rs3742052	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	35	85	0	0.530303	0	A|0.748;G|0.252	0.252	strong	.	COQ5	26	.	NM_032314	exon1	c.T24C	p.A8A	CCATAGAGCACAG	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	89	34	103	0	0.382022	0	C|0.605;T|0.395	0.395	strong	.	DENND5B	114	.	NM_144973	exon2	c.G155A	p.R52K	GTTCTTCTCAAAG	.	PASS	Atlas-SNP
HLA-G	3135	hgsc.bcm.edu	37	6	29797639	29797639	+	Silent	SNP	C	C	T	rs1049033	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	140	105	147	0	0.75	0	C|0.738;T|0.262	0.262	strong	.	HLA-G	90	.	NM_002127	exon6	c.C942T	p.G314G	TGCTGGCCTGGTT	.	PASS	Atlas-SNP
NLRC5	84166	hgsc.bcm.edu	37	16	57080528	57080528	+	Missense_Mutation	SNP	C	C	A	rs289723	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	126	56	126	0	0.444444	0	T|0.002;G|0.001	.	strong	.	NLRC5	186	.	NM_032206	exon21	c.C3313A	p.Q1105K	TTCCGTCAGCGCT	.	PASS	Atlas-SNP
IQUB	154865	hgsc.bcm.edu	37	7	123119990	123119990	+	Silent	SNP	T	T	C	rs10500091	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	121	68	162	0	0.561983	0	T|0.782;C|0.218	0.218	strong	.	IQUB	117	.	NM_178827	exon8	c.A1269G	p.Q423Q	AAAAGATTGGTTA	.	PASS	Atlas-SNP
CAPN11	11131	hgsc.bcm.edu	37	6	44141088	44141088	+	Missense_Mutation	SNP	G	G	A	rs6938938	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	19	10	36	0	0.526316	0	G|0.864;A|0.136	0.136	strong	.	CAPN11	66	.	NM_007058	exon7	c.G796A	p.V266M	AAGGCCGTGGAGC	.	PASS	Atlas-SNP
PRPS2	5634	hgsc.bcm.edu	37	X	12809661	12809661	+	Silent	SNP	G	G	A	rs1731469	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	50	45	0	0.806452	0	G|0.430;A|0.570	0.570	strong	.	PRPS2	41	.	NM_001039091	exon1	c.G45A	p.L15L	GGACCTGTCCCAG	.	PASS	Atlas-SNP
HLA-C	3107	hgsc.bcm.edu	37	6	31239417	31239417	+	Missense_Mutation	SNP	C	C	T	rs2308557	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	180	23	169	0	0.127778	0	T|0.404;G|0.000;C|0.595;A|0.000	0.404	strong	.	HLA-C	92	.	NM_002117	exon2	c.G302A	p.S101N	CGCAGGCTCACTC	.	PASS	Atlas-SNP
CCDC116	164592	hgsc.bcm.edu	37	22	21988599	21988599	+	Missense_Mutation	SNP	G	G	A	rs371513	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	45	23	28	0	0.511111	0	G|0.847;A|0.153	0.153	strong	.	CCDC116	56	.	NM_152612	exon3	c.G361A	p.G121R	AGTGGTGGACGGC	.	PASS	Atlas-SNP
FOXE1	2304	hgsc.bcm.edu	37	9	100616583	100616583	+	Silent	SNP	T	T	C	rs3021523	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	77	40	89	0	0.519481	0	T|0.177;C|0.823	0.823	strong	.	FOXE1	19	.	NM_004473	exon1	c.T387C	p.L129L	GGCGCTTGACCCC	.	PASS	Atlas-SNP
SLCO6A1	133482	hgsc.bcm.edu	37	5	101724472	101724472	+	Missense_Mutation	SNP	C	C	T	rs72779942	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	198	94	226	0	0.474747	0	C|0.987;T|0.013	0.013	strong	SLCO6A1,caecum,carcinoma,-1,1	SLCO6A1	153	1	NM_173488	exon12	c.G1937A	p.R646Q	ACATCCCGTAAAA	.	PASS	Atlas-SNP
ABCA13	154664	hgsc.bcm.edu	37	7	48313881	48313881	+	Missense_Mutation	SNP	T	T	C	rs17712299	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	39	31	57	0	0.794872	0	T|0.884;C|0.116	0.116	strong	.	ABCA13	1192	.	NM_152701	exon17	c.T4618C	p.F1540L	AATCAGTTTCAAA	.	PASS	Atlas-SNP
CUTC	51076	hgsc.bcm.edu	37	10	101502968	101502968	+	Silent	SNP	A	A	G	rs3740076	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	212	103	279	0	0.485849	0	A|0.931;G|0.069	0.069	strong	.	CUTC	32	.	NM_015960	exon4	c.A252G	p.P84P	TCGGCCACGGGGA	.	PASS	Atlas-SNP
MUC6	4588	hgsc.bcm.edu	37	11	1016825	1016825	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	825	38	607	0	0.0460606	0	.	.	none	MUC6_ENST00000421673,NS,carcinoma,-1,2	MUC6	408	2	NM_005961	exon31	c.C5976T	p.T1992T	GGTAGTGGTGGTC	.	PASS	Atlas-SNP
ROR2	4920	hgsc.bcm.edu	37	9	94495595	94495595	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	101	8	96	0	0.0792079	0	.	.	none	.	ROR2	167	.	NM_004560	exon6	c.G746A	p.R249H	AGCTCACGCGGCT	.	PASS	Atlas-SNP
SLC4A9	83697	hgsc.bcm.edu	37	5	139740454	139740454	+	Silent	SNP	C	C	T	rs34507975	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	133	56	112	0	0.421053	0	C|0.790;T|0.210	0.210	strong	.	SLC4A9	125	.	NM_001258428	exon2	c.C360T	p.H120H	CCCCCACGTGCCC	.	PASS	Atlas-SNP
ZNF561	93134	hgsc.bcm.edu	37	19	9721218	9721218	+	Silent	SNP	G	G	A	rs138137635	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	33	57	0	0.540984	0	G|0.999;A|0.001	0.001	strong	.	ZNF561	64	.	NM_152289	exon6	c.C1119T	p.A373A	AGTGAAGGCTTTC	.	PASS	Atlas-SNP
TCEB3B	51224	hgsc.bcm.edu	37	18	44561619	44561619	+	Missense_Mutation	SNP	G	G	C	rs61738602	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	115	56	82	0	0.486957	0	C|0.074;G|0.926;T|0.000	0.074	strong	.	TCEB3B	141	.	NM_016427	exon1	c.C17G	p.T6S	AGCGTAGTGGACC	.	PASS	Atlas-SNP
ZNF845	91664	hgsc.bcm.edu	37	19	53856349	53856349	+	Missense_Mutation	SNP	A	A	T	rs55874600	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79	78	92	0	0.987342	0	A|0.782;T|0.218	0.218	strong	.	ZNF845	101	.	NM_138374	exon4	c.A2421T	p.E807D	TAATGAATGTGGC	.	PASS	Atlas-SNP
NR6A1	2649	hgsc.bcm.edu	37	9	127300464	127300464	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	108	2	97	0	0.0185185	0	.	.	none	NR6A1,NS,carcinoma,-1,1	NR6A1	38	1	NM_033334	exon6	c.G731A	p.R244H	AGGCTGCGAGCTT	.	scavenged	Atlas-SNP
NSUN4	387338	hgsc.bcm.edu	37	1	46827456	46827456	+	Missense_Mutation	SNP	A	A	G	rs9865	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	290	154	235	0	0.531034	0	A|0.862;G|0.138	0.138	strong	.	NSUN4	26	.	NM_199044	exon6	c.A1093G	p.I365V	CTGGTAATACCAA	.	PASS	Atlas-SNP
LENG1	79165	hgsc.bcm.edu	37	19	54662043	54662043	+	Missense_Mutation	SNP	C	C	T	rs35089861	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	139	56	121	0	0.402878	0	C|0.964;T|0.036	0.036	strong	.	LENG1	19	.	NM_024316	exon2	c.G289A	p.E97K	CTTCCTCGTACTC	.	PASS	Atlas-SNP
PCDH17	27253	hgsc.bcm.edu	37	13	58208047	58208047	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	10	47	0	0.15873	0	.	.	none	PCDH17,colon,carcinoma,-1,1	PCDH17	304	1	NM_001040429	exon1	c.A1367C	p.K456T	CCACCAAGTCGTT	.	PASS	Atlas-SNP
CERS2	29956	hgsc.bcm.edu	37	1	150940625	150940625	+	Missense_Mutation	SNP	T	T	G	rs267738	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	38	22	53	1	0.578947	0.0188679	T|0.878;G|0.122	0.122	strong	LASS2,colon,carcinoma,0,1	.	.	1	NM_022075	exon4	c.A344C	p.E115A	CAACGCTCTACCT	.	scavenged	Atlas-SNP
C19orf55	148137	hgsc.bcm.edu	37	19	36258842	36258842	+	Missense_Mutation	SNP	G	G	C	rs231217	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	18	10	22	0	0.555556	0	G|0.901;C|0.099	0.099	strong	.	C19orf55	39	.	NM_001039887	exon9	c.G1095C	p.K365N	AGTCAAGGCCTCG	.	PASS	Atlas-SNP
KIAA0232	9778	hgsc.bcm.edu	37	4	6843852	6843852	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	34	3	37	0	0.0882353	0	.	.	none	KIAA0232,bladder,carcinoma,-1,1	KIAA0232	102	1	NM_014743	exon4	c.A290G	p.K97R	AGAGTAAGAAAAA	.	scavenged	Atlas-SNP
KRTAP10-6	386674	hgsc.bcm.edu	37	21	46011298	46011298	+	Silent	SNP	G	G	A	rs74695406		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	196	5	156	0	0.0255102	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
WDR81	124997	hgsc.bcm.edu	37	17	1637302	1637302	+	Silent	SNP	A	A	G	rs3809872	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	33	63	0	0.392857	0	A|0.257;G|0.743	0.743	strong	.	WDR81	180	.	NM_001163809	exon7	c.A4971G	p.L1657L	ACCCCTAAGCAGC	.	PASS	Atlas-SNP
FAT1	2195	hgsc.bcm.edu	37	4	187629137	187629137	+	Silent	SNP	A	A	G	rs4862726	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	41	17	54	0	0.414634	0	A|0.975;G|0.025	0.025	strong	.	FAT1	500	.	NM_005245	exon2	c.T1845C	p.F615F	TAAACTAAAGAAA	.	PASS	Atlas-SNP
PITRM1	10531	hgsc.bcm.edu	37	10	3207632	3207632	+	Missense_Mutation	SNP	A	A	G	rs3814596	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	124	55	110	1	0.443548	0.00909091	A|0.857;G|0.143	0.143	strong	PITRM1,colon,carcinoma,0,1	PITRM1	109	1	NM_014889	exon5	c.T506C	p.F169S	CATGGGAAAAAGG	.	scavenged	Atlas-SNP
OR5P2	120065	hgsc.bcm.edu	37	11	7817538	7817538	+	Missense_Mutation	SNP	T	T	C	rs7949771	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60	60	72	0	1	0	T|0.748;C|0.252	0.252	strong	.	OR5P2	68	.	NM_153444	exon1	c.A952G	p.N318D	CATTATTTGAAGT	.	PASS	Atlas-SNP
FMN2	56776	hgsc.bcm.edu	37	1	240371112	240371112	+	Silent	SNP	G	G	T	rs71646889	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51	13	62	1	0.254902	0.016129	A|0.000;G|0.879;T|0.121	0.121	strong	FMN2,NS,carcinoma,0,4	FMN2	451	4	NM_020066	exon5	c.G3000T	p.P1000P	CCCTCCGCCCCCA	.	scavenged	Atlas-SNP
AQP11	282679	hgsc.bcm.edu	37	11	77301341	77301341	+	Missense_Mutation	SNP	G	G	A	rs2276415	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98	88	91	0	0.897959	0	G|0.873;A|0.127	0.127	strong	.	AQP11	14	.	NM_173039	exon1	c.G304A	p.G102S	CCGTGCGGCGTGA	.	PASS	Atlas-SNP
GPR144	347088	hgsc.bcm.edu	37	9	127217284	127217284	+	Missense_Mutation	SNP	G	G	A	rs77622235	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	39	53	0	0.464286	0	G|0.990;A|0.010	0.010	strong	.	GPR144	33	.	NM_001161808	exon7	c.G1327A	p.G443R	GCCCTCGGGGCTG	.	PASS	Atlas-SNP
CENPJ	55835	hgsc.bcm.edu	37	13	25487103	25487103	+	Missense_Mutation	SNP	T	T	C	rs35498994	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	95	44	95	0	0.463158	0	A|0.000;C|0.138;T|0.862	0.138	strong	.	CENPJ	116	.	NM_018451	exon2	c.A61G	p.M21V	TGGTCATCCACTG	.	PASS	Atlas-SNP
GBP6	163351	hgsc.bcm.edu	37	1	89846152	89846152	+	Missense_Mutation	SNP	C	C	T	rs4582772	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69	38	62	0	0.550725	0	C|0.929;T|0.071	0.071	strong	.	GBP6	87	.	NM_198460	exon6	c.C833T	p.T278I	CAAGAACCAAGAC	.	PASS	Atlas-SNP
CD180	4064	hgsc.bcm.edu	37	5	66492387	66492387	+	Missense_Mutation	SNP	C	C	T	rs377501004		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	88	6	64	0	0.0681818	0	.	.	weak	.	CD180	78	.	NM_005582	exon1	c.G83A	p.C28Y	TCAATGCACATCT	.	PASS	Atlas-SNP
EPCAM	4072	hgsc.bcm.edu	37	2	47601106	47601106	+	Missense_Mutation	SNP	T	T	C	rs1126497	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91	48	68	0	0.527473	0	T|0.385;C|0.615	0.615	strong	.	EPCAM	27	.	NM_002354	exon3	c.T344C	p.M115T	CCTCCATGTGCTG	.	PASS	Atlas-SNP
ABCA13	154664	hgsc.bcm.edu	37	7	48547511	48547511	+	Missense_Mutation	SNP	C	C	A	rs78634768	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	95	59	136	0	0.621053	0	C|0.989;A|0.011	0.011	strong	.	ABCA13	1192	.	NM_152701	exon50	c.C13390A	p.L4464M	ATCGTGCTGGGAT	.	PASS	Atlas-SNP
XIAP	331	hgsc.bcm.edu	37	X	123034511	123034511	+	Missense_Mutation	SNP	A	A	C	rs5956583	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	302	76	196	0	0.251656	0	A|0.624;0|0.022	.	strong	.	XIAP	56	.	NM_001204401	exon6	c.A1268C	p.Q423P	GTATGCAAGATGA	.	PASS	Atlas-SNP
FAM35A	54537	hgsc.bcm.edu	37	10	88911841	88911841	+	Missense_Mutation	SNP	A	A	G	rs77879311	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	89	45	101	0	0.505618	0	A|0.850;G|0.150	0.150	strong	.	FAM35A	48	.	NM_019054	exon3	c.A730G	p.S244G	TTTCTCAGTATAA	.	PASS	Atlas-SNP
FBXO34	55030	hgsc.bcm.edu	37	14	55817708	55817708	+	Silent	SNP	T	T	C	rs10144418	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	148	146	166	0	0.986486	0	T|0.655;C|0.345	0.345	strong	FBXO34,NS,carcinoma,0,1	FBXO34	61	1	NM_017943	exon2	c.T600C	p.Y200Y	AGTCTATGCTGGG	.	PASS	Atlas-SNP
SLC52A3	113278	hgsc.bcm.edu	37	20	744450	744450	+	Silent	SNP	G	G	A	rs3746805	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49	47	61	0	0.959184	0	G|0.667;A|0.333	0.333	strong	.	.	.	.	NM_033409	exon3	c.C765T	p.L255L	ATTGAGGAGGTCT	.	PASS	Atlas-SNP
TGS1	96764	hgsc.bcm.edu	37	8	56711713	56711713	+	Missense_Mutation	SNP	A	A	G	rs10109493	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	33	15	42	0	0.454545	0	A|0.876;G|0.124	0.124	strong	.	TGS1	66	.	NM_024831	exon8	c.A1783G	p.T595A	CTAGCAACTGTTC	.	PASS	Atlas-SNP
BLVRA	644	hgsc.bcm.edu	37	7	43810764	43810764	+	Missense_Mutation	SNP	G	G	A	rs699512	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	62	93	0	1	0	G|0.184;A|0.816	0.816	strong	.	BLVRA	26	.	NM_001253823	exon3	c.G7A	p.A3T	ATGAATGCAGAGG	.	PASS	Atlas-SNP
THSD7A	221981	hgsc.bcm.edu	37	7	11581134	11581134	+	Silent	SNP	T	T	C	rs2074603	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	176	176	197	0	1	0	T|0.532;C|0.468	0.468	strong	.	THSD7A	219	.	NM_015204	exon6	c.A1734G	p.A578A	TCTCACTGCTTTC	.	PASS	Atlas-SNP
SLCO2A1	6578	hgsc.bcm.edu	37	3	133666209	133666209	+	Missense_Mutation	SNP	C	C	T	rs34550074	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	96	52	107	0	0.541667	0	C|0.732;T|0.268	0.268	strong	SLCO2A1,NS,carcinoma,0,1	SLCO2A1	72	1	NM_005630	exon9	c.G1186A	p.A396T	GAATGGCTTGTAG	.	PASS	Atlas-SNP
CD68	968	hgsc.bcm.edu	37	17	7484101	7484101	+	Missense_Mutation	SNP	C	C	A	rs9901673	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	162	83	153	0	0.512346	0	C|0.830;A|0.170	0.170	strong	.	CD68	17	.	NM_001251	exon4	c.C760A	p.Q254K	GCAGCACGTAAGT	.	PASS	Atlas-SNP
APBA3	9546	hgsc.bcm.edu	37	19	3753769	3753769	+	Silent	SNP	C	C	T	rs3746120	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	31	9	18	0	0.290323	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
C1orf94	84970	hgsc.bcm.edu	37	1	34663411	34663411	+	Missense_Mutation	SNP	C	C	G	rs1414474	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	77	43	84	0	0.558442	0	C|0.796;G|0.204	0.204	strong	.	C1orf94	156	.	NM_001134734	exon2	c.C906G	p.D302E	TCCTGACAAGCTC	.	PASS	Atlas-SNP
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057958	46057958	+	Silent	SNP	C	C	T	rs4818951	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	206	74	154	0	0.359223	0	C|0.368;T|0.632	0.632	strong	.	KRTAP10-10	37	.	NM_181688	exon1	c.C624T	p.S208S	CCCCTCCTGCGGT	.	PASS	Atlas-SNP
REG3A	5068	hgsc.bcm.edu	37	2	79385787	79385787	+	Missense_Mutation	SNP	G	G	A	rs77686105	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	90	11	137	0	0.122222	0	G|0.894;A|0.106	0.106	strong	.	REG3A	76	.	NM_138938	exon2	c.C185T	p.T62I	GCATCTGTCCAGG	.	PASS	Atlas-SNP
TLR10	81793	hgsc.bcm.edu	37	4	38774785	38774785	+	Silent	SNP	A	A	G	rs10776482	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	39	79	0	0.481481	0	A|0.739;G|0.261	0.261	strong	TLR10,colon,carcinoma,0,1	TLR10	87	1	NM_001017388	exon2	c.T2427C	p.D809D	TAGACAATCTGTT	.	PASS	Atlas-SNP
LRP1	4035	hgsc.bcm.edu	37	12	57593101	57593101	+	Silent	SNP	G	G	A	rs1140648	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57	55	59	0	0.964912	0	G|0.449;A|0.551	0.551	strong	.	LRP1	428	.	NM_002332	exon61	c.G9783A	p.T3261T	GACCACGGGCACC	.	PASS	Atlas-SNP
STAM	8027	hgsc.bcm.edu	37	10	17756596	17756596	+	Silent	SNP	T	T	C	rs12221	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	118	49	111	0	0.415254	0	T|0.815;C|0.185	0.185	strong	STAM,NS,carcinoma,0,1	STAM	60	1	NM_003473	exon14	c.T1440C	p.Y480Y	AGTATATAGTCCT	.	PASS	Atlas-SNP
BCMO1	53630	hgsc.bcm.edu	37	16	81295780	81295780	+	Silent	SNP	C	C	A	rs35683292	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79	35	63	0	0.443038	0	C|0.965;A|0.035	0.035	strong	.	BCMO1	53	.	NM_017429	exon4	c.C363A	p.T121T	TTTCACCGACAAC	.	PASS	Atlas-SNP
LALBA	3906	hgsc.bcm.edu	37	12	48962869	48962869	+	Silent	SNP	A	A	G	rs2232566	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	117	54	107	0	0.461538	0	A|0.903;G|0.097	0.097	strong	.	LALBA	9	.	NM_002289	exon2	c.T288C	p.C96C	ACTGTCACAGGAG	.	PASS	Atlas-SNP
CFHR2	3080	hgsc.bcm.edu	37	1	196918724	196918724	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	219	14	235	0	0.0639269	0	.	.	none	.	CFHR2	73	.	NM_005666	exon2	c.T198A	p.F66L	ATCCTTTTGGACT	.	PASS	Atlas-SNP
LRRC47	57470	hgsc.bcm.edu	37	1	3701663	3701663	+	Silent	SNP	T	T	C	rs2298227	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	34	106	0	0.459459	0	T|0.882;C|0.118	0.118	strong	.	LRRC47	42	.	NM_020710	exon3	c.A1182G	p.P394P	GTCCTGTGGGGGC	.	PASS	Atlas-SNP
FCGBP	8857	hgsc.bcm.edu	37	19	40389741	40389741	+	Missense_Mutation	SNP	A	A	G	rs3746009	bycluster;byfrequency;by2hit2allele;byhapmap	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	593	212	741	132	0.357504	0.178138	A|0.200;G|0.800	0.800	strong	FCGBP,NS,neuroblastoma,0,3	FCGBP	416	3	NM_003890	exon18	c.T8441C	p.V2814A	TTACCCACATGGC	.	scavenged	Atlas-SNP
SGK223	0	hgsc.bcm.edu	37	8	8234219	8234219	+	Missense_Mutation	SNP	G	G	A	rs4840955	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	32	13	25	0	0.40625	0	G|0.631;A|0.369	0.369	strong	.	.	.	.	NM_001080826	exon2	c.C1700T	p.P567L	GCCAGCGGTGACA	.	PASS	Atlas-SNP
SVEP1	79987	hgsc.bcm.edu	37	9	113261483	113261483	+	Missense_Mutation	SNP	C	C	T	rs872665	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	122	65	133	0	0.532787	0	C|0.731;T|0.269	0.269	strong	.	SVEP1	326	.	NM_153366	exon7	c.G1519A	p.V507I	TGATGACATCTTT	.	PASS	Atlas-SNP
MAP2K3	5606	hgsc.bcm.edu	37	17	21203964	21203964	+	Silent	SNP	C	C	G	rs34458870	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	13	71	0	0.213115	0	C|0.853;G|0.147	0.147	strong	MAP2K3_ENST00000316920,NS,lymphoid_neoplasm,0,1	MAP2K3	135	1	NM_145109	exon4	c.C273G	p.A91A	CATGGCCGTGAAG	.	PASS	Atlas-SNP
PIWIL4	143689	hgsc.bcm.edu	37	11	94320237	94320237	+	Silent	SNP	T	T	C	rs7110167	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	15	62	0	0.227273	0	T|0.476;C|0.524	0.524	strong	PIWIL4,NS,carcinoma,+2,1	PIWIL4	70	1	NM_152431	exon7	c.T738C	p.F246F	TGGGTTTGCCATT	.	scavenged	Atlas-SNP
PAOX	196743	hgsc.bcm.edu	37	10	135205009	135205009	+	Silent	SNP	C	C	G	rs1046178	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57	56	53	0	0.982456	0	C|0.165;G|0.835	0.835	strong	.	PAOX	82	.	NM_207128	exon6	c.C1428G	p.P476P	GGGACCCTCATTT	.	PASS	Atlas-SNP
AGGF1	55109	hgsc.bcm.edu	37	5	76359024	76359024	+	Missense_Mutation	SNP	C	C	A	rs34400049	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	129	127	161	0	0.984496	0	A|0.225;C|0.775	0.225	strong	.	AGGF1	71	.	NM_018046	exon14	c.C2092A	p.P698T	ACTAAGCCTCAAA	.	PASS	Atlas-SNP
PLEKHM1	9842	hgsc.bcm.edu	37	17	43552717	43552717	+	Silent	SNP	G	G	C	rs147243132	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	171	161	226	1	0.94152	0.00442478	G|0.873;C|0.127	0.127	strong	PLEKHM1,caecum,carcinoma,-1,1	PLEKHM1	69	1	NM_014798	exon4	c.C672G	p.S224S	AGAATGGGAAATG	.	PASS	Atlas-SNP
XRCC3	7517	hgsc.bcm.edu	37	14	104165753	104165753	+	Missense_Mutation	SNP	G	G	A	rs861539	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	108	61	122	0	0.564815	0	G|0.729;A|0.271	0.271	strong	XRCC3,NS,carcinoma,0,1	XRCC3	16	1	NM_005432	exon8	c.C722T	p.T241M	CGCAGCGTGGCCC	.	PASS	Atlas-SNP
UCP3	7352	hgsc.bcm.edu	37	11	73717254	73717254	+	Silent	SNP	A	A	G	rs1800006	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	5	37	0	0.0943396	0	A|0.651;G|0.349	0.349	strong	.	UCP3	31	.	NM_003356	exon3	c.T297C	p.Y99Y	GGAGTCATAGAGG	.	PASS	Atlas-SNP
KANSL1	284058	hgsc.bcm.edu	37	17	44117119	44117119	+	Missense_Mutation	SNP	A	A	G	rs34043286	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	116	116	107	1	1	0.00934579	A|0.853;G|0.147	0.147	strong	.	.	.	.	NM_001193466	exon8	c.T2152C	p.S718P	GAGCTGAATCTGG	.	PASS	Atlas-SNP
SLC16A1	6566	hgsc.bcm.edu	37	1	113456546	113456546	+	Missense_Mutation	SNP	A	A	T	rs1049434	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	273	129	283	0	0.472527	0	A|0.340;T|0.660	0.660	strong	.	SLC16A1	61	.	NM_001166496	exon5	c.T1470A	p.D490E	CCCTCCATCTGTG	.	PASS	Atlas-SNP
CBR3	874	hgsc.bcm.edu	37	21	37518582	37518582	+	Silent	SNP	G	G	A	rs17849671	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79	78	65	0	0.987342	0	G|0.964;A|0.036	0.036	strong	CBR3,NS,carcinoma,+1,1	CBR3	11	1	NM_001236	exon3	c.G606A	p.T202T	GGTCACGGTCTTA	.	PASS	Atlas-SNP
PCDHA1	56147	hgsc.bcm.edu	37	5	140167033	140167033	+	Silent	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100	18	116	0	0.18	0	.	.	none	.	PCDHA1	387	.	NM_031411	exon1	c.T1158G	p.T386T	GGTGACTTGCTCC	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68	66	89	2	0.970588	0.0224719	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	.	scavenged	Atlas-SNP
TAF4B	6875	hgsc.bcm.edu	37	18	23854692	23854692	+	Silent	SNP	C	C	T	rs17224558	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	116	56	123	0	0.482759	0	C|0.875;T|0.125	0.125	strong	.	TAF4B	71	.	NM_005640	exon4	c.C663T	p.T221T	AACTACCCTGAAG	.	PASS	Atlas-SNP
HEATR5B	54497	hgsc.bcm.edu	37	2	37227797	37227797	+	Missense_Mutation	SNP	C	C	G	rs62621396	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	129	59	133	0	0.457364	0	C|0.896;G|0.104	0.104	strong	.	HEATR5B	185	.	NM_019024	exon33	c.G5477C	p.G1826A	TGAACGCCAGCCT	.	PASS	Atlas-SNP
PCDHGB4	8641	hgsc.bcm.edu	37	5	140769293	140769293	+	Silent	SNP	C	C	T	rs150721796	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	31	16	26	0	0.516129	0	C|0.964;T|0.036	0.036	strong	.	PCDHGB4	125	.	NM_032098	exon1	c.C1842T	p.L614L	CGGGCTCTTCAGC	.	PASS	Atlas-SNP
MYH2	4620	hgsc.bcm.edu	37	17	10448769	10448769	+	Silent	SNP	A	A	T	rs11078850	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	92	43	99	0	0.467391	0	A|0.586;T|0.414	0.414	strong	.	MYH2	390	.	NM_017534	exon5	c.T399A	p.P133P	ATACACAGGCAGC	.	PASS	Atlas-SNP
KRT73	319101	hgsc.bcm.edu	37	12	53012128	53012128	+	Missense_Mutation	SNP	C	C	T	rs35417182	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	35	85	0	0.466667	0	C|0.927;T|0.073	0.073	strong	.	KRT73	101	.	NM_175068	exon1	c.G181A	p.V61M	TGGCCACATTGAA	.	PASS	Atlas-SNP
REC8	9985	hgsc.bcm.edu	37	14	24647814	24647814	+	Silent	SNP	T	T	C	rs1885711	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69	29	53	0	0.42029	0	T|0.305;C|0.695	0.695	strong	.	REC8	47	.	NM_001048205	exon13	c.T996C	p.P332P	ACAGCCTATGGTG	.	PASS	Atlas-SNP
ABCA13	154664	hgsc.bcm.edu	37	7	48285485	48285485	+	Missense_Mutation	SNP	C	C	T	rs1880738	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93	26	121	1	0.27957	0.00826446	C|0.624;T|0.376	0.376	strong	ABCA13_ENST00000435803,NS,carcinoma,0,2	ABCA13	1192	2	NM_152701	exon13	c.C1517T	p.P506L	TCTGCCCGAATGG	.	scavenged	Atlas-SNP
ATP13A4	84239	hgsc.bcm.edu	37	3	193272556	193272556	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	118	12	124	0	0.101695	0	.	.	none	.	ATP13A4	154	.	NM_032279	exon1	c.G33A	p.L11L	ATTGAGCAGAGCG	.	PASS	Atlas-SNP
MORC4	79710	hgsc.bcm.edu	37	X	106221389	106221389	+	Missense_Mutation	SNP	T	T	C	rs41304048	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79	19	51	0	0.240506	0	T|0.984;C|0.016	0.016	strong	.	MORC4	155	.	NM_001085354	exon8	c.A977G	p.N326S	TTACTATTCTTGC	.	PASS	Atlas-SNP
DKKL1	27120	hgsc.bcm.edu	37	19	49878115	49878115	+	Missense_Mutation	SNP	G	G	A	rs1054770	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	26	70	0	0.490566	0	G|0.733;A|0.267	0.267	strong	.	DKKL1	23	.	NM_014419	exon5	c.G559A	p.G187S	GAGGGCGGCCACT	.	PASS	Atlas-SNP
CARD14	79092	hgsc.bcm.edu	37	17	78171944	78171944	+	Missense_Mutation	SNP	G	G	C	rs2066964	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	43	22	48	0	0.511628	0	G|0.621;C|0.379	0.379	strong	CARD14_ENST00000309710,colon,carcinoma,0,2	CARD14	98	2	NM_024110	exon12	c.G1641C	p.R547S	TGGAAGGCTTGAT	.	PASS	Atlas-SNP
DUSP12	11266	hgsc.bcm.edu	37	1	161721707	161721707	+	Silent	SNP	C	C	T	rs1063178	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	280	137	282	1	0.489286	0.0035461	C|0.639;N|0.000	.	strong	.	DUSP12	20	.	NM_007240	exon3	c.C510T	p.Y170Y	GGGATACGAAGTG	.	PASS	Atlas-SNP
OR10Q1	219960	hgsc.bcm.edu	37	11	57995777	57995777	+	Missense_Mutation	SNP	G	G	A	rs11229301	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	97	52	83	0	0.536082	0	G|0.865;A|0.135	0.135	strong	OR10Q1,NS,carcinoma,+1,2	OR10Q1	79	2	NM_001004471	exon1	c.C571T	p.R191C	CCAGGCGCAGGAC	.	PASS	Atlas-SNP
CD200R1	131450	hgsc.bcm.edu	37	3	112642572	112642572	+	Silent	SNP	T	T	C	rs79556290	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	161	72	168	0	0.447205	0	T|0.954;C|0.046	0.046	strong	.	CD200R1	91	.	NM_138806	exon8	c.A999G	p.A333A	CTCAGATGCCTTC	.	PASS	Atlas-SNP
PXK	54899	hgsc.bcm.edu	37	3	58382846	58382846	+	Silent	SNP	C	C	T	rs3191903	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93	39	86	0	0.419355	0	C|0.701;T|0.299	0.299	strong	.	PXK	89	.	NM_017771	exon10	c.C903T	p.C301C	CACTTGCCGGCTG	.	PASS	Atlas-SNP
RFPL4A	342931	hgsc.bcm.edu	37	19	56273285	56273285	+	Missense_Mutation	SNP	A	A	G	rs2019945	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	347	126	422	2	0.363112	0.00473934	.	.	weak	ENSG00000188683,NS,carcinoma,0,1	RFPL4A	8	1	NM_001145014	exon2	c.A119G	p.K40R	TCCAGAAGGAGCC	.	scavenged	Atlas-SNP
LTN1	26046	hgsc.bcm.edu	37	21	30339120	30339120	+	Missense_Mutation	SNP	C	C	A	rs34191159	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	42	53	0	0.591549	0	C|0.836;A|0.164	0.164	strong	.	LTN1	141	.	NM_015565	exon10	c.G1831T	p.G611C	CCCAGCCTTCAAT	.	PASS	Atlas-SNP
NSRP1	84081	hgsc.bcm.edu	37	17	28511978	28511978	+	Silent	SNP	G	G	A	rs1979572	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	29	95	0	0.391892	0	G|0.483;A|0.517	0.517	strong	.	NSRP1	49	.	NM_032141	exon7	c.G963A	p.Q321Q	GCACCAGCAGAAG	.	PASS	Atlas-SNP
PRAME	23532	hgsc.bcm.edu	37	22	22893394	22893394	+	Missense_Mutation	SNP	A	A	T	rs41310248	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	41	25	45	0	0.609756	0	A|0.978;T|0.022	0.022	strong	.	PRAME	78	.	NM_206954	exon4	c.T139A	p.L47M	GCAGCAACTCCAG	.	PASS	Atlas-SNP
PCSK5	5125	hgsc.bcm.edu	37	9	78937974	78937974	+	Missense_Mutation	SNP	C	C	T	rs3001772	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55	55	54	0	1	0	C|0.517;T|0.483	0.483	strong	.	PCSK5	329	.	NM_001190482	exon31	c.C4028T	p.T1343M	AGTGCACGCCTGA	.	PASS	Atlas-SNP
RAB19	401409	hgsc.bcm.edu	37	7	140125750	140125750	+	Missense_Mutation	SNP	T	T	C	rs2948386	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48	23	68	0	0.479167	0	T|0.830;C|0.170	0.170	strong	.	RAB19	21	.	NM_001008749	exon4	c.T454C	p.Y152H	GAGAAGTACGGCC	.	PASS	Atlas-SNP
EXD1	161829	hgsc.bcm.edu	37	15	41483682	41483682	+	Silent	SNP	A	A	G	rs1971131	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	8	76	0	0.170213	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
NKX1-2	390010	hgsc.bcm.edu	37	10	126138345	126138345	+	Silent	SNP	C	C	T	rs112863004	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	58	23	56	0	0.396552	0	C|0.946;T|0.054	0.054	strong	.	NKX1-2	6	.	NM_001146340	exon1	c.G168A	p.G56G	ATCTTTCCCCGCT	.	PASS	Atlas-SNP
DOCK5	80005	hgsc.bcm.edu	37	8	25230168	25230168	+	Silent	SNP	C	C	T	rs2271108	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100	43	91	0	0.43	0	C|0.562;T|0.438	0.438	strong	DOCK5,NS,carcinoma,0,1	DOCK5	167	1	NM_024940	exon35	c.C3618T	p.D1206D	GCTGGACTATAGA	.	PASS	Atlas-SNP
DSPP	1834	hgsc.bcm.edu	37	4	88536553	88536553	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83	7	117	0	0.0843373	0	.	.	none	DSPP,NS,carcinoma,0,3	DSPP	174	3	NM_014208	exon5	c.C2739T	p.D913D	CAGTGACAGCAGT	.	PASS	Atlas-SNP
OR10H2	26538	hgsc.bcm.edu	37	19	15839174	15839174	+	Silent	SNP	C	C	T	rs74730938		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	219	85	183	0	0.388128	0	T|1.000;|0.000	1.000	weak	.	OR10H2	59	.	NM_013939	exon1	c.C321T	p.F107F	CAGCTTCGGCTTC	.	PASS	Atlas-SNP
LILRB4	11006	hgsc.bcm.edu	37	19	55178162	55178162	+	Missense_Mutation	SNP	A	A	G	rs11574576	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	97	54	96	0	0.556701	0	A|0.646;C|0.000;G|0.354	0.354	strong	.	LILRB4	86	.	NM_006847	exon10	c.A1003G	p.N335D	GTGAAGAACACAC	.	PASS	Atlas-SNP
ADH4	127	hgsc.bcm.edu	37	4	100048414	100048414	+	Missense_Mutation	SNP	T	T	C	rs1126671	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	123	123	154	0	1	0	T|0.213;C|0.787	0.787	strong	.	ADH4	35	.	NM_000670	exon7	c.A925G	p.I309V	GAAAAATAGTCAA	.	PASS	Atlas-SNP
SUGP1	57794	hgsc.bcm.edu	37	19	19413092	19413092	+	Missense_Mutation	SNP	C	C	T	rs17751061	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	112	60	98	0	0.535714	0	C|0.891;T|0.109	0.109	strong	.	SUGP1	63	.	NM_172231	exon7	c.G869A	p.R290H	TTCTCACGGTTGT	.	PASS	Atlas-SNP
OR2T29	343563	hgsc.bcm.edu	37	1	248722659	248722659	+	Missense_Mutation	SNP	C	C	T	rs2105243	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	428	150	356	0	0.350467	0	C|0.250;T|0.750	0.750	weak	.	OR2T29	8	.	NM_001004694	exon1	c.G134A	p.G45E	GCATTTCCAGACA	.	PASS	Atlas-SNP
SECISBP2L	9728	hgsc.bcm.edu	37	15	49293194	49293194	+	Missense_Mutation	SNP	C	C	A	rs11854184	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	208	204	222	0	0.980769	0	C|0.860;A|0.140	0.140	strong	.	SECISBP2L	118	.	NM_001193489	exon15	c.G2128T	p.V710L	CTCTTACAGGATC	.	PASS	Atlas-SNP
CCDC91	55297	hgsc.bcm.edu	37	12	28412372	28412372	+	Missense_Mutation	SNP	G	G	A	rs11049488	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79	38	71	0	0.481013	0	G|0.816;A|0.184	0.184	strong	.	CCDC91	63	.	NM_018318	exon2	c.G106A	p.A36T	TTTCCTGCAGGTA	.	PASS	Atlas-SNP
PDE6C	5146	hgsc.bcm.edu	37	10	95389041	95389041	+	Silent	SNP	G	G	A	rs714550	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	118	116	137	0	0.983051	0	G|0.622;A|0.378	0.378	strong	.	PDE6C	97	.	NM_006204	exon8	c.G1098A	p.A366A	CCCTGCGGATGAA	.	PASS	Atlas-SNP
ASGR2	433	hgsc.bcm.edu	37	17	7011225	7011225	+	Silent	SNP	T	T	G	rs61731746	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	109	48	88	0	0.440367	0	T|0.891;G|0.109	0.109	strong	ASGR2,NS,carcinoma,0,1	ASGR2	38	1	NM_080912	exon5	c.A354C	p.G118G	GCTGCCTCCTGGA	.	PASS	Atlas-SNP
BAIAP2L1	55971	hgsc.bcm.edu	37	7	97922851	97922851	+	Silent	SNP	C	C	T	rs12728	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	88	88	82	0	1	0	C|0.634;T|0.366	0.366	strong	.	BAIAP2L1	61	.	NM_018842	exon14	c.G1518A	p.S506S	GGGTGCCGAGCGA	.	PASS	Atlas-SNP
CASP7	840	hgsc.bcm.edu	37	10	115457264	115457264	+	Missense_Mutation	SNP	T	T	G	rs11555408	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83	54	94	0	0.650602	0	T|0.889;G|0.111	0.111	strong	.	CASP7	21	.	NM_001267057	exon2	c.T236G	p.I79S	AGATGATCAGGGC	.	PASS	Atlas-SNP
CPXM2	119587	hgsc.bcm.edu	37	10	125528048	125528048	+	Silent	SNP	G	G	A	rs1219725	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	24	23	19	0	0.958333	0	G|0.654;A|0.346	0.346	strong	.	CPXM2	120	.	NM_198148	exon9	c.C1293T	p.Y431Y	CCCTTCGTAGGCC	.	PASS	Atlas-SNP
SCLY	51540	hgsc.bcm.edu	37	2	238999883	238999883	+	Silent	SNP	T	T	C	rs1128552	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	226	113	180	1	0.5	0.00555556	T|0.801;C|0.199	0.199	strong	SCLY,NS,carcinoma,0,1	SCLY	51	1	NM_016510	exon8	c.T933C	p.A311A	GATTGCTGGCCTT	.	scavenged	Atlas-SNP
PODXL	5420	hgsc.bcm.edu	37	7	131196062	131196062	+	Silent	SNP	C	C	T	rs17744792	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	109	53	79	0	0.486239	0	C|0.871;T|0.129	0.129	strong	.	PODXL	53	.	NM_001018111	exon2	c.G231A	p.S77S	CTTGACCGAGGCC	.	PASS	Atlas-SNP
THRB	7068	hgsc.bcm.edu	37	3	24184995	24184995	+	Silent	SNP	G	G	A	rs3752874	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	147	75	150	0	0.510204	0	G|0.858;A|0.142	0.142	strong	.	THRB	52	.	NM_000461	exon7	c.C735T	p.F245F	TACCAGGAATTTC	.	PASS	Atlas-SNP
FLRT1	23769	hgsc.bcm.edu	37	11	63884453	63884453	+	Silent	SNP	C	C	T	rs3751120	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	59	18	79	0	0.305085	0	C|0.702;T|0.298	0.298	strong	.	FLRT1	46	.	NM_013280	exon2	c.C714T	p.R238R	CCAGCGCATCGCC	.	PASS	Atlas-SNP
OR8B4	283162	hgsc.bcm.edu	37	11	124294377	124294377	+	Missense_Mutation	SNP	A	A	G	rs4057750	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85	73	108	0	0.858824	0	A|0.742;G|0.258	0.258	strong	OR8B4,NS,carcinoma,+1,1	OR8B4	60	1	NM_001005196	exon1	c.T391C	p.Y131H	CCATGTAGAGCAG	.	PASS	Atlas-SNP
PCNXL3	399909	hgsc.bcm.edu	37	11	65387012	65387012	+	Silent	SNP	C	C	T	rs57318451	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44	22	49	0	0.5	0	C|0.904;T|0.096	0.096	strong	.	PCNXL3	140	.	NM_032223	exon7	c.C1710T	p.A570A	AGCGGCCGAGGAG	.	PASS	Atlas-SNP
ANKS3	124401	hgsc.bcm.edu	37	16	4748825	4748825	+	Silent	SNP	C	C	T	rs841214	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	54	56	1	1	0.0178571	C|0.602;T|0.398	0.398	strong	ANKS3,NS,carcinoma,0,1	ANKS3	44	1	NM_133450	exon13	c.G1527A	p.Q509Q	GAGCTCCTGCATC	.	scavenged	Atlas-SNP
FMNL2	114793	hgsc.bcm.edu	37	2	153435434	153435434	+	Silent	SNP	C	C	T	rs16831399	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	50	13	47	0	0.26	0	C|0.842;N|0.000	.	strong	.	FMNL2	75	.	NM_052905	exon8	c.C738T	p.H246H	TCCACACGCTGTC	.	PASS	Atlas-SNP
CARNS1	57571	hgsc.bcm.edu	37	11	67186271	67186271	+	Missense_Mutation	SNP	C	C	A	rs868167	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	58	11	52	0	0.189655	0	C|0.835;A|0.165	0.165	strong	.	CARNS1	60	.	NM_001166222	exon5	c.C409A	p.P137T	AAGGTGCCAGCAC	.	PASS	Atlas-SNP
GRIA2	2891	hgsc.bcm.edu	37	4	158238830	158238830	+	Silent	SNP	T	T	C	rs4302506	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	149	75	161	0	0.503356	0	T|0.364;C|0.636	0.636	strong	GRIA2_ENST00000264426,NS,carcinoma,0,2	GRIA2	358	2	NM_000826	exon5	c.T687C	p.H229H	AAAACATGTTAAA	.	PASS	Atlas-SNP
PZP	5858	hgsc.bcm.edu	37	12	9321501	9321501	+	Missense_Mutation	SNP	C	C	T	rs3213832	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	39	52	0	0.58209	0	C|0.907;T|0.093	0.093	strong	.	PZP	422	.	NM_002864	exon17	c.G2071A	p.V691M	CAGACACGGAAGG	.	PASS	Atlas-SNP
CLCN7	1186	hgsc.bcm.edu	37	16	1506130	1506130	+	Silent	SNP	C	C	T	rs41286695	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	24	14	26	0	0.583333	0	C|0.973;T|0.027	0.027	strong	.	CLCN7	53	.	NM_001287	exon10	c.G900A	p.A300A	TCCAAACGCCGCT	.	PASS	Atlas-SNP
TCTN2	79867	hgsc.bcm.edu	37	12	124179417	124179417	+	Silent	SNP	T	T	C	rs7966867	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	194	82	194	0	0.42268	0	C|0.521;N|0.000	0.521	strong	.	TCTN2	50	.	NM_024809	exon10	c.T1128C	p.P376P	AACCCCTAGAATT	.	PASS	Atlas-SNP
NUP62CL	54830	hgsc.bcm.edu	37	X	106396455	106396455	+	Silent	SNP	A	A	G	rs1285590	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	220	59	143	0	0.268182	0	A|0.553;G|0.447	0.447	strong	.	NUP62CL	10	.	NM_017681	exon7	c.T477C	p.R159R	CTGGTCACGCGTA	.	PASS	Atlas-SNP
SPACA7	122258	hgsc.bcm.edu	37	13	113053470	113053470	+	Missense_Mutation	SNP	T	T	A	rs10816	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80	57	155	2	0.7125	0.0129032	T|0.343;A|0.657	0.657	strong	SPACA7,NS,adenoma,0,1	SPACA7	36	1	NM_145248	exon4	c.T332A	p.V111D	TTGAGGTCAAAAT	.	scavenged	Atlas-SNP
B4GALNT4	338707	hgsc.bcm.edu	37	11	380395	380395	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55	4	70	0	0.0727273	0	.	.	none	B4GALNT4,NS,carcinoma,+1,1	B4GALNT4	83	1	NM_178537	exon18	c.C2819T	p.A940V	CCTTCGCGCCCGT	.	PASS	Atlas-SNP
DNAH8	1769	hgsc.bcm.edu	37	6	38800164	38800164	+	Missense_Mutation	SNP	G	G	A	rs9357283	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	115	24	103	0	0.208696	0	G|0.840;A|0.160	0.160	strong	DNAH8_ENST00000359357,NS,carcinoma,0,1	DNAH8	1239	1	NM_001206927	exon31	c.G4255A	p.E1419K	TCTGTGGAAGTTT	.	PASS	Atlas-SNP
PREX2	80243	hgsc.bcm.edu	37	8	69046409	69046409	+	Silent	SNP	G	G	A	rs3793379	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	65	29	67	0	0.446154	0	G|0.894;A|0.106	0.106	strong	PREX2,colon,carcinoma,+1,1	PREX2	614	1	NM_024870	exon32	c.G3882A	p.K1294K	CAGCAAGGAAAAT	.	PASS	Atlas-SNP
AP2M1	1173	hgsc.bcm.edu	37	3	183901281	183901281	+	Silent	SNP	G	G	A	rs2231224	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	147	57	150	0	0.387755	0	G|0.921;A|0.079	0.079	strong	.	AP2M1	35	.	NM_001025205	exon11	c.G1179A	p.A393A	ATTCGCGCCCTCT	.	PASS	Atlas-SNP
CTXN3	613212	hgsc.bcm.edu	37	5	126993249	126993249	+	Silent	SNP	G	G	C	rs45074	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	31	50	0	0.508197	0	G|0.308;C|0.692	0.692	strong	.	CTXN3	19	.	NM_001048252	exon3	c.G36C	p.V12V	CCTAGTGCCCCTT	.	PASS	Atlas-SNP
IGHMBP2	3508	hgsc.bcm.edu	37	11	68705820	68705820	+	Missense_Mutation	SNP	G	G	A	rs2275996	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	27	7	26	0	0.259259	0	G|0.983;A|0.017	0.017	strong	.	IGHMBP2	83	.	NM_002180	exon14	c.G2782A	p.E928K	CTGCCCGAGGTAT	.	PASS	Atlas-SNP
PRSS1	5644	hgsc.bcm.edu	37	7	142458437	142458437	+	Silent	SNP	C	C	T	rs372637371		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	156	17	208	1	0.108974	0.00480769	.	.	weak	PRSS1,NS,carcinoma,0,1	PRSS1	68	1	NM_002769	exon2	c.C72T	p.I24I	CAAGATCGTTGGG	.	scavenged	Atlas-SNP
C6orf15	29113	hgsc.bcm.edu	37	6	31079703	31079703	+	Missense_Mutation	SNP	C	C	G	rs2233978	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	122	18	107	0	0.147541	0	C|0.892;G|0.108	0.108	strong	.	C6orf15	29	.	NM_014070	exon2	c.G433C	p.A145P	CCGGAGCGAGGGC	.	PASS	Atlas-SNP
PEX14	5195	hgsc.bcm.edu	37	1	10689942	10689942	+	Silent	SNP	G	G	T	rs11539794	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72	70	54	0	0.972222	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
MLPH	79083	hgsc.bcm.edu	37	2	238427194	238427194	+	Missense_Mutation	SNP	T	T	C	rs3751109	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	134	72	185	0	0.537313	0	T|0.795;C|0.205	0.205	strong	.	MLPH	41	.	NM_001042467	exon5	c.T458C	p.L153P	CTGAACTGATATC	.	PASS	Atlas-SNP
NT5M	56953	hgsc.bcm.edu	37	17	17250197	17250197	+	Missense_Mutation	SNP	G	G	A	rs145194793	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	77	40	63	0	0.519481	0	G|0.997;A|0.003	0.003	strong	.	NT5M	17	.	NM_020201	exon5	c.G623A	p.R208H	CCCCCCGCCGCAG	.	PASS	Atlas-SNP
CAMLG	819	hgsc.bcm.edu	37	5	134076812	134076812	+	Missense_Mutation	SNP	G	G	A	rs12657663	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83	40	72	0	0.481928	0	G|0.890;A|0.110	0.110	strong	.	CAMLG	27	.	NM_001745	exon2	c.G232A	p.V78I	CTCAGCGTTCCTT	.	PASS	Atlas-SNP
CDC42BPA	8476	hgsc.bcm.edu	37	1	227216662	227216662	+	Silent	SNP	T	T	C	rs1929861	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	34	11	39	0	0.323529	0	T|0.544;C|0.456	0.456	strong	.	CDC42BPA	528	.	NM_003607	exon29	c.A4023G	p.K1341K	AATTTCTTTAAAT	.	PASS	Atlas-SNP
RNF5	6048	hgsc.bcm.edu	37	6	32147696	32147696	+	Silent	SNP	G	G	A	rs3130349	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	191	139	175	0	0.727749	0	G|0.863;A|0.137	0.137	strong	.	RNF5	16	.	NM_006913	exon4	c.G315A	p.P105P	AGCTCCGGAGAGC	.	PASS	Atlas-SNP
NLRC5	84166	hgsc.bcm.edu	37	16	57091977	57091977	+	Silent	SNP	T	T	C	rs7206703	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44	17	47	0	0.386364	0	T|0.893;C|0.107	0.107	strong	.	NLRC5	186	.	NM_032206	exon27	c.T3747C	p.D1249D	CTACAGTCTCTCA	.	PASS	Atlas-SNP
HHIPL2	79802	hgsc.bcm.edu	37	1	222713631	222713631	+	Missense_Mutation	SNP	G	G	C	rs3748666	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	66	82	0	1	0	G|0.678;C|0.322	0.322	strong	.	HHIPL2	122	.	NM_024746	exon4	c.C1171G	p.H391D	TGCCATGTGAGCC	.	PASS	Atlas-SNP
PTBP2	58155	hgsc.bcm.edu	37	1	97235290	97235290	+	Silent	SNP	A	A	G	rs139414147	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	89	33	100	0	0.370787	0	A|0.998;G|0.002	0.002	strong	.	PTBP2	62	.	NM_021190	exon4	c.A147G	p.G49G	TAAAGGAGAAGAT	.	PASS	Atlas-SNP
TMEM120B	144404	hgsc.bcm.edu	37	12	122186317	122186317	+	Missense_Mutation	SNP	G	G	A	rs28655666	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	164	83	156	0	0.506098	0	G|0.502;A|0.498	0.498	strong	TMEM120B_ENST00000449592,brain,glioma,0,2	TMEM120B	43	2	NM_001080825	exon3	c.G274A	p.D92N	TTCTTCGACATGG	.	PASS	Atlas-SNP
LIMD2	80774	hgsc.bcm.edu	37	17	61776651	61776651	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	96	20	112	0	0.208333	0	.	.	none	.	LIMD2	6	.	NM_030576	exon2	c.A8T	p.Q3L	GCAGCCTGGAACA	.	PASS	Atlas-SNP
RXFP2	122042	hgsc.bcm.edu	37	13	32371361	32371361	+	Missense_Mutation	SNP	A	A	G	rs17076657	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	176	88	175	0	0.5	0	A|0.855;G|0.145	0.145	strong	RXFP2,NS,carcinoma,-2,1	RXFP2	95	1	NM_130806	exon17	c.A1810G	p.I604V	TTTCTCATCATTG	.	PASS	Atlas-SNP
PRR14L	253143	hgsc.bcm.edu	37	22	32113269	32113269	+	Missense_Mutation	SNP	C	C	A	rs112531886	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	117	58	119	0	0.495726	0	C|0.969;A|0.031	0.031	strong	PRR14L_ENST00000397493,NS,carcinoma,0,2	PRR14L	198	2	NM_173566	exon4	c.G556T	p.V186L	TCTGTACATTTCC	.	PASS	Atlas-SNP
SWT1	54823	hgsc.bcm.edu	37	1	185171869	185171869	+	Missense_Mutation	SNP	A	A	G	rs6698109	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	134	67	128	0	0.5	0	A|0.699;G|0.301	0.301	strong	.	SWT1	88	.	NM_017673	exon11	c.A1607G	p.H536R	TATTACACTTATC	.	PASS	Atlas-SNP
WASF3	10810	hgsc.bcm.edu	37	13	27257004	27257004	+	Missense_Mutation	SNP	C	C	T	rs17084492	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	31	16	42	0	0.516129	0	C|0.957;T|0.043	0.043	strong	.	WASF3	68	.	NM_006646	exon9	c.C1244T	p.S415L	CTCTTTCGTCCTC	.	PASS	Atlas-SNP
OMA1	115209	hgsc.bcm.edu	37	1	58999896	58999896	+	Silent	SNP	C	C	A	rs41287650	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	231	89	281	0	0.385281	0	C|1.000;A|0.000	0.000	strong	.	OMA1	50	.	NM_145243	exon4	c.G837T	p.G279G	AGAGATCCCTGGA	.	PASS	Atlas-SNP
BTNL8	79908	hgsc.bcm.edu	37	5	180374523	180374523	+	Missense_Mutation	SNP	G	G	A	rs7724813	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	191	107	245	0	0.560209	0	G|0.732;A|0.268	0.268	strong	BTNL8_ENST00000340184,NS,carcinoma,0,2	BTNL8	114	2	NM_001159708	exon4	c.G685A	p.E229K	TTTTTCGAGCCTA	.	PASS	Atlas-SNP
UTP18	51096	hgsc.bcm.edu	37	17	49338275	49338275	+	Silent	SNP	G	G	A	rs8907	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	13	13	20	0	1	0	G|0.909;A|0.091	0.091	strong	.	UTP18	28	.	NM_016001	exon1	c.G330A	p.L110L	GCGTCTGCGAGGC	.	PASS	Atlas-SNP
RSAD1	55316	hgsc.bcm.edu	37	17	48561871	48561871	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	43	12	34	0	0.27907	0	.	.	none	RSAD1,NS,carcinoma,+2,1	RSAD1	36	1	NM_018346	exon8	c.G1176A	p.E392E	GCAGGAGCTGCTG	.	PASS	Atlas-SNP
HSPG2	3339	hgsc.bcm.edu	37	1	22160043	22160043	+	Missense_Mutation	SNP	C	C	T	rs2229493	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110	53	122	0	0.481818	0	T|0.098;G|0.000;C|0.902;A|0.000	0.098	strong	.	HSPG2	311	.	NM_005529	exon79	c.G10895A	p.R3632Q	TGGGGTCGGACTG	.	PASS	Atlas-SNP
FAM71B	153745	hgsc.bcm.edu	37	5	156589660	156589660	+	Missense_Mutation	SNP	C	C	T	rs147753755	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	197	93	196	0	0.472081	0	C|0.997;T|0.003	0.003	strong	.	FAM71B	145	.	NM_130899	exon2	c.G1616A	p.R539K	AGGCTCCTTAAAA	.	PASS	Atlas-SNP
OAS2	4939	hgsc.bcm.edu	37	12	113448288	113448288	+	Missense_Mutation	SNP	A	A	G	rs15895	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	25	13	31	0	0.52	0	T|0.004;G|0.782	0.782	strong	.	OAS2	86	.	NM_016817	exon11	c.A2159G	p.X720W	ACTTCTAGAGATC	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179457147	179457147	+	Missense_Mutation	SNP	G	G	A	rs16866406	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110	40	117	0	0.363636	0	G|0.808;A|0.191	0.191	strong	.	TTN	18412	.	NM_001267550	exon301	c.C59585T	p.P19862L	CCAGCTGGATTCT	.	PASS	Atlas-SNP
ACPT	93650	hgsc.bcm.edu	37	19	51294098	51294098	+	Missense_Mutation	SNP	C	C	T	rs145475625	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51	25	68	0	0.490196	0	C|0.964;T|0.036	0.036	strong	ACPT,NS,carcinoma,0,1	ACPT	43	1	NM_033068	exon3	c.C284T	p.P95L	TGAGTCCGGAGTA	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29910402	29910402	+	Silent	SNP	G	G	A	rs1136656	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	12	85	0	0.190476	0	G|0.870;A|0.130	0.130	strong	.	HLA-A	89	.	NM_001242758	exon1	c.G72A	p.A24A	CTGGGCGGGTGAG	.	PASS	Atlas-SNP
FAM220A	84792	hgsc.bcm.edu	37	7	6370194	6370194	+	Missense_Mutation	SNP	C	C	T	rs6952125	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	135	88	92	0	0.651852	0	C|0.342;N|0.000	.	strong	.	.	.	.	NM_001037163	exon2	c.G592A	p.V198M	GATACACGTGCAG	.	PASS	Atlas-SNP
OTUD4	54726	hgsc.bcm.edu	37	4	146063471	146063471	+	Missense_Mutation	SNP	C	C	T	rs151020153	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	65	35	50	0	0.538462	0	C|0.998;T|0.002	0.002	strong	.	OTUD4	120	.	NM_001102653	exon18	c.G1504A	p.V502M	AAGACACATGTTC	.	PASS	Atlas-SNP
ANPEP	290	hgsc.bcm.edu	37	15	90334240	90334240	+	Silent	SNP	A	A	G	rs25654	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	176	79	170	0	0.448864	0	A|0.675;G|0.325	0.325	strong	.	ANPEP	124	.	NM_001150	exon19	c.T2613C	p.I871I	TTGCCCAATGACG	.	PASS	Atlas-SNP
ACVR2A	92	hgsc.bcm.edu	37	2	148657117	148657117	+	Silent	SNP	G	G	A	rs1128919	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	33	33	41	0	1	0	G|0.657;A|0.343	0.343	strong	.	ACVR2A	125	.	NM_001616	exon3	c.G354A	p.P118P	TTTTCCGGAGATG	.	PASS	Atlas-SNP
BICD1	636	hgsc.bcm.edu	37	12	32481369	32481369	+	Silent	SNP	C	C	T	rs34447944	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93	32	110	0	0.344086	0	C|0.940;T|0.060	0.060	strong	BICD1,colon,carcinoma,0,1	BICD1	89	1	NM_001714	exon5	c.C1980T	p.A660A	GCTAGCCCCCATG	.	PASS	Atlas-SNP
TMEM232	642987	hgsc.bcm.edu	37	5	109960989	109960989	+	Silent	SNP	A	A	G	rs61730920	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	210	93	207	0	0.442857	0	A|0.859;G|0.141	0.141	strong	.	TMEM232	57	.	NM_001039763	exon7	c.T747C	p.Y249Y	GTTCTCATATCTT	.	PASS	Atlas-SNP
PRRG4	79056	hgsc.bcm.edu	37	11	32852172	32852172	+	Missense_Mutation	SNP	G	G	A	rs33962176	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44	19	53	0	0.431818	0	G|0.902;A|0.098	0.098	strong	PRRG4,NS,carcinoma,0,1	PRRG4	15	1	NM_024081	exon2	c.G97A	p.E33K	GCGGGAGAAGAAG	.	PASS	Atlas-SNP
DNAJC10	54431	hgsc.bcm.edu	37	2	183584755	183584755	+	Missense_Mutation	SNP	G	G	A	rs6729801	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	23	23	30	0	1	0	G|0.597;A|0.403	0.403	strong	.	DNAJC10	76	.	NM_001271581	exon4	c.G226A	p.D76N	CATGGCGATTTTT	.	PASS	Atlas-SNP
DOCK5	80005	hgsc.bcm.edu	37	8	25222165	25222165	+	Missense_Mutation	SNP	A	A	G	rs2271111	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	146	57	184	0	0.390411	0	A|0.749;G|0.251	0.251	strong	DOCK5,NS,carcinoma,0,1	DOCK5	167	1	NM_024940	exon30	c.A3068G	p.Q1023R	TAAATCAGTTTGC	.	PASS	Atlas-SNP
SEC23B	10483	hgsc.bcm.edu	37	20	18513372	18513372	+	Missense_Mutation	SNP	C	C	T	rs17807673	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	111	48	122	0	0.432432	0	C|0.909;T|0.091	0.091	strong	SEC23B,NS,carcinoma,-1,1	SEC23B	70	1	NM_032985	exon11	c.C1298T	p.P433L	AAGGACCGTGTGT	.	PASS	Atlas-SNP
CEP290	80184	hgsc.bcm.edu	37	12	88505078	88505078	+	Silent	SNP	T	T	C	rs2468255	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	196	87	209	0	0.443878	0	T|0.224;C|0.776	0.776	strong	.	CEP290	195	.	NM_025114	exon22	c.A2268G	p.S756S	AACATTTGATCCT	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	108	16	103	0	0.148148	0	C|0.778;T|0.222	0.222	strong	.	SNRNP48	32	.	NM_152551	exon1	c.C134T	p.P45L	TGGATCCCGGGGA	.	PASS	Atlas-SNP
PLEC	5339	hgsc.bcm.edu	37	8	145004185	145004185	+	Silent	SNP	C	C	T	rs78012434	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	77	36	70	0	0.467532	0	C|0.963;T|0.037	0.037	strong	.	PLEC	1144	.	NM_201380	exon22	c.G3069A	p.L1023L	CACGTGCAACTGG	.	PASS	Atlas-SNP
ANKRD6	22881	hgsc.bcm.edu	37	6	90340276	90340276	+	Silent	SNP	G	G	A	rs3210511	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	108	49	85	0	0.453704	0	G|0.381;A|0.619	0.619	strong	.	ANKRD6	51	.	NM_001242809	exon16	c.G1737A	p.S579S	GCTGTCGTCTTCT	.	PASS	Atlas-SNP
OR1S2	219958	hgsc.bcm.edu	37	11	57971171	57971171	+	Silent	SNP	C	C	T	rs200697120	byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	155	23	208	0	0.148387	0	C|0.928;T|0.072	0.072	strong	.	OR1S2	119	.	NM_001004459	exon1	c.G483A	p.S161S	GAACCACGAGATG	.	PASS	Atlas-SNP
WDFY4	57705	hgsc.bcm.edu	37	10	50013402	50013402	+	Missense_Mutation	SNP	T	T	C	rs2170132	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	29	13	23	0	0.448276	0	T|0.443;C|0.557	0.557	strong	.	WDFY4	205	.	NM_020945	exon26	c.T4582C	p.S1528P	AAGATCTCCACCA	.	PASS	Atlas-SNP
GCNT2	2651	hgsc.bcm.edu	37	6	10587056	10587056	+	Silent	SNP	A	A	G	rs71548508	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	133	26	161	0	0.195489	0	A|0.899;G|0.101	0.101	strong	GCNT2_ENST00000265012,NS,carcinoma,0,1	GCNT2	123	1	NM_145655	exon1	c.A834G	p.L278L	TGTTCTACGTGAC	.	PASS	Atlas-SNP
PDE5A	8654	hgsc.bcm.edu	37	4	120474859	120474859	+	Silent	SNP	A	A	G	rs11947234	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	160	68	148	0	0.425	0	A|0.732;G|0.268	0.268	strong	.	PDE5A	83	.	NM_001083	exon8	c.T1242C	p.Y414Y	TTTGACATACTGA	.	PASS	Atlas-SNP
MLXIPL	51085	hgsc.bcm.edu	37	7	73010191	73010191	+	Missense_Mutation	SNP	C	C	T	rs149244334	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	35	16	52	0	0.457143	0	C|0.999;T|0.001	0.001	strong	.	MLXIPL	54	.	NM_032951	exon14	c.G2167A	p.E723K	TGAGCTCCTCAAT	.	PASS	Atlas-SNP
LAMA5	3911	hgsc.bcm.edu	37	20	60903419	60903419	+	Silent	SNP	C	C	T	rs7262393	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	28	68	0	0.459016	0	C|0.782;T|0.218	0.218	strong	LAMA5,colon,carcinoma,0,1	LAMA5	268	1	NM_005560	exon35	c.G4530A	p.L1510L	GCACAGCAGGCAG	.	PASS	Atlas-SNP
FAM160A2	84067	hgsc.bcm.edu	37	11	6239139	6239139	+	Silent	SNP	A	A	G	rs11040809	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	19	9	29	0	0.473684	0	A|0.841;G|0.159;N|0.000;T|0.000	0.159	strong	.	FAM160A2	100	.	NM_032127	exon9	c.T1719C	p.R573R	ACCACGACGTGCC	.	PASS	Atlas-SNP
F13A1	2162	hgsc.bcm.edu	37	6	6152140	6152140	+	Missense_Mutation	SNP	C	C	T	rs5987	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	43	11	51	0	0.255814	0	C|0.943;T|0.057	0.057	strong	.	F13A1	135	.	NM_000129	exon14	c.G1951A	p.V651I	ACTCAACTGTCAC	.	PASS	Atlas-SNP
NOP9	161424	hgsc.bcm.edu	37	14	24771285	24771285	+	Missense_Mutation	SNP	G	G	A	rs4280164	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	104	58	108	0	0.557692	0	G|0.835;A|0.165	0.165	strong	.	.	.	.	NM_174913	exon4	c.G923A	p.S308N	ACCTGAGTACTCG	.	PASS	Atlas-SNP
CTAGE5	4253	hgsc.bcm.edu	37	14	39769122	39769122	+	Missense_Mutation	SNP	A	A	C	rs34761053	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60	25	85	0	0.416667	0	A|0.995;C|0.005	0.005	strong	.	CTAGE5	75	.	NM_001247989	exon9	c.A742C	p.K248Q	AAACAGAAAGTAA	.	PASS	Atlas-SNP
SPERT	220082	hgsc.bcm.edu	37	13	46287373	46287373	+	Nonsense_Mutation	SNP	C	C	A	rs80072371	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	78	28	40	0	0.358974	0	C|0.930;A|0.070	0.070	strong	SPERT,caecum,carcinoma,0,1	SPERT	54	1	NM_152719	exon3	c.C213A	p.C71X	TCGCTGCGCGCAG	.	PASS	Atlas-SNP
HDGFRP2	0	hgsc.bcm.edu	37	19	4493708	4493708	+	Silent	SNP	A	A	G	rs892161	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80	30	119	0	0.375	0	A|0.431;G|0.569	0.569	strong	HDGF2,NS,carcinoma,0,1	.	.	1	NM_032631	exon7	c.A687G	p.P229P	GGCGCCATCAGCC	.	PASS	Atlas-SNP
PM20D1	148811	hgsc.bcm.edu	37	1	205812912	205812912	+	Missense_Mutation	SNP	A	A	G	rs7518979	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49	26	62	0	0.530612	0	A|0.764;G|0.236	0.236	strong	.	PM20D1	56	.	NM_152491	exon6	c.T710C	p.I237T	ACTGCAATCCTGT	.	PASS	Atlas-SNP
FUT6	2528	hgsc.bcm.edu	37	19	5831840	5831840	+	Missense_Mutation	SNP	C	C	T	rs17855739	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	234	101	267	0	0.431624	0	C|0.878;T|0.122	0.122	strong	FUT6,NS,carcinoma,+2,1	FUT6	30	1	NM_000150	exon3	c.G739A	p.E247K	AGTTCTCGAAGGC	.	PASS	Atlas-SNP
SMC5	23137	hgsc.bcm.edu	37	9	72933774	72933774	+	Missense_Mutation	SNP	A	A	G	rs11142365	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	109	46	102	0	0.422018	0	A|0.888;G|0.112	0.112	strong	.	SMC5	96	.	NM_015110	exon15	c.A2045G	p.H682R	GCAAACATCTGGA	.	PASS	Atlas-SNP
KRTAP12-1	353332	hgsc.bcm.edu	37	21	46101993	46101993	+	Missense_Mutation	SNP	C	C	T	rs55881656	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	150	70	113	0	0.466667	0	C|0.947;T|0.053	0.053	strong	.	KRTAP12-1	9	.	NM_181686	exon1	c.G46A	p.A16T	TGGGCGCGCAGCA	.	PASS	Atlas-SNP
FRMD1	79981	hgsc.bcm.edu	37	6	168462626	168462626	+	Silent	SNP	G	G	A	rs12197610	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	65	29	63	0	0.446154	0	G|0.739;A|0.261	0.261	strong	FRMD1,NS,carcinoma,-1,1	FRMD1	52	1	NM_024919	exon8	c.C906T	p.P302P	TGCTGCGGGCAGC	.	PASS	Atlas-SNP
FCGBP	8857	hgsc.bcm.edu	37	19	40408128	40408128	+	Silent	SNP	C	C	T	rs4803310	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	283	155	292	1	0.547703	0.00342466	C|0.824;T|0.176	0.176	strong	FCGBP,NS,malignant_melanoma,0,2	FCGBP	416	2	NM_003890	exon9	c.G4593A	p.E1531E	AGGGCACTCCATG	.	PASS	Atlas-SNP
HSPG2	3339	hgsc.bcm.edu	37	1	22168801	22168801	+	Missense_Mutation	SNP	T	T	C	rs2229491	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	35	80	0	0.460526	0	T|0.899;G|0.000;C|0.101;A|0.000	0.101	strong	.	HSPG2	311	.	NM_005529	exon68	c.A8983G	p.S2995G	GGCCGCTGGCTGC	.	PASS	Atlas-SNP
MYH15	22989	hgsc.bcm.edu	37	3	108189627	108189627	+	Missense_Mutation	SNP	C	C	T	rs4299484	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110	57	85	0	0.518182	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
CELSR1	9620	hgsc.bcm.edu	37	22	46762360	46762360	+	Silent	SNP	G	G	A	rs56325154	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	107	52	95	0	0.485981	0	G|0.993;A|0.007	0.007	strong	.	CELSR1	242	.	NM_014246	exon30	c.C8223T	p.N2741N	GGTGGTGTTGCAG	.	PASS	Atlas-SNP
LZTR1	8216	hgsc.bcm.edu	37	22	21348914	21348914	+	Silent	SNP	C	C	T	rs4822790	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	11	65	0	0.211538	0	C|0.855;T|0.145	0.145	strong	.	LZTR1	99	.	NM_006767	exon15	c.C1683T	p.R561R	GTGCCGCCTGGAG	.	PASS	Atlas-SNP
KLHL23	151230	hgsc.bcm.edu	37	2	170592709	170592709	+	Silent	SNP	A	A	G	rs2288331	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	59	29	46	0	0.491525	0	A|0.835;G|0.165	0.165	strong	.	KLHL23	52	.	NM_144711	exon2	c.A1185G	p.K395K	AGAGAAATGGATT	.	PASS	Atlas-SNP
PCDHGA9	56107	hgsc.bcm.edu	37	5	140783628	140783628	+	Missense_Mutation	SNP	A	A	G	rs375910829		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	139	71	124	0	0.510791	0	.	.	weak	.	PCDHGA9	110	.	NM_032089	exon1	c.A1109G	p.N370S	TTTTCAATGCTCA	.	PASS	Atlas-SNP
FGA	2243	hgsc.bcm.edu	37	4	155507590	155507590	+	Missense_Mutation	SNP	T	T	C	rs6050	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83	43	105	1	0.518072	0.00952381	T|0.700;C|0.300	0.300	strong	FGA,NS,carcinoma,0,1	FGA	179	1	NM_000508	exon5	c.A991G	p.T331A	TTCCAGTACTTCC	.	scavenged	Atlas-SNP
SSTR4	6754	hgsc.bcm.edu	37	20	23016970	23016970	+	Missense_Mutation	SNP	T	T	G	rs3746726	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	123	56	132	0	0.455285	0	T|0.674;G|0.326	0.326	strong	SSTR4,colon,carcinoma,0,1	SSTR4	83	1	NM_001052	exon1	c.T850G	p.F284V	AACCTCTTCGTGA	.	PASS	Atlas-SNP
KLHL5	51088	hgsc.bcm.edu	37	4	39064162	39064162	+	Missense_Mutation	SNP	A	A	C	rs2711941	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	149	147	173	0	0.986577	0	A|0.260;C|0.740	0.740	strong	.	KLHL5	75	.	NM_015990	exon1	c.A28C	p.I10L	TTACATATTTTTG	.	PASS	Atlas-SNP
INPP5E	56623	hgsc.bcm.edu	37	9	139324740	139324740	+	Silent	SNP	C	C	T	rs10870182	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48	21	68	0	0.4375	0	C|0.894;T|0.106	0.106	strong	.	INPP5E	18	.	NM_019892	exon9	c.G1791A	p.P597P	TCGCCCCGGCCTC	.	PASS	Atlas-SNP
NOTCH4	4855	hgsc.bcm.edu	37	6	32168771	32168771	+	Silent	SNP	G	G	T	rs3134942	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	103	86	90	0	0.834951	0	G|0.909;T|0.091	0.091	strong	NOTCH4,colon,carcinoma,0,1	NOTCH4	201	1	NM_004557	exon23	c.C4152A	p.V1384V	ACCCATGACCACC	.	PASS	Atlas-SNP
SFTA2	389376	hgsc.bcm.edu	37	6	30899524	30899524	+	Missense_Mutation	SNP	T	T	C	rs3131787	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	74	77	0	0.850575	0	T|0.854;C|0.146	0.146	strong	.	SFTA2	6	.	NM_205854	exon2	c.A110G	p.N37S	GAGGAATTTGTCA	.	PASS	Atlas-SNP
COL5A3	50509	hgsc.bcm.edu	37	19	10084460	10084460	+	Missense_Mutation	SNP	A	A	G	rs62638750	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	28	13	35	0	0.464286	0	A|0.992;G|0.008	0.008	strong	.	COL5A3	243	.	NM_015719	exon49	c.T3584C	p.V1195A	TGACCAACTCCTC	.	PASS	Atlas-SNP
ENPP5	59084	hgsc.bcm.edu	37	6	46135795	46135795	+	Missense_Mutation	SNP	T	T	C	rs34432940	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	40	60	0	0.493827	0	T|0.993;C|0.007	0.007	strong	.	ENPP5	44	.	NM_021572	exon2	c.A205G	p.I69V	TTGTAATAAAAAC	.	PASS	Atlas-SNP
OR11H12	440153	hgsc.bcm.edu	37	14	19377881	19377881	+	Missense_Mutation	SNP	G	G	A	rs138502172	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	357	25	301	0	0.070028	0	G|0.973;A|0.027	0.027	strong	OR11H12,NS,carcinoma,0,1	OR11H12	58	1	NM_001013354	exon1	c.G288A	p.M96I	CAAGATGTTGGTC	.	scavenged	Atlas-SNP
RASA1	5921	hgsc.bcm.edu	37	5	86564564	86564564	+	Missense_Mutation	SNP	C	C	T	rs111840875	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	27	68	0	0.435484	0	C|0.982;T|0.018	0.018	strong	.	RASA1	213	.	NM_002890	exon1	c.C296T	p.A99V	GTGCTGCTGCTGG	.	PASS	Atlas-SNP
OR2D3	120775	hgsc.bcm.edu	37	11	6942952	6942952	+	Silent	SNP	T	T	C	rs2035844	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	225	126	244	0	0.56	0	T|0.667;C|0.333	0.333	strong	.	OR2D3	51	.	NM_001004684	exon1	c.T720C	p.T240T	CTCCACTGTTATC	.	PASS	Atlas-SNP
PSME4	23198	hgsc.bcm.edu	37	2	54176359	54176359	+	Silent	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	23	59	0	0.310811	0	.	.	none	.	PSME4	247	.	NM_014614	exon2	c.T304C	p.L102L	CATACAATAACTT	.	PASS	Atlas-SNP
ZNF154	7710	hgsc.bcm.edu	37	19	58213773	58213773	+	Missense_Mutation	SNP	G	G	C	rs2188736	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	160	73	157	0	0.45625	0	G|0.847;C|0.153	0.153	strong	.	ZNF154	34	.	NM_001085384	exon3	c.C544G	p.L182V	TGTGAAGTCTCCA	.	PASS	Atlas-SNP
DOCK1	1793	hgsc.bcm.edu	37	10	129160458	129160458	+	Silent	SNP	G	G	A	rs2296635	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	44	101	0	0.586667	0	G|0.808;A|0.192	0.192	strong	.	DOCK1	188	.	NM_001380	exon33	c.G3351A	p.S1117S	CCATTCGACCCGA	.	PASS	Atlas-SNP
PGD	5226	hgsc.bcm.edu	37	1	10473196	10473196	+	Silent	SNP	C	C	T	rs2229687	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	35	57	0	0.564516	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
CLEC4F	165530	hgsc.bcm.edu	37	2	71043461	71043461	+	Missense_Mutation	SNP	C	C	T	rs722896	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	115	77	158	0	0.669565	0	C|0.704;T|0.296	0.296	strong	.	CLEC4F	95	.	NM_173535	exon4	c.G1052A	p.R351H	TCCAGACGGCCAT	.	PASS	Atlas-SNP
FLNC	2318	hgsc.bcm.edu	37	7	128488734	128488734	+	Missense_Mutation	SNP	G	G	A	rs2291569	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	43	23	33	0	0.534884	0	G|0.921;A|0.079	0.079	strong	.	FLNC	339	.	NM_001127487	exon27	c.G4700A	p.R1567Q	ACGCACGGGACGC	.	PASS	Atlas-SNP
TMEM51	55092	hgsc.bcm.edu	37	1	15546077	15546077	+	Silent	SNP	G	G	A	rs3753313	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	92	43	112	1	0.467391	0.00892857	G|0.767;A|0.233	0.233	strong	TMEM51,NS,lymphoid_neoplasm,+1,1	TMEM51	28	1	NM_018022	exon3	c.G600A	p.P200P	GAAACCGCTGAAA	.	scavenged	Atlas-SNP
ZNF211	10520	hgsc.bcm.edu	37	19	58153000	58153000	+	Silent	SNP	T	T	C	rs3746218	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	30	12	21	0	0.4	0	T|0.792;C|0.208	0.208	strong	.	ZNF211	78	.	NM_001265597	exon5	c.T1341C	p.F447F	AAACTTTAGCCTG	.	PASS	Atlas-SNP
SYNE3	161176	hgsc.bcm.edu	37	14	95906321	95906321	+	Missense_Mutation	SNP	G	G	A	rs9671369	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	29	29	36	0	1	0	G|0.638;A|0.362	0.362	strong	SYNE3_ENST00000334258,NS,carcinoma,0,3	SYNE3	130	3	NM_152592	exon11	c.C2003T	p.T668M	TTTTGCGTGGTCA	.	PASS	Atlas-SNP
LAMA5	3911	hgsc.bcm.edu	37	20	60899182	60899182	+	Missense_Mutation	SNP	C	C	T	rs11698080	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	77	40	96	0	0.519481	0	C|0.759;T|0.241	0.241	strong	LAMA5,caecum,carcinoma,0,1	LAMA5	268	1	NM_005560	exon43	c.G5722A	p.A1908T	AGGGGGCGCTGGG	.	PASS	Atlas-SNP
HSPG2	3339	hgsc.bcm.edu	37	1	22180723	22180723	+	Silent	SNP	C	C	T	rs12742444	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	99	56	107	0	0.565657	0	C|0.971;G|0.000;T|0.029	0.029	strong	.	HSPG2	311	.	NM_005529	exon50	c.G6402A	p.V2134V	GTGGAGCACAGAC	.	PASS	Atlas-SNP
DARC	2532	hgsc.bcm.edu	37	1	159175527	159175527	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	103	50	116	0	0.485437	0	.	.	none	.	DARC	76	.	NM_001122951	exon1	c.G304A	p.A102T	GTCCTGGCACAGC	.	PASS	Atlas-SNP
ZNF750	79755	hgsc.bcm.edu	37	17	80788465	80788465	+	Silent	SNP	T	T	C	rs12938126	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	119	55	106	0	0.462185	0	T|0.600;C|0.400	0.400	strong	.	ZNF750	60	.	NM_024702	exon3	c.A1725G	p.A575A	AGGTTCTGCAGCT	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	40	13	27	0	0.325	0	C|0.753;N|0.000	.	strong	.	OR6N1	96	.	NM_001005185	exon1	c.G28A	p.A10T	ATTCTGCTACCTG	.	PASS	Atlas-SNP
HLA-C	3107	hgsc.bcm.edu	37	6	31238931	31238931	+	Missense_Mutation	SNP	G	G	C	rs697743	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	154	13	111	1	0.0844156	0.00900901	G|0.777;C|0.108;A|0.115	0.108	strong	HLA-C_ENST00000383329,NS,carcinoma,0,4	HLA-C	92	4	NM_002117	exon3	c.C538G	p.L180V	CTCTCAGCTGCTC	.	scavenged	Atlas-SNP
ADAMTS18	170692	hgsc.bcm.edu	37	16	77325285	77325285	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	129	31	138	0	0.24031	0	.	.	none	ADAMTS18,NS,carcinoma,+1,2	ADAMTS18	270	2	NM_199355	exon21	c.C3280T	p.R1094X	ATCTTCGCTCTGG	.	PASS	Atlas-SNP
WDR81	124997	hgsc.bcm.edu	37	17	1639350	1639350	+	Silent	SNP	C	C	T	rs117522064	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48	33	47	0	0.6875	0	C|0.978;T|0.022	0.022	strong	.	WDR81	180	.	NM_001163809	exon9	c.C5343T	p.G1781G	ACTGGGCGGTGGG	.	PASS	Atlas-SNP
TUBA3D	113457	hgsc.bcm.edu	37	2	132237927	132237927	+	Missense_Mutation	SNP	C	C	A	rs76585620	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	137	13	215	0	0.0948905	0	C|0.500;A|0.500	0.500	weak	TUBA3D,trunk,malignant_melanoma,0,1	TUBA3D	60	1	NM_080386	exon4	c.C661A	p.R221S	ATTGAACGTCCCA	.	scavenged	Atlas-SNP
SETD5	55209	hgsc.bcm.edu	37	3	9483818	9483818	+	Nonsense_Mutation	SNP	C	C	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	17	31	0	0.361702	0	.	.	none	.	SETD5	210	.	NM_001080517	exon10	c.C966G	p.Y322X	ACCATACCCCTTT	.	PASS	Atlas-SNP
APMAP	57136	hgsc.bcm.edu	37	20	24954303	24954303	+	Silent	SNP	G	G	C	rs148400044	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	102	57	98	0	0.558824	0	G|0.998;C|0.002	0.002	strong	.	APMAP	3	.	NM_020531	exon4	c.C399G	p.A133A	AAACCGGGCAATG	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	16	10	15	0	0.625	0	C|0.662;T|0.338	0.338	strong	.	.	.	.	NM_001243312	exon3	c.C419T	p.A140V	ATGGGGCAAATGC	.	PASS	Atlas-SNP
SLC39A6	25800	hgsc.bcm.edu	37	18	33702162	33702162	+	Silent	SNP	G	G	A	rs3737466	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	131	75	108	0	0.572519	0	G|0.903;A|0.097	0.097	strong	.	SLC39A6	81	.	NM_012319	exon5	c.C1212T	p.F404F	ATGACTGAAAAGT	.	PASS	Atlas-SNP
FREM1	158326	hgsc.bcm.edu	37	9	14819370	14819370	+	Missense_Mutation	SNP	G	G	T	rs7023244	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73	42	73	0	0.575342	0	G|0.830;T|0.170	0.170	strong	.	FREM1	261	.	NM_144966	exon15	c.C2408A	p.S803Y	GCATCAGAAATTA	.	PASS	Atlas-SNP
DAPP1	27071	hgsc.bcm.edu	37	4	100784980	100784980	+	Silent	SNP	C	C	T	rs3737484	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51	17	60	0	0.333333	0	C|0.705;T|0.295	0.295	strong	.	DAPP1	47	.	NM_014395	exon7	c.C654T	p.F218F	ACAATTCGATTAT	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	19	76	0	0.365385	0	G|0.777;A|0.223	0.223	strong	.	FHAD1	78	.	NM_052929	exon4	c.G545A	p.R182H	ACGCCCGCAAGCC	.	PASS	Atlas-SNP
CYP27A1	1593	hgsc.bcm.edu	37	2	219677690	219677690	+	Silent	SNP	A	A	G	rs61733619	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	137	53	128	0	0.386861	0	A|0.983;G|0.017	0.017	strong	.	CYP27A1	52	.	NM_000784	exon5	c.A888G	p.Q296Q	GGCCCAACTGCAG	.	PASS	Atlas-SNP
TAS2R42	353164	hgsc.bcm.edu	37	12	11338669	11338669	+	Missense_Mutation	SNP	C	C	T	rs1669412	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	28	82	0	0.459016	0	C|0.762;T|0.238	0.238	strong	.	TAS2R42	30	.	NM_181429	exon1	c.G875A	p.R292Q	GTCTGTCGCAGCT	.	PASS	Atlas-SNP
IL32	9235	hgsc.bcm.edu	37	16	3119167	3119167	+	Silent	SNP	T	T	C	rs4786372	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	257	122	206	0	0.474708	0	T|0.235;C|0.765	0.765	strong	.	IL32	32	.	NM_004221	exon7	c.T378C	p.V126V	CGGGGTTCTGGCC	.	PASS	Atlas-SNP
CPSF3L	54973	hgsc.bcm.edu	37	1	1249187	1249187	+	Silent	SNP	G	G	A	rs12142199	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	175	174	173	1	0.994286	0.00578035	G|0.517;A|0.483	0.483	strong	.	CPSF3L	33	.	NM_001256456	exon11	c.C900T	p.F300F	CTGCACGAAAGTC	.	PASS	Atlas-SNP
ANKH	56172	hgsc.bcm.edu	37	5	14741984	14741984	+	Silent	SNP	T	T	C	rs2288474	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	148	67	151	0	0.452703	0	T|0.932;C|0.068	0.068	strong	ANKH,NS,carcinoma,0,1	ANKH	64	1	NM_054027	exon8	c.A963G	p.A321A	GTGGGCTGCCGTG	.	PASS	Atlas-SNP
LRIG1	26018	hgsc.bcm.edu	37	3	66434668	66434668	+	Silent	SNP	G	G	A	rs34993786	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	223	82	236	0	0.367713	0	A|0.031;C|0.000;G|0.969	0.031	strong	.	LRIG1	138	.	NM_015541	exon14	c.C1818T	p.H606H	TATGTCGTGGGGC	.	PASS	Atlas-SNP
MIS18BP1	55320	hgsc.bcm.edu	37	14	45711340	45711340	+	Missense_Mutation	SNP	G	G	C	rs34168608	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	142	66	158	0	0.464789	0	G|0.991;C|0.009	0.009	strong	.	MIS18BP1	92	.	NM_018353	exon4	c.C1040G	p.P347R	AGTCTTGGTGTTG	.	PASS	Atlas-SNP
CEACAM4	1089	hgsc.bcm.edu	37	19	42132314	42132314	+	Missense_Mutation	SNP	G	G	C	rs1126454	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	50	25	54	0	0.5	0	G|0.462;C|0.537	0.537	strong	.	CEACAM4	42	.	NM_001817	exon2	c.C85G	p.H29D	GCGGGTGCCAGAA	.	PASS	Atlas-SNP
PPP1R15A	23645	hgsc.bcm.edu	37	19	49379167	49379167	+	Silent	SNP	C	C	T	rs524	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	104	44	80	0	0.423077	0	C|0.647;T|0.353	0.353	strong	.	PPP1R15A	48	.	NM_014330	exon3	c.C1962T	p.A654A	TGTGGCCACACCT	.	PASS	Atlas-SNP
PRMT8	56341	hgsc.bcm.edu	37	12	3701464	3701464	+	Silent	SNP	G	G	A	rs34000611	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	43	14	50	0	0.325581	0	G|0.881;A|0.119	0.119	strong	PRMT8_ENST00000452611,NS,carcinoma,+1,2	PRMT8	97	2	NM_019854	exon9	c.G1047A	p.R349R	TGTCCGGAGGGGG	.	PASS	Atlas-SNP
GPRIN1	114787	hgsc.bcm.edu	37	5	176026138	176026138	+	Missense_Mutation	SNP	T	T	A	rs201635586	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85	22	134	0	0.258824	0	T|0.795;A|0.205	0.205	strong	.	GPRIN1	77	.	NM_052899	exon2	c.A698T	p.E233V	GGATCCTCCTTCC	.	PASS	Atlas-SNP
SBF1	6305	hgsc.bcm.edu	37	22	50893668	50893668	+	Silent	SNP	C	C	G	rs374064130		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	56	35	57	0	0.625	0	.	.	weak	.	SBF1	211	.	NM_002972	exon33	c.G4539C	p.L1513L	GCAGTCCAGGAAC	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	46	25	60	0	0.543478	0	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	.	PASS	Atlas-SNP
PPL	5493	hgsc.bcm.edu	37	16	4935636	4935636	+	Missense_Mutation	SNP	G	G	A	rs2075639	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100	48	119	0	0.48	0	G|0.915;A|0.085	0.085	strong	.	PPL	168	.	NM_002705	exon22	c.C3020T	p.A1007V	TCATCCGCCTGGG	.	PASS	Atlas-SNP
OR4L1	122742	hgsc.bcm.edu	37	14	20528207	20528207	+	Missense_Mutation	SNP	G	G	A	rs1958715	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	96	49	96	0	0.510417	0	G|0.535;A|0.465	0.465	strong	.	OR4L1	98	.	NM_001004717	exon1	c.G4A	p.D2N	TAAATGGATCTTA	.	PASS	Atlas-SNP
WNK2	65268	hgsc.bcm.edu	37	9	96030979	96030979	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91	28	109	0	0.307692	0	.	.	none	.	WNK2	277	.	NM_006648	exon18	c.A3984T	p.E1328D	CCCTGAATCTTCG	.	PASS	Atlas-SNP
ZFP2	80108	hgsc.bcm.edu	37	5	178358857	178358857	+	Silent	SNP	C	C	T	rs61744382	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	16	10	17	0	0.625	0	C|0.925;T|0.075	0.075	strong	.	ZFP2	70	.	NM_030613	exon5	c.C543T	p.T181T	TCACACCGGAGAG	.	PASS	Atlas-SNP
TNK1	8711	hgsc.bcm.edu	37	17	7286266	7286266	+	Silent	SNP	C	C	T	rs1554947	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	89	48	90	0	0.539326	0	C|0.631;T|0.369	0.369	strong	.	TNK1	31	.	NM_003985	exon2	c.C21T	p.S7S	TGGCTCCCTGTGG	.	PASS	Atlas-SNP
COL6A6	131873	hgsc.bcm.edu	37	3	130311551	130311551	+	Silent	SNP	A	A	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	108	28	131	0	0.259259	0	.	.	none	COL6A6_ENST00000358511,bladder,carcinoma,+1,2	COL6A6	497	2	NM_001102608	exon14	c.A4356T	p.G1452G	CAGAGGACTAAAT	.	PASS	Atlas-SNP
TMEM173	340061	hgsc.bcm.edu	37	5	138861078	138861078	+	Missense_Mutation	SNP	C	C	T	rs11554776	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	134	63	129	2	0.470149	0.0155039	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	.	scavenged	Atlas-SNP
TMCO3	55002	hgsc.bcm.edu	37	13	114175038	114175038	+	Missense_Mutation	SNP	G	G	A	rs7319493	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69	16	89	0	0.231884	0	G|0.835;A|0.165	0.165	strong	.	TMCO3	77	.	NM_017905	exon8	c.G1333A	p.A445T	GCCAGTGCATCTT	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	144	60	123	0	0.416667	0	A|0.264;G|0.736	0.736	strong	.	KRTAP12-4	10	.	NM_198698	exon1	c.T330C	p.T110T	GCAGCCAGTGGGG	.	PASS	Atlas-SNP
OR2L3	391192	hgsc.bcm.edu	37	1	248224227	248224227	+	Missense_Mutation	SNP	T	T	C	rs146249174	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	223	107	234	0	0.479821	0	T|0.992;C|0.008	0.008	strong	.	OR2L3	97	.	NM_001004687	exon1	c.T244C	p.S82P	ATGGCATCTGATT	.	PASS	Atlas-SNP
MAPT	4137	hgsc.bcm.edu	37	17	44061036	44061036	+	Missense_Mutation	SNP	T	T	C	rs62063787	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	105	105	101	1	1	0.00990099	T|0.849;C|0.151	0.151	strong	.	MAPT	135	.	NM_001123066	exon6	c.T866C	p.V289A	CCAGTGTAGGGCG	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	192	191	190	1	0.994792	0.00526316	G|0.433;A|0.567	0.567	strong	.	MYO3B	320	.	NM_001083615	exon6	c.G585A	p.P195P	CACCCCGTTCTGG	.	PASS	Atlas-SNP
ZBTB3	79842	hgsc.bcm.edu	37	11	62521475	62521475	+	Silent	SNP	T	T	C	rs72929471	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	105	51	103	0	0.485714	0	T|0.821;C|0.179	0.179	strong	.	ZBTB3	47	.	NM_024784	exon1	c.A60G	p.R20R	TCTTTTTCGCTCC	.	PASS	Atlas-SNP
EIF2B5	8893	hgsc.bcm.edu	37	3	183860335	183860335	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	240	5	249	2	0.0208333	0.00803213	.	.	none	EIF2B5,colon,carcinoma,-1,1	EIF2B5	62	1	NM_003907	exon10	c.G1490T	p.W497L	ACCTCTGGAAAGC	.	scavenged	Atlas-SNP
GIMAP7	168537	hgsc.bcm.edu	37	7	150217335	150217335	+	Silent	SNP	G	G	T	rs3735079	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48	18	56	0	0.375	0	G|0.893;T|0.107	0.107	strong	.	GIMAP7	47	.	NM_153236	exon2	c.G273T	p.G91G	CCCAGGGCCCCAT	.	PASS	Atlas-SNP
MTMR11	10903	hgsc.bcm.edu	37	1	149906167	149906167	+	Missense_Mutation	SNP	T	T	G	rs41302101	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91	47	80	0	0.516484	0	T|0.948;G|0.052	0.052	strong	.	MTMR11	136	.	NM_001145862	exon7	c.A600C	p.E200D	CCAGTCTTCCGCT	.	PASS	Atlas-SNP
USP45	85015	hgsc.bcm.edu	37	6	99894086	99894086	+	Missense_Mutation	SNP	C	C	G	rs41288947	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94	46	85	0	0.489362	0	C|0.737;G|0.263	0.263	strong	.	USP45	56	.	NM_001080481	exon14	c.G1562C	p.R521T	CTGGATCTGAACA	.	PASS	Atlas-SNP
ZNF682	91120	hgsc.bcm.edu	37	19	20135066	20135066	+	Silent	SNP	G	G	T	rs61739376	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	34	83	0	0.507463	0	G|0.937;T|0.063	0.063	strong	.	ZNF682	51	.	NM_033196	exon2	c.C123A	p.V41V	CAGAGAGACCAGG	.	PASS	Atlas-SNP
ACSM3	6296	hgsc.bcm.edu	37	16	20796387	20796387	+	Missense_Mutation	SNP	G	G	C	rs5716	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60	26	54	0	0.433333	0	G|0.919;C|0.081	0.081	strong	.	ACSM3	113	.	NM_202000	exon8	c.G1101C	p.K367N	AAACAAGACGGGC	.	PASS	Atlas-SNP
ZDHHC11	79844	hgsc.bcm.edu	37	5	843723	843723	+	Missense_Mutation	SNP	C	C	A	rs71273553		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	379	93	122	0	0.245383	0	C|0.500;A|0.500	0.500	weak	ZDHHC11_ENST00000424784,rectum,carcinoma,0,2	ZDHHC11	97	2	NM_024786	exon4	c.G620T	p.R207M	TCATACCTGGGGT	.	PASS	Atlas-SNP
OR51B6	390058	hgsc.bcm.edu	37	11	5373497	5373497	+	Missense_Mutation	SNP	G	G	C	rs7106330	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	179	74	204	0	0.413408	0	G|0.883;C|0.117	0.117	strong	.	OR51B6	53	.	NM_001004750	exon1	c.G760C	p.V254L	ACTGTAGTTTGTC	.	PASS	Atlas-SNP
DHDH	27294	hgsc.bcm.edu	37	19	49445817	49445817	+	Missense_Mutation	SNP	T	T	C	rs11666105	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	39	56	0	0.464286	0	T|0.634;C|0.366	0.366	strong	.	DHDH	35	.	NM_014475	exon5	c.T740C	p.V247A	GCATGGTACAGGT	.	PASS	Atlas-SNP
TAS2R20	259295	hgsc.bcm.edu	37	12	11149720	11149720	+	Missense_Mutation	SNP	A	A	G	rs10845280	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	121	46	143	0	0.380165	0	A|0.670;G|0.329	0.329	strong	.	TAS2R20	17	.	NM_176889	exon1	c.T755C	p.F252S	ATCTTAAAATTCC	.	PASS	Atlas-SNP
FAM122B	159090	hgsc.bcm.edu	37	X	133923139	133923139	+	Silent	SNP	T	T	C	rs17317849	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	197	150	155	0	0.761421	0	0|0.003;C|0.018	0.018	strong	.	FAM122B	20	.	NM_001170756	exon5	c.A309G	p.Q103Q	CCATGATTGGCTT	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57	22	67	0	0.385965	0	G|0.796;A|0.204	0.204	strong	.	C1orf85	41	.	NM_001256608	exon4	c.C607T	p.P203S	GGGCTGGTCGGCT	.	PASS	Atlas-SNP
CCDC114	93233	hgsc.bcm.edu	37	19	48800338	48800338	+	Silent	SNP	A	A	G	rs7252988	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49	47	85	0	0.959184	0	A|0.435;G|0.565	0.565	strong	.	CCDC114	100	.	NM_144577	exon14	c.T1908C	p.S636S	CGAATCAGACGCT	.	PASS	Atlas-SNP
BTNL8	79908	hgsc.bcm.edu	37	5	180338368	180338368	+	Missense_Mutation	SNP	A	A	G	rs2276995	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	176	174	167	0	0.988636	0	A|0.529;G|0.471	0.471	strong	BTNL8,colon,carcinoma,-2,1	BTNL8	114	1	NM_001159708	exon3	c.A427G	p.T143A	TCCATCACGGGAT	.	PASS	Atlas-SNP
RNF20	56254	hgsc.bcm.edu	37	9	104309445	104309445	+	Silent	SNP	T	T	C	rs2273976	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	129	47	148	0	0.364341	0	T|0.867;C|0.133	0.133	strong	.	RNF20	110	.	NM_019592	exon8	c.T921C	p.Y307Y	GGTGTATGGAGCG	.	PASS	Atlas-SNP
RNF213	57674	hgsc.bcm.edu	37	17	78272294	78272294	+	Missense_Mutation	SNP	C	C	T	rs72849841	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100	55	116	0	0.55	0	C|0.869;T|0.131	0.131	strong	RNF213_ENST00000456466,colon,carcinoma,-1,3	RNF213	766	3	NM_001256071	exon11	c.C2186T	p.P729L	TCTCACCGTTCCG	.	PASS	Atlas-SNP
PPP4R4	57718	hgsc.bcm.edu	37	14	94722815	94722815	+	Silent	SNP	G	G	A	rs114970142	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	35	13	41	0	0.371429	0	G|0.989;A|0.011	0.011	strong	.	PPP4R4	107	.	NM_058237	exon17	c.G1884A	p.L628L	CTACCTGTTGCCC	.	PASS	Atlas-SNP
CHST8	64377	hgsc.bcm.edu	37	19	34262922	34262922	+	Missense_Mutation	SNP	C	C	T	rs149660944	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	103	51	112	0	0.495146	0	C|0.995;T|0.005	0.005	strong	.	CHST8	70	.	NM_001127895	exon5	c.C229T	p.R77W	GTCACTCGGGACT	.	PASS	Atlas-SNP
SMG6	23293	hgsc.bcm.edu	37	17	2186100	2186100	+	Silent	SNP	C	C	T	rs749240	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	235	119	218	0	0.506383	0	C|0.573;N|0.001	.	strong	.	SMG6	97	.	NM_017575	exon8	c.G2502A	p.Q834Q	CCGCCACTGGTCA	.	PASS	Atlas-SNP
TADA2B	93624	hgsc.bcm.edu	37	4	7055796	7055796	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	88	3	119	0	0.0340909	0	.	.	none	TADA2B,colon,adenoma,0,1	TADA2B	29	1	NM_152293	exon2	c.T278C	p.M93T	AAGATATGGCTGC	.	scavenged	Atlas-SNP
KRTAP4-11	653240	hgsc.bcm.edu	37	17	39274150	39274150	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51	7	57	2	0.137255	0.0350877	.	.	none	KRTAP4-11,NS,carcinoma,0,5	KRTAP4-11	94	5	NM_033059	exon1	c.A418T	p.S140C	AGATGCTGCAGCT	.	scavenged	Atlas-SNP
LIMD1	8994	hgsc.bcm.edu	37	3	45637253	45637253	+	Silent	SNP	C	C	T	rs267237	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	50	22	72	0	0.44	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
SHD	56961	hgsc.bcm.edu	37	19	4280186	4280186	+	Silent	SNP	C	C	T	rs10419363	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93	45	116	0	0.483871	0	C|0.681;N|0.000	.	strong	.	SHD	33	.	NM_020209	exon1	c.C126T	p.F42F	GGACTTCGAGGAC	.	PASS	Atlas-SNP
ZNF587	84914	hgsc.bcm.edu	37	19	58371274	58371274	+	Silent	SNP	G	G	T	rs10405892	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	230	21	194	0	0.0913043	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
PCDHB7	56129	hgsc.bcm.edu	37	5	140553784	140553784	+	Silent	SNP	C	C	T	rs7702701	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	90	41	86	0	0.455556	0	C|0.934;T|0.066	0.066	strong	.	PCDHB7	231	.	NM_018940	exon1	c.C1368T	p.Y456Y	CTCCTACACCCTG	.	PASS	Atlas-SNP
ROR2	4920	hgsc.bcm.edu	37	9	94499797	94499797	+	Silent	SNP	A	A	G	rs16907720	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	30	14	36	0	0.466667	0	A|0.902;G|0.098	0.098	strong	.	ROR2	167	.	NM_004560	exon5	c.T498C	p.D166D	GTAATCATCCCTG	.	PASS	Atlas-SNP
PRRC2C	23215	hgsc.bcm.edu	37	1	171509275	171509275	+	Silent	SNP	T	T	C	rs75723046	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100	44	112	0	0.44	0	T|0.997;C|0.003	0.003	strong	.	.	.	.	NM_015172	exon16	c.T2664C	p.D888D	TACTGATGCAAAT	.	PASS	Atlas-SNP
DCDC2	51473	hgsc.bcm.edu	37	6	24302049	24302049	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	131	10	131	0	0.0763359	0	.	.	none	.	DCDC2	53	.	NM_001195610	exon5	c.A451C	p.N151H	CTGGGTTTATGAG	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1272793	1272793	+	Missense_Mutation	SNP	C	C	T	rs56159668	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	90	43	86	0	0.477778	0	C|0.992;T|0.008	0.008	strong	.	MUC5B	473	.	NM_002458	exon31	c.C14683T	p.P4895S	ACGGTTCCCAGCT	.	PASS	Atlas-SNP
SLC1A7	6512	hgsc.bcm.edu	37	1	53600078	53600078	+	Silent	SNP	A	A	G	rs3737989	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80	43	66	0	0.5375	0	A|0.820;G|0.180	0.180	strong	.	SLC1A7	65	.	NM_006671	exon2	c.T159C	p.P53P	CTCTCCAGGGAAC	.	PASS	Atlas-SNP
KLK14	43847	hgsc.bcm.edu	37	19	51584951	51584951	+	Missense_Mutation	SNP	T	T	C	rs35287116	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	31	124	0	0.369048	0	T|0.653;C|0.347	0.347	strong	.	KLK14	49	.	NM_022046	exon4	c.A98G	p.Q33R	TGGCTCTGTGTCA	.	PASS	Atlas-SNP
TMSB10	9168	hgsc.bcm.edu	37	2	85133216	85133216	+	Silent	SNP	G	G	A	rs7148	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	111	83	179	1	0.747748	0.00558659	A|0.049;C|0.000;G|0.951	0.049	strong	.	TMSB10	2	.	NM_021103	exon2	c.G75A	p.E25E	GCAGGAGAAGAAC	.	PASS	Atlas-SNP
ALPK3	57538	hgsc.bcm.edu	37	15	85383640	85383640	+	Missense_Mutation	SNP	G	G	A	rs3803405	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	22	47	0	0.407407	0	G|0.815;A|0.185	0.185	strong	.	ALPK3	289	.	NM_020778	exon5	c.G1736A	p.G579E	CACGGGGGCCTGG	.	PASS	Atlas-SNP
KIF15	56992	hgsc.bcm.edu	37	3	44881909	44881909	+	Silent	SNP	A	A	G	rs76526953	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57	28	67	0	0.491228	0	A|0.943;G|0.057	0.057	strong	.	KIF15	103	.	NM_020242	exon28	c.A3381G	p.Q1127Q	GAGGCAACTAGAA	.	PASS	Atlas-SNP
PITRM1	10531	hgsc.bcm.edu	37	10	3206027	3206027	+	Silent	SNP	A	A	G	rs4609511	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	54	63	0	1	0	A|0.358;G|0.642	0.642	strong	.	PITRM1	109	.	NM_014889	exon7	c.T681C	p.P227P	GTGGTCAGGAAGA	.	PASS	Atlas-SNP
C1orf189	388701	hgsc.bcm.edu	37	1	154178079	154178079	+	Silent	SNP	G	G	A	rs74957241	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	35	83	0	0.492958	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
ZBTB16	7704	hgsc.bcm.edu	37	11	114118019	114118019	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	131	25	110	0	0.19084	0	.	.	none	.	ZBTB16	101	.	NM_006006	exon6	c.A1724G	p.E575G	CCTACGAGTGCAA	.	PASS	Atlas-SNP
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32551935	32551935	+	Silent	SNP	G	G	A	rs11554463	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	13	6	38	0	0.461538	0	T|0.033;G|0.900;A|0.067	0.067	strong	.	HLA-DRB1	41	.	NM_002124	exon2	c.C321T	p.Y107Y	TCTGCAGTAGGTG	.	PASS	Atlas-SNP
DENND6B	414918	hgsc.bcm.edu	37	22	50752150	50752150	+	Missense_Mutation	SNP	C	C	T	rs68178377	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	21	62	0	0.388889	0	C|0.747;T|0.253	0.253	strong	.	.	.	.	NM_001001794	exon15	c.G1207A	p.V403M	TCTGCACGCCCTG	.	PASS	Atlas-SNP
KRT72	140807	hgsc.bcm.edu	37	12	52985293	52985293	+	Silent	SNP	A	A	G	rs12824366	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	116	51	157	0	0.439655	0	A|0.651;G|0.349	0.349	strong	.	KRT72	70	.	NM_001146225	exon5	c.T918C	p.I306I	TAGGGCAATCTCC	.	PASS	Atlas-SNP
OTUD6B	51633	hgsc.bcm.edu	37	8	92097062	92097062	+	Missense_Mutation	SNP	G	G	A	rs3210518	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	88	45	119	0	0.511364	0	G|0.954;A|0.046	0.046	strong	.	OTUD6B	28	.	NM_016023	exon7	c.G938A	p.R313Q	TTACACGGTTGGT	.	PASS	Atlas-SNP
LRIG2	9860	hgsc.bcm.edu	37	1	113637308	113637308	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	209	94	239	0	0.449761	0	.	.	none	.	LRIG2	67	.	NM_014813	exon6	c.A734G	p.K245R	CTTTGAAAATGCA	.	PASS	Atlas-SNP
IL19	29949	hgsc.bcm.edu	37	1	207013248	207013248	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	183	2	191	0	0.010929	0	.	.	none	IL19_ENST00000340758,NS,carcinoma,+1,2	IL19	31	2	NM_153758	exon4	c.G378A	p.R126R	GGACAGGGTGTTC	.	scavenged	Atlas-SNP
PCDH1	5097	hgsc.bcm.edu	37	5	141248437	141248437	+	Silent	SNP	G	G	A	rs142655578	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	225	100	231	0	0.444444	0	G|0.990;A|0.010	0.010	strong	.	PCDH1	119	.	NM_032420	exon2	c.C600T	p.N200N	CACACCGTTGGGA	.	PASS	Atlas-SNP
DIMT1	27292	hgsc.bcm.edu	37	5	61694379	61694379	+	Silent	SNP	T	T	C	rs247264	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	208	205	224	0	0.985577	0	T|0.437;C|0.563	0.563	strong	.	.	.	.	NM_014473	exon6	c.A405G	p.S135S	AAAAGGTGAAGAG	.	PASS	Atlas-SNP
WDR81	124997	hgsc.bcm.edu	37	17	1637458	1637458	+	Silent	SNP	G	G	A	rs8065251	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	22	9	22	0	0.409091	0	G|0.782;A|0.218	0.218	strong	WDR81_ENST00000437219,NS,carcinoma,0,3	WDR81	180	3	NM_001163809	exon7	c.G5127A	p.P1709P	GGCCCCGCAGCAC	.	scavenged	Atlas-SNP
SSH3	54961	hgsc.bcm.edu	37	11	67079177	67079177	+	Missense_Mutation	SNP	G	G	A	rs1573536	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	77	16	61	0	0.207792	0	G|0.958;A|0.042	0.042	strong	.	SSH3	54	.	NM_017857	exon14	c.G1799A	p.R600H	AGTCCCGCCAGTC	.	PASS	Atlas-SNP
BRWD1	54014	hgsc.bcm.edu	37	21	40582823	40582823	+	Silent	SNP	C	C	T	rs75046572	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	116	74	74	0	0.637931	0	C|0.970;T|0.030	0.030	strong	.	BRWD1	325	.	NM_018963	exon35	c.G3933A	p.T1311T	ATAGTTCGTAGCT	.	PASS	Atlas-SNP
P2RX6	9127	hgsc.bcm.edu	37	22	21377650	21377650	+	Missense_Mutation	SNP	G	G	A	rs2277838	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48	25	47	0	0.520833	0	G|0.895;A|0.105	0.105	strong	.	.	.	.	NM_005446	exon7	c.G725A	p.R242H	TGTTCCGCATTGG	.	PASS	Atlas-SNP
CTSE	1510	hgsc.bcm.edu	37	1	206319201	206319201	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	88	13	102	0	0.147727	0	.	.	none	.	CTSE	72	.	NM_001910	exon3	c.G326A	p.C109Y	TGTACTGCACTAG	.	PASS	Atlas-SNP
SLIT1	6585	hgsc.bcm.edu	37	10	98820528	98820528	+	Silent	SNP	C	C	G	rs33970910	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	101	46	85	0	0.455446	0	C|0.870;G|0.130	0.130	strong	.	SLIT1	154	.	NM_003061	exon9	c.G810C	p.G270G	CACGCGCCCCGCT	.	PASS	Atlas-SNP
CAGE1	285782	hgsc.bcm.edu	37	6	7374207	7374207	+	Missense_Mutation	SNP	T	T	G	rs2876098	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	114	69	120	0	0.605263	0	T|0.882;G|0.118	0.118	strong	.	CAGE1	165	.	NM_001170693	exon5	c.A845C	p.E282A	CAGTTCTCCCGAC	.	PASS	Atlas-SNP
ANKRD50	57182	hgsc.bcm.edu	37	4	125592869	125592869	+	Silent	SNP	G	G	A	rs114589928	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	33	97	0	0.383721	0	G|0.994;A|0.006	0.006	strong	.	ANKRD50	136	.	NM_020337	exon4	c.C1563T	p.A521A	TTCTAAGGCTTGT	.	PASS	Atlas-SNP
MYO15A	51168	hgsc.bcm.edu	37	17	18058521	18058521	+	Silent	SNP	C	C	T	rs712272	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	22	62	0	0.349206	0	C|0.696;T|0.304	0.304	strong	.	MYO15A	268	.	NM_016239	exon45	c.C8322T	p.S2774S	CTTCTCCCGCATC	.	PASS	Atlas-SNP
HIST1H3J	8356	hgsc.bcm.edu	37	6	27858310	27858310	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	8	93	0	0.0987654	0	.	.	none	.	HIST1H3J	16	.	NM_003535	exon1	c.C261T	p.S87S	CGCCGAGCTCTGG	.	PASS	Atlas-SNP
CPAMD8	27151	hgsc.bcm.edu	37	19	17104379	17104379	+	Silent	SNP	G	G	A	rs75991134	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100	51	99	0	0.51	0	G|0.966;A|0.034	0.034	strong	.	CPAMD8	192	.	NM_015692	exon12	c.C1254T	p.P418P	GCCATCGGGGTAG	.	PASS	Atlas-SNP
KIAA1211	57482	hgsc.bcm.edu	37	4	57181629	57181629	+	Missense_Mutation	SNP	C	C	T	rs61750793	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	27	18	36	0	0.666667	0	C|0.760;T|0.240	0.240	strong	.	KIAA1211	178	.	NM_020722	exon8	c.C1961T	p.P654L	CTAAGCCCCGCCA	.	PASS	Atlas-SNP
ENPP7	339221	hgsc.bcm.edu	37	17	77709383	77709383	+	Missense_Mutation	SNP	C	C	T	rs148221256	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73	23	85	0	0.315068	0	C|0.998;T|0.002	0.002	strong	.	ENPP7	63	.	NM_178543	exon3	c.C941T	p.A314V	AGGAGGCGTTCCC	.	PASS	Atlas-SNP
GMPPA	29926	hgsc.bcm.edu	37	2	220371035	220371035	+	Silent	SNP	C	C	G	rs1046474	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	64	76	0	1	0	C|0.888;G|0.112	0.112	strong	.	GMPPA	50	.	NM_205847	exon12	c.C1053G	p.A351A	CTGGGCCCGCGTG	.	PASS	Atlas-SNP
ADAMTS13	11093	hgsc.bcm.edu	37	9	136308542	136308542	+	Silent	SNP	C	C	T	rs3124767	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	25	19	19	0	0.76	0	C|0.512;T|0.488	0.488	strong	.	ADAMTS13	113	.	NM_139027	exon19	c.C2280T	p.G760G	TGGGGGCGGCCTG	.	PASS	Atlas-SNP
SCML4	256380	hgsc.bcm.edu	37	6	108067907	108067907	+	Missense_Mutation	SNP	C	C	T	rs142985964	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	35	85	0	0.555556	0	C|0.999;T|0.001	0.001	strong	.	SCML4	65	.	NM_198081	exon4	c.G473A	p.G158D	ATCTCACCACCAT	.	PASS	Atlas-SNP
OSGIN1	29948	hgsc.bcm.edu	37	16	83992895	83992895	+	Missense_Mutation	SNP	A	A	G	rs150635654	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79	37	80	0	0.468354	0	A|0.999;G|0.001	0.001	strong	.	OSGIN1	33	.	NM_182981	exon3	c.A98G	p.Y33C	TGTCCTACCTGCT	.	PASS	Atlas-SNP
MYLK	4638	hgsc.bcm.edu	37	3	123411589	123411589	+	Silent	SNP	G	G	A	rs40305	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	31	71	0	0.5	0	G|0.525;A|0.475	0.475	strong	.	MYLK	224	.	NM_053025	exon19	c.C3558T	p.T1186T	ATCCACGGTGACT	.	PASS	Atlas-SNP
ARHGAP30	257106	hgsc.bcm.edu	37	1	161017556	161017556	+	Silent	SNP	C	C	T	rs2774279	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	38	71	0	0.469136	0	C|0.752;T|0.248	0.248	strong	.	ARHGAP30	105	.	NM_001025598	exon12	c.G3255A	p.R1085R	ATATGACCTGCGC	.	PASS	Atlas-SNP
ALS2CR11	151254	hgsc.bcm.edu	37	2	202436684	202436684	+	Silent	SNP	T	T	A	rs55872838	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	134	56	150	0	0.41791	0	T|0.948;A|0.052	0.052	strong	.	ALS2CR11	194	.	NM_001168217	exon8	c.A813T	p.P271P	TCTTTCTGGAGGT	.	PASS	Atlas-SNP
ELF1	1997	hgsc.bcm.edu	37	13	41515286	41515286	+	Missense_Mutation	SNP	T	T	A	rs1056820	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	146	105	89	1	0.719178	0.011236	T|0.513;A|0.487	0.487	strong	ELF1,colon,carcinoma,0,1	ELF1	65	1	NM_172373	exon8	c.A1027T	p.T343S	GAACTGTAGTGGC	.	scavenged	Atlas-SNP
TMEM120B	144404	hgsc.bcm.edu	37	12	122186268	122186268	+	Silent	SNP	C	C	T	rs28651018	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	180	89	171	0	0.494444	0	C|0.500;G|0.000;T|0.499	0.499	strong	.	TMEM120B	43	.	NM_001080825	exon3	c.C225T	p.L75L	GGAGCTCGTTCAG	.	PASS	Atlas-SNP
ARHGAP24	83478	hgsc.bcm.edu	37	4	86844835	86844835	+	Silent	SNP	A	A	G	rs6824722	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82	42	86	0	0.512195	0	A|0.669;G|0.331	0.331	strong	.	ARHGAP24	116	.	NM_001025616	exon4	c.A303G	p.E101E	TCATGAAAGCTAC	.	PASS	Atlas-SNP
MXRA5	25878	hgsc.bcm.edu	37	X	3241050	3241050	+	Silent	SNP	G	G	A	rs1635247	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	120	118	107	1	0.983333	0.00934579	0|0.003;A|0.559	0.559	strong	.	MXRA5	815	.	NM_015419	exon5	c.C2676T	p.S892S	CTTCTCGGAAAGG	.	PASS	Atlas-SNP
ATAD2	29028	hgsc.bcm.edu	37	8	124360487	124360487	+	Silent	SNP	G	G	A	rs77106954	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73	26	124	0	0.356164	0	G|0.979;A|0.021	0.021	strong	.	ATAD2	160	.	NM_014109	exon15	c.C1833T	p.H611H	CCTGGTGTGAATC	.	PASS	Atlas-SNP
RPS6KA4	8986	hgsc.bcm.edu	37	11	64138805	64138805	+	Silent	SNP	T	T	C	rs11542299	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	65	28	54	0	0.430769	0	T|0.729;C|0.271	0.271	strong	RPS6KA4_ENST00000334205,NS,carcinoma,+1,2	RPS6KA4	85	2	NM_003942	exon17	c.T2172C	p.N724N	GGAGAATGCACCC	.	PASS	Atlas-SNP
COL27A1	85301	hgsc.bcm.edu	37	9	117029826	117029826	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	4	53	0	0.0655738	0	.	.	none	.	COL27A1	200	.	NM_032888	exon34	c.G3490A	p.A1164T	GGGGAAGCCGGGA	.	PASS	Atlas-SNP
ACP6	51205	hgsc.bcm.edu	37	1	147124310	147124310	+	Silent	SNP	T	T	G	rs2153463	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91	51	49	0	0.56044	0	G|0.729;N|0.000	0.729	strong	.	ACP6	36	.	NM_016361	exon7	c.A823C	p.R275R	TCATCCTTGCAAA	.	PASS	Atlas-SNP
MDN1	23195	hgsc.bcm.edu	37	6	90482397	90482397	+	Missense_Mutation	SNP	T	T	C	rs12110451	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	58	19	58	0	0.327586	0	T|0.817;C|0.183	0.183	strong	.	MDN1	478	.	NM_014611	exon14	c.A1978G	p.I660V	GCTCGATGAGAAC	.	PASS	Atlas-SNP
DCHS2	54798	hgsc.bcm.edu	37	4	155411939	155411939	+	Missense_Mutation	SNP	A	A	C	rs17373874	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	119	119	190	1	1	0.00526316	A|0.634;C|0.366	0.366	strong	.	DCHS2	594	.	NM_001142552	exon1	c.T569G	p.V190G	TGGGCAACTGGCA	.	PASS	Atlas-SNP
SHMT1	6470	hgsc.bcm.edu	37	17	18232096	18232096	+	Missense_Mutation	SNP	G	G	A	rs1979277	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	31	16	36	0	0.516129	0	G|0.719;A|0.281	0.281	strong	SHMT1,colon,carcinoma,0,1	SHMT1	36	1	NM_004169	exon12	c.C1420T	p.L474F	GGAAGAGAGAGGC	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9056513	9056513	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	97	2	101	0	0.0206186	0	.	.	none	MUC16_ENST00000397910,NS,carcinoma,-2,2	MUC16	4315	2	NM_024690	exon3	c.C30933T	p.G10311G	CCCAGGGCCTGAC	.	scavenged	Atlas-SNP
CTLA4	1493	hgsc.bcm.edu	37	2	204732714	204732714	+	Missense_Mutation	SNP	A	A	G	rs231775	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	128	68	114	0	0.53125	0	A|0.592;G|0.408	0.408	strong	.	CTLA4	24	.	NM_005214	exon1	c.A49G	p.T17A	CTGGCTACCAGGA	.	PASS	Atlas-SNP
EPHX2	2053	hgsc.bcm.edu	37	8	27401964	27401964	+	Silent	SNP	A	A	C	rs1126452	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98	98	107	0	1	0	A|0.594;C|0.406	0.406	strong	EPHX2,NS,carcinoma,+2,1	EPHX2	57	1	NM_001979	exon19	c.A1593C	p.P531P	CAGGCCAACCGAG	.	PASS	Atlas-SNP
SAMD9	54809	hgsc.bcm.edu	37	7	92733975	92733975	+	Missense_Mutation	SNP	G	G	A	rs78564070	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	96	41	141	0	0.427083	0	G|0.947;A|0.053	0.053	strong	SAMD9,NS,carcinoma,+1,1	SAMD9	239	1	NM_001193307	exon2	c.C1436T	p.T479M	GAAATCGTCTCAT	.	PASS	Atlas-SNP
SLFN11	91607	hgsc.bcm.edu	37	17	33680811	33680811	+	Missense_Mutation	SNP	C	C	A	rs9898983	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	115	72	115	0	0.626087	0	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
SLC52A1	55065	hgsc.bcm.edu	37	17	4937351	4937351	+	Silent	SNP	G	G	T	rs56126318	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91	51	99	0	0.56044	0	G|0.931;T|0.069	0.069	strong	GPR172B,NS,carcinoma,+1,1	.	.	1	NM_017986	exon3	c.C433A	p.R145R	AAGACCGTAAGAA	.	PASS	Atlas-SNP
FCGBP	8857	hgsc.bcm.edu	37	19	40368391	40368391	+	Silent	SNP	G	G	A	rs76288738	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	286	39	259	0	0.136364	0	G|0.967;A|0.033	0.033	strong	.	FCGBP	416	.	NM_003890	exon28	c.C12957T	p.D4319D	AAGAATGTCACGG	.	PASS	Atlas-SNP
ZNF236	7776	hgsc.bcm.edu	37	18	74639433	74639433	+	Silent	SNP	G	G	A	rs117481741	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	43	43	36	0	1	0	G|0.992;A|0.008	0.008	strong	.	ZNF236	325	.	NM_007345	exon24	c.G4368A	p.P1456P	AGGCCCGCTGTCT	.	PASS	Atlas-SNP
ND4	0	hgsc.bcm.edu	37	MT	12088	12088	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	17	6	6	0	0.352941	0	.	.	none	.	.	.	.	ENST00000361381	exon1	c.C1329T	p.P443P	ATCCCCCATTCTC	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9083143	9083143	+	Missense_Mutation	SNP	G	G	A	rs7245949	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	175	81	157	0	0.462857	0	G|0.771;A|0.229	0.229	strong	.	MUC16	4315	.	NM_024690	exon1	c.C8672T	p.T2891I	TCAAATGTCAAGG	.	PASS	Atlas-SNP
SGK196	0	hgsc.bcm.edu	37	8	42977591	42977591	+	Silent	SNP	G	G	C	rs34040483	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85	38	90	0	0.447059	0	G|0.992;C|0.008	0.008	strong	.	.	.	.	NM_032237	exon5	c.G624C	p.L208L	CGACCTGCCGAAG	.	PASS	Atlas-SNP
HNRNPCL1	343069	hgsc.bcm.edu	37	1	12907843	12907843	+	Silent	SNP	T	T	G	rs2982093	bycluster;by2hit2allele	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	236	45	227	0	0.190678	0	T|1.000;|0.000	.	weak	HNRNPCL1,NS,carcinoma,-1,1	HNRNPCL1	68	1	NM_001013631	exon2	c.A300C	p.S100S	CGCTGCTGATCGT	.	PASS	Atlas-SNP
C1QTNF9	338872	hgsc.bcm.edu	37	13	24895631	24895631	+	Missense_Mutation	SNP	T	T	A	rs78083136	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	228	42	205	0	0.184211	0	T|0.930;A|0.070	0.070	strong	.	C1QTNF9	22	.	NM_178540	exon4	c.T727A	p.C243S	TTCACGTGCCACA	.	PASS	Atlas-SNP
PREX2	80243	hgsc.bcm.edu	37	8	69009268	69009268	+	Silent	SNP	C	C	T	rs3812458	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	88	31	70	0	0.352273	0	C|0.740;T|0.260	0.260	strong	.	PREX2	614	.	NM_025170	exon22	c.C2385T	p.F795F	CAAATTCAACACT	.	PASS	Atlas-SNP
DMBT1	1755	hgsc.bcm.edu	37	10	124330421	124330421	+	Missense_Mutation	SNP	C	C	G	rs75209396	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	192	94	161	0	0.489583	0	C|0.950;G|0.050	0.050	strong	.	DMBT1	677	.	NM_007329	exon4	c.C155G	p.S52W	TTCCCTCGGAGTC	.	PASS	Atlas-SNP
OAS3	4940	hgsc.bcm.edu	37	12	113398919	113398919	+	Silent	SNP	G	G	A	rs2072136	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	45	81	0	0.555556	0	G|0.696;N|0.000	.	strong	.	OAS3	63	.	NM_006187	exon8	c.G1701A	p.S567S	CTACTCGAGGCTC	.	PASS	Atlas-SNP
DNAJC11	55735	hgsc.bcm.edu	37	1	6705874	6705874	+	Missense_Mutation	SNP	G	G	C	rs200454	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	111	63	83	0	0.567568	0	G|0.786;C|0.214	0.214	strong	.	DNAJC11	93	.	NM_018198	exon8	c.C869G	p.T290S	TGGCTGGTTTTAG	.	PASS	Atlas-SNP
HYAL4	23553	hgsc.bcm.edu	37	7	123517000	123517000	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	171	89	185	0	0.520468	0	.	.	none	.	HYAL4	65	.	NM_012269	exon5	c.G1237A	p.G413R	GAGGACGGGGAGT	.	PASS	Atlas-SNP
AFAP1	60312	hgsc.bcm.edu	37	4	7857230	7857230	+	Silent	SNP	C	C	T	rs61742221	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69	67	86	0	0.971014	0	C|0.700;T|0.300	0.300	strong	.	AFAP1	93	.	NM_001134647	exon4	c.G297A	p.P99P	GCTCAGCGGCACA	.	PASS	Atlas-SNP
DSCAML1	57453	hgsc.bcm.edu	37	11	117308795	117308795	+	Silent	SNP	G	G	A	rs2253440	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	117	93	111	0	0.794872	0	G|0.808;A|0.192	0.192	strong	DSCAML1,colon,carcinoma,0,1	DSCAML1	286	1	NM_020693	exon25	c.C4428T	p.F1476F	TAGCACGAAGCCT	.	PASS	Atlas-SNP
UNC13D	201294	hgsc.bcm.edu	37	17	73827205	73827205	+	Missense_Mutation	SNP	T	T	C	rs1135688	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	63	59	0	1	0	T|0.510;C|0.490	0.490	strong	.	UNC13D	68	.	NM_199242	exon27	c.A2599G	p.K867E	GGGCCTTGGGTGG	.	PASS	Atlas-SNP
MAP1B	4131	hgsc.bcm.edu	37	5	71494906	71494906	+	Silent	SNP	G	G	A	rs61734262	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	34	18	51	0	0.529412	0	G|0.900;A|0.100	0.100	strong	.	MAP1B	243	.	NM_005909	exon5	c.G5724A	p.K1908K	TGAGAAGATAGAG	.	PASS	Atlas-SNP
AIPL1	23746	hgsc.bcm.edu	37	17	6337404	6337404	+	Silent	SNP	G	G	A	rs11650007	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	89	38	100	0	0.426966	0	G|0.983;A|0.017	0.017	strong	.	AIPL1	34	.	NM_014336	exon2	c.C111T	p.F37F	GGTGCGGAAATGA	.	PASS	Atlas-SNP
SH3RF3	344558	hgsc.bcm.edu	37	2	110065896	110065896	+	Missense_Mutation	SNP	C	C	T	rs192679474	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	97	42	114	0	0.43299	0	C|0.998;T|0.002	0.002	strong	.	SH3RF3	62	.	NM_001099289	exon8	c.C2099T	p.S700F	CCACATCCAGCCC	.	PASS	Atlas-SNP
NAALADL2	254827	hgsc.bcm.edu	37	3	174974265	174974265	+	Silent	SNP	C	C	T	rs192980349	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	102	48	118	0	0.470588	0	C|0.999;T|0.001	0.001	strong	.	NAALADL2	86	.	NM_207015	exon4	c.C885T	p.N295N	AAAAAACGTAACA	.	PASS	Atlas-SNP
BTBD6	90135	hgsc.bcm.edu	37	14	105716034	105716034	+	Silent	SNP	C	C	T	rs2816606	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72	43	67	0	0.597222	0	C|0.776;T|0.224	0.224	strong	.	BTBD6	24	.	NM_033271	exon5	c.C483T	p.Y161Y	TCTGTACGCTGCT	.	PASS	Atlas-SNP
ZKSCAN2	342357	hgsc.bcm.edu	37	16	25255506	25255506	+	Silent	SNP	C	C	T	rs11642611	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	35	73	0	0.466667	0	C|0.698;T|0.302	0.302	strong	.	ZKSCAN2	90	.	NM_001012981	exon6	c.G1581A	p.K527K	TTTGCTCTTCCGA	.	PASS	Atlas-SNP
SLC11A2	4891	hgsc.bcm.edu	37	12	51386066	51386066	+	Silent	SNP	A	A	G	rs1048230	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	40	60	0	0.45977	0	A|0.856;G|0.144	0.144	strong	.	SLC11A2	51	.	NM_001174125	exon13	c.T1341C	p.I447I	GATGGCAATAGAG	.	PASS	Atlas-SNP
ACADSB	36	hgsc.bcm.edu	37	10	124768583	124768583	+	Missense_Mutation	SNP	G	G	A	rs12263012	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	44	102	0	0.505747	0	G|0.772;A|0.228	0.228	strong	ACADSB,NS,carcinoma,0,1	ACADSB	45	1	NM_001609	exon1	c.G38A	p.R13K	GCAGCAGGCTGGT	.	PASS	Atlas-SNP
ATG2B	55102	hgsc.bcm.edu	37	14	96800027	96800027	+	Missense_Mutation	SNP	C	C	T	rs183527316	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98	50	81	0	0.510204	0	C|0.998;T|0.002	0.002	strong	.	ATG2B	169	.	NM_018036	exon8	c.G1205A	p.R402H	TTACCACGGCTAG	.	PASS	Atlas-SNP
WDR52	55779	hgsc.bcm.edu	37	3	113085143	113085143	+	Missense_Mutation	SNP	T	T	C	rs74521061	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	185	95	180	0	0.513514	0	T|0.978;C|0.022	0.022	strong	.	WDR52	151	.	NM_001164496	exon19	c.A2458G	p.M820V	ACATCATAACTTT	.	PASS	Atlas-SNP
NTRK1	4914	hgsc.bcm.edu	37	1	156848995	156848995	+	Silent	SNP	C	C	T	rs6337	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85	39	94	0	0.458824	0	C|0.533;T|0.467	0.467	strong	.	NTRK1	287	.	NM_002529	exon15	c.C1887T	p.A629A	GCTGGCCGTGGCT	.	PASS	Atlas-SNP
CIDEC	63924	hgsc.bcm.edu	37	3	9918861	9918861	+	Silent	SNP	C	C	A	rs456168	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68	41	48	0	0.602941	0	C|0.678;A|0.322	0.322	strong	CIDEC,NS,carcinoma,0,1	CIDEC	22	1	NM_001199623	exon3	c.G135T	p.L45L	CTCCGACAGCAGC	.	PASS	Atlas-SNP
OR2B2	81697	hgsc.bcm.edu	37	6	27879982	27879982	+	Missense_Mutation	SNP	A	A	G	rs61742093	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68	53	78	0	0.779412	0	A|0.943;G|0.057	0.057	strong	.	OR2B2	54	.	NM_033057	exon1	c.T116C	p.I39T	CCAAAGATTGTCA	.	PASS	Atlas-SNP
CNRIP1	25927	hgsc.bcm.edu	37	2	68511584	68511584	+	Silent	SNP	A	A	G	rs735815	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	52	61	0	0.981132	0	A|0.599;G|0.401	0.401	strong	CNRIP1_ENST00000409559,NS,carcinoma,0,1	CNRIP1	45	1	NM_001111101	exon3	c.T363C	p.S121S	TGTAAGAGAGATC	.	PASS	Atlas-SNP
GRM1	2911	hgsc.bcm.edu	37	6	146755515	146755515	+	Silent	SNP	T	T	G	rs6923864	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	59	21	140	10	0.355932	0.0714286	T|0.366;G|0.634	0.634	strong	GRM1,NS,carcinoma,+2,1	GRM1	419	1	NM_000838	exon9	c.T3168G	p.G1056G	CCCCGGTGGTCCC	.	scavenged	Atlas-SNP
ABCD4	5826	hgsc.bcm.edu	37	14	74766352	74766352	+	Silent	SNP	A	A	G	rs2301345	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	99	47	125	0	0.474747	0	A|0.717;G|0.283	0.283	strong	.	ABCD4	54	.	NM_005050	exon3	c.T184C	p.L62L	GGATCAAGCCAAC	.	PASS	Atlas-SNP
PPFIBP2	8495	hgsc.bcm.edu	37	11	7662851	7662851	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	92	24	94	0	0.26087	0	.	.	none	.	PPFIBP2	87	.	NM_003621	exon16	c.A1517C	p.K506T	GGGGAAAGTAAGT	.	PASS	Atlas-SNP
HIST2H3D	653604	hgsc.bcm.edu	37	1	149784843	149784843	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	238	15	239	0	0.0630252	0	.	.	none	.	HIST2H3D	15	.	NM_001123375	exon1	c.C394T	p.R132C	CCCCGCGGATGCG	.	PASS	Atlas-SNP
RBM11	54033	hgsc.bcm.edu	37	21	15599466	15599466	+	Missense_Mutation	SNP	A	A	G	rs7280643	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	196	69	169	0	0.352041	0	A|0.907;G|0.093	0.093	strong	RBM11,NS,carcinoma,0,1	RBM11	41	1	NM_144770	exon5	c.A698G	p.H233R	GGACTCACCAACA	.	PASS	Atlas-SNP
OR52E4	390081	hgsc.bcm.edu	37	11	5906291	5906291	+	Missense_Mutation	SNP	T	T	C	rs11823842	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	139	74	152	0	0.532374	0	T|0.627;C|0.373	0.373	strong	.	OR52E4	65	.	NM_001005165	exon1	c.T769C	p.F257L	CCAGCATTTTTTT	.	PASS	Atlas-SNP
PREX1	57580	hgsc.bcm.edu	37	20	47267940	47267940	+	Silent	SNP	G	G	A	rs61748372	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69	34	67	0	0.492754	0	A|0.145;C|0.000;G|0.855	0.145	strong	.	PREX1	441	.	NM_020820	exon22	c.C2649T	p.T883T	CTTGGCGGTGAGG	.	PASS	Atlas-SNP
KANSL1	284058	hgsc.bcm.edu	37	17	44110532	44110532	+	Silent	SNP	G	G	A	rs36076725	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	136	136	155	0	1	0	A|0.143;C|0.000;G|0.856;T|0.000	0.143	strong	.	.	.	.	NM_001193466	exon13	c.C2751T	p.F917F	GGCGGCGAAGGCT	.	PASS	Atlas-SNP
C7	730	hgsc.bcm.edu	37	5	40964885	40964885	+	Missense_Mutation	SNP	A	A	T	rs60714178	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	155	80	120	0	0.516129	0	A|0.902;T|0.098	0.098	strong	.	C7	136	.	NM_000587	exon14	c.A1792T	p.T598S	GTGTACACTTGCA	.	PASS	Atlas-SNP
WDR11	55717	hgsc.bcm.edu	37	10	122645376	122645376	+	Silent	SNP	A	A	T	rs7899928	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	29	59	0	0.537037	0	A|0.640;T|0.360	0.360	strong	WDR11,NS,carcinoma,0,1	WDR11	95	1	NM_018117	exon15	c.A1899T	p.A633A	ACTTGCAACTCGA	.	PASS	Atlas-SNP
SERPINA9	327657	hgsc.bcm.edu	37	14	94933473	94933473	+	Missense_Mutation	SNP	C	C	A	rs28618118	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	163	70	177	0	0.429448	0	C|0.677;A|0.323	0.323	strong	.	SERPINA9	105	.	NM_175739	exon3	c.G929T	p.R310I	CACTTTCTCAGTG	.	PASS	Atlas-SNP
OR2T3	343173	hgsc.bcm.edu	37	1	248637381	248637381	+	Missense_Mutation	SNP	G	G	A	rs139789199	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	344	54	419	0	0.156977	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
GIMAP1-GIMAP5	0	hgsc.bcm.edu	37	7	150440043	150440043	+	Silent	SNP	C	C	T	rs1046355	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83	34	99	0	0.409639	0	C|0.620;T|0.380	0.380	strong	.	.	.	.	NM_001199577	exon6	c.C1428T	p.L476L	GGCGCTCCTCAGA	.	PASS	Atlas-SNP
TJP2	9414	hgsc.bcm.edu	37	9	71862987	71862987	+	Silent	SNP	G	G	A	rs2095876	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57	57	42	0	1	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
ZNF665	79788	hgsc.bcm.edu	37	19	53668549	53668549	+	Silent	SNP	T	T	G	rs10409924	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	70	37	56	0	0.528571	0	T|0.774;G|0.226	0.226	strong	.	ZNF665	136	.	NM_024733	exon4	c.A1194C	p.G398G	CTTTTCTCCGGTA	.	PASS	Atlas-SNP
OR10W1	81341	hgsc.bcm.edu	37	11	58034543	58034543	+	Missense_Mutation	SNP	C	C	T	rs10792156	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	168	74	157	0	0.440476	0	C|0.523;T|0.477	0.477	strong	OR10W1,NS,malignant_melanoma,-1,1	OR10W1	58	1	NM_207374	exon1	c.G788A	p.R263Q	ATGAACCGATCTT	.	PASS	Atlas-SNP
PDILT	204474	hgsc.bcm.edu	37	16	20410488	20410488	+	Silent	SNP	G	G	A	rs7185940	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93	44	85	0	0.473118	0	G|0.676;A|0.324	0.324	strong	.	PDILT	120	.	NM_174924	exon2	c.C135T	p.L45L	CACTAGGAGACTG	.	PASS	Atlas-SNP
C5orf52	100190949	hgsc.bcm.edu	37	5	157102159	157102159	+	Missense_Mutation	SNP	G	G	A	rs10051838	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	90	44	114	0	0.488889	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
OTOP3	347741	hgsc.bcm.edu	37	17	72943126	72943126	+	Silent	SNP	G	G	A	rs8066909	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	56	56	87	0	1	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
MYO7B	4648	hgsc.bcm.edu	37	2	128367451	128367451	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	116	13	177	0	0.112069	0	.	.	none	.	MYO7B	359	.	NM_001080527	exon24	c.C3052T	p.L1018L	GTCATCCTGAGGT	.	PASS	Atlas-SNP
SGK1	6446	hgsc.bcm.edu	37	6	134495218	134495218	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	70	21	62	0	0.3	0	.	.	none	SGK1_ENST00000528577,NS,lymphoid_neoplasm,0,4	SGK1	387	4	NM_001143676	exon5	c.C438T	p.H146H	TTCAGGGCTGCAG	.	PASS	Atlas-SNP
MYO5B	4645	hgsc.bcm.edu	37	18	47398549	47398549	+	Silent	SNP	G	G	A	rs3826579	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	122	61	121	0	0.5	0	G|0.718;A|0.282	0.282	strong	.	MYO5B	178	.	NM_001080467	exon27	c.C3591T	p.Y1197Y	ACTATTGTAGGCC	.	PASS	Atlas-SNP
HEPACAM	220296	hgsc.bcm.edu	37	11	124793716	124793716	+	Silent	SNP	G	G	A	rs10790716	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	51	60	0	0.822581	0	G|0.814;A|0.186	0.186	strong	.	HEPACAM	64	.	NM_152722	exon3	c.C618T	p.R206R	GAGCACGCGGGTG	.	PASS	Atlas-SNP
TTC12	54970	hgsc.bcm.edu	37	11	113234603	113234603	+	Silent	SNP	G	G	A	rs34940277	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94	74	89	0	0.787234	0	G|0.999;A|0.001	0.001	strong	.	TTC12	66	.	NM_017868	exon20	c.G1770A	p.T590T	CTGCACGAATAGT	.	PASS	Atlas-SNP
ZNF91	7644	hgsc.bcm.edu	37	19	23545250	23545250	+	Silent	SNP	A	A	G	rs1044095	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	50	49	41	0	0.98	0	A|0.600;G|0.400	0.400	strong	ZNF91_ENST00000300619,caecum,carcinoma,0,2	ZNF91	349	2	NM_003430	exon4	c.T531C	p.T177T	CTTTCCAGTATGT	.	PASS	Atlas-SNP
MTUS1	57509	hgsc.bcm.edu	37	8	17532715	17532715	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	128	27	92	0	0.210938	0	.	.	none	.	MTUS1	144	.	NM_001001924	exon8	c.T2885G	p.V962G	AGGTTAACAAGTT	.	PASS	Atlas-SNP
ARHGAP15	55843	hgsc.bcm.edu	37	2	144194565	144194565	+	Silent	SNP	C	C	T	rs17230746	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	119	86	149	0	0.722689	0	C|0.853;T|0.147	0.147	strong	.	ARHGAP15	99	.	NM_018460	exon8	c.C657T	p.Y219Y	TCACTACGACAGT	.	PASS	Atlas-SNP
CCRL2	9034	hgsc.bcm.edu	37	3	46450297	46450297	+	Missense_Mutation	SNP	A	A	G	rs3204850	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	189	84	185	0	0.444444	0	A|0.948;G|0.052	0.052	strong	.	CCRL2	23	.	NM_001130910	exon2	c.A763G	p.I255V	TTTGCCATAATGG	.	PASS	Atlas-SNP
SP140L	93349	hgsc.bcm.edu	37	2	231258150	231258150	+	Missense_Mutation	SNP	C	C	T	rs7590429	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	36	10	41	0	0.277778	0	C|0.605;T|0.395	0.395	strong	.	SP140L	68	.	NM_138402	exon13	c.C1129T	p.P377S	AATCCTCCAAGAA	.	PASS	Atlas-SNP
SCN10A	6336	hgsc.bcm.edu	37	3	38748833	38748833	+	Silent	SNP	T	T	C	rs6790627	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	227	103	217	0	0.453745	0	T|0.796;C|0.204	0.204	strong	SCN10A,NS,carcinoma,0,1	SCN10A	359	1	NM_006514	exon25	c.A4323G	p.K1441K	GTAGTATTTCTTC	.	PASS	Atlas-SNP
EPPK1	83481	hgsc.bcm.edu	37	8	144947062	144947062	+	Silent	SNP	C	C	T	rs7819087	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	113	70	123	0	0.619469	0	C|0.955;T|0.045	0.045	strong	.	EPPK1	199	.	NM_031308	exon1	c.G360A	p.T120T	ATAGCCCGTAGTG	.	PASS	Atlas-SNP
KCNMB2	10242	hgsc.bcm.edu	37	3	178546026	178546026	+	Silent	SNP	T	T	C	rs9831934	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	107	52	116	0	0.485981	0	T|0.360;C|0.640	0.640	strong	.	KCNMB2	35	.	NM_005832	exon5	c.T288C	p.N96N	ATTTAATTGCTCC	.	PASS	Atlas-SNP
ITPKB	3707	hgsc.bcm.edu	37	1	226923938	226923938	+	Missense_Mutation	SNP	A	A	C	rs6667260	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	59	57	0	0.967213	0	A|0.444;C|0.556	0.556	strong	ITPKB_ENST00000429204,NS,carcinoma,0,1	ITPKB	158	1	NM_002221	exon2	c.T1222G	p.S408A	TCAGGGAATCAGA	.	PASS	Atlas-SNP
FHL2	2274	hgsc.bcm.edu	37	2	105977776	105977776	+	Silent	SNP	G	G	A	rs3087523	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	78	32	72	0	0.410256	0	G|0.921;A|0.079	0.079	strong	FHL2,colon,carcinoma,0,1	FHL2	18	1	NM_001039492	exon7	c.C804T	p.D268D	GATGTCGTCCCTC	.	PASS	Atlas-SNP
NLRP6	171389	hgsc.bcm.edu	37	11	284341	284341	+	Silent	SNP	G	G	A	rs7108246	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	78	42	57	0	0.538462	0	G|0.961;A|0.039	0.039	strong	NALP6,colon,carcinoma,+1,1	NLRP6	4	1	NM_138329	exon6	c.G2313A	p.A771A	TGAGGCGGGACTG	.	PASS	Atlas-SNP
C1orf127	148345	hgsc.bcm.edu	37	1	11024271	11024271	+	Silent	SNP	G	G	T	rs11121662	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79	47	58	0	0.594937	0	G|0.919;T|0.081	0.081	strong	.	C1orf127	134	.	NM_001170754	exon5	c.C430A	p.R144R	CACTCCGCTCCAA	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	27	13	30	0	0.481481	0	T|0.723;C|0.277	0.277	strong	KIAA0649,NS,carcinoma,0,1	.	.	1	NM_014811	exon4	c.T293C	p.V98A	TGGCTGTCTGTGG	.	scavenged	Atlas-SNP
CFHR1	3078	hgsc.bcm.edu	37	1	196801042	196801042	+	Silent	SNP	G	G	T	rs4230	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	537	237	284	0	0.441341	0	G|0.519;T|0.481	0.481	strong	CFHR1,right_upper_lobe,carcinoma,+1,2	CFHR1	47	2	NM_002113	exon6	c.G906T	p.R302R	TAAACGGGGATAT	.	PASS	Atlas-SNP
DHRS3	9249	hgsc.bcm.edu	37	1	12640650	12640650	+	Silent	SNP	C	C	T	rs11540058	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	121	62	121	0	0.512397	0	C|0.868;T|0.132	0.132	strong	.	DHRS3	18	.	NM_004753	exon2	c.G240A	p.T80T	CTCCTCCGTCGTC	.	PASS	Atlas-SNP
MORC1	27136	hgsc.bcm.edu	37	3	108719470	108719470	+	Silent	SNP	C	C	G	rs3762698	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	106	55	114	0	0.518868	0	C|0.734;G|0.266	0.266	strong	.	MORC1	211	.	NM_014429	exon21	c.G2121C	p.L707L	AAAGTTCAGACTC	.	PASS	Atlas-SNP
CDHR1	92211	hgsc.bcm.edu	37	10	85960395	85960395	+	Silent	SNP	A	A	G	rs4933975	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	165	80	184	0	0.484848	0	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	.	PASS	Atlas-SNP
CD276	80381	hgsc.bcm.edu	37	15	73994847	73994847	+	Missense_Mutation	SNP	C	C	A	rs7173476	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	115	59	129	0	0.513043	0	C|0.813;A|0.187	0.187	strong	.	CD276	29	.	NM_025240	exon3	c.C331A	p.R111S	CTGCAGCGCGTGC	.	PASS	Atlas-SNP
IFT140	9742	hgsc.bcm.edu	37	16	1608082	1608082	+	Silent	SNP	A	A	G	rs2076436	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	118	59	129	0	0.5	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
SPATA17	128153	hgsc.bcm.edu	37	1	217856626	217856626	+	Silent	SNP	G	G	A	rs12068167	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	133	67	146	0	0.503759	0	G|0.826;A|0.174	0.174	strong	.	SPATA17	59	.	NM_138796	exon5	c.G318A	p.R106R	CTATAGGGTTCGG	.	PASS	Atlas-SNP
PZP	5858	hgsc.bcm.edu	37	12	9317784	9317784	+	Missense_Mutation	SNP	A	A	G	rs2277413	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	139	72	128	0	0.517986	0	A|0.677;G|0.323	0.323	strong	.	PZP	422	.	NM_002864	exon19	c.T2438C	p.V813A	GTGAAGACCTCTC	.	PASS	Atlas-SNP
GPR123	84435	hgsc.bcm.edu	37	10	134942166	134942166	+	Silent	SNP	A	A	G	rs2806452	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	46	20	63	0	0.434783	0	A|0.559;G|0.441	0.441	strong	.	GPR123	118	.	NM_001083909	exon7	c.A834G	p.S278S	GGTGTCACAGGGC	.	PASS	Atlas-SNP
TRPV1	7442	hgsc.bcm.edu	37	17	3494361	3494361	+	Silent	SNP	G	G	A	rs222748	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	154	68	163	0	0.441558	0	G|0.863;A|0.137	0.137	strong	TRPV1_ENST00000399756,caecum,carcinoma,0,2	TRPV1	99	2	NM_018727	exon4	c.C501T	p.H167H	TCCGTCGTGCAGG	.	PASS	Atlas-SNP
OR5P2	120065	hgsc.bcm.edu	37	11	7818056	7818056	+	Missense_Mutation	SNP	T	T	C	rs73406604	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	38	38	55	0	1	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
USP42	84132	hgsc.bcm.edu	37	7	6193752	6193752	+	Missense_Mutation	SNP	G	G	A	rs61753119	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	9	4	26	0	0.444444	0	G|0.919;A|0.081	0.081	strong	USP42_ENST00000306177,NS,carcinoma,0,2	USP42	138	2	NM_032172	exon15	c.G2567A	p.S856N	GGTTGAGTCCGGC	.	scavenged	Atlas-SNP
PARP12	64761	hgsc.bcm.edu	37	7	139724555	139724555	+	Silent	SNP	C	C	T	rs3735352	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	35	114	0	0.432099	0	T|0.364;G|0.008;C|0.628	0.364	strong	.	PARP12	59	.	NM_022750	exon12	c.G1911A	p.P637P	GGCCGGCGGACGG	.	PASS	Atlas-SNP
PLEKHS1	79949	hgsc.bcm.edu	37	10	115529576	115529576	+	Missense_Mutation	SNP	T	T	A	rs41292632	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	46	29	47	0	0.630435	0	T|0.838;A|0.162	0.162	strong	.	PLEKHS1	19	.	NM_024889	exon7	c.T469A	p.F157I	ACCCTCTTCTACT	.	PASS	Atlas-SNP
ANKRD30A	91074	hgsc.bcm.edu	37	10	37421199	37421199	+	Missense_Mutation	SNP	C	C	T	rs34042320	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	214	99	204	1	0.462617	0.00490196	C|0.962;T|0.038	0.038	strong	ANKRD30A_ENST00000602533,NS,carcinoma,-1,3	ANKRD30A	448	3	NM_052997	exon4	c.C374T	p.T125M	CCATAACGAAAAG	.	scavenged	Atlas-SNP
HIST1H3J	8356	hgsc.bcm.edu	37	6	27858421	27858421	+	Silent	SNP	A	A	G	rs200973	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	55	83	0	0.820895	0	A|0.839;G|0.161	0.161	strong	.	HIST1H3J	16	.	NM_003535	exon1	c.T150C	p.R50R	GATCTCACGCAAG	.	PASS	Atlas-SNP
PYCRL	65263	hgsc.bcm.edu	37	8	144689289	144689289	+	Missense_Mutation	SNP	C	C	T	rs11549789	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	58	28	67	0	0.482759	0	C|0.935;T|0.065	0.065	strong	.	PYCRL	14	.	NM_023078	exon3	c.G206A	p.R69Q	GTGGTCCGGCAAC	.	PASS	Atlas-SNP
CETN1	1068	hgsc.bcm.edu	37	18	580623	580623	+	Missense_Mutation	SNP	T	T	C	rs61734344	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	40	17	51	0	0.425	0	T|0.833;C|0.167	0.167	strong	.	CETN1	48	.	NM_004066	exon1	c.T215C	p.M72T	AGAAAATGATCTC	.	PASS	Atlas-SNP
AOAH	313	hgsc.bcm.edu	37	7	36656035	36656035	+	Missense_Mutation	SNP	G	G	C	rs3735386	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	42	16	62	0	0.380952	0	G|0.910;C|0.090	0.090	strong	.	AOAH	79	.	NM_001637	exon11	c.C797G	p.A266G	AAATGAGCCCCAG	.	PASS	Atlas-SNP
DNMBP	23268	hgsc.bcm.edu	37	10	101715899	101715899	+	Silent	SNP	G	G	A	rs2862923	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	118	115	132	0	0.974576	0	G|0.534;A|0.466	0.466	strong	.	DNMBP	173	.	NM_015221	exon4	c.C1332T	p.P444P	AAGGTCGGGGTAC	.	PASS	Atlas-SNP
ZNF407	55628	hgsc.bcm.edu	37	18	72347482	72347482	+	Silent	SNP	T	T	C	rs12327359	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	90	40	90	0	0.444444	0	T|0.567;C|0.433	0.433	strong	ZNF407,NS,carcinoma,0,1	ZNF407	231	1	NM_001146190	exon1	c.T4507C	p.L1503L	TTATTTTTACATA	.	PASS	Atlas-SNP
PIGB	9488	hgsc.bcm.edu	37	15	55632859	55632859	+	Missense_Mutation	SNP	G	G	T	rs678892	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	130	130	172	1	1	0.00581395	G|0.418;T|0.582	0.582	strong	.	PIGB	36	.	NM_004855	exon8	c.G896T	p.W299L	AGAACTGGGGAAC	.	PASS	Atlas-SNP
ZFP2	80108	hgsc.bcm.edu	37	5	178359075	178359075	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44	17	27	0	0.386364	0	.	.	none	.	ZFP2	70	.	NM_030613	exon5	c.G761C	p.S254T	GTCAAAGCATGCA	.	PASS	Atlas-SNP
TRIM3	10612	hgsc.bcm.edu	37	11	6477831	6477831	+	Silent	SNP	C	C	T	rs10606	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	26	69	0	0.553191	0	C|0.791;T|0.209	0.209	strong	TRIM3,NS,lymphoid_neoplasm,0,1	TRIM3	67	1	NM_001248006	exon6	c.G1125A	p.P375P	TGGCACCGGAAGG	.	PASS	Atlas-SNP
B4GALNT2	124872	hgsc.bcm.edu	37	17	47210469	47210469	+	Missense_Mutation	SNP	G	G	A	rs117575112	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	42	23	27	0	0.547619	0	G|0.954;A|0.046	0.046	strong	.	B4GALNT2	67	.	NM_153446	exon1	c.G82A	p.E28K	ACGCCCGAGTGTG	.	PASS	Atlas-SNP
TLR10	81793	hgsc.bcm.edu	37	4	38776180	38776180	+	Silent	SNP	C	C	A	rs11096956	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	106	56	110	0	0.528302	0	C|0.732;A|0.268	0.268	strong	TLR10,NS,malignant_melanoma,-2,2	TLR10	87	2	NM_001017388	exon2	c.G1032T	p.P344P	ATAATTCGGGAAA	.	PASS	Atlas-SNP
LPA	4018	hgsc.bcm.edu	37	6	161007538	161007538	+	Missense_Mutation	SNP	G	G	C	rs7765803	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	28	85	0	0.378378	0	G|0.569;C|0.431	0.431	strong	.	LPA	237	.	NM_005577	exon26	c.C4072G	p.L1358V	TGAGGAGAGTTGA	.	PASS	Atlas-SNP
EPPK1	83481	hgsc.bcm.edu	37	8	144941940	144941940	+	Silent	SNP	G	G	A	rs73715514	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	117	58	112	0	0.495726	0	G|0.951;A|0.049	0.049	strong	.	EPPK1	199	.	NM_031308	exon1	c.C5482T	p.L1828L	TTTCCAGCAATTT	.	PASS	Atlas-SNP
GCNT4	51301	hgsc.bcm.edu	37	5	74324548	74324548	+	Missense_Mutation	SNP	G	G	A	rs3811987	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	108	43	102	0	0.398148	0	G|0.584;A|0.416	0.416	strong	GCNT4,NS,carcinoma,0,1	GCNT4	46	1	NM_016591	exon1	c.C1315T	p.P439S	CTGAGGGCAAAGT	.	PASS	Atlas-SNP
FAM5C	339479	hgsc.bcm.edu	37	1	190067970	190067970	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	135	35	96	0	0.259259	0	.	.	none	FAM5C,colon,carcinoma,-2,1	FAM5C	343	1	NM_199051	exon8	c.A1479C	p.Q493H	GAGATCTTGCAGG	.	PASS	Atlas-SNP
NPW	283869	hgsc.bcm.edu	37	16	2070568	2070568	+	Missense_Mutation	SNP	A	A	C	rs2286472	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	36	15	45	1	0.416667	0.0222222	A|0.624;C|0.376	0.376	strong	NPW,NS,carcinoma,0,2	NPW	4	2	NM_001099456	exon2	c.A446C	p.D149A	CGGTGGACCCCGC	.	scavenged	Atlas-SNP
ZNF860	344787	hgsc.bcm.edu	37	3	32031135	32031135	+	Silent	SNP	A	A	G	rs6419811	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	102	100	134	0	0.980392	0	A|0.567;G|0.433	0.433	strong	ZNF860_ENST00000360311,NS,carcinoma,0,6	ZNF860	96	6	NM_001137674	exon2	c.A564G	p.S188S	TTCCTCAGTTCTA	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1101078	1101078	+	Missense_Mutation	SNP	A	A	G	rs11245954	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93	60	109	0	0.645161	0	A|0.924;G|0.076	0.076	strong	.	MUC2	614	.	NM_002457	exon42	c.A7465G	p.S2489G	AGGTGCAGCCAGA	.	PASS	Atlas-SNP
ABCA13	154664	hgsc.bcm.edu	37	7	48315796	48315796	+	Missense_Mutation	SNP	C	C	A	rs1880736	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	35	35	58	0	1	0	C|0.216;A|0.784	0.784	strong	.	ABCA13	1192	.	NM_152701	exon17	c.C6533A	p.A2178E	CTAGAGCAGGCAA	.	PASS	Atlas-SNP
FRAS1	80144	hgsc.bcm.edu	37	4	78987157	78987157	+	Missense_Mutation	SNP	A	A	G	rs4859905	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	307	148	326	1	0.482085	0.00306748	A|0.473;G|0.527	0.527	strong	.	FRAS1	779	.	NM_001166133	exon2	c.A95G	p.D32G	ATCAGGATTCCTT	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	50	50	39	0	1	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
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057393	46057393	+	Missense_Mutation	SNP	T	T	A	rs2838602	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	114	46	90	0	0.403509	0	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
CCDC22	28952	hgsc.bcm.edu	37	X	49103224	49103224	+	Silent	SNP	G	G	A	rs2294020	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	35	8	34	0	0.228571	0	0|0.005;A|0.488	0.488	strong	.	CCDC22	69	.	NM_014008	exon7	c.G747A	p.Q249Q	GCTGCAGAAGCAA	.	PASS	Atlas-SNP
RNFT1	51136	hgsc.bcm.edu	37	17	58031412	58031412	+	Silent	SNP	A	A	G	rs11368	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	187	186	172	0	0.994652	0	A|0.499;G|0.501	0.501	strong	.	RNFT1	30	.	NM_016125	exon8	c.T1167C	p.I389I	CTGACAAATGAGA	.	PASS	Atlas-SNP
KIF16B	55614	hgsc.bcm.edu	37	20	16410559	16410559	+	Silent	SNP	A	A	T	rs34550969	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	32	21	59	0	0.65625	0	A|0.898;T|0.102	0.102	strong	.	KIF16B	305	.	NM_001199865	exon13	c.T1371A	p.I457I	GATGCCAATCAAA	.	PASS	Atlas-SNP
WDR81	124997	hgsc.bcm.edu	37	17	1630992	1630992	+	Silent	SNP	G	G	A	rs9912287	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	90	48	89	0	0.533333	0	G|0.790;A|0.208	0.208	strong	.	WDR81	180	.	NM_001163809	exon1	c.G2739A	p.L913L	GGTGCTGAAGGAC	.	PASS	Atlas-SNP
SLC39A14	23516	hgsc.bcm.edu	37	8	22262418	22262418	+	Silent	SNP	A	A	G	rs2293144	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93	92	69	0	0.989247	0	A|0.386;G|0.614	0.614	strong	.	SLC39A14	59	.	NM_001135153	exon2	c.A195G	p.L65L	GGCCCTACTCAAC	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44	34	43	0	0.772727	0	C|0.820;T|0.180	0.180	strong	.	DDR1	213	.	NM_001202522	exon10	c.C1406T	p.P469L	CCACTCCGCTCCC	.	PASS	Atlas-SNP
KIR3DL1	3811	hgsc.bcm.edu	37	19	55340841	55340841	+	Silent	SNP	G	G	C	rs150471749	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	9	9	36	0	1	0	G|0.905;C|0.096	0.096	strong	.	KIR3DL1	174	.	NM_013289	exon7	c.G1026C	p.L342L	CATTCTGATTGGG	.	PASS	Atlas-SNP
ASIP	434	hgsc.bcm.edu	37	20	32856838	32856838	+	Silent	SNP	C	C	A	rs36093428	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	35	62	0	0.660377	0	C|0.994;A|0.006	0.006	strong	.	ASIP	6	.	NM_001672	exon3	c.C264A	p.P88P	GACCCCCCTATCT	.	PASS	Atlas-SNP
TMC4	147798	hgsc.bcm.edu	37	19	54664209	54664209	+	Missense_Mutation	SNP	G	G	C	rs36657	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	35	70	1	0.432099	0.0142857	G|0.492;C|0.508	0.508	strong	TMC4_ENST00000416963,NS,carcinoma,0,2	TMC4	89	2	NM_001145303	exon14	c.C2065G	p.Q689E	CCGTCTGTCTCTG	.	scavenged	Atlas-SNP
PNPLA3	80339	hgsc.bcm.edu	37	22	44342116	44342116	+	Missense_Mutation	SNP	A	A	G	rs2294918	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	41	87	0	0.471264	0	A|0.280;G|0.720	0.720	strong	.	PNPLA3	53	.	NM_025225	exon9	c.A1300G	p.K434E	TCCCCCAAGGGCT	.	PASS	Atlas-SNP
SYNJ2	8871	hgsc.bcm.edu	37	6	158507981	158507981	+	Silent	SNP	G	G	A	rs2296506	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	18	15	14	0	0.833333	0	G|0.477;A|0.523	0.523	strong	SYNJ2,NS,carcinoma,0,1	SYNJ2	111	1	NM_003898	exon23	c.G3303A	p.R1101R	CAACCGGCCTCGG	.	PASS	Atlas-SNP
EIF2AK1	27102	hgsc.bcm.edu	37	7	6066461	6066461	+	Silent	SNP	T	T	C	rs2639	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	191	70	101	1	0.366492	0.00990099	T|0.699;C|0.301	0.301	strong	EIF2AK1,NS,carcinoma,0,1	EIF2AK1	76	1	NM_014413	exon14	c.A1662G	p.P554P	TTGCACTGGACAC	.	scavenged	Atlas-SNP
LPO	4025	hgsc.bcm.edu	37	17	56344867	56344867	+	Silent	SNP	G	G	A	rs8178409	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	48	100	0	0.551724	0	G|0.824;A|0.176	0.176	strong	.	LPO	73	.	NM_006151	exon12	c.G1851A	p.P617P	TGAGCCGCTGGTG	.	PASS	Atlas-SNP
UCHL1	7345	hgsc.bcm.edu	37	4	41259633	41259633	+	Missense_Mutation	SNP	C	C	A	rs5030732	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	21	9	43	0	0.428571	0	C|0.758;A|0.242	0.242	strong	.	UCHL1	19	.	NM_004181	exon3	c.C53A	p.S18Y	TGCTGTCCCGGCT	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228496014	228496014	+	Silent	SNP	G	G	A	rs876180	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94	39	98	0	0.414894	0	G|0.776;A|0.224	0.224	strong	OBSCN_ENST00000570156,NS,carcinoma,0,3	OBSCN	2142	3	NM_001271223	exon58	c.G15540A	p.T5180T	CGTGACGCCCGAG	.	PASS	Atlas-SNP
CCR2	729230	hgsc.bcm.edu	37	3	46399581	46399581	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	143	51	168	0	0.356643	0	.	.	none	.	CCR2	103	.	NM_001123041	exon2	c.A563C	p.Y188S	CTGTTTATGTCTG	.	PASS	Atlas-SNP
SOX5	6660	hgsc.bcm.edu	37	12	23757393	23757393	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	124	9	137	0	0.0725806	0	.	.	none	.	SOX5	134	.	NM_006940	exon9	c.C1092A	p.N364K	ACCAAGGTTGCCT	.	PASS	Atlas-SNP
GCH1	2643	hgsc.bcm.edu	37	14	55369053	55369053	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	41	15	40	0	0.365854	0	.	.	none	.	GCH1	16	.	NM_000161	exon1	c.A329G	p.Q110R	GTCTCCTGGTAGC	.	PASS	Atlas-SNP
SAMD9	54809	hgsc.bcm.edu	37	7	92734983	92734983	+	Missense_Mutation	SNP	A	A	G	rs6969691	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	151	78	165	0	0.516556	0	A|0.818;G|0.182	0.182	strong	.	SAMD9	239	.	NM_001193307	exon2	c.T428C	p.I143T	TCTTCTATGAGCT	.	PASS	Atlas-SNP
PLEKHA4	57664	hgsc.bcm.edu	37	19	49368843	49368843	+	Missense_Mutation	SNP	T	T	C	rs506425	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	117	52	102	0	0.444444	0	T|0.549;G|0.003	.	strong	.	PLEKHA4	70	.	NM_001161354	exon3	c.A109G	p.I37V	CGTGGATCTTGTT	.	PASS	Atlas-SNP
TNRC18	84629	hgsc.bcm.edu	37	7	5352949	5352949	+	Missense_Mutation	SNP	G	G	C	rs76882791	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44	29	21	0	0.659091	0	G|0.869;C|0.131	0.131	strong	.	TNRC18	311	.	NM_001080495	exon27	c.C7573G	p.L2525V	GGGCGAGGTCCCC	.	PASS	Atlas-SNP
FOXS1	2307	hgsc.bcm.edu	37	20	30433139	30433139	+	Silent	SNP	G	G	A	rs6089096	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	41	77	0	0.577465	0	G|0.929;A|0.071	0.071	strong	.	FOXS1	29	.	NM_004118	exon1	c.C207T	p.N69N	TGACAGGTTGTGG	.	PASS	Atlas-SNP
SEC16A	9919	hgsc.bcm.edu	37	9	139371786	139371786	+	Silent	SNP	A	A	C	rs6560632	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	122	63	117	0	0.516393	0	A|0.601;C|0.399	0.399	strong	.	SEC16A	249	.	NM_014866	exon3	c.T282G	p.V94V	GTGAGGAACAAGC	.	PASS	Atlas-SNP
GNAQ	2776	hgsc.bcm.edu	37	9	80537112	80537112	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	135	3	114	0	0.0222222	0	.	.	none	GNAQ,NS,carcinoma,0,2	GNAQ	384	2	NM_002072	exon2	c.A286T	p.T96S	TGAGTGTGTCCAT	.	scavenged	Atlas-SNP
DNAJA2	10294	hgsc.bcm.edu	37	16	47007480	47007480	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	40	11	39	0	0.275	0	.	.	none	.	DNAJA2	28	.	NM_005880	exon1	c.G4A	p.A2T	CGTTAGCCATGGC	.	PASS	Atlas-SNP
KLK3	354	hgsc.bcm.edu	37	19	51359497	51359497	+	Silent	SNP	T	T	C	rs11573	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	76	84	0	1	0	T|0.629;C|0.371	0.371	strong	.	KLK3	76	.	NM_001030050	exon2	c.T48C	p.G16G	TGCAGGTGCTGCA	.	PASS	Atlas-SNP
PABPC4	8761	hgsc.bcm.edu	37	1	40036944	40036944	+	Silent	SNP	G	G	A	rs61743745	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	154	80	135	0	0.519481	0	G|0.982;A|0.018	0.018	strong	.	PABPC4	56	.	NM_001135653	exon3	c.C465T	p.I155I	CTTCTCGATGGCC	.	PASS	Atlas-SNP
TAS2R43	259289	hgsc.bcm.edu	37	12	11244166	11244166	+	Silent	SNP	G	G	C	rs35720106	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	97	83	27	0	0.85567	0	G|0.614;C|0.386	0.386	strong	TAS2R43,NS,carcinoma,0,2	TAS2R43	19	2	NM_176884	exon1	c.C663G	p.T221T	GACCTTGGTGCTG	.	PASS	Atlas-SNP
OR1L3	26735	hgsc.bcm.edu	37	9	125437664	125437664	+	Missense_Mutation	SNP	T	T	G	rs56304399	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	132	72	124	0	0.545455	0	T|0.993;G|0.007	0.007	strong	.	OR1L3	51	.	NM_001005234	exon1	c.T256G	p.L86V	AACTTCTTATCAG	.	PASS	Atlas-SNP
ZFP90	146198	hgsc.bcm.edu	37	16	68598007	68598007	+	Silent	SNP	A	A	G	rs1177648	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68	68	77	0	1	0	A|0.462;G|0.538	0.538	strong	ZFP90,NS,carcinoma,+1,1	ZFP90	67	1	NM_133458	exon4	c.A1317G	p.Q439Q	CACTCAAGATGAA	.	PASS	Atlas-SNP
FAM114A1	92689	hgsc.bcm.edu	37	4	38933859	38933859	+	Missense_Mutation	SNP	G	G	A	rs17429619	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	244	86	218	0	0.352459	0	G|0.869;A|0.131	0.131	strong	.	FAM114A1	42	.	NM_138389	exon12	c.G1327A	p.V443I	CAGGAAGTATACA	.	PASS	Atlas-SNP
PRKACG	5568	hgsc.bcm.edu	37	9	71628207	71628207	+	Missense_Mutation	SNP	G	G	C	rs3730386	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	113	54	81	0	0.477876	0	G|0.707;C|0.293	0.293	strong	.	PRKACG	65	.	NM_002732	exon1	c.C802G	p.H268D	GCAGATGCTTGAG	.	PASS	Atlas-SNP
DEPTOR	64798	hgsc.bcm.edu	37	8	120940652	120940652	+	Silent	SNP	C	C	T	rs16893299	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	46	25	48	0	0.543478	0	C|0.743;T|0.257	0.257	strong	.	DEPTOR	41	.	NM_022783	exon2	c.C135T	p.H45H	GCTGCACGAAGAA	.	PASS	Atlas-SNP
HRC	3270	hgsc.bcm.edu	37	19	49658345	49658345	+	Silent	SNP	G	G	A	rs117942355	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	27	67	0	0.442623	0	G|1.000;A|0.000	0.000	strong	.	HRC	85	.	NM_002152	exon1	c.C150T	p.S50S	CTCCTCGGAGAGC	.	PASS	Atlas-SNP
TMEM61	199964	hgsc.bcm.edu	37	1	55457710	55457710	+	Silent	SNP	G	G	A	rs2500326	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	65	65	52	0	1	0	G|0.200;A|0.800	0.800	strong	.	TMEM61	22	.	NM_182532	exon3	c.G567A	p.A189A	TTCTGCGGAGACG	.	PASS	Atlas-SNP
NDRG4	65009	hgsc.bcm.edu	37	16	58545426	58545426	+	Silent	SNP	A	A	G	rs42945	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	121	120	153	1	0.991736	0.00653595	A|0.274;G|0.726	0.726	strong	.	NDRG4	29	.	NM_001130487	exon16	c.A1122G	p.S374S	CCACTCAGAGAGC	.	PASS	Atlas-SNP
KIF5B	3799	hgsc.bcm.edu	37	10	32320002	32320002	+	Missense_Mutation	SNP	G	G	A	rs35441986	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79	44	83	0	0.556962	0	G|0.998;A|0.002	0.002	strong	.	KIF5B	81	.	NM_004521	exon14	c.C1580T	p.S527L	CCTACCGATTTCT	.	PASS	Atlas-SNP
C1orf94	84970	hgsc.bcm.edu	37	1	34663180	34663180	+	Silent	SNP	G	G	A	rs3795412	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79	44	72	0	0.556962	0	G|0.833;A|0.167	0.167	strong	.	C1orf94	156	.	NM_001134734	exon2	c.G675A	p.R225R	GGACAGGGGCCGC	.	PASS	Atlas-SNP
LCE1E	353135	hgsc.bcm.edu	37	1	152760106	152760106	+	Missense_Mutation	SNP	G	G	A	rs56313719	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	490	204	497	0	0.416327	0	G|0.913;A|0.087	0.087	strong	LCE1E,neck,malignant_melanoma,-1,1	LCE1E	26	1	NM_178353	exon2	c.G331A	p.G111S	GGCAGCGGCCAGC	.	PASS	Atlas-SNP
TRIM16	10626	hgsc.bcm.edu	37	17	15531942	15531942	+	Missense_Mutation	SNP	C	C	A	rs62070417	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57	23	58	0	0.403509	0	C|0.785;A|0.215	0.215	strong	.	TRIM16	45	.	NM_006470	exon9	c.G1682T	p.G561V	GCAGTCCCCACCA	.	PASS	Atlas-SNP
VPS35	55737	hgsc.bcm.edu	37	16	46705710	46705710	+	Silent	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	202	4	185	0	0.019802	0	.	.	none	VPS35,NS,carcinoma,0,1	VPS35	49	1	NM_018206	exon12	c.A1431G	p.E477E	AGGGTCTTCTACA	.	scavenged	Atlas-SNP
PRSS3	5646	hgsc.bcm.edu	37	9	33798052	33798052	+	Silent	SNP	C	C	T	rs377380263		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	6	84	0	0.0810811	0	.	.	weak	PRSS3_ENST00000361005,NS,carcinoma,0,3	PRSS3	79	3	NM_007343	exon3	c.C597T	p.S199S	CATCTCCGGCTGG	.	scavenged	Atlas-SNP
EPS8L2	64787	hgsc.bcm.edu	37	11	720197	720197	+	Silent	SNP	C	C	T	rs3087546	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	138	60	149	1	0.434783	0.00671141	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	.	scavenged	Atlas-SNP
OR13C2	392376	hgsc.bcm.edu	37	9	107367008	107367008	+	Missense_Mutation	SNP	T	T	C	rs10156474	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	195	91	162	0	0.466667	0	T|0.639;C|0.361	0.361	strong	.	OR13C2	46	.	NM_001004481	exon1	c.A901G	p.K301E	CATCCTTGTTTCT	.	PASS	Atlas-SNP
KLHL4	56062	hgsc.bcm.edu	37	X	86887244	86887244	+	Silent	SNP	C	C	T	rs222084	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	118	116	103	0	0.983051	0	0|0.003;T|0.605	0.605	strong	.	KLHL4	263	.	NM_019117	exon7	c.C1359T	p.T453T	CAGGACCAACAGT	.	PASS	Atlas-SNP
FGFR4	2264	hgsc.bcm.edu	37	5	176516631	176516631	+	Missense_Mutation	SNP	G	G	A	rs1966265	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	148	73	164	0	0.493243	0	G|0.804;A|0.196	0.196	strong	.	FGFR4	174	.	NM_022963	exon1	c.G28A	p.V10I	TTGGGGGTCCTGC	.	PASS	Atlas-SNP
ZNF469	84627	hgsc.bcm.edu	37	16	88501034	88501034	+	Missense_Mutation	SNP	G	G	C	rs12598474	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	22	52	0	0.407407	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
BBS12	166379	hgsc.bcm.edu	37	4	123664457	123664457	+	Silent	SNP	C	C	T	rs13135445	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83	83	127	0	1	0	C|0.818;T|0.182	0.182	strong	.	BBS12	63	.	NM_001178007	exon3	c.C1410T	p.C470C	GGTCTGCGTGACC	.	PASS	Atlas-SNP
COL12A1	1303	hgsc.bcm.edu	37	6	75827165	75827165	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	22	98	0	0.328358	0	.	.	none	COL12A1,NS,carcinoma,0,1	COL12A1	385	1	NM_004370	exon47	c.C7452T	p.D2484D	AAAGTCGTCCACA	.	PASS	Atlas-SNP
GRIK4	2900	hgsc.bcm.edu	37	11	120823608	120823608	+	Silent	SNP	G	G	A	rs2298725	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	115	19	120	0	0.165217	0	G|0.752;A|0.248	0.248	strong	.	GRIK4	149	.	NM_014619	exon13	c.G1635A	p.P545P	TTCTCCGGGCGTC	.	PASS	Atlas-SNP
ALDH9A1	223	hgsc.bcm.edu	37	1	165638577	165638577	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	201	69	200	0	0.343284	0	.	.	none	.	ALDH9A1	75	.	NM_000696	exon7	c.A1041C	p.E347D	TGTATCTTCCAGA	.	PASS	Atlas-SNP
MYO6	4646	hgsc.bcm.edu	37	6	76572352	76572352	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	124	6	133	0	0.0483871	0	.	.	none	.	MYO6	124	.	NM_004999	exon16	c.T1586G	p.L529W	ATATTTTGGATGA	.	PASS	Atlas-SNP
SGK223	0	hgsc.bcm.edu	37	8	8234218	8234218	+	Silent	SNP	C	C	T	rs4840954	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	31	13	25	0	0.419355	0	C|0.631;T|0.369	0.369	strong	.	.	.	.	NM_001080826	exon2	c.G1701A	p.P567P	AGCCAGCGGTGAC	.	PASS	Atlas-SNP
MAGEB18	286514	hgsc.bcm.edu	37	X	26157220	26157220	+	Missense_Mutation	SNP	C	C	T	rs5944317	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	131	32	98	0	0.244275	0	C|0.372;T|0.628	0.628	strong	.	MAGEB18	67	.	NM_173699	exon2	c.C118T	p.P40S	CCCTCCCCTGCCT	.	PASS	Atlas-SNP
CST2	1470	hgsc.bcm.edu	37	20	23805955	23805955	+	Silent	SNP	C	C	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	95	3	121	1	0.0315789	0.00826446	.	.	none	CST2,colon,carcinoma,-2,1	CST2	39	1	NM_001322	exon2	c.G234T	p.V78V	CCCGCCCACGATC	.	scavenged	Atlas-SNP
MATN3	4148	hgsc.bcm.edu	37	2	20202929	20202929	+	Silent	SNP	C	C	T	rs28452699	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110	48	104	0	0.436364	0	C|0.827;T|0.173	0.173	strong	.	MATN3	28	.	NM_002381	exon3	c.G909A	p.T303T	TGAACACGTTTTC	.	PASS	Atlas-SNP
PCDHB10	56126	hgsc.bcm.edu	37	5	140573442	140573442	+	Silent	SNP	C	C	G	rs622424	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	102	47	85	0	0.460784	0	C|0.549;G|0.451	0.451	strong	.	PCDHB10	177	.	NM_018930	exon1	c.C1317G	p.V439V	AACGGTCCTGGTC	.	PASS	Atlas-SNP
ACSL3	2181	hgsc.bcm.edu	37	2	223783841	223783841	+	Silent	SNP	G	G	A	rs13000358	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	158	88	176	0	0.556962	0	G|0.963;A|0.037	0.037	strong	.	ACSL3	107	.	NM_203372	exon6	c.G726A	p.P242P	GCCACCGACCTGG	.	PASS	Atlas-SNP
B4GALNT3	283358	hgsc.bcm.edu	37	12	661656	661656	+	Missense_Mutation	SNP	A	A	G	rs7298766	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	242	113	259	0	0.466942	0	A|0.704;G|0.296	0.296	strong	.	B4GALNT3	64	.	NM_173593	exon13	c.A1232G	p.K411R	ACATCAAGATTGA	.	PASS	Atlas-SNP
SYNPO2	171024	hgsc.bcm.edu	37	4	119948046	119948046	+	Missense_Mutation	SNP	A	A	C	rs17263971	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	109	45	87	0	0.412844	0	A|0.774;C|0.226	0.226	strong	.	SYNPO2	353	.	NM_001128934	exon3	c.A522C	p.Q174H	CTCCCAAAGAGGA	.	PASS	Atlas-SNP
FBN3	84467	hgsc.bcm.edu	37	19	8176640	8176640	+	Missense_Mutation	SNP	C	C	T	rs12975322	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	107	47	109	0	0.439252	0	C|0.722;T|0.278	0.278	strong	FBN3,colon,carcinoma,0,1	FBN3	300	1	NM_032447	exon31	c.G3976A	p.V1326I	GGGAGACGCATTC	.	PASS	Atlas-SNP
GRID1	2894	hgsc.bcm.edu	37	10	87898729	87898729	+	Silent	SNP	G	G	A	rs17106320	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	30	89	0	0.46875	0	G|0.823;A|0.177	0.177	strong	.	GRID1	204	.	NM_017551	exon4	c.C573T	p.D191D	AGAGACGTCAAGG	.	PASS	Atlas-SNP
PIK3C2G	5288	hgsc.bcm.edu	37	12	18473928	18473928	+	Silent	SNP	T	T	C	rs12309666	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	197	102	230	0	0.517766	0	T|0.786;C|0.214	0.214	strong	PIK3C2G,NS,carcinoma,0,1	PIK3C2G	315	1	NM_004570	exon7	c.T1170C	p.N390N	TCTGAATCAACTT	.	PASS	Atlas-SNP
KRT72	140807	hgsc.bcm.edu	37	12	52994955	52994955	+	Silent	SNP	G	G	A	rs61747192	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44	23	57	0	0.522727	0	G|0.856;A|0.144	0.144	strong	.	KRT72	70	.	NM_001146225	exon1	c.C282T	p.P94P	GCCCCCGGGTGGG	.	PASS	Atlas-SNP
MYBPC2	4606	hgsc.bcm.edu	37	19	50957397	50957397	+	Missense_Mutation	SNP	G	G	A	rs25665	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	127	127	132	0	1	0	G|0.772;A|0.227	0.227	strong	.	MYBPC2	103	.	NM_004533	exon17	c.G1870A	p.V624I	AACCCCGTCGGCG	.	PASS	Atlas-SNP
NPHP4	261734	hgsc.bcm.edu	37	1	5937327	5937327	+	Silent	SNP	C	C	T	rs3747990	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	160	159	196	0	0.99375	0	C|0.906;T|0.094	0.094	strong	.	NPHP4	119	.	NM_015102	exon20	c.G2643A	p.A881A	CACGTCCGCCAGC	.	PASS	Atlas-SNP
PPP1R17	10842	hgsc.bcm.edu	37	7	31732089	31732089	+	Missense_Mutation	SNP	C	C	G	rs3735422	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	65	19	92	0	0.292308	0	C|0.856;G|0.144	0.144	strong	C7orf16,NS,carcinoma,0,1	.	.	1	NM_006658	exon2	c.C34G	p.L12V	CTGGAACTCTCAG	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9072975	9072975	+	Missense_Mutation	SNP	G	G	A	rs17000816	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	332	135	326	0	0.406626	0	G|0.810;A|0.190	0.190	strong	MUC16_ENST00000397910,rectum,carcinoma,0,3	MUC16	4315	3	NM_024690	exon3	c.C14471T	p.T4824M	GGATGCGTTGTCT	.	PASS	Atlas-SNP
BTNL8	79908	hgsc.bcm.edu	37	5	180374534	180374534	+	Silent	SNP	G	G	A	rs3733756	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	197	197	264	1	1	0.00378788	G|0.508;A|0.492	0.492	strong	BTNL8_ENST00000340184,NS,carcinoma,0,2	BTNL8	114	2	NM_001159708	exon4	c.G696A	p.S232S	TATATCGTGGCAC	.	PASS	Atlas-SNP
RGPD4	285190	hgsc.bcm.edu	37	2	108475928	108475928	+	Missense_Mutation	SNP	C	C	T	rs2912841		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	211	15	172	0	0.0710901	0	.	.	weak	RGPD4,extremity,malignant_melanoma,0,1	RGPD4	112	1	NM_182588	exon11	c.C1552T	p.L518F	CTGCCCCTTCCTG	.	scavenged	Atlas-SNP
P2RY8	286530	hgsc.bcm.edu	37	X	1585084	1585084	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	15	120	0	0.172414	0	.	.	none	.	P2RY8	53	.	NM_178129	exon2	c.T368G	p.L123R	ACCCCCAGGAAGC	.	PASS	Atlas-SNP
ANKRD18B	441459	hgsc.bcm.edu	37	9	33566234	33566234	+	Silent	SNP	C	C	T	rs79153255		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	39	88	0	0.448276	0	T|1.000;|0.000	1.000	weak	.	ANKRD18B	46	.	NM_001244752	exon13	c.C2289T	p.A763A	TATGGCCGAGAAG	.	PASS	Atlas-SNP
PARP12	64761	hgsc.bcm.edu	37	7	139727135	139727135	+	Silent	SNP	G	G	A	rs2286196	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	135	75	120	0	0.555556	0	G|0.728;T|0.002	.	strong	.	PARP12	59	.	NM_022750	exon10	c.C1569T	p.F523F	AAAGTAGAAAGGC	.	PASS	Atlas-SNP
EXPH5	23086	hgsc.bcm.edu	37	11	108409784	108409784	+	Missense_Mutation	SNP	T	T	A	rs2640785	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	117	19	89	0	0.162393	0	T|0.797;A|0.203	0.203	strong	.	EXPH5	193	.	NM_015065	exon3	c.A410T	p.E137V	GAAGTCTCCTTTC	.	PASS	Atlas-SNP
FAM135B	51059	hgsc.bcm.edu	37	8	139160926	139160926	+	Silent	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49	13	41	0	0.265306	0	.	.	none	.	FAM135B	423	.	NM_015912	exon14	c.T3285C	p.F1095F	CTGATAAAAACTG	.	PASS	Atlas-SNP
HDC	3067	hgsc.bcm.edu	37	15	50534514	50534514	+	Missense_Mutation	SNP	T	T	G	rs2073440	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	117	53	132	0	0.452991	0	T|0.929;G|0.071	0.071	strong	.	HDC	86	.	NM_002112	exon12	c.A1932C	p.E644D	GCTGCATTCAGGA	.	PASS	Atlas-SNP
ADH4	127	hgsc.bcm.edu	37	4	100045616	100045616	+	Missense_Mutation	SNP	C	C	T	rs1126673	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	145	142	151	0	0.97931	0	C|0.225;T|0.775	0.775	strong	.	ADH4	35	.	NM_000670	exon9	c.G1120A	p.V374I	TTCGGACGCTGTT	.	PASS	Atlas-SNP
KIR3DL1	3811	hgsc.bcm.edu	37	19	55330019	55330019	+	Missense_Mutation	SNP	C	C	T	rs143159382	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	8	8	33	0	1	0	C|0.884;T|0.116	0.116	strong	.	KIR3DL1	174	.	NM_013289	exon3	c.C320T	p.S107L	GGTGGTCGGCACC	.	PASS	Atlas-SNP
GALNT10	55568	hgsc.bcm.edu	37	5	153783753	153783753	+	Silent	SNP	C	C	T	rs6580076	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	116	52	124	1	0.448276	0.00806452	C|0.733;T|0.267	0.267	strong	GALNT10,NS,carcinoma,0,1	GALNT10	70	1	NM_198321	exon8	c.C1146T	p.A382A	CCCGGCCGGAGTC	.	scavenged	Atlas-SNP
RTN4RL1	146760	hgsc.bcm.edu	37	17	1840732	1840732	+	Silent	SNP	G	G	A	rs372962204		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	38	66	0	0.5	0	.	.	weak	.	RTN4RL1	21	.	NM_178568	exon2	c.C384T	p.H128H	GAGGGCGTGAAGC	.	PASS	Atlas-SNP
SEC24D	9871	hgsc.bcm.edu	37	4	119736613	119736613	+	Silent	SNP	C	C	T	rs115118317	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	29	67	0	0.386667	0	C|0.960;T|0.040	0.040	strong	SEC24D,NS,carcinoma,-1,1	SEC24D	96	1	NM_014822	exon5	c.G666A	p.P222P	CTGCTGCGGAGGA	.	PASS	Atlas-SNP
MAP1B	4131	hgsc.bcm.edu	37	5	71491950	71491950	+	Missense_Mutation	SNP	T	T	C	rs143194383	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83	49	74	0	0.590361	0	T|1.000;C|0.000	0.000	strong	.	MAP1B	243	.	NM_005909	exon5	c.T2768C	p.I923T	ACGACATTGAAAA	.	PASS	Atlas-SNP
MXRA5	25878	hgsc.bcm.edu	37	X	3241284	3241284	+	Silent	SNP	A	A	G	rs1635248	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82	82	76	0	1	0	A|0.511;0|0.003	.	strong	.	MXRA5	815	.	NM_015419	exon5	c.T2442C	p.S814S	TTCTAGACTCAAG	.	PASS	Atlas-SNP
CTU2	348180	hgsc.bcm.edu	37	16	88780175	88780175	+	Missense_Mutation	SNP	G	G	A	rs4782321	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	95	40	98	0	0.421053	0	G|0.912;A|0.088	0.088	strong	.	CTU2	66	.	NM_001012759	exon9	c.G994A	p.V332I	CCAGCCGTCGACA	.	PASS	Atlas-SNP
KCNJ2	3759	hgsc.bcm.edu	37	17	68171425	68171425	+	Missense_Mutation	SNP	G	G	A	rs199473653		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	306	85	285	0	0.277778	0	.	.	weak	.	KCNJ2	74	.	NM_000891	exon2	c.G245A	p.R82Q	GCTGGCGGTGGAT	.	PASS	Atlas-SNP
MRPL28	10573	hgsc.bcm.edu	37	16	420140	420140	+	Missense_Mutation	SNP	G	G	A	rs3194151	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	41	20	56	0	0.487805	0	G|0.896;A|0.104	0.104	strong	.	MRPL28	15	.	NM_006428	exon2	c.C79T	p.H27Y	GGTAGTGGCCGGG	.	PASS	Atlas-SNP
OR2W5	441932	hgsc.bcm.edu	37	1	247655275	247655275	+	Silent	SNP	T	T	C	rs12141850	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	139	65	123	0	0.467626	0	T|0.648;C|0.352	0.352	strong	.	OR2W5	97	.	NM_001004698	exon1	c.T846C	p.H282H	TCGTCATTCCCAG	.	PASS	Atlas-SNP
PHF10	55274	hgsc.bcm.edu	37	6	170110404	170110404	+	Silent	SNP	T	T	C	rs17860601	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	147	62	163	0	0.421769	0	T|0.969;C|0.031	0.031	strong	.	PHF10	76	.	NM_018288	exon9	c.A1041G	p.K347K	TTTGTCTTTTGAT	.	PASS	Atlas-SNP
ENTPD1	953	hgsc.bcm.edu	37	10	97471746	97471746	+	Silent	SNP	G	G	A	rs200247284	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	33	64	0	0.434211	0	G|0.994;A|0.006	0.006	strong	.	ENTPD1	44	.	NM_001098175	exon1	c.G33A	p.Q11Q	CCAGCAGAAGGGT	.	PASS	Atlas-SNP
ALDH3B2	222	hgsc.bcm.edu	37	11	67431914	67431914	+	Missense_Mutation	SNP	G	G	A	rs17856219	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79	55	67	0	0.696203	0	G|0.913;A|0.087	0.087	strong	ALDH3B2,NS,carcinoma,0,1	ALDH3B2	46	1	NM_001031615	exon8	c.C826T	p.R276W	CCTGCCGGTTGAT	.	PASS	Atlas-SNP
NBR1	4077	hgsc.bcm.edu	37	17	41342737	41342737	+	Silent	SNP	G	G	A	rs200554551	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	107	48	124	0	0.448598	0	G|0.997;A|0.003	0.003	strong	.	NBR1	55	.	NM_031862	exon9	c.G807A	p.P269P	TGAACCGTTCTGT	.	PASS	Atlas-SNP
CSMD1	64478	hgsc.bcm.edu	37	8	2820895	2820895	+	Silent	SNP	C	C	T	rs35515847	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44	24	45	0	0.545455	0	C|0.991;T|0.009	0.009	strong	.	CSMD1	1469	.	NM_033225	exon60	c.G9303A	p.P3101P	CACCGGCGGCGGC	.	PASS	Atlas-SNP
CDH23	64072	hgsc.bcm.edu	37	10	73558886	73558886	+	Missense_Mutation	SNP	G	G	A	rs4747194	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	28	72	0	0.528302	0	G|0.658;A|0.342	0.342	strong	CDH23,NS,carcinoma,0,1	CDH23	365	1	NM_022124	exon49	c.G7073A	p.R2358Q	CCAACCGGACAGT	.	PASS	Atlas-SNP
ALK	238	hgsc.bcm.edu	37	2	29543736	29543736	+	Missense_Mutation	SNP	A	A	G	rs35093491	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	97	48	80	0	0.494845	0	A|0.973;G|0.027	0.027	strong	.	ALK	533	.	NM_004304	exon7	c.T1427C	p.V476A	AAACCCACAGGCA	.	PASS	Atlas-SNP
CCDC153	283152	hgsc.bcm.edu	37	11	119064558	119064558	+	Silent	SNP	G	G	A	rs12417928	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	6	47	0	0.09375	0	G|0.934;A|0.066	0.066	strong	.	CCDC153	19	.	NM_001145018	exon4	c.C174T	p.S58S	GTCTTCGGAAGCC	.	PASS	Atlas-SNP
ACOT4	122970	hgsc.bcm.edu	37	14	74061757	74061757	+	Missense_Mutation	SNP	A	A	G	rs141714008		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	122	59	153	0	0.483607	0	A|1.000;G|0.000	0.000	weak	.	ACOT4	25	.	NM_152331	exon3	c.A665G	p.K222R	AGGTAAAAGGCCC	.	PASS	Atlas-SNP
NELL1	4745	hgsc.bcm.edu	37	11	20939776	20939776	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	96	20	90	0	0.208333	0	.	.	none	.	NELL1	179	.	NM_006157	exon6	c.A652T	p.T218S	TATATAACACAGT	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29911272	29911272	+	Missense_Mutation	SNP	T	T	G	rs76185201	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	101	55	125	0	0.544554	0	A|0.001;G|0.178;T|0.821	0.178	strong	HLA-A,colon,carcinoma,0,1	HLA-A	89	1	NM_001242758	exon3	c.T571G	p.W191G	GTGGAGTGGCTCC	.	PASS	Atlas-SNP
SLC16A13	201232	hgsc.bcm.edu	37	17	6942111	6942111	+	Silent	SNP	G	G	T	rs33979567	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	40	85	0	0.45977	0	G|0.773;T|0.227	0.227	strong	SLC16A13,colon,carcinoma,0,1	SLC16A13	28	1	NM_201566	exon3	c.G984T	p.V328V	CTCCGTGCTGCCT	.	PASS	Atlas-SNP
SLC38A8	146167	hgsc.bcm.edu	37	16	84070500	84070500	+	Silent	SNP	C	C	G	rs1317524	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	37	16	46	0	0.432432	0	C|0.617;G|0.383	0.383	strong	.	SLC38A8	60	.	NM_001080442	exon2	c.G195C	p.S65S	GACCAACGAGACC	.	PASS	Atlas-SNP
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32629936	32629936	+	Missense_Mutation	SNP	C	C	T	rs1049107	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	38	14	35	0	0.368421	0	C|0.812;T|0.188	0.188	strong	.	HLA-DQB1	15	.	NM_002123	exon3	c.G469A	p.G157S	TCTGGCCTGGATA	.	PASS	Atlas-SNP
HLX	3142	hgsc.bcm.edu	37	1	221053545	221053545	+	Missense_Mutation	SNP	T	T	C	rs12141189	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	36	12	67	5	0.333333	0.0746269	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
MUC5B	727897	hgsc.bcm.edu	37	11	1272800	1272800	+	Missense_Mutation	SNP	C	C	T	rs55693520	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	33	84	0	0.407407	0	C|0.974;T|0.026	0.026	strong	MUC5B,NS,carcinoma,0,2	MUC5B	473	2	NM_002458	exon31	c.C14690T	p.S4897L	CCAGCTCGTCCAC	.	PASS	Atlas-SNP
DDR1	780	hgsc.bcm.edu	37	6	30864829	30864829	+	Silent	SNP	T	T	C	rs1049623	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	166	129	168	0	0.777108	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
FBN3	84467	hgsc.bcm.edu	37	19	8176569	8176569	+	Silent	SNP	G	G	A	rs35306870	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	129	63	132	0	0.488372	0	G|0.761;A|0.239	0.239	strong	FBN3,colon,carcinoma,0,1	FBN3	300	1	NM_032447	exon31	c.C4047T	p.C1349C	CTGGCGGCAGGTG	.	PASS	Atlas-SNP
CHN2	1124	hgsc.bcm.edu	37	7	29440195	29440195	+	Silent	SNP	C	C	T	rs34045356	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44	34	35	0	0.772727	0	C|0.932;T|0.068	0.068	strong	.	CHN2	98	.	NM_004067	exon6	c.C327T	p.H109H	CTTCCACGACGGG	.	PASS	Atlas-SNP
CACFD1	11094	hgsc.bcm.edu	37	9	136333487	136333487	+	Missense_Mutation	SNP	G	G	A	rs3094381	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	6	5	5	0	0.833333	0	G|0.912;A|0.088	0.088	strong	.	CACFD1	1	.	NM_001242369	exon5	c.G454A	p.A152T	TCCTTCGCAGCCC	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	65	56	0	0.970149	0	A|0.643;G|0.357	0.357	strong	.	ARHGAP42	32	.	NM_152432	exon10	c.A1014G	p.R338R	CAAACGATTCTGC	.	PASS	Atlas-SNP
NOP9	161424	hgsc.bcm.edu	37	14	24772965	24772965	+	Silent	SNP	C	C	A	rs116960868	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	111	56	112	0	0.504505	0	C|0.990;A|0.010	0.010	strong	C14orf21,colon,carcinoma,-2,1	.	.	1	NM_174913	exon7	c.C1312A	p.R438R	TCATCCCGGCAAG	.	PASS	Atlas-SNP
FRAS1	80144	hgsc.bcm.edu	37	4	79437155	79437155	+	Silent	SNP	C	C	T	rs3749487	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	142	67	143	0	0.471831	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
PSD4	23550	hgsc.bcm.edu	37	2	113940839	113940839	+	Missense_Mutation	SNP	G	G	C	rs4849167	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	86	149	0	1	0	G|0.507;C|0.493	0.493	strong	.	PSD4	74	.	NM_012455	exon2	c.G806C	p.G269A	CCTGGGGGGCTTC	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	106	38	124	0	0.358491	0	G|0.737;A|0.263	0.263	strong	.	MSH4	147	.	NM_002440	exon2	c.G289A	p.A97T	ACAGTTGCATCAA	.	PASS	Atlas-SNP
BSND	7809	hgsc.bcm.edu	37	1	55474262	55474262	+	Silent	SNP	G	G	A	rs33938617	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	22	43	0	0.407407	0	G|0.824;A|0.176	0.176	strong	.	BSND	36	.	NM_057176	exon4	c.G924A	p.P308P	CCTCCCGGACAAG	.	PASS	Atlas-SNP
SDCCAG3	10807	hgsc.bcm.edu	37	9	139299637	139299637	+	Missense_Mutation	SNP	C	C	T	rs3812577	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	26	75	0	0.346667	0	C|0.886;T|0.114	0.114	strong	.	SDCCAG3	41	.	NM_001039707	exon7	c.G911A	p.R304Q	AACTTCCGCTCAA	.	PASS	Atlas-SNP
RYR1	6261	hgsc.bcm.edu	37	19	38995510	38995510	+	Silent	SNP	T	T	C	rs2915951	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	89	40	82	0	0.449438	0	T|0.653;C|0.347	0.347	strong	RYR1,NS,carcinoma,0,1	RYR1	708	1	NM_001042723	exon51	c.T8190C	p.D2730D	AGTGGATGCTGAA	.	PASS	Atlas-SNP
FCGR2B	2213	hgsc.bcm.edu	37	1	161642985	161642985	+	Silent	SNP	G	G	A	rs182968886	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	322	217	528	1	0.673913	0.00189394	G|0.895;A|0.105	0.105	strong	.	FCGR2B	33	.	NM_001002274	exon4	c.G612A	p.L204L	CACGCTGTACTCA	.	PASS	Atlas-SNP
THAP10	56906	hgsc.bcm.edu	37	15	71184278	71184278	+	Silent	SNP	G	G	T	rs2959174	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60	30	76	0	0.5	0	G|0.471;T|0.529	0.529	strong	.	THAP10	19	.	NM_020147	exon1	c.C334A	p.R112R	CTCCTCGCGTGTC	.	PASS	Atlas-SNP
GPR37	2861	hgsc.bcm.edu	37	7	124404371	124404371	+	Silent	SNP	G	G	A	rs61744942	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	65	29	59	0	0.446154	0	G|0.889;A|0.111	0.111	strong	GPR37,rectum,carcinoma,-1,1	GPR37	89	1	NM_005302	exon1	c.C660T	p.A220A	ATTCTGGGCCAGC	.	PASS	Atlas-SNP
QRICH2	84074	hgsc.bcm.edu	37	17	74289705	74289705	+	Missense_Mutation	SNP	A	A	G	rs6501880	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	383	179	313	0	0.467363	0	A|0.564;G|0.436	0.436	strong	.	QRICH2	143	.	NM_032134	exon4	c.T605C	p.L202S	CTGGCCAAGGGTA	.	PASS	Atlas-SNP
INPP5E	56623	hgsc.bcm.edu	37	9	139326304	139326304	+	Silent	SNP	G	G	A	rs10870188	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	104	61	104	0	0.586538	0	G|0.898;A|0.102	0.102	strong	INPP5E,NS,carcinoma,0,1	INPP5E	18	1	NM_019892	exon7	c.C1521T	p.H507H	CTGGTCGTGCTGC	.	PASS	Atlas-SNP
HSD3B1	3283	hgsc.bcm.edu	37	1	120057158	120057158	+	Silent	SNP	C	C	T	rs6203	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	139	139	164	0	1	0	C|0.647;T|0.353	0.353	strong	.	HSD3B1	53	.	NM_000862	exon4	c.C1012T	p.L338L	CGAGATCTGGCGT	.	PASS	Atlas-SNP
APOB	338	hgsc.bcm.edu	37	2	21231524	21231524	+	Missense_Mutation	SNP	G	G	A	rs676210	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	201	201	237	0	1	0	G|0.731;A|0.269	0.269	strong	.	APOB	761	.	NM_000384	exon26	c.C8216T	p.P2739L	AATTCTGGTATGT	.	PASS	Atlas-SNP
CEP192	55125	hgsc.bcm.edu	37	18	13056333	13056333	+	Silent	SNP	C	C	T	rs2282541	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	123	64	110	0	0.520325	0	C|0.713;T|0.287	0.287	strong	.	CEP192	340	.	NM_032142	exon19	c.C3744T	p.H1248H	TGTGCACGCACTC	.	PASS	Atlas-SNP
OR2T34	127068	hgsc.bcm.edu	37	1	248737230	248737230	+	Missense_Mutation	SNP	T	T	C	rs199863869	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	180	59	135	0	0.327778	0	T|0.875;C|0.125	0.125	strong	OR2T34,NS,carcinoma,0,1	OR2T34	72	1	NM_001001821	exon1	c.A829G	p.M277V	CCATCATGTCCTG	.	scavenged	Atlas-SNP
PLA2G4F	255189	hgsc.bcm.edu	37	15	42434254	42434254	+	Silent	SNP	G	G	A	rs655427	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	62	70	0	1	0	G|0.540;N|0.000	.	strong	.	PLA2G4F	75	.	NM_213600	exon20	c.C2478T	p.N826N	CTCCACGTTGTTC	.	PASS	Atlas-SNP
SRP68	6730	hgsc.bcm.edu	37	17	74056413	74056413	+	Silent	SNP	C	C	T	rs2665998	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	25	63	0	0.337838	0	C|0.433;T|0.567	0.567	strong	SRP68,NS,carcinoma,-2,1	SRP68	61	1	NM_014230	exon7	c.G813A	p.E271E	GAGACCCTCAGTG	.	PASS	Atlas-SNP
PSG1	5669	hgsc.bcm.edu	37	19	43382374	43382374	+	Missense_Mutation	SNP	C	C	G	rs707744	bycluster;byfrequency;by2hit2allele	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	124	46	147	0	0.370968	0	C|0.695;G|0.305	0.305	strong	.	PSG1	196	.	NM_001184826	exon2	c.G121C	p.E41Q	TTGGCTCGGCTTC	.	PASS	Atlas-SNP
OR10K2	391107	hgsc.bcm.edu	37	1	158390252	158390252	+	Silent	SNP	T	T	G	rs12239443	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	189	105	181	0	0.555556	0	T|0.635;G|0.365	0.365	strong	.	OR10K2	69	.	NM_001004476	exon1	c.A405C	p.L135L	TCCCATTAGCACT	.	PASS	Atlas-SNP
STRN	6801	hgsc.bcm.edu	37	2	37111123	37111123	+	Missense_Mutation	SNP	G	G	A	rs80243841	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	214	110	206	0	0.514019	0	G|0.984;A|0.016	0.016	strong	.	STRN	71	.	NM_003162	exon9	c.C1138T	p.P380S	TGCTGGGTCTGGA	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	107	63	112	0	0.588785	0	T|0.719;C|0.281	0.281	strong	.	METTL11B	18	.	NM_001136107	exon3	c.T448C	p.S150P	ATGGAATCCTTTC	.	PASS	Atlas-SNP
PTPRS	5802	hgsc.bcm.edu	37	19	5273571	5273571	+	Silent	SNP	T	T	G	rs1141371	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	105	104	129	0	0.990476	0	T|0.785;G|0.215;A|0.000	0.215	strong	.	PTPRS	169	.	NM_130854	exon4	c.A261C	p.A87A	TGCCCCTGCACTC	.	PASS	Atlas-SNP
HERC2	8924	hgsc.bcm.edu	37	15	28517436	28517436	+	Silent	SNP	T	T	C	rs75181529	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	155	64	110	0	0.412903	0	T|0.500;C|0.500	0.500	weak	.	HERC2	501	.	NM_004667	exon9	c.A1008G	p.P336P	CAAAAGTGGGGCG	.	PASS	Atlas-SNP
RSPH6A	81492	hgsc.bcm.edu	37	19	46313918	46313918	+	Silent	SNP	C	C	G	rs141102105	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	33	93	0	0.515625	0	C|0.997;G|0.003	0.003	strong	RSPH6A,NS,carcinoma,-2,1	RSPH6A	70	1	NM_030785	exon2	c.G831C	p.A277A	GAACAGCGCCTTC	.	PASS	Atlas-SNP
LMX1A	4009	hgsc.bcm.edu	37	1	165322487	165322487	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	38	11	36	0	0.289474	0	.	.	none	.	LMX1A	87	.	NM_001174069	exon3	c.G89T	p.S30I	TTGGGGCTCACCG	.	PASS	Atlas-SNP
KANK1	23189	hgsc.bcm.edu	37	9	712599	712599	+	Silent	SNP	C	C	T	rs11789987	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	35	70	0	0.492958	0	C|0.719;T|0.281	0.281	strong	KANK1_ENST00000382303,colon,carcinoma,0,2	KANK1	231	2	NM_001256876	exon7	c.C1833T	p.N611N	TGTGAACGACCTC	.	PASS	Atlas-SNP
UBQLNL	143630	hgsc.bcm.edu	37	11	5536415	5536415	+	Silent	SNP	C	C	T	rs10769023	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	228	102	172	0	0.447368	0	C|0.719;T|0.281	0.281	strong	.	UBQLNL	74	.	NM_145053	exon1	c.G1257A	p.E419E	GCTCTGCTCATCT	.	PASS	Atlas-SNP
SLC4A2	6522	hgsc.bcm.edu	37	7	150763655	150763655	+	Silent	SNP	T	T	A	rs2229549	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	40	40	42	0	1	0	T|0.406;A|0.594	0.594	strong	.	SLC4A2	98	.	NM_003040	exon6	c.T630A	p.T210T	TGGCACTGCAGGG	.	PASS	Atlas-SNP
SH3TC1	54436	hgsc.bcm.edu	37	4	8220029	8220029	+	Missense_Mutation	SNP	G	G	A	rs1281138	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	34	21	73	0	0.617647	0	G|0.980;A|0.020	0.020	strong	SH3TC1,colon,carcinoma,-2,1	SH3TC1	105	1	NM_018986	exon8	c.G871A	p.D291N	CCCATCGACGATG	.	PASS	Atlas-SNP
TFEC	22797	hgsc.bcm.edu	37	7	115580893	115580893	+	Silent	SNP	G	G	A	rs34298819	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	147	70	153	0	0.47619	0	G|0.988;A|0.012	0.012	strong	.	TFEC	51	.	NM_012252	exon8	c.C756T	p.S252S	AGGATGGCTCTGC	.	PASS	Atlas-SNP
MLPH	79083	hgsc.bcm.edu	37	2	238449107	238449107	+	Silent	SNP	A	A	G	rs2271809	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44	44	42	0	1	0	A|0.549;C|0.000;G|0.450;T|0.000	0.450	strong	MLPH,NS,carcinoma,0,2	MLPH	41	2	NM_024101	exon10	c.A1221G	p.E407E	GGAGGAAGCCAAG	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85	85	94	0	1	0	A|0.416;G|0.584	0.584	strong	.	SLFN12	56	.	NM_018042	exon2	c.T502C	p.C168R	CAACACAGGGCCT	.	PASS	Atlas-SNP
GNS	2799	hgsc.bcm.edu	37	12	65141588	65141588	+	Silent	SNP	C	C	T	rs2230291	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	229	108	225	0	0.471616	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
GOLGA6L1	283767	hgsc.bcm.edu	37	15	22743086	22743086	+	Missense_Mutation	SNP	C	C	T	rs201721928	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	13	54	0	0.175676	0	.	.	weak	.	GOLGA6L1	20	.	NM_001001413	exon8	c.C1471T	p.R491W	AAGATACGGAAGC	.	PASS	Atlas-SNP
STK10	6793	hgsc.bcm.edu	37	5	171533656	171533656	+	Silent	SNP	C	C	T	rs2306962	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	108	48	131	0	0.444444	0	C|0.351;T|0.649	0.649	strong	.	STK10	100	.	NM_005990	exon6	c.G756A	p.S252S	AGGGTCCGACTTG	.	PASS	Atlas-SNP
COMT	1312	hgsc.bcm.edu	37	22	19951207	19951207	+	Silent	SNP	C	C	G	rs4818	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	70	29	82	0	0.414286	0	C|0.677;G|0.323	0.323	strong	.	COMT	10	.	NM_000754	exon4	c.C408G	p.L136L	GAGGCTCATCACC	.	PASS	Atlas-SNP
BTNL3	10917	hgsc.bcm.edu	37	5	180432416	180432416	+	Silent	SNP	C	C	T	rs78885278	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	151	145	127	0	0.960265	0	T|1.000;|0.000	1.000	weak	BTNL3,NS,carcinoma,+1,1	BTNL3	55	1	NM_197975	exon8	c.C945T	p.P315P	AGCTCCCCAGGAG	.	PASS	Atlas-SNP
PEG3	5178	hgsc.bcm.edu	37	19	57335959	57335959	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	135	35	140	0	0.259259	0	.	.	none	.	PEG3	414	.	NM_001146184	exon3	c.A65G	p.E22G	TCTAGCTCATACA	.	PASS	Atlas-SNP
PLEKHS1	79949	hgsc.bcm.edu	37	10	115540411	115540411	+	Silent	SNP	T	T	C	rs11196483	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44	23	42	0	0.522727	0	T|0.631;C|0.369	0.369	strong	.	PLEKHS1	19	.	NM_001193435	exon11	c.T972C	p.A324A	CCATGCTGCATCC	.	PASS	Atlas-SNP
TAS2R20	259295	hgsc.bcm.edu	37	12	11150046	11150046	+	Missense_Mutation	SNP	G	G	T	rs12226920	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	96	44	85	0	0.458333	0	G|0.671;T|0.329	0.329	strong	.	TAS2R20	17	.	NM_176889	exon1	c.C429A	p.H143Q	CACAAGGTGACAA	.	PASS	Atlas-SNP
VWF	7450	hgsc.bcm.edu	37	12	6167196	6167196	+	Silent	SNP	A	A	G	rs1800379	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	23	65	0	0.489362	0	T|0.125;G|0.330	0.330	strong	VWF,colon,carcinoma,0,2	VWF	338	2	NM_000552	exon14	c.T1548C	p.Y516Y	CCCGGCATAGACG	.	PASS	Atlas-SNP
TG	7038	hgsc.bcm.edu	37	8	133899051	133899051	+	Silent	SNP	G	G	A	rs116254142	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	95	39	119	0	0.410526	0	G|0.994;A|0.006	0.006	strong	TG,NS,carcinoma,0,1	TG	416	1	NM_003235	exon9	c.G1434A	p.V478V	TTTGGTGAATGTT	.	PASS	Atlas-SNP
PLEC	5339	hgsc.bcm.edu	37	8	145024570	145024570	+	Missense_Mutation	SNP	C	C	A	rs200335928	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	35	13	46	0	0.371429	0	A|0.005;C|0.996	0.005	weak	.	PLEC	1144	.	NM_201380	exon1	c.G305T	p.R102L	ACGGGGCGGCGCA	.	PASS	Atlas-SNP
HIST2H2AC	8338	hgsc.bcm.edu	37	1	149858806	149858806	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	209	11	211	0	0.0526316	0	.	.	none	HIST2H2AC,NS,carcinoma,0,3	HIST2H2AC	75	3	NM_003517	exon1	c.G282A	p.L94L	GGAACTGAACAAG	.	PASS	Atlas-SNP
C10orf137	26098	hgsc.bcm.edu	37	10	127412393	127412393	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	102	17	113	0	0.166667	0	.	.	none	.	C10orf137	153	.	NM_015608	exon4	c.T398C	p.L133P	AAAAACTCCTGAA	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9087758	9087758	+	Missense_Mutation	SNP	G	G	A	rs12611293	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	338	141	329	0	0.41716	0	G|0.812;A|0.188	0.188	strong	.	MUC16	4315	.	NM_024690	exon1	c.C4057T	p.H1353Y	TTGGATGGTTTTC	.	PASS	Atlas-SNP
CDH23	64072	hgsc.bcm.edu	37	10	73544086	73544086	+	Missense_Mutation	SNP	G	G	A	rs3802711	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82	37	87	0	0.451219	0	G|0.843;A|0.157	0.157	strong	.	CDH23	365	.	NM_022124	exon40	c.G5411A	p.R1804Q	GGGTCCGGAAGGA	.	PASS	Atlas-SNP
NT5C1B	93034	hgsc.bcm.edu	37	2	18767638	18767638	+	Missense_Mutation	SNP	A	A	G	rs147855918	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	130	59	113	0	0.453846	0	A|0.997;G|0.003	0.003	strong	.	NT5C1B	72	.	NM_001199087	exon4	c.T371C	p.L124P	TTCCGCAGTGATG	.	PASS	Atlas-SNP
IL22RA1	58985	hgsc.bcm.edu	37	1	24448084	24448084	+	Silent	SNP	G	G	A	rs17852648	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68	26	75	0	0.382353	0	G|0.765;A|0.235	0.235	strong	IL22RA1,NS,carcinoma,0,1	IL22RA1	62	1	NM_021258	exon7	c.C936T	p.P312P	TCCTGCGGGCTCC	.	PASS	Atlas-SNP
HTR3A	3359	hgsc.bcm.edu	37	11	113860425	113860425	+	Silent	SNP	A	A	G	rs1176713	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44	11	29	0	0.25	0	G|0.258;N|0.000	0.258	strong	.	HTR3A	93	.	NM_213621	exon8	c.A1491G	p.L497L	CCTGCTAGCGGTG	.	PASS	Atlas-SNP
SPESP1	246777	hgsc.bcm.edu	37	15	69238445	69238445	+	Missense_Mutation	SNP	G	G	A	rs3743093	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	134	66	118	0	0.492537	0	G|0.426;A|0.574	0.574	strong	.	SPESP1	39	.	NM_145658	exon2	c.G572A	p.G191E	GCATTGGGATCTC	.	PASS	Atlas-SNP
IMPG1	3617	hgsc.bcm.edu	37	6	76633385	76633385	+	Missense_Mutation	SNP	C	C	T	rs3778005	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	109	36	110	0	0.330275	0	C|0.832;T|0.168	0.168	strong	.	IMPG1	143	.	NM_001563	exon16	c.G2282A	p.S761N	TTAACACTAGTTT	.	PASS	Atlas-SNP
ZEB2	9839	hgsc.bcm.edu	37	2	145274844	145274844	+	Splice_Site	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	50	27	56	0	0.54	0	.	.	none	ZEB2,NS,NS,0,1	ZEB2	218	1	NM_001171653	exon3	c.73+1G>A	.	TTCTTACCGTTTT	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	108	44	94	0	0.407407	0	T|0.815;C|0.185	0.185	strong	.	ALPK3	289	.	NM_020778	exon10	c.T4865C	p.L1622P	GTGGCCTTCGGAA	.	PASS	Atlas-SNP
PRPSAP1	5635	hgsc.bcm.edu	37	17	74307737	74307737	+	Silent	SNP	T	T	C	rs10459	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93	37	108	0	0.397849	0	T|0.766;C|0.234	0.234	strong	.	PRPSAP1	32	.	NM_002766	exon10	c.A1044G	p.Q348Q	GGGACATTGCAGC	.	PASS	Atlas-SNP
PCDH9	5101	hgsc.bcm.edu	37	13	67802190	67802190	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	154	54	103	0	0.350649	0	.	.	none	.	PCDH9	252	.	NM_203487	exon2	c.T383A	p.I128K	ATTTTTATTTTGA	.	PASS	Atlas-SNP
NUP62	23636	hgsc.bcm.edu	37	19	50412396	50412396	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85	39	66	0	0.458824	0	.	.	none	NUP62,NS,carcinoma,0,2	NUP62	50	2	NM_153719	exon3	c.G669A	p.A223A	TATTGACGCAAAG	.	PASS	Atlas-SNP
RAP1GAP	5909	hgsc.bcm.edu	37	1	21932625	21932625	+	Silent	SNP	G	G	A	rs2275365	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	40	60	0	0.47619	0	G|0.893;A|0.107	0.107	strong	.	RAP1GAP	119	.	NM_001145658	exon18	c.C1554T	p.T518T	GGACACGGTGTTG	.	PASS	Atlas-SNP
FAT4	79633	hgsc.bcm.edu	37	4	126402890	126402890	+	Silent	SNP	G	G	A	rs6824160	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	27	68	0	0.442623	0	G|0.890;A|0.110	0.110	strong	.	FAT4	1752	.	NM_024582	exon15	c.G12813A	p.V4271V	TACTGTGAAGGTG	.	PASS	Atlas-SNP
RASL12	51285	hgsc.bcm.edu	37	15	65347405	65347405	+	Silent	SNP	G	G	A	rs2232762	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	62	64	0	0.96875	0	G|0.606;A|0.394	0.394	strong	.	RASL12	32	.	NM_016563	exon5	c.C633T	p.T211T	CCGCGCGGTGAGC	.	PASS	Atlas-SNP
ZCRB1	85437	hgsc.bcm.edu	37	12	42707711	42707711	+	Silent	SNP	C	C	T	rs141493486		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	132	2	137	0	0.0151515	0	.	.	weak	ZCRB1,upper_arm,malignant_melanoma,0,1	ZCRB1	20	1	NM_033114	exon6	c.G411A	p.K137K	TTTTTTCTTTTTT	.	scavenged	Atlas-SNP
PCSK5	5125	hgsc.bcm.edu	37	9	78938043	78938043	+	Missense_Mutation	SNP	G	G	A	rs2495207	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	92	41	91	0	0.445652	0	G|0.668;A|0.332	0.332	strong	.	PCSK5	329	.	NM_001190482	exon31	c.G4097A	p.R1366H	ACTCGCGCCACTG	.	PASS	Atlas-SNP
B3GALT5	10317	hgsc.bcm.edu	37	21	41033062	41033062	+	Silent	SNP	G	G	A	rs734412	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	25	72	0	0.333333	0	G|0.950;A|0.050	0.050	strong	.	B3GALT5	40	.	NM_033170	exon3	c.G576A	p.R192R	CATCAGGCAGCCA	.	PASS	Atlas-SNP
DHODH	1723	hgsc.bcm.edu	37	16	72042682	72042682	+	Missense_Mutation	SNP	A	A	C	rs3213422	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	131	130	139	0	0.992366	0	A|0.433;C|0.567	0.567	strong	DHODH,colon,carcinoma,0,1	DHODH	33	1	NM_001361	exon1	c.A19C	p.K7Q	CACCTGAAAGTGA	.	PASS	Atlas-SNP
CCDC50	152137	hgsc.bcm.edu	37	3	191097966	191097966	+	Missense_Mutation	SNP	T	T	C	rs293813	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	105	50	110	1	0.47619	0.00909091	T|0.396;C|0.603	0.603	strong	CCDC50,NS,carcinoma,0,1	CCDC50	39	1	NM_178335	exon7	c.T995C	p.M332T	GAGTGATGAAAGA	.	scavenged	Atlas-SNP
MFSD6L	162387	hgsc.bcm.edu	37	17	8700982	8700982	+	Missense_Mutation	SNP	C	C	T	rs2242373	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	32	14	38	0	0.4375	0	C|0.815;T|0.185	0.185	strong	.	MFSD6L	46	.	NM_152599	exon1	c.G1457A	p.R486H	TCCATGCGGGGAG	.	PASS	Atlas-SNP
GRIN2A	2903	hgsc.bcm.edu	37	16	9857231	9857231	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	32	99	0	0.372093	0	.	.	none	GRIN2A,colon,carcinoma,0,1	GRIN2A	366	1	NM_001134408	exon14	c.G3827A	p.R1276H	TGGCAACGAGTGT	.	PASS	Atlas-SNP
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057806	46057806	+	Missense_Mutation	SNP	G	G	A	rs4818950	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	99	51	107	0	0.515152	0	G|0.392;A|0.608	0.608	strong	.	KRTAP10-10	37	.	NM_181688	exon1	c.G472A	p.V158M	TGCTATGTGCCTG	.	PASS	Atlas-SNP
SLC15A1	6564	hgsc.bcm.edu	37	13	99340771	99340771	+	Silent	SNP	G	G	A	rs8187832	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110	72	84	0	0.654545	0	G|0.925;A|0.075	0.075	strong	.	SLC15A1	92	.	NM_005073	exon19	c.C1527T	p.N509N	GCTGATGTTTGCA	.	PASS	Atlas-SNP
NUP188	23511	hgsc.bcm.edu	37	9	131767668	131767668	+	Silent	SNP	A	A	C	rs2287363	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	43	20	34	0	0.465116	0	A|0.553;C|0.447	0.447	strong	.	NUP188	140	.	NM_015354	exon40	c.A4596C	p.S1532S	CTCCTCAAAGCAG	.	PASS	Atlas-SNP
IGSF10	285313	hgsc.bcm.edu	37	3	151165641	151165641	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	201	11	197	0	0.0547264	0	.	.	none	.	IGSF10	279	.	NM_178822	exon4	c.A2128C	p.K710Q	TGTGTTTTCCAAC	.	PASS	Atlas-SNP
MST1L	11223	hgsc.bcm.edu	37	1	17084569	17084569	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	214	13	264	1	0.0607477	0.00378788	.	.	none	Q13209_HUMAN,NS,carcinoma,0,2	.	.	2	NM_001271733	exon12	c.C1529T	p.T510M	TAGCCCGTGAGAG	.	scavenged	Atlas-SNP
DPP10	57628	hgsc.bcm.edu	37	2	116447277	116447277	+	Silent	SNP	G	G	A	rs35766316	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	78	58	106	0	0.74359	0	G|0.928;A|0.072	0.072	strong	DPP10_ENST00000410059,ear,carcinoma,+1,4	DPP10	415	4	NM_001178034	exon6	c.G468A	p.S156S	TTATTCGTATACT	.	PASS	Atlas-SNP
SUPT20H	55578	hgsc.bcm.edu	37	13	37583831	37583831	+	Missense_Mutation	SNP	G	G	A	rs9469	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	209	89	211	0	0.425837	0	G|0.646;A|0.354	0.354	strong	.	.	.	.	NM_001014286	exon26	c.C2318T	p.T773M	GTTGGCGTGCCTC	.	PASS	Atlas-SNP
OR5AU1	390445	hgsc.bcm.edu	37	14	21623489	21623489	+	Silent	SNP	C	C	T	rs45462402	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	44	88	0	0.52381	0	C|0.637;T|0.363	0.363	strong	.	OR5AU1	46	.	NM_001004731	exon1	c.G696A	p.G232G	GGGTGGCCCATCA	.	PASS	Atlas-SNP
KRTAP19-5	337972	hgsc.bcm.edu	37	21	31874241	31874241	+	Silent	SNP	G	G	T	rs150340950	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	23	57	0	0.348485	0	G|0.975;T|0.025	0.025	strong	KRTAP19-5,NS,carcinoma,-2,1	KRTAP19-5	32	1	NM_181611	exon1	c.C168A	p.R56R	GCAGCTGCGGTAT	.	PASS	Atlas-SNP
LDHAL6B	92483	hgsc.bcm.edu	37	15	59499228	59499228	+	Missense_Mutation	SNP	C	C	T	rs3809529	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	30	78	0	0.394737	0	C|0.613;T|0.387	0.387	strong	.	LDHAL6B	30	.	NM_033195	exon1	c.C89T	p.P30L	TGTGTCCGCGTCA	.	PASS	Atlas-SNP
PCDHB7	56129	hgsc.bcm.edu	37	5	140554484	140554484	+	Missense_Mutation	SNP	G	G	T	rs1811236	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	121	34	134	0	0.280992	0	G|0.943;T|0.057	0.057	strong	.	PCDHB7	231	.	NM_018940	exon1	c.G2068T	p.V690L	CTGGTGGTGGCGT	.	PASS	Atlas-SNP
POM121L2	94026	hgsc.bcm.edu	37	6	27278340	27278340	+	Missense_Mutation	SNP	A	A	G	rs147268352	by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110	24	79	0	0.218182	0	A|0.999;G|0.001	0.001	strong	.	POM121L2	61	.	NM_033482	exon1	c.T1610C	p.I537T	CCCAAAATCGGTT	.	PASS	Atlas-SNP
DOCK10	55619	hgsc.bcm.edu	37	2	225727431	225727431	+	Silent	SNP	T	T	C	rs7589474	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	92	31	116	0	0.336957	0	T|0.830;C|0.170	0.170	strong	.	DOCK10	308	.	NM_014689	exon14	c.A1635G	p.Q545Q	GCAGAATTGTCTG	.	PASS	Atlas-SNP
ATP2C2	9914	hgsc.bcm.edu	37	16	84485677	84485677	+	Missense_Mutation	SNP	T	T	A	rs62640926	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	88	47	97	0	0.534091	0	T|0.946;A|0.054	0.054	strong	.	ATP2C2	75	.	NM_014861	exon18	c.T1811A	p.L604Q	ATGCCCTGGAGAC	.	PASS	Atlas-SNP
GLTSCR2	29997	hgsc.bcm.edu	37	19	48248925	48248925	+	Silent	SNP	C	C	A	rs144346550	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	138	75	112	0	0.543478	0	C|0.981;A|0.019	0.019	strong	.	GLTSCR2	45	.	NM_015710	exon1	c.C109A	p.R37R	AGGCGGCGGCGGC	.	PASS	Atlas-SNP
TRIM77	390231	hgsc.bcm.edu	37	11	89447375	89447375	+	Missense_Mutation	SNP	C	C	T	rs17221124	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	10	62	0	0.133333	0	C|0.957;T|0.043	0.043	strong	.	.	.	.	NM_001146162	exon3	c.C523T	p.R175W	AATTTGCGGAGCA	.	PASS	Atlas-SNP
PCSK5	5125	hgsc.bcm.edu	37	9	78942956	78942956	+	Silent	SNP	A	A	G	rs2259969	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	104	102	115	0	0.980769	0	A|0.492;G|0.508	0.508	strong	.	PCSK5	329	.	NM_001190482	exon32	c.A4290G	p.S1430S	CTCATCATCTGGG	.	PASS	Atlas-SNP
WNT9A	7483	hgsc.bcm.edu	37	1	228113046	228113046	+	Silent	SNP	C	C	T	rs8192629	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	41	101	0	0.506173	0	C|0.927;T|0.073	0.073	strong	.	WNT9A	39	.	NM_003395	exon2	c.G270A	p.A90A	CTCGAGCGCACTC	.	PASS	Atlas-SNP
CYP4A22	284541	hgsc.bcm.edu	37	1	47609489	47609489	+	Missense_Mutation	SNP	T	T	C	rs10789501	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	174	88	195	0	0.505747	0	T|0.527;C|0.473	0.473	strong	.	CYP4A22	60	.	NM_001010969	exon6	c.T691C	p.C231R	TTTTGCTGTATGA	.	PASS	Atlas-SNP
KBTBD2	25948	hgsc.bcm.edu	37	7	32909182	32909182	+	Silent	SNP	G	G	A	rs752730	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	77	19	105	0	0.246753	0	G|0.819;A|0.181	0.181	strong	.	KBTBD2	37	.	NM_015483	exon4	c.C1647T	p.Y549Y	GGTGACGTATTTA	.	PASS	Atlas-SNP
DZIP1L	199221	hgsc.bcm.edu	37	3	137787041	137787041	+	Missense_Mutation	SNP	C	C	T	rs115489792	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	25	70	0	0.390625	0	C|0.980;T|0.020	0.020	strong	.	DZIP1L	88	.	NM_173543	exon13	c.G1784A	p.G595E	TGCAGTCCGGGGC	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	96	45	88	0	0.46875	0	G|0.833;T|0.167	0.167	strong	.	NMB	14	.	NM_205858	exon2	c.C217A	p.P73T	TGTGGGGAGCTGT	.	PASS	Atlas-SNP
CACNA1G	8913	hgsc.bcm.edu	37	17	48703752	48703752	+	Silent	SNP	T	T	C	rs739925	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	117	58	132	0	0.495726	0	T|0.603;G|0.006	.	strong	.	CACNA1G	659	.	NM_018896	exon38	c.T6774C	p.P2258P	CCGGCCTACGTCC	.	PASS	Atlas-SNP
SDCCAG8	10806	hgsc.bcm.edu	37	1	243579112	243579112	+	Silent	SNP	G	G	A	rs10927011	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	262	134	211	0	0.51145	0	G|0.576;A|0.424	0.424	strong	.	SDCCAG8	73	.	NM_006642	exon14	c.G1725A	p.E575E	AATGGAGGCCCAG	.	PASS	Atlas-SNP
KCNE3	10008	hgsc.bcm.edu	37	11	74168411	74168411	+	Silent	SNP	A	A	G	rs2270676	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	119	28	134	0	0.235294	0	A|0.881;G|0.119	0.119	strong	.	KCNE3	7	.	NM_005472	exon3	c.T198C	p.F66F	AAATAGAAACATG	.	PASS	Atlas-SNP
RHOD	29984	hgsc.bcm.edu	37	11	66834252	66834252	+	Silent	SNP	C	C	T	rs2282502	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	111	111	70	0	1	0	C|0.683;G|0.000;T|0.317	0.317	strong	.	RHOD	8	.	NM_014578	exon3	c.C264T	p.D88D	CCCTGACGCCAGC	.	PASS	Atlas-SNP
TSPAN18	90139	hgsc.bcm.edu	37	11	44940828	44940828	+	Missense_Mutation	SNP	G	G	A	rs2291334	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82	82	96	0	1	0	G|0.711;A|0.289	0.289	strong	TSPAN18,colon,carcinoma,-2,1	TSPAN18	38	1	NM_130783	exon6	c.G397A	p.V133I	ACAGACGTCTTCT	.	PASS	Atlas-SNP
EPB41L2	2037	hgsc.bcm.edu	37	6	131179302	131179302	+	Missense_Mutation	SNP	C	C	G	rs61731767	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98	48	81	0	0.489796	0	C|0.961;G|0.039	0.039	strong	.	EPB41L2	96	.	NM_001431	exon19	c.G2992C	p.E998Q	CCAACTCTGTTTC	.	PASS	Atlas-SNP
OR4C6	219432	hgsc.bcm.edu	37	11	55432843	55432843	+	Silent	SNP	G	G	A	rs191322588	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	246	3	254	0	0.0121951	0	G|1.000;A|0.000	0.000	strong	OR4C6,NS,carcinoma,0,1	OR4C6	114	1	NM_001004704	exon1	c.G201A	p.L67L	CCTTTTGGATGTC	.	scavenged	Atlas-SNP
SMU1	55234	hgsc.bcm.edu	37	9	33062128	33062128	+	Silent	SNP	G	G	A	rs2274764	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	59	29	62	0	0.491525	0	G|0.960;A|0.040	0.040	strong	.	SMU1	29	.	NM_018225	exon5	c.C549T	p.T183T	ATCTATGGTCATA	.	PASS	Atlas-SNP
ESPL1	9700	hgsc.bcm.edu	37	12	53682326	53682326	+	Silent	SNP	G	G	A	rs1110720	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	60	53	0	0.967742	0	G|0.402;A|0.598	0.598	strong	.	ESPL1	158	.	NM_012291	exon20	c.G4551A	p.G1517G	AGGTGGGAAGACT	.	PASS	Atlas-SNP
CCDC15	80071	hgsc.bcm.edu	37	11	124857192	124857192	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	137	20	138	0	0.145985	0	.	.	none	.	CCDC15	134	.	NM_025004	exon8	c.A1070C	p.K357T	GTGTTAAGCCAGA	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	62	67	1	0.815789	0.0149254	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	.	scavenged	Atlas-SNP
FAIM3	9214	hgsc.bcm.edu	37	1	207078467	207078467	+	Missense_Mutation	SNP	G	G	A	rs41304091	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	23	65	0	0.359375	0	G|0.992;A|0.008	0.008	strong	.	FAIM3	36	.	NM_005449	exon8	c.C1070T	p.A357V	GATGGGGCATGGA	.	PASS	Atlas-SNP
PTBP1	5725	hgsc.bcm.edu	37	19	808586	808586	+	Silent	SNP	C	C	G	rs13169	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	65	33	76	0	0.507692	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
TMPRSS6	164656	hgsc.bcm.edu	37	22	37499386	37499386	+	Silent	SNP	C	C	T	rs11704654	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	42	71	1	0.488372	0.0140845	C|0.825;T|0.175	0.175	strong	TMPRSS6,NS,carcinoma,-2,2	TMPRSS6	99	2	NM_153609	exon2	c.G99A	p.P33P	CCCCTCCGGCTCC	.	scavenged	Atlas-SNP
SLC22A11	55867	hgsc.bcm.edu	37	11	64337280	64337280	+	Silent	SNP	G	G	A	rs34836439	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44	20	38	0	0.454545	0	G|0.996;A|0.004	0.004	strong	.	SLC22A11	54	.	NM_018484	exon9	c.G1539A	p.P513P	CCTCCCGGAGACC	.	PASS	Atlas-SNP
BRDT	676	hgsc.bcm.edu	37	1	92445257	92445257	+	Missense_Mutation	SNP	C	C	G	rs3088232	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	147	145	193	0	0.986395	0	C|0.838;G|0.162	0.162	strong	.	BRDT	133	.	NM_001242806	exon8	c.C1242G	p.N414K	AGGGAACTCTTCT	.	PASS	Atlas-SNP
RIMBP2	23504	hgsc.bcm.edu	37	12	130912757	130912757	+	Silent	SNP	C	C	T	rs2277356	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80	35	83	1	0.4375	0.0120482	C|0.786;T|0.214	0.214	strong	RIMBP2,NS,carcinoma,0,2	RIMBP2	220	2	NM_015347	exon12	c.G2328A	p.R776R	GGGCCGCCTCCTT	.	scavenged	Atlas-SNP
OR5P2	120065	hgsc.bcm.edu	37	11	7818313	7818313	+	Silent	SNP	C	C	T	rs73406609	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	41	41	68	0	1	0	C|0.741;T|0.259	0.259	strong	.	OR5P2	68	.	NM_153444	exon1	c.G177A	p.L59L	GTGGCTCAGAAAG	.	PASS	Atlas-SNP
ANO7	50636	hgsc.bcm.edu	37	2	242149010	242149010	+	Missense_Mutation	SNP	C	C	T	rs57677160	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	182	103	172	0	0.565934	0	C|0.812;T|0.188	0.188	strong	ANO7,NS,carcinoma,+2,1	ANO7	136	1	NM_001001891	exon13	c.C1481T	p.A494V	GCCGCGCGCGCCG	.	PASS	Atlas-SNP
PFKM	5213	hgsc.bcm.edu	37	12	48526712	48526712	+	Missense_Mutation	SNP	G	G	A	rs2228500	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	46	104	0	0.534884	0	G|0.825;A|0.175	0.175	strong	.	PFKM	117	.	NM_001166686	exon7	c.G512A	p.R171Q	GACTCCGAGCTGC	.	PASS	Atlas-SNP
TBC1D9	23158	hgsc.bcm.edu	37	4	141598126	141598126	+	Silent	SNP	C	C	T	rs2303911	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83	36	67	0	0.433735	0	C|0.866;G|0.000;T|0.133	0.133	strong	.	TBC1D9	198	.	NM_015130	exon6	c.G981A	p.Q327Q	AAACATCTGCCCC	.	PASS	Atlas-SNP
COL4A2	1284	hgsc.bcm.edu	37	13	111102770	111102770	+	Silent	SNP	C	C	T	rs78615289	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	18	8	28	0	0.444444	0	C|0.984;T|0.016	0.016	strong	.	COL4A2	178	.	NM_001846	exon20	c.C1308T	p.P436P	AGGACCCCCCGGG	.	PASS	Atlas-SNP
QRSL1	55278	hgsc.bcm.edu	37	6	107100396	107100396	+	Missense_Mutation	SNP	A	A	G	rs34221917	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72	70	88	0	0.972222	0	A|0.962;G|0.038	0.038	strong	.	QRSL1	30	.	NM_018292	exon7	c.A788G	p.N263S	CTATTAATAAACC	.	PASS	Atlas-SNP
BAZ1A	11177	hgsc.bcm.edu	37	14	35263983	35263983	+	Silent	SNP	T	T	C	rs17102745	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	96	47	94	0	0.489583	0	T|0.899;C|0.101	0.101	strong	.	BAZ1A	128	.	NM_182648	exon11	c.A1335G	p.Q445Q	CTCATCTTGAAGA	.	PASS	Atlas-SNP
C6orf141	135398	hgsc.bcm.edu	37	6	49519048	49519048	+	Missense_Mutation	SNP	G	G	T	rs199917136	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	115	59	132	0	0.513043	0	.	.	weak	.	C6orf141	7	.	NM_001145652	exon1	c.G543T	p.M181I	TCGCATGACCACG	.	PASS	Atlas-SNP
BLMH	642	hgsc.bcm.edu	37	17	28576076	28576076	+	Missense_Mutation	SNP	T	T	C	rs1050565	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	122	46	95	0	0.377049	0	T|0.728;C|0.272	0.272	strong	.	BLMH	42	.	NM_000386	exon12	c.A1327G	p.I443V	GCAGGATAATGGG	.	PASS	Atlas-SNP
FPGT	8790	hgsc.bcm.edu	37	1	74670172	74670172	+	Silent	SNP	A	A	G	rs12046751	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94	46	93	0	0.489362	0	A|0.697;G|0.303	0.303	strong	.	FPGT	77	.	NM_003838	exon4	c.A441G	p.K147K	ATTAAAACTAGCC	.	PASS	Atlas-SNP
SERPINB10	5273	hgsc.bcm.edu	37	18	61582867	61582867	+	Missense_Mutation	SNP	A	A	G	rs8097425	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	147	81	148	0	0.55102	0	A|0.582;G|0.418	0.418	strong	.	SERPINB10	53	.	NM_005024	exon1	c.A123G	p.I41M	GACCATAGTGTAT	.	PASS	Atlas-SNP
RPS6KA3	6197	hgsc.bcm.edu	37	X	20204461	20204461	+	Silent	SNP	G	G	T	rs2230488	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	135	88	86	0	0.651852	0	0|0.003;T|0.273	0.273	strong	.	RPS6KA3	110	.	NM_004586	exon10	c.C798A	p.L266L	GAAAGGGAGTGTA	.	PASS	Atlas-SNP
KIAA0753	9851	hgsc.bcm.edu	37	17	6511781	6511781	+	Silent	SNP	A	A	G	rs4796519	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	70	37	84	1	0.528571	0.0119048	A|0.360;G|0.640	0.640	strong	KIAA0753,colon,carcinoma,-1,1	KIAA0753	63	1	NM_014804	exon10	c.T1716C	p.A572A	CCATGCAGCACTG	.	scavenged	Atlas-SNP
CYP2F1	1572	hgsc.bcm.edu	37	19	41622189	41622189	+	Silent	SNP	G	G	A	rs305968	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	46	80	0	0.547619	0	G|0.601;A|0.399	0.399	strong	.	CYP2F1	60	.	NM_000774	exon2	c.G96A	p.P32P	GCCTCCGGGACCC	.	PASS	Atlas-SNP
CISD1	55847	hgsc.bcm.edu	37	10	60036963	60036963	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	213	4	205	0	0.0187793	0	.	.	none	CISD1,NS,carcinoma,-1,2	CISD1	7	2	NM_018464	exon2	c.C118T	p.R40X	GATCATCGAAATA	.	scavenged	Atlas-SNP
NSD1	64324	hgsc.bcm.edu	37	5	176721272	176721272	+	Silent	SNP	G	G	C	rs11740250	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	33	15	33	0	0.454545	0	G|0.836;C|0.164	0.164	strong	.	NSD1	416	.	NM_022455	exon23	c.G6903C	p.G2301G	CGCTGGGTCAGGG	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	117	51	120	0	0.435897	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
MRPS12	6183	hgsc.bcm.edu	37	19	39421979	39421979	+	Silent	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94	27	84	0	0.287234	0	.	.	none	.	MRPS12	11	.	NM_033362	exon2	c.T45G	p.T15T	CCTAACTTGTGGT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195512103	195512103	+	Silent	SNP	G	G	A	rs437805	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	232	28	244	0	0.12069	0	G|0.898;A|0.102	0.102	strong	.	MUC4	1505	.	NM_018406	exon2	c.C6348T	p.T2116T	AGCATCGGTGTCA	.	PASS	Atlas-SNP
TAS2R31	259290	hgsc.bcm.edu	37	12	11183512	11183512	+	Silent	SNP	A	A	G	rs12370363	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	116	39	140	0	0.336207	0	A|0.785;G|0.215	0.215	strong	.	TAS2R31	24	.	NM_176885	exon1	c.T423C	p.A141A	TTGACAAGCCAAA	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29912086	29912086	+	Silent	SNP	G	G	A	rs2231092	byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	132	26	118	0	0.19697	0	G|0.580;A|0.420	0.420	strong	.	HLA-A	89	.	NM_001242758	exon4	c.G807A	p.A269A	GTGGGCGGCTGTG	.	PASS	Atlas-SNP
C6orf226	441150	hgsc.bcm.edu	37	6	42858524	42858524	+	Missense_Mutation	SNP	C	C	T	rs61732354	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	151	82	114	0	0.543046	0	C|0.982;T|0.018	0.018	strong	.	C6orf226	8	.	NM_001008739	exon1	c.G3A	p.M1I	ACGCTCCATGTCG	.	PASS	Atlas-SNP
TCP10L	140290	hgsc.bcm.edu	37	21	33956579	33956579	+	Silent	SNP	T	T	C	rs2017816	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	189	189	131	0	1	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
HLA-C	3107	hgsc.bcm.edu	37	6	31239449	31239449	+	Missense_Mutation	SNP	C	C	G	rs28626310	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	190	186	191	0	0.978947	0	C|0.840;G|0.160	0.160	strong	.	HLA-C	92	.	NM_002117	exon2	c.G270C	p.K90N	CTTGTACTTCTGT	.	PASS	Atlas-SNP
WBSCR17	64409	hgsc.bcm.edu	37	7	71177023	71177023	+	Silent	SNP	G	G	A	rs75947590	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	58	28	57	0	0.482759	0	G|0.998;A|0.002	0.002	strong	.	WBSCR17	208	.	NM_022479	exon11	c.G1689A	p.K563K	GAACAAGGGCACG	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	140	102	111	0	0.728571	0	A|0.517;0|0.025	.	strong	.	GPR112	459	.	NM_153834	exon6	c.A828G	p.I276M	ACCTATATTTGCA	.	PASS	Atlas-SNP
S100A7A	338324	hgsc.bcm.edu	37	1	153391729	153391729	+	Missense_Mutation	SNP	G	G	A	rs56232841		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	258	117	214	0	0.453488	0	.	.	weak	S100A7A,rectum,carcinoma,0,2	S100A7A	24	2	NM_176823	exon3	c.G250A	p.A84T	ATAGCCGCAGACT	.	PASS	Atlas-SNP
PRSS36	146547	hgsc.bcm.edu	37	16	31152818	31152818	+	Missense_Mutation	SNP	C	C	T	rs117442264	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	32	12	25	0	0.375	0	C|0.990;T|0.010	0.010	strong	.	PRSS36	50	.	NM_001258291	exon12	c.G1873A	p.V625I	CCAGGACCCAGCC	.	PASS	Atlas-SNP
PIFO	128344	hgsc.bcm.edu	37	1	111891170	111891170	+	Missense_Mutation	SNP	A	A	C	rs15396	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	50	83	0	0.581395	0	A|0.957;C|0.043	0.043	strong	.	.	.	.	NM_181643	exon4	c.A291C	p.K97N	CCAGAAAGTAAGT	.	PASS	Atlas-SNP
ZC3H12C	85463	hgsc.bcm.edu	37	11	110035262	110035262	+	Silent	SNP	A	A	G	rs1026608	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85	16	61	0	0.188235	0	A|0.746;G|0.254	0.254	strong	.	ZC3H12C	83	.	NM_033390	exon6	c.A1452G	p.R484R	CAAACGAGGTGCT	.	PASS	Atlas-SNP
SPANXE	171489	hgsc.bcm.edu	37	X	140785741	140785741	+	Missense_Mutation	SNP	A	A	C	rs144554749	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	587	81	372	0	0.13799	0	.	.	weak	.	.	.	.	NM_145665	exon2	c.T175G	p.F59V	TTTTAAAGTTCCT	.	PASS	Atlas-SNP
EP400	57634	hgsc.bcm.edu	37	12	132508389	132508389	+	Silent	SNP	A	A	G	rs7133119	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	179	92	165	0	0.513967	0	A|0.700;G|0.300	0.300	strong	EP400,NS,carcinoma,0,1	EP400	370	1	NM_015409	exon24	c.A4758G	p.P1586P	TCAGCCAGAGACG	.	PASS	Atlas-SNP
PPT2	9374	hgsc.bcm.edu	37	6	32122472	32122472	+	Missense_Mutation	SNP	C	C	A	rs3096696	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	99	83	91	0	0.838384	0	C|0.825;A|0.175	0.175	strong	.	PPT2	19	.	NM_138717	exon2	c.C119A	p.A40E	ACCGCGCGTCCTA	.	PASS	Atlas-SNP
CEP57	9702	hgsc.bcm.edu	37	11	95564259	95564259	+	Missense_Mutation	SNP	A	A	G	rs644799	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	135	17	141	0	0.125926	0	T|0.005;G|0.275;C|0.007;N|0.000;A|0.713	0.275	strong	CEP57,colon,carcinoma,0,1	CEP57	40	1	NM_014679	exon11	c.A1342G	p.R448G	GAAGAAAGAAACA	.	PASS	Atlas-SNP
TSNARE1	203062	hgsc.bcm.edu	37	8	143425406	143425406	+	Silent	SNP	C	C	T	rs80309837	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	56	30	54	0	0.535714	0	C|0.971;T|0.029	0.029	strong	.	TSNARE1	59	.	NM_145003	exon4	c.G666A	p.T222T	CACGGGCGTGAGA	.	PASS	Atlas-SNP
MAP2K2	5605	hgsc.bcm.edu	37	19	4102449	4102449	+	Silent	SNP	G	G	A	rs17851657	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	36	12	24	0	0.333333	0	G|0.865;A|0.135	0.135	strong	MAP2K2_ENST00000262948,NS,carcinoma,0,1	MAP2K2	72	1	NM_030662	exon4	c.C453T	p.D151D	GCCGCCGTCCTAG	.	PASS	Atlas-SNP
PLXNB3	5365	hgsc.bcm.edu	37	X	153035798	153035798	+	Missense_Mutation	SNP	G	G	A	rs2266879	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	145	141	102	0	0.972414	0	G|0.542;A|0.458	0.458	strong	.	PLXNB3	208	.	NM_001163257	exon10	c.G1861A	p.V621I	GACCACGTCACTG	.	PASS	Atlas-SNP
AFAP1	60312	hgsc.bcm.edu	37	4	7780582	7780582	+	Missense_Mutation	SNP	C	C	T	rs41264705	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	31	31	27	0	1	0	C|0.800;T|0.200	0.200	strong	.	AFAP1	93	.	NM_001134647	exon14	c.G1804A	p.V602M	ACGCCACGGGGGG	.	PASS	Atlas-SNP
ZNF302	55900	hgsc.bcm.edu	37	19	35175592	35175592	+	Missense_Mutation	SNP	G	G	A	rs78654759		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	34	69	0	0.53125	0	G|0.500;A|0.500	0.500	weak	ZNF302,right_upper_lobe,carcinoma,+1,1	ZNF302	27	1	NM_018443	exon5	c.G650A	p.S217N	TCCTCAGTCGCCA	.	scavenged	Atlas-SNP
DOCK11	139818	hgsc.bcm.edu	37	X	117700141	117700141	+	Silent	SNP	A	A	G	rs2286977	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	121	45	78	0	0.371901	0	0|0.012;G|0.317	0.317	strong	.	DOCK11	185	.	NM_144658	exon8	c.A867G	p.A289A	AACAGCACAAGGT	.	PASS	Atlas-SNP
PARP1	142	hgsc.bcm.edu	37	1	226573364	226573364	+	Silent	SNP	A	A	G	rs1805414	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	24	61	0	0.461538	0	A|0.543;G|0.457	0.457	strong	.	PARP1	100	.	NM_001618	exon7	c.T852C	p.A284A	GCCATCAGCTACT	.	PASS	Atlas-SNP
OGFR	11054	hgsc.bcm.edu	37	20	61444660	61444660	+	Missense_Mutation	SNP	C	C	A	rs61743079	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	8	3	4	0	0.375	0	C|0.981;A|0.019	0.019	weak	OGFR,NS,neuroblastoma,0,1	OGFR	63	1	NM_007346	exon7	c.C1693A	p.R565S	GGCCCCCGCCCGG	.	scavenged	Atlas-SNP
RAB21	23011	hgsc.bcm.edu	37	12	72148943	72148943	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	11	9	0	0	0.818182	.	.	.	none	.	RAB21	17	.	NM_014999	exon1	c.G34A	p.A12T	GGGGCGGCGGCGG	.	PASS	Atlas-SNP
NEU4	129807	hgsc.bcm.edu	37	2	242758203	242758203	+	Silent	SNP	T	T	C	rs2293763	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	90	32	138	1	0.355556	0.00724638	T|0.640;C|0.360	0.360	strong	NEU4,NS,carcinoma,0,1	NEU4	39	1	NM_001167599	exon4	c.T1323C	p.A441A	GCCGGCTCCTGAG	.	scavenged	Atlas-SNP
PCDHB10	56126	hgsc.bcm.edu	37	5	140572729	140572729	+	Missense_Mutation	SNP	C	C	T	rs189437073	bycluster;by1000genomes;alternate_allele	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	2	118	0	0.0232558	0	C|0.997;A|0.003	.	alt	PCDHB10,NS,lymphoid_neoplasm,0,1	PCDHB10	177	1	NM_018930	exon1	c.C604T	p.R202W	CTGGATCGGGAGG	.	scavenged	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179582327	179582327	+	Missense_Mutation	SNP	C	C	T	rs13390491	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	227	108	240	0	0.475771	0	C|0.774;T|0.226	0.226	strong	.	TTN	18412	.	NM_001267550	exon87	c.G25274A	p.S8425N	ATGTGGCTCTGGT	.	PASS	Atlas-SNP
MED24	9862	hgsc.bcm.edu	37	17	38186106	38186106	+	Silent	SNP	C	C	T	rs11555255	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	136	69	135	0	0.507353	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
JAKMIP1	152789	hgsc.bcm.edu	37	4	6062160	6062160	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83	29	92	0	0.349398	0	.	.	none	.	JAKMIP1	250	.	NM_001099433	exon11	c.G1635A	p.E545E	TCCCTTCTCAACC	.	PASS	Atlas-SNP
HSD17B7	51478	hgsc.bcm.edu	37	1	162760622	162760622	+	Missense_Mutation	SNP	G	G	C	rs116929795	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	273	135	301	1	0.494505	0.00332226	G|0.996;C|0.004	0.004	strong	.	HSD17B7	25	.	NM_016371	exon1	c.G32C	p.S11T	GGGCTAGCAGGTG	.	PASS	Atlas-SNP
STX1A	6804	hgsc.bcm.edu	37	7	73122923	73122923	+	Silent	SNP	A	A	G	rs2228607	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	70	90	0	0.985915	0	A|0.473;G|0.527	0.527	strong	.	STX1A	16	.	NM_004603	exon3	c.T204C	p.D68D	ACTCTCATCGGGG	.	PASS	Atlas-SNP
TIMP1	7076	hgsc.bcm.edu	37	X	47444985	47444985	+	Silent	SNP	T	T	C	rs4898	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	102	102	73	0	1	0	T|0.536;C|0.464	0.464	strong	.	TIMP1	12	.	NM_003254	exon5	c.T372C	p.F124F	CAGTTTTGTGGCT	.	PASS	Atlas-SNP
DTHD1	401124	hgsc.bcm.edu	37	4	36317970	36317970	+	Silent	SNP	T	T	C	rs9995922	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72	42	68	0	0.583333	0	T|0.642;C|0.358	0.358	strong	.	DTHD1	63	.	NM_001170700	exon7	c.T1827C	p.S609S	CTATAGTTGCCCT	.	PASS	Atlas-SNP
C16orf71	146562	hgsc.bcm.edu	37	16	4790273	4790273	+	Silent	SNP	G	G	A	rs859305	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	103	101	108	1	0.980583	0.00925926	G|0.414;A|0.586	0.586	strong	.	C16orf71	46	.	NM_139170	exon4	c.G396A	p.E132E	TGGTGAGGTCAGC	.	PASS	Atlas-SNP
DHX37	57647	hgsc.bcm.edu	37	12	125461976	125461976	+	Missense_Mutation	SNP	C	C	T	rs33931896	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	155	66	143	0	0.425806	0	C|0.980;T|0.020	0.020	strong	.	DHX37	114	.	NM_032656	exon5	c.G799A	p.E267K	GGTGCTCGGCCAC	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29911957	29911957	+	Silent	SNP	G	G	A	rs77380700		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	280	26	178	0	0.0928571	0	.	.	weak	.	HLA-A	89	.	NM_001242758	exon4	c.G678A	p.R226R	CCTGAGGTGCTGG	.	PASS	Atlas-SNP
TRO	7216	hgsc.bcm.edu	37	X	54951464	54951464	+	Missense_Mutation	SNP	C	C	T	rs45448595	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	213	150	156	0	0.704225	0	C|0.970;T|0.030	0.030	strong	.	TRO	246	.	NM_016157	exon6	c.C1448T	p.P483L	ATTTCCCAGAAAT	.	PASS	Atlas-SNP
TNFRSF8	943	hgsc.bcm.edu	37	1	12164437	12164437	+	Silent	SNP	C	C	T	rs2230622	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	43	90	0	0.494253	0	C|0.611;A|0.050	.	strong	.	TNFRSF8	70	.	NM_001243	exon4	c.C270T	p.D90D	CTTAGACGACCTC	.	PASS	Atlas-SNP
IGSF8	93185	hgsc.bcm.edu	37	1	160062340	160062340	+	Silent	SNP	G	G	A	rs41265757	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	67	61	0	1	0	G|0.910;A|0.090	0.090	strong	.	IGSF8	59	.	NM_052868	exon5	c.C1458T	p.D486D	CTCTCCGTCCTCT	.	PASS	Atlas-SNP
ZNF423	23090	hgsc.bcm.edu	37	16	49671218	49671218	+	Silent	SNP	C	C	T	rs16947741	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	155	75	152	0	0.483871	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
KCNH7	90134	hgsc.bcm.edu	37	2	163228507	163228507	+	Silent	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	77	33	117	0	0.428571	0	.	.	none	KCNH7,NS,carcinoma,0,1	KCNH7	378	1	NM_033272	exon16	c.T3423G	p.T1141T	AAGTGAAGTCAAG	.	PASS	Atlas-SNP
HELZ2	85441	hgsc.bcm.edu	37	20	62194238	62194238	+	Silent	SNP	C	C	T	rs34996572	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	70	33	67	0	0.471429	0	C|0.984;T|0.016	0.016	strong	.	.	.	.	NM_001037335	exon9	c.G5937A	p.P1979P	CCCCTGCGGCGTC	.	PASS	Atlas-SNP
CCDC64B	146439	hgsc.bcm.edu	37	16	3085335	3085335	+	Missense_Mutation	SNP	G	G	C	rs7204908	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	88	44	109	3	0.5	0.0275229	G|0.592;C|0.408	0.408	strong	CCDC64B,NS,carcinoma,0,1	CCDC64B	19	1	NM_001103175	exon1	c.C163G	p.Q55E	TCTGCTGCAGCTG	.	scavenged	Atlas-SNP
ALDH1A1	216	hgsc.bcm.edu	37	9	75545882	75545882	+	Silent	SNP	G	G	A	rs13959	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	43	85	0	0.511905	0	G|0.598;A|0.402	0.402	strong	.	ALDH1A1	98	.	NM_000689	exon3	c.C225T	p.S75S	CCACGGGGATCCA	.	PASS	Atlas-SNP
OR10H2	26538	hgsc.bcm.edu	37	19	15839459	15839459	+	Silent	SNP	G	G	A	rs11669315	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	136	67	117	0	0.492647	0	G|0.839;A|0.161	0.161	strong	.	OR10H2	59	.	NM_013939	exon1	c.G606A	p.L202L	GGGCTTGGTATGT	.	PASS	Atlas-SNP
HRNR	388697	hgsc.bcm.edu	37	1	152186614	152186614	+	Silent	SNP	C	C	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	1337	55	507	1	0.0411369	0.00197239	.	.	none	HRNR,NS,carcinoma,0,1	HRNR	403	1	NM_001009931	exon3	c.G7491C	p.S2497S	ACAGCTCGATGAC	.	scavenged	Atlas-SNP
PKHD1	5314	hgsc.bcm.edu	37	6	51720838	51720838	+	Silent	SNP	T	T	C	rs9349603	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	146	67	147	0	0.458904	0	T|0.577;C|0.423	0.423	strong	.	PKHD1	927	.	NM_170724	exon49	c.A7764G	p.L2588L	CATGGTTAAATCA	.	PASS	Atlas-SNP
SMYD1	150572	hgsc.bcm.edu	37	2	88387508	88387508	+	Silent	SNP	C	C	A	rs113636517	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	191	132	239	1	0.691099	0.0041841	C|0.995;A|0.005	0.005	strong	.	SMYD1	95	.	NM_198274	exon3	c.C442A	p.R148R	GACCTGCGGGTGG	.	PASS	Atlas-SNP
AK7	122481	hgsc.bcm.edu	37	14	96944878	96944878	+	Silent	SNP	G	G	A	rs76293597	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	120	64	93	0	0.533333	0	G|0.957;A|0.043	0.043	strong	.	AK7	69	.	NM_152327	exon15	c.G1632A	p.A544A	CGTGGCGGGGACC	.	PASS	Atlas-SNP
BLVRA	644	hgsc.bcm.edu	37	7	43846603	43846603	+	Silent	SNP	A	A	G	rs7738	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55	18	84	0	0.327273	0	A|0.555;G|0.445	0.445	strong	.	BLVRA	26	.	NM_001253823	exon9	c.A660G	p.G220G	AAAAGGACCTGGT	.	PASS	Atlas-SNP
CDC20B	166979	hgsc.bcm.edu	37	5	54410099	54410099	+	Missense_Mutation	SNP	G	G	A	rs444527	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	125	69	124	0	0.552	0	G|0.861;A|0.139	0.139	strong	CDC20B,bladder,carcinoma,+2,2	CDC20B	61	2	NM_001170402	exon12	c.C1507T	p.R503W	ACACCCGGGTCTG	.	PASS	Atlas-SNP
ONECUT2	9480	hgsc.bcm.edu	37	18	55143766	55143766	+	Silent	SNP	C	C	T	rs3745074	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	43	109	0	0.494253	0	C|0.638;T|0.362	0.362	strong	ONECUT2,NS,carcinoma,+1,1	ONECUT2	42	1	NM_004852	exon2	c.C1326T	p.F442F	ACTCTTCGCCATC	.	PASS	Atlas-SNP
CLDN16	10686	hgsc.bcm.edu	37	3	190106074	190106074	+	Missense_Mutation	SNP	G	G	C	rs3214506	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	155	86	179	0	0.554839	0	G|0.753;C|0.247	0.247	strong	.	CLDN16	59	.	NM_006580	exon1	c.G166C	p.A56P	GCCAGGGCTGGTG	.	PASS	Atlas-SNP
CDH17	1015	hgsc.bcm.edu	37	8	95158259	95158259	+	Silent	SNP	G	G	A	rs2251734	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	147	68	126	0	0.462585	0	G|0.692;A|0.308	0.308	strong	.	CDH17	119	.	NM_004063	exon15	c.C2064T	p.F688F	AGCCTCGAAAATG	.	PASS	Atlas-SNP
RBM44	375316	hgsc.bcm.edu	37	2	238725962	238725962	+	Missense_Mutation	SNP	G	G	A	rs182474506	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	99	44	103	0	0.444444	0	G|0.999;A|0.001	0.001	strong	.	RBM44	167	.	NM_001080504	exon3	c.G403A	p.D135N	GAATTAGATCCTG	.	PASS	Atlas-SNP
PDE4DIP	9659	hgsc.bcm.edu	37	1	144863438	144863438	+	Missense_Mutation	SNP	G	G	T	rs140993521	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	182	17	206	1	0.0934066	0.00485437	.	.	weak	PDE4DIP_ENST00000369356,NS,carcinoma,0,2	PDE4DIP	817	2	NM_014644	exon37	c.C5965A	p.Q1989K	TGTGCTGCAGTCT	.	scavenged	Atlas-SNP
GPRC6A	222545	hgsc.bcm.edu	37	6	117114290	117114290	+	Missense_Mutation	SNP	A	A	G	rs35937022	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	142	141	95	0	0.992958	0	A|0.803;G|0.197	0.197	strong	.	GPRC6A	152	.	NM_148963	exon6	c.T1796C	p.I599T	GAGAGAATCAGGA	.	PASS	Atlas-SNP
MAPT	4137	hgsc.bcm.edu	37	17	44071294	44071294	+	Silent	SNP	T	T	C	rs62063845	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	90	90	93	0	1	0	T|0.860;C|0.140	0.140	strong	.	MAPT	135	.	NM_001123066	exon10	c.T1512C	p.T504T	AGCGACTAAGCAA	.	PASS	Atlas-SNP
ZNF37A	7587	hgsc.bcm.edu	37	10	38407519	38407519	+	Silent	SNP	A	A	G	rs176889	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	41	41	65	0	1	0	A|0.502;G|0.498	0.498	strong	.	ZNF37A	118	.	NM_003421	exon7	c.A1440G	p.S480S	GAAGTCAGCCCTA	.	PASS	Atlas-SNP
CRISP1	167	hgsc.bcm.edu	37	6	49814379	49814379	+	Missense_Mutation	SNP	T	T	C	rs3209304	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	114	56	130	0	0.491228	0	T|0.762;G|0.006;C|0.078;A|0.154	0.078	strong	.	CRISP1	45	.	NM_001205220	exon5	c.A289G	p.T97A	AAAAGGTATCTGA	.	PASS	Atlas-SNP
PPAP2C	8612	hgsc.bcm.edu	37	19	288062	288062	+	Silent	SNP	G	G	A	rs11542542	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	171	61	132	0	0.356725	0	G|0.935;A|0.065	0.065	strong	PPAP2C_ENST00000269812,NS,carcinoma,0,2	PPAP2C	38	2	NM_177543	exon2	c.C225T	p.H75H	GAGCCCGTGGGTG	.	PASS	Atlas-SNP
DDX51	317781	hgsc.bcm.edu	37	12	132625027	132625027	+	Silent	SNP	G	G	A	rs61942919	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	32	87	0	0.380952	0	G|0.995;A|0.005	0.005	strong	DDX51,NS,carcinoma,-1,1	DDX51	33	1	NM_175066	exon11	c.C1614T	p.R538R	CCCGTAGCGCGAG	.	PASS	Atlas-SNP
ZNF131	7690	hgsc.bcm.edu	37	5	43173541	43173541	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85	38	87	0	0.447059	0	.	.	none	.	ZNF131	51	.	NM_003432	exon7	c.C1074T	p.Y358Y	GCTCTACGAATGC	.	PASS	Atlas-SNP
NCK1	4690	hgsc.bcm.edu	37	3	136664737	136664737	+	Missense_Mutation	SNP	C	C	T	rs13320485	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	142	79	124	0	0.556338	0	C|0.989;T|0.011	0.011	strong	.	NCK1	26	.	NM_006153	exon3	c.C539T	p.A180V	AATTAGCAGCAGT	.	PASS	Atlas-SNP
ARHGAP30	257106	hgsc.bcm.edu	37	1	161017761	161017761	+	Missense_Mutation	SNP	C	C	T	rs112388093	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	52	83	0	0.597701	0	C|0.980;T|0.020	0.020	strong	.	ARHGAP30	105	.	NM_001025598	exon12	c.G3050A	p.R1017Q	TGGGTTCGCCGAA	.	PASS	Atlas-SNP
TTC7A	57217	hgsc.bcm.edu	37	2	47177617	47177617	+	Silent	SNP	C	C	T	rs61738825	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	28	62	0	0.373333	0	C|0.928;T|0.072	0.072	strong	.	TTC7A	80	.	NM_020458	exon2	c.C300T	p.S100S	GATGAGCGAAGCC	.	PASS	Atlas-SNP
RBMXL3	139804	hgsc.bcm.edu	37	X	114425238	114425238	+	Missense_Mutation	SNP	G	G	A	rs55718100	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	35	12	34	0	0.342857	0	G|0.930;A|0.070	0.070	strong	.	RBMXL3	83	.	NM_001145346	exon1	c.G1234A	p.G412S	AGTTACGGCCAGA	.	PASS	Atlas-SNP
HHLA2	11148	hgsc.bcm.edu	37	3	108081277	108081277	+	Missense_Mutation	SNP	C	C	A	rs6779094	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	38	74	0	0.452381	0	C|0.868;A|0.132	0.132	strong	.	HHLA2	95	.	NM_007072	exon7	c.C1092A	p.S364R	TTGGAGCGTAAAA	.	PASS	Atlas-SNP
BTBD2	55643	hgsc.bcm.edu	37	19	1986520	1986520	+	Silent	SNP	G	G	A	rs7253519	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	135	66	137	0	0.488889	0	A|0.103;C|0.000;G|0.897	0.103	strong	BTBD2,NS,carcinoma,0,1	BTBD2	31	1	NM_017797	exon9	c.C1545T	p.D515D	CTGGCCGTCCTCC	.	PASS	Atlas-SNP
COL15A1	1306	hgsc.bcm.edu	37	9	101804366	101804366	+	Missense_Mutation	SNP	T	T	C	rs35901514	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	37	54	0	0.552239	0	T|0.993;C|0.007	0.007	strong	.	COL15A1	211	.	NM_001855	exon24	c.T2551C	p.F851L	CCTGGCTTTCCAG	.	PASS	Atlas-SNP
CCDC135	84229	hgsc.bcm.edu	37	16	57762401	57762401	+	Missense_Mutation	SNP	T	T	C	rs2923147	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	160	90	167	0	0.5625	0	T|0.627;C|0.373	0.373	strong	CCDC135,NS,carcinoma,0,1	CCDC135	97	1	NM_032269	exon16	c.T2296C	p.C766R	CTAACATGCTGGC	.	PASS	Atlas-SNP
GATC	283459	hgsc.bcm.edu	37	12	120884328	120884328	+	Silent	SNP	C	C	T	rs2235217	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69	33	58	0	0.478261	0	C|0.744;T|0.256	0.256	strong	.	GATC	12	.	NM_176818	exon1	c.C45T	p.G15G	TCTGGGCGGGCGC	.	PASS	Atlas-SNP
EPPK1	83481	hgsc.bcm.edu	37	8	144940331	144940331	+	Missense_Mutation	SNP	C	C	T	rs200585601	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	176	45	131	1	0.255682	0.00763359	C|0.997;T|0.003	0.003	weak	EPPK1,NS,carcinoma,0,6	EPPK1	199	6	NM_031308	exon1	c.G7091A	p.R2364Q	CCGCGCCGGTAGG	.	scavenged	Atlas-SNP
MAP10	54627	hgsc.bcm.edu	37	1	232941354	232941354	+	Silent	SNP	G	G	T	rs12567597	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	27	18	20	0	0.666667	0	G|0.858;T|0.142	0.142	strong	.	.	.	.	NM_019090	exon1	c.G585T	p.L195L	CGGTCTGTGCCCC	.	PASS	Atlas-SNP
FREM1	158326	hgsc.bcm.edu	37	9	14801738	14801738	+	Missense_Mutation	SNP	G	G	C	rs16932300	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	206	101	236	0	0.490291	0	G|0.839;C|0.161	0.161	strong	.	FREM1	261	.	NM_144966	exon21	c.C3606G	p.S1202R	GTCTTTGCTAAAC	.	PASS	Atlas-SNP
DPP4	1803	hgsc.bcm.edu	37	2	162929979	162929979	+	Silent	SNP	A	A	G	rs17574	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57	23	99	0	0.403509	0	A|0.720;G|0.280	0.280	strong	.	DPP4	90	.	NM_001935	exon2	c.T24C	p.L8L	TCCCAGAAGAACC	.	PASS	Atlas-SNP
CARD11	84433	hgsc.bcm.edu	37	7	2983886	2983886	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	199	88	174	0	0.442211	0	.	.	none	CARD11,colon,carcinoma,-1,6	CARD11	339	6	NM_032415	exon5	c.A644T	p.K215M	ATGTTCTTCTCCT	.	PASS	Atlas-SNP
USP13	8975	hgsc.bcm.edu	37	3	179424788	179424788	+	Missense_Mutation	SNP	T	T	C	rs141550831	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	150	89	157	0	0.593333	0	T|0.999;C|0.001	0.001	strong	USP13,NS,carcinoma,-1,1	USP13	117	1	NM_003940	exon5	c.T544C	p.W182R	GACACGTGGGAAA	.	PASS	Atlas-SNP
ZBBX	79740	hgsc.bcm.edu	37	3	167000256	167000256	+	Missense_Mutation	SNP	G	G	C	rs12638625	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	129	54	158	0	0.418605	0	G|0.622;C|0.378	0.378	strong	.	ZBBX	299	.	NM_001199201	exon20	c.C2024G	p.A675G	AAATTTGCTGTTG	.	PASS	Atlas-SNP
NEBL	10529	hgsc.bcm.edu	37	10	21134282	21134282	+	Missense_Mutation	SNP	C	C	G	rs41277370	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	45	22	30	0	0.488889	0	C|0.937;G|0.063	0.063	strong	NEBL,NS,carcinoma,0,1	NEBL	199	1	NM_006393	exon12	c.G1132C	p.D378H	CAAAATCCTCTTT	.	PASS	Atlas-SNP
CARNS1	57571	hgsc.bcm.edu	37	11	67191449	67191449	+	Silent	SNP	T	T	C	rs1790747	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	70	13	81	0	0.185714	0	T|0.648;C|0.352	0.352	strong	.	CARNS1	60	.	NM_001166222	exon10	c.T2230C	p.L744L	GGGCGGTTGCTGG	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228412228	228412228	+	Missense_Mutation	SNP	G	G	A	rs1757153	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	130	56	151	0	0.430769	0	G|0.756;A|0.244	0.244	strong	.	OBSCN	2142	.	NM_001271223	exon10	c.G2998A	p.A1000T	GCCAGTGCCACAC	.	PASS	Atlas-SNP
SEL1L2	80343	hgsc.bcm.edu	37	20	13912308	13912308	+	Missense_Mutation	SNP	C	C	T	rs143129534	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	108	40	98	1	0.37037	0.0102041	C|0.988;T|0.012	0.012	strong	SEL1L2,colon,carcinoma,-1,1	SEL1L2	103	1	NM_001271539	exon3	c.G224A	p.R75H	ATTTTACGTTGAT	.	scavenged	Atlas-SNP
ESRP1	54845	hgsc.bcm.edu	37	8	95690579	95690579	+	Silent	SNP	T	T	C	rs12677519	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	96	96	98	0	1	0	T|0.494;C|0.506	0.506	strong	.	ESRP1	148	.	NM_001122825	exon13	c.T1800C	p.N600N	CATGAATTACACA	.	PASS	Atlas-SNP
JAG1	182	hgsc.bcm.edu	37	20	10653469	10653469	+	Silent	SNP	C	C	T	rs1051415	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	36	46	0	0.486486	0	C|0.922;T|0.078	0.078	strong	.	JAG1	213	.	NM_000214	exon2	c.G267A	p.G89G	GGGCCCCCCGGCC	.	PASS	Atlas-SNP
CHPT1	56994	hgsc.bcm.edu	37	12	102108301	102108301	+	Silent	SNP	T	T	C	rs2066920	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	165	85	151	0	0.515152	0	C|0.107;T|0.893	0.107	strong	.	CHPT1	27	.	NM_020244	exon3	c.T441C	p.A147A	GGGAGCTTCAATT	.	PASS	Atlas-SNP
ARHGAP18	93663	hgsc.bcm.edu	37	6	129929191	129929191	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	38	9	25	0	0.236842	0	.	.	none	.	ARHGAP18	52	.	NM_033515	exon9	c.T1129G	p.C377G	CTTGGCAAAGATT	.	PASS	Atlas-SNP
SETX	23064	hgsc.bcm.edu	37	9	135172412	135172412	+	Silent	SNP	A	A	G	rs2296869	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	88	45	71	0	0.511364	0	A|0.628;G|0.372	0.372	strong	.	SETX	234	.	NM_015046	exon14	c.T5811C	p.D1937D	CTTTTGATCTTCA	.	PASS	Atlas-SNP
NACAD	23148	hgsc.bcm.edu	37	7	45120282	45120282	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	115	74	131	0	0.643478	0	.	.	none	.	NACAD	44	.	NM_001146334	exon7	c.G4631A	p.R1544Q	AGAGCCCGCACGG	.	PASS	Atlas-SNP
C9orf50	375759	hgsc.bcm.edu	37	9	132375432	132375432	+	Missense_Mutation	SNP	C	C	T	rs2302779	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	29	39	0	0.467742	0	C|0.835;T|0.165	0.165	strong	.	C9orf50	25	.	NM_199350	exon6	c.G1142A	p.R381Q	CTGCTTCGCGGCC	.	PASS	Atlas-SNP
GPBP1L1	60313	hgsc.bcm.edu	37	1	46095272	46095272	+	Silent	SNP	T	T	C	rs1135812	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	34	107	0	0.395349	0	T|0.709;C|0.291;A|0.000	0.291	strong	.	GPBP1L1	43	.	NM_021639	exon12	c.A1248G	p.K416K	GAACTCTTTGAGC	.	PASS	Atlas-SNP
ATXN7	6314	hgsc.bcm.edu	37	3	63967900	63967900	+	Missense_Mutation	SNP	A	A	G	rs1053338	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98	44	115	0	0.44898	0	A|0.876;G|0.124	0.124	strong	.	ATXN7	126	.	NM_000333	exon7	c.A791G	p.K264R	ATCCGAAAATGGA	.	PASS	Atlas-SNP
DPYSL4	10570	hgsc.bcm.edu	37	10	134013906	134013906	+	Silent	SNP	C	C	T	rs56326856	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	102	49	100	0	0.480392	0	C|0.833;T|0.167	0.167	strong	DPYSL4,caecum,carcinoma,+1,8	DPYSL4	91	8	NM_006426	exon9	c.C858T	p.D286D	CACCGACGGTTCA	.	PASS	Atlas-SNP
PARP11	57097	hgsc.bcm.edu	37	12	3931308	3931308	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93	12	87	0	0.129032	0	.	.	none	.	PARP11	39	.	NM_020367	exon5	c.C360T	p.N120N	GGCCTCGTTTTCA	.	PASS	Atlas-SNP
PCSK1N	27344	hgsc.bcm.edu	37	X	48690749	48690749	+	Silent	SNP	C	C	T	rs11538178	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	13	10	10	0	0.769231	0	C|0.763;T|0.237	0.237	strong	.	PCSK1N	6	.	NM_013271	exon2	c.G117A	p.E39E	GCGGGGCTCCTGC	.	PASS	Atlas-SNP
MAPT	4137	hgsc.bcm.edu	37	17	44061278	44061278	+	Missense_Mutation	SNP	C	C	T	rs17651549	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	36	36	31	0	1	0	C|0.867;T|0.133	0.133	strong	.	MAPT	135	.	NM_001123066	exon6	c.C1108T	p.R370W	GTCAGCCGGGTCC	.	PASS	Atlas-SNP
KRT32	3882	hgsc.bcm.edu	37	17	39620399	39620399	+	Silent	SNP	C	C	T	rs12948056	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	138	69	174	0	0.5	0	C|0.683;N|0.000	.	strong	KRT32,rectum,carcinoma,0,1	KRT32	57	1	NM_002278	exon5	c.G927A	p.Q309Q	GTCTGACTGGTAG	.	PASS	Atlas-SNP
ZC3H3	23144	hgsc.bcm.edu	37	8	144522387	144522387	+	Nonsense_Mutation	SNP	G	G	T	rs2272754	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	77	34	68	0	0.441558	0	G|0.879;T|0.121	0.121	strong	.	ZC3H3	75	.	NM_015117	exon11	c.C2639A	p.S880X	GGGGATGAGGAGG	.	PASS	Atlas-SNP
FLNC	2318	hgsc.bcm.edu	37	7	128470838	128470838	+	Silent	SNP	C	C	T	rs3734972	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	253	144	199	0	0.56917	0	C|0.885;T|0.115	0.115	strong	.	FLNC	339	.	NM_001127487	exon1	c.C147T	p.H49H	TGAGCACCTCAAG	.	PASS	Atlas-SNP
OR2L8	391190	hgsc.bcm.edu	37	1	248112554	248112554	+	Missense_Mutation	SNP	T	T	C	rs202165563		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	178	22	157	0	0.123596	0	.	.	weak	OR2L8,trunk,malignant_melanoma,0,1	OR2L8	92	1	NM_001001963	exon1	c.T395C	p.L132P	ACTATCTCATCCG	.	scavenged	Atlas-SNP
SACS	26278	hgsc.bcm.edu	37	13	23911820	23911820	+	Silent	SNP	A	A	G	rs4143768	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	35	16	52	0	0.457143	0	A|0.760;G|0.240	0.240	strong	.	SACS	871	.	NM_014363	exon10	c.T6195C	p.I2065I	TTCTTGAATATTT	.	PASS	Atlas-SNP
CCDC15	80071	hgsc.bcm.edu	37	11	124862514	124862514	+	Silent	SNP	A	A	G	rs6590113	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	43	45	0	0.826923	0	A|0.728;G|0.272	0.272	strong	.	CCDC15	134	.	NM_025004	exon10	c.A2070G	p.E690E	GAGAGAAGAATTG	.	PASS	Atlas-SNP
SLC28A3	64078	hgsc.bcm.edu	37	9	86920236	86920236	+	Silent	SNP	T	T	C	rs7867504	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	116	48	102	0	0.413793	0	C|0.517;N|0.000	0.517	strong	SLC28A3,NS,carcinoma,-1,1	SLC28A3	72	1	NM_001199633	exon4	c.A267G	p.T89T	ACATACTGTGTCA	.	PASS	Atlas-SNP
ENPP2	5168	hgsc.bcm.edu	37	8	120569823	120569823	+	Missense_Mutation	SNP	G	G	A	rs61738778	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	106	51	120	0	0.481132	0	G|0.996;A|0.004	0.004	strong	.	ENPP2	254	.	NM_006209	exon26	c.C2686T	p.R896C	AGCTGCGGCTGGT	.	PASS	Atlas-SNP
ARFGAP3	26286	hgsc.bcm.edu	37	22	43195147	43195147	+	Silent	SNP	A	A	G	rs1128013	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	35	35	38	0	1	0	A|0.557;G|0.443	0.443	strong	.	ARFGAP3	48	.	NM_014570	exon15	c.T1431C	p.S477S	CAGCACACTGGAC	.	PASS	Atlas-SNP
DNHD1	144132	hgsc.bcm.edu	37	11	6569896	6569896	+	Missense_Mutation	SNP	G	G	A	rs11606889	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	24	50	0	0.444444	0	G|0.887;A|0.113	0.113	strong	.	DNHD1	198	.	NM_144666	exon24	c.G7120A	p.V2374M	TATGTGGTGGACC	.	PASS	Atlas-SNP
ETFB	2109	hgsc.bcm.edu	37	19	51857774	51857774	+	Missense_Mutation	SNP	T	T	G	rs143144671	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	42	67	0	0.591549	0	T|0.998;G|0.002	0.002	strong	.	ETFB	46	.	NM_001014763	exon1	c.A119C	p.E40A	AGCCATTCCTGGG	.	PASS	Atlas-SNP
REST	5978	hgsc.bcm.edu	37	4	57797414	57797414	+	Missense_Mutation	SNP	C	C	T	rs3796529	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	70	26	68	0	0.371429	0	C|0.784;T|0.216	0.216	strong	REST,NS,carcinoma,0,1	REST	104	1	NM_001193508	exon4	c.C2390T	p.P797L	GGGAGCCACCTCC	.	PASS	Atlas-SNP
PEG3	5178	hgsc.bcm.edu	37	19	57327503	57327503	+	Silent	SNP	A	A	G	rs33931963	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	220	119	246	0	0.540909	0	A|0.767;G|0.233	0.233	strong	ZIM2_ENST00000326441,NS,carcinoma,-1,2	PEG3	414	2	NM_001146184	exon9	c.T2307C	p.Y769Y	TGCCTCATAGACA	.	PASS	Atlas-SNP
NUMA1	4926	hgsc.bcm.edu	37	11	71726785	71726785	+	Silent	SNP	A	A	G	rs17161802	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	16	89	0	0.186047	0	A|0.992;G|0.008	0.008	strong	.	NUMA1	142	.	NM_006185	exon15	c.T1764C	p.A588A	CTCTGCAGCAGTG	.	PASS	Atlas-SNP
ABCG2	9429	hgsc.bcm.edu	37	4	89061114	89061114	+	Missense_Mutation	SNP	C	C	T	rs2231137	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	138	57	175	0	0.413043	0	C|0.925;T|0.075	0.075	strong	.	ABCG2	151	.	NM_004827	exon2	c.G34A	p.V12M	GTGACACTGGGAT	.	PASS	Atlas-SNP
FAM24B	196792	hgsc.bcm.edu	37	10	124610027	124610027	+	Missense_Mutation	SNP	G	G	A	rs1891110	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	116	116	125	0	1	0	G|0.475;A|0.525	0.525	strong	.	FAM24B	9	.	NM_001204364	exon3	c.C5T	p.P2L	ATGACAGGCATAA	.	PASS	Atlas-SNP
ATP10D	57205	hgsc.bcm.edu	37	4	47560002	47560002	+	Missense_Mutation	SNP	C	C	A	rs34208443	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85	37	56	0	0.435294	0	C|0.865;A|0.135	0.135	strong	ATP10D,NS,carcinoma,-1,1	ATP10D	168	1	NM_020453	exon12	c.C2146A	p.P716T	GGACAGCCATTGG	.	PASS	Atlas-SNP
IL11	3589	hgsc.bcm.edu	37	19	55879872	55879872	+	Silent	SNP	C	C	T	rs1126757	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	117	117	113	0	1	0	C|0.636;T|0.364	0.364	strong	.	IL11	16	.	NM_000641	exon3	c.G246A	p.A82A	TGCCCCCGCACTC	.	PASS	Atlas-SNP
RYR1	6261	hgsc.bcm.edu	37	19	39002725	39002725	+	Silent	SNP	A	A	G	rs2071089	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	164	65	153	0	0.396341	0	A|0.669;G|0.331	0.331	strong	.	RYR1	708	.	NM_001042723	exon62	c.A9186G	p.P3062P	CGCCCCAGCTGTG	.	PASS	Atlas-SNP
PON2	5445	hgsc.bcm.edu	37	7	95041016	95041016	+	Missense_Mutation	SNP	G	G	C	rs12026	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	135	59	150	0	0.437037	0	G|0.746;C|0.253	0.253	strong	PON2,rectum,carcinoma,-1,1	PON2	32	1	NM_000305	exon5	c.C443G	p.A148G	TTTTCTGCTTCTT	.	PASS	Atlas-SNP
PRR22	163154	hgsc.bcm.edu	37	19	5783905	5783905	+	Missense_Mutation	SNP	G	G	A	rs3745640	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	36	12	24	0	0.333333	0	G|0.702;A|0.298	0.298	strong	.	PRR22	25	.	NM_001134316	exon3	c.C353T	p.P118L	GGCTGAGGCTCCA	.	PASS	Atlas-SNP
LONRF3	79836	hgsc.bcm.edu	37	X	118108785	118108785	+	Silent	SNP	T	T	C	rs3813933	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	99	98	66	0	0.989899	0	T|0.560;C|0.440	0.440	strong	.	LONRF3	138	.	NM_001031855	exon1	c.T42C	p.A14A	GCCCGCTGAGGTC	.	PASS	Atlas-SNP
CSPG4	1464	hgsc.bcm.edu	37	15	75981976	75981976	+	Missense_Mutation	SNP	C	C	T	rs200493777		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	156	7	118	0	0.0448718	0	C|0.999;T|0.001	0.001	weak	CSPG4,NS,carcinoma,0,2	CSPG4	175	2	NM_001897	exon3	c.G1430A	p.R477H	CCATGGCGTGCCC	.	scavenged	Atlas-SNP
TTC40	54777	hgsc.bcm.edu	37	10	134648279	134648279	+	Missense_Mutation	SNP	C	C	T	rs12356978	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	29	56	0	0.54717	0	C|0.955;T|0.045	0.045	strong	.	TTC40	100	.	NM_001200049	exon48	c.G6745A	p.E2249K	CTGGTTCCTACCG	.	PASS	Atlas-SNP
SGK3	23678	hgsc.bcm.edu	37	8	67748231	67748231	+	Silent	SNP	G	G	A	rs35809374	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	131	59	137	0	0.450382	0	G|0.875;A|0.125	0.125	strong	.	SGK3	92	.	NM_001033578	exon10	c.G663A	p.P221P	ACATCCGTTTTTG	.	PASS	Atlas-SNP
RAI1	10743	hgsc.bcm.edu	37	17	17698254	17698254	+	Silent	SNP	G	G	A	rs8067439	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44	21	52	0	0.477273	0	G|0.457;A|0.543	0.543	strong	.	RAI1	121	.	NM_030665	exon3	c.G1992A	p.P664P	GGAGCCGGAGGCC	.	PASS	Atlas-SNP
ZFAND6	54469	hgsc.bcm.edu	37	15	80414094	80414094	+	Silent	SNP	A	A	G	rs56296028	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	141	71	124	0	0.503546	0	A|0.996;G|0.004	0.004	strong	.	ZFAND6	18	.	NM_001242913	exon5	c.A195G	p.Q65Q	AGTTCAATGCACA	.	PASS	Atlas-SNP
SEC24C	9632	hgsc.bcm.edu	37	10	75527708	75527708	+	Silent	SNP	A	A	G	rs4746147	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	233	124	195	0	0.532189	0	A|0.856;G|0.144	0.144	strong	SEC24C,NS,carcinoma,0,1	SEC24C	86	1	NM_198597	exon15	c.A2124G	p.T708T	GGCCACACTCTCT	.	PASS	Atlas-SNP
RHCE	6006	hgsc.bcm.edu	37	1	25717365	25717365	+	Missense_Mutation	SNP	C	C	G	rs609320	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	146	61	150	0	0.417808	0	C|0.855;G|0.145	0.145	strong	.	RHCE	36	.	NM_138618	exon5	c.G676C	p.A226P	GCAGAGCAGAGTT	.	PASS	Atlas-SNP
MED12L	116931	hgsc.bcm.edu	37	3	151090424	151090424	+	Missense_Mutation	SNP	G	G	A	rs3732765	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	95	95	93	0	1	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
MUC16	94025	hgsc.bcm.edu	37	19	9060572	9060572	+	Silent	SNP	G	G	A	rs56405542	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	216	97	197	0	0.449074	0	G|0.788;A|0.212	0.212	strong	.	MUC16	4315	.	NM_024690	exon3	c.C26874T	p.G8958G	TGGGAGGCCTGGA	.	PASS	Atlas-SNP
NUP107	57122	hgsc.bcm.edu	37	12	69082805	69082805	+	Silent	SNP	G	G	A	rs2259588	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	89	50	80	0	0.561798	0	G|0.777;A|0.223	0.223	strong	NUP107,NS,carcinoma,+2,1	NUP107	88	1	NM_020401	exon2	c.G72A	p.R24R	TGCACGGAAACAG	.	PASS	Atlas-SNP
PPL	5493	hgsc.bcm.edu	37	16	4934564	4934564	+	Silent	SNP	C	C	G	rs1049207	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	39	68	0	0.448276	0	C|0.573;G|0.427	0.427	strong	.	PPL	168	.	NM_002705	exon22	c.G4092C	p.L1364L	GGCCCGCAGGCCT	.	PASS	Atlas-SNP
YY1AP1	55249	hgsc.bcm.edu	37	1	155658085	155658085	+	Silent	SNP	T	T	C	rs2666826	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	42	19	59	0	0.452381	0	T|0.472;C|0.528	0.528	strong	YY1AP1_ENST00000368339,NS,carcinoma,0,1	YY1AP1	104	1	NM_001198904	exon1	c.A171G	p.E57E	GATCGTTTCCCCT	.	PASS	Atlas-SNP
RBL2	5934	hgsc.bcm.edu	37	16	53503943	53503943	+	Silent	SNP	C	C	G	rs11540358	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	99	99	104	0	1	0	C|0.706;G|0.294	0.294	strong	.	RBL2	115	.	NM_005611	exon15	c.C2091G	p.R697R	TGGGCGCATGCCC	.	PASS	Atlas-SNP
WNK2	65268	hgsc.bcm.edu	37	9	96030957	96030957	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	95	27	116	0	0.284211	0	.	.	none	.	WNK2	277	.	NM_006648	exon18	c.A3962G	p.H1321R	CTGAGCACCCCGC	.	PASS	Atlas-SNP
MOV10	4343	hgsc.bcm.edu	37	1	113239382	113239382	+	Silent	SNP	G	G	A	rs17030651	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83	37	82	0	0.445783	0	G|0.803;A|0.197	0.197	strong	MOV10,NS,carcinoma,+2,1	MOV10	74	1	NM_020963	exon14	c.G2112A	p.E704E	GCTGGAGCGGCTG	.	PASS	Atlas-SNP
DDR2	4921	hgsc.bcm.edu	37	1	162737116	162737116	+	Silent	SNP	C	C	G	rs2298258	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	141	68	156	1	0.482269	0.00641026	C|0.718;G|0.282	0.282	strong	DDR2_ENST00000367922,NS,carcinoma,+2,1	DDR2	228	1	NM_001014796	exon12	c.C1260G	p.L420L	CATCCTCTGGAGG	.	scavenged	Atlas-SNP
GPR133	283383	hgsc.bcm.edu	37	12	131622735	131622735	+	Silent	SNP	T	T	C	rs7302341	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	33	21	40	0	0.636364	0	T|0.416;C|0.584	0.584	strong	.	GPR133	136	.	NM_198827	exon24	c.T2490C	p.S830S	CAGCTCTGCCCGC	.	PASS	Atlas-SNP
CDH17	1015	hgsc.bcm.edu	37	8	95188850	95188850	+	Missense_Mutation	SNP	T	T	C	rs2243518	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	267	259	325	1	0.970037	0.00307692	T|0.193;C|0.807	0.807	strong	.	CDH17	119	.	NM_004063	exon5	c.A343G	p.K115E	TCACTTTTATGGT	.	PASS	Atlas-SNP
DLGAP2	9228	hgsc.bcm.edu	37	8	1514009	1514009	+	Missense_Mutation	SNP	C	C	A	rs2301963	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	22	57	0	0.333333	0	C|0.556;A|0.444	0.444	strong	.	DLGAP2	292	.	NM_004745	exon3	c.C1151A	p.P384Q	TCCTACCAGAGCC	.	PASS	Atlas-SNP
PEG3	5178	hgsc.bcm.edu	37	19	57328920	57328920	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	127	3	149	0	0.023622	0	.	.	none	ZIM2_ENST00000326441,NS,carcinoma,-1,2	PEG3	414	2	NM_001146184	exon9	c.A890T	p.K297I	GTTGATTTTTTGG	.	scavenged	Atlas-SNP
GPR123	84435	hgsc.bcm.edu	37	10	134942319	134942319	+	Silent	SNP	C	C	T	rs2806453	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	24	12	22	0	0.5	0	C|0.959;T|0.041	0.041	strong	.	GPR123	118	.	NM_001083909	exon7	c.C987T	p.P329P	CCACCCCGCACTT	.	PASS	Atlas-SNP
LTBP1	4052	hgsc.bcm.edu	37	2	33335818	33335818	+	Silent	SNP	C	C	T	rs17012574	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	181	91	172	0	0.502762	0	C|0.952;T|0.048	0.048	strong	.	LTBP1	317	.	NM_206943	exon4	c.C1033T	p.L345L	TTTCAGCGTGAGT	.	PASS	Atlas-SNP
ANKRD26	22852	hgsc.bcm.edu	37	10	27353007	27353007	+	Missense_Mutation	SNP	T	T	C	rs12359281	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	32	21	27	0	0.65625	0	T|0.945;C|0.055	0.055	strong	.	ANKRD26	179	.	NM_014915	exon12	c.A1273G	p.I425V	CAGAGATACTCTG	.	PASS	Atlas-SNP
GPR87	53836	hgsc.bcm.edu	37	3	151011969	151011969	+	Silent	SNP	G	G	A	rs1048408	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	126	58	142	0	0.460317	0	G|0.533;A|0.467	0.467	strong	.	GPR87	52	.	NM_023915	exon3	c.C1065T	p.Y355Y	ATCAGTGTAATCA	.	PASS	Atlas-SNP
SNAPC4	6621	hgsc.bcm.edu	37	9	139275204	139275204	+	Silent	SNP	A	A	C	rs3812570	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	47	59	0	1	0	A|0.591;C|0.409	0.409	strong	.	SNAPC4	82	.	NM_003086	exon19	c.T2487G	p.V829V	AAGATGAACTGGT	.	PASS	Atlas-SNP
DEK	7913	hgsc.bcm.edu	37	6	18264210	18264210	+	Silent	SNP	G	G	A	rs11544757	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	27	6	25	0	0.222222	0	G|0.838;C|0.000;A|0.162	0.162	strong	.	DEK	31	.	NM_003472	exon2	c.C9T	p.A3A	GGCCGAGGCGGAC	.	PASS	Atlas-SNP
TBCK	93627	hgsc.bcm.edu	37	4	107133919	107133919	+	Silent	SNP	A	A	G	rs17036613	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	255	130	302	2	0.509804	0.00662252	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	.	scavenged	Atlas-SNP
GPER	2852	hgsc.bcm.edu	37	7	1132153	1132153	+	Silent	SNP	G	G	A	rs3808352	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	27	7	33	0	0.259259	0	G|0.875;A|0.125	0.125	strong	.	GPER	25	.	NM_001505	exon2	c.G789A	p.A263A	CCTCGCGGTGGTG	.	PASS	Atlas-SNP
ARMC5	79798	hgsc.bcm.edu	37	16	31473275	31473275	+	Missense_Mutation	SNP	A	A	G	rs35923277	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	104	51	111	0	0.490385	0	A|0.964;G|0.036	0.036	strong	.	ARMC5	94	.	NM_024742	exon2	c.A508G	p.I170V	GACAGCATCCAGA	.	PASS	Atlas-SNP
PRAMEF2	65122	hgsc.bcm.edu	37	1	12919891	12919891	+	Nonsense_Mutation	SNP	G	G	T	rs75411676	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	131	46	121	0	0.351145	0	G|0.952;T|0.048	0.048	strong	.	PRAMEF2	85	.	NM_023014	exon3	c.G631T	p.E211X	GAGCTGGAAATTC	.	PASS	Atlas-SNP
LAMA1	284217	hgsc.bcm.edu	37	18	7008591	7008591	+	Missense_Mutation	SNP	T	T	C	rs662471	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	22	54	0	0.349206	0	T|0.753;C|0.247	0.247	strong	.	LAMA1	458	.	NM_005559	exon28	c.A4018G	p.M1340V	CCTCCATTGAAAT	.	PASS	Atlas-SNP
EBI3	10148	hgsc.bcm.edu	37	19	4236996	4236996	+	Missense_Mutation	SNP	G	G	A	rs4740	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	56	32	67	0	0.571429	0	A|0.399;C|0.003	0.399	strong	.	EBI3	15	.	NM_005755	exon5	c.G601A	p.V201I	TACTACGTCCAAG	.	PASS	Atlas-SNP
ASXL3	80816	hgsc.bcm.edu	37	18	31324934	31324934	+	Missense_Mutation	SNP	A	A	G	rs7232237	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	45	45	58	0	1	0	A|0.319;G|0.681	0.681	strong	.	ASXL3	405	.	NM_030632	exon12	c.A5122G	p.M1708V	CAGAACATGAAAG	.	PASS	Atlas-SNP
GCSAML	148823	hgsc.bcm.edu	37	1	247719769	247719769	+	Splice_Site	SNP	G	G	A	rs56043070	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	35	16	35	0	0.457143	0	G|0.941;A|0.059	0.059	strong	.	.	.	.	NM_145278	exon2	c.89+1G>A	.	AAAACGGTAAGAA	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1080954	1080954	+	Silent	SNP	G	G	A	rs11245929	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	117	56	122	1	0.478632	0.00819672	G|0.919;A|0.081	0.081	strong	MUC2_ENST00000441003,NS,carcinoma,0,2	MUC2	614	2	NM_002457	exon10	c.G1338A	p.T446T	GAAGACGGTGGTG	.	scavenged	Atlas-SNP
OTC	5009	hgsc.bcm.edu	37	X	38262964	38262964	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	59	18	47	0	0.305085	0	.	.	none	.	OTC	60	.	NM_000531	exon6	c.G634A	p.G212R	AAATTCGGAATGC	.	PASS	Atlas-SNP
CDCP1	64866	hgsc.bcm.edu	37	3	45153708	45153708	+	Silent	SNP	G	G	A	rs35501071	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	113	61	87	0	0.539823	0	G|0.844;A|0.156	0.156	strong	CDCP1,colon,carcinoma,0,1	CDCP1	61	1	NM_178181	exon3	c.C522T	p.I174I	GGTTCCGATCCTG	.	PASS	Atlas-SNP
SPAG17	200162	hgsc.bcm.edu	37	1	118583408	118583408	+	Silent	SNP	G	G	A	rs10923477	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	133	69	146	0	0.518797	0	G|0.677;A|0.323	0.323	strong	.	SPAG17	263	.	NM_206996	exon22	c.C3111T	p.Y1037Y	ATACAGGTAGTAA	.	PASS	Atlas-SNP
RBM19	9904	hgsc.bcm.edu	37	12	114261053	114261053	+	Silent	SNP	G	G	A	rs11066773	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	28	13	43	0	0.464286	0	G|0.894;A|0.106	0.106	strong	.	RBM19	117	.	NM_001146699	exon24	c.C2859T	p.S953S	CTCCTCGCTGTCG	.	PASS	Atlas-SNP
ARHGEF28	64283	hgsc.bcm.edu	37	5	73148481	73148481	+	Missense_Mutation	SNP	G	G	A	rs2973566	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	148	63	131	0	0.425676	0	G|0.830;A|0.170	0.170	strong	.	.	.	.	NM_001080479	exon14	c.G1754A	p.R585K	AGCAAAGAGCTTA	.	PASS	Atlas-SNP
SMOX	54498	hgsc.bcm.edu	37	20	4158164	4158164	+	Silent	SNP	C	C	A	rs11552911	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	45	25	51	0	0.555556	0	C|0.950;A|0.050	0.050	strong	.	SMOX	119	.	NM_175839	exon3	c.C375A	p.T125T	CCTTACCAACCAC	.	PASS	Atlas-SNP
CHRNE	1145	hgsc.bcm.edu	37	17	4802329	4802329	+	Silent	SNP	G	G	A	rs33978919	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	41	62	0	0.672131	0	G|0.820;A|0.180	0.180	strong	.	CHRNE	25	.	NM_000080	exon11	c.C1293T	p.A431A	GCTCTCGGCCACG	.	PASS	Atlas-SNP
SFI1	9814	hgsc.bcm.edu	37	22	32014161	32014161	+	Silent	SNP	G	G	A	rs55735011	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	147	86	161	1	0.585034	0.00621118	G|0.959;A|0.041	0.041	strong	SFI1,NS,carcinoma,0,1	SFI1	78	1	NM_001007467	exon32	c.G3573A	p.P1191P	GGAGCCGGGGCCT	.	scavenged	Atlas-SNP
ARHGAP30	257106	hgsc.bcm.edu	37	1	161019040	161019040	+	Missense_Mutation	SNP	G	G	C	rs3813609	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	32	93	0	0.395062	0	G|0.539;C|0.461	0.461	strong	.	ARHGAP30	105	.	NM_001025598	exon12	c.C1771G	p.L591V	AGTCCAGGGAACA	.	PASS	Atlas-SNP
RASSF1	11186	hgsc.bcm.edu	37	3	50369546	50369546	+	Missense_Mutation	SNP	C	C	A	rs2073498	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	44	78	0	0.52381	0	C|0.925;A|0.075	0.075	strong	.	RASSF1	46	.	NM_170714	exon3	c.G409T	p.A137S	TCTCAGCTTGAGA	.	PASS	Atlas-SNP
PINX1	54984	hgsc.bcm.edu	37	8	10692242	10692242	+	Silent	SNP	G	G	A	rs1052523	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	32	82	0	0.450704	0	G|0.958;A|0.042	0.042	strong	.	PINX1	38	.	NM_017884	exon2	c.C63T	p.A21A	ACTCCAGGCAGTG	.	PASS	Atlas-SNP
LTB	4050	hgsc.bcm.edu	37	6	31549604	31549604	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80	27	69	0	0.3375	0	.	.	none	.	LTB	19	.	NM_002341	exon2	c.C195T	p.A65A	TTGCTGGGCCTGT	.	PASS	Atlas-SNP
ANKRD18B	441459	hgsc.bcm.edu	37	9	33568789	33568789	+	Silent	SNP	T	T	G	rs10971566	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80	43	41	0	0.5375	0	T|0.756;G|0.244	0.244	strong	.	ANKRD18B	46	.	NM_001244752	exon15	c.T2886G	p.L962L	AAATCTTAATAGT	.	PASS	Atlas-SNP
ZFHX3	463	hgsc.bcm.edu	37	16	72992221	72992221	+	Silent	SNP	G	G	A	rs61735550	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	161	70	188	0	0.434783	0	G|0.830;A|0.170	0.170	strong	.	ZFHX3	404	.	NM_006885	exon2	c.C1824T	p.S608S	CTCTGTGCTTTCA	.	PASS	Atlas-SNP
CHST1	8534	hgsc.bcm.edu	37	11	45671241	45671241	+	Silent	SNP	C	C	G	rs7115779	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	25	11	27	0	0.44	0	C|0.989;G|0.011	0.011	strong	CHST1,colon,adenoma,0,1	CHST1	81	1	NM_003654	exon4	c.G1233C	p.S411S	GGGTCACGAGAAG	.	PASS	Atlas-SNP
INPP4B	8821	hgsc.bcm.edu	37	4	143033778	143033778	+	Silent	SNP	T	T	C	rs3822141	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	115	54	118	0	0.469565	0	C|0.057;T|0.943	0.057	strong	.	INPP4B	132	.	NM_003866	exon23	c.A2193G	p.L731L	AATCTGTAGAGGT	.	PASS	Atlas-SNP
PPP1R15A	23645	hgsc.bcm.edu	37	19	49377918	49377918	+	Missense_Mutation	SNP	G	G	T	rs35087747	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	30	79	0	0.491803	0	A|0.000;C|0.000;G|0.864;T|0.136	0.136	strong	.	PPP1R15A	48	.	NM_014330	exon2	c.G1428T	p.R476S	CCAGAGGGCCCAC	.	PASS	Atlas-SNP
RASGRF1	5923	hgsc.bcm.edu	37	15	79284127	79284127	+	Missense_Mutation	SNP	C	C	A	rs28603308	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	96	39	100	0	0.40625	0	C|0.986;A|0.014	0.014	strong	.	RASGRF1	168	.	NM_002891	exon22	c.G3085T	p.V1029L	CCTTCACGCCTTC	.	PASS	Atlas-SNP
SNRNP200	23020	hgsc.bcm.edu	37	2	96963419	96963419	+	Missense_Mutation	SNP	T	T	C	rs142729495	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	115	63	133	2	0.547826	0.0150376	T|0.996;C|0.004	0.004	strong	SNRNP200,NS,lymphoid_neoplasm,0,1	SNRNP200	195	1	NM_014014	exon10	c.A1159G	p.M387V	TGTCCATTCGAGA	.	scavenged	Atlas-SNP
TM6SF1	53346	hgsc.bcm.edu	37	15	83781631	83781631	+	Missense_Mutation	SNP	C	C	T	rs1989	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	135	75	145	0	0.555556	0	C|0.934;T|0.066	0.066	strong	.	TM6SF1	38	.	NM_001144903	exon2	c.C175T	p.P59S	AAACCACCCCGGG	.	PASS	Atlas-SNP
PDIA2	64714	hgsc.bcm.edu	37	16	334732	334732	+	Silent	SNP	C	C	T	rs45593734	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	6	4	5	0	0.666667	0	C|0.886;T|0.114	0.114	strong	.	PDIA2	51	.	NM_006849	exon3	c.C480T	p.D160D	GGAGGACGAGGCG	.	PASS	Atlas-SNP
SMURF1	57154	hgsc.bcm.edu	37	7	98650051	98650051	+	Silent	SNP	G	G	C	rs219797	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	34	15	22	0	0.441176	0	G|0.362;C|0.638	0.638	strong	.	SMURF1	58	.	NM_020429	exon7	c.C498G	p.S166S	AGGCCCGGAGTCT	.	PASS	Atlas-SNP
SH3PXD2A	9644	hgsc.bcm.edu	37	10	105362209	105362209	+	Silent	SNP	T	T	C	rs4917396	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	104	102	115	0	0.980769	0	T|0.147;C|0.853	0.853	strong	.	SH3PXD2A	90	.	NM_014631	exon14	c.A2682G	p.K894K	GTCTGATTTGCCT	.	PASS	Atlas-SNP
ZNF860	344787	hgsc.bcm.edu	37	3	32031643	32031643	+	Missense_Mutation	SNP	A	A	G	rs13065048	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	135	133	225	0	0.985185	0	A|0.615;G|0.385	0.385	strong	.	ZNF860	96	.	NM_001137674	exon2	c.A1072G	p.T358A	CACCTCACACAAC	.	PASS	Atlas-SNP
EMR3	84658	hgsc.bcm.edu	37	19	14758168	14758168	+	Missense_Mutation	SNP	G	G	A	rs34226397	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	95	50	92	0	0.526316	0	G|0.679;A|0.321	0.321	strong	.	EMR3	99	.	NM_032571	exon8	c.C707T	p.A236V	GCAATGGCACTGG	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73	73	55	0	1	0	T|0.495;C|0.505	0.505	strong	.	MST1R	205	.	NM_001244937	exon4	c.A1568G	p.Q523R	GGGCCTTGGATAG	.	PASS	Atlas-SNP
MRPL38	64978	hgsc.bcm.edu	37	17	73895744	73895744	+	Missense_Mutation	SNP	G	G	A	rs1128878	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57	21	54	0	0.368421	0	G|0.999;A|0.001	0.001	strong	.	MRPL38	26	.	NM_032478	exon7	c.C722T	p.P241L	TTACCCGGGATGT	.	PASS	Atlas-SNP
ANXA9	8416	hgsc.bcm.edu	37	1	150958836	150958836	+	Missense_Mutation	SNP	A	A	G	rs267733	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69	33	90	0	0.478261	0	A|0.906;G|0.094	0.094	strong	.	ANXA9	28	.	NM_003568	exon8	c.A497G	p.D166G	TGGATGACATCAC	.	PASS	Atlas-SNP
PPP1R15A	23645	hgsc.bcm.edu	37	19	49377319	49377319	+	Missense_Mutation	SNP	A	A	G	rs610308	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	31	61	0	0.382716	0	A|0.546;G|0.454	0.454	strong	.	PPP1R15A	48	.	NM_014330	exon2	c.A829G	p.K277E	GCACACAAAGAAA	.	PASS	Atlas-SNP
LEPR	3953	hgsc.bcm.edu	37	1	66102617	66102617	+	Silent	SNP	A	A	G	rs61781316	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44	17	71	0	0.386364	0	A|0.997;G|0.003	0.003	strong	.	LEPR	284	.	NM_002303	exon20	c.A3417G	p.A1139A	TTTTGCATCTTAC	.	PASS	Atlas-SNP
MECOM	2122	hgsc.bcm.edu	37	3	169098992	169098992	+	Missense_Mutation	SNP	G	G	A	rs7622799	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	97	46	117	0	0.474227	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
FHAD1	114827	hgsc.bcm.edu	37	1	15702130	15702130	+	Silent	SNP	A	A	G	rs17368978	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	41	15	44	0	0.365854	0	A|0.944;G|0.056	0.056	strong	.	FHAD1	78	.	NM_052929	exon27	c.A3543G	p.L1181L	ATTTCTAGATTTA	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48	26	20	0	0.541667	0	G|0.653;A|0.347	0.347	strong	.	CENPQ	23	.	NM_018132	exon4	c.G187A	p.G63R	AAACACGGAAAGA	.	PASS	Atlas-SNP
ITGBL1	9358	hgsc.bcm.edu	37	13	102220193	102220193	+	Missense_Mutation	SNP	G	G	T	rs1140605	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	28	20	48	0	0.714286	0	G|0.897;T|0.103	0.103	strong	.	ITGBL1	83	.	NM_004791	exon3	c.G460T	p.A154S	TCTAATGCAGGTA	.	PASS	Atlas-SNP
KLK14	43847	hgsc.bcm.edu	37	19	51584916	51584916	+	Missense_Mutation	SNP	G	G	A	rs2569491	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	78	31	123	0	0.397436	0	G|0.632;A|0.368	0.368	strong	.	KLK14	49	.	NM_022046	exon4	c.C133T	p.H45Y	ACGTATGGCCACC	.	PASS	Atlas-SNP
BAZ1A	11177	hgsc.bcm.edu	37	14	35242828	35242828	+	Silent	SNP	G	G	A	rs2275145	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	214	211	239	0	0.985981	0	G|0.500;A|0.500	0.500	strong	.	BAZ1A	128	.	NM_013448	exon20	c.C3102T	p.D1034D	TTCTACGTCTTCA	.	PASS	Atlas-SNP
C17orf112	100506650	hgsc.bcm.edu	37	17	51063068	51063068	+	Silent	SNP	A	A	G	rs12450084	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91	41	97	0	0.450549	0	A|0.933;G|0.067	0.067	strong	.	.	.	.	NM_001243552	exon1	c.A30G	p.V10V	CTTCGTAGCATTT	.	PASS	Atlas-SNP
C3orf30	152405	hgsc.bcm.edu	37	3	118867047	118867047	+	Missense_Mutation	SNP	C	C	G	rs9289122	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	213	101	208	0	0.474178	0	C|0.521;G|0.479	0.479	strong	.	C3orf30	64	.	NM_152539	exon2	c.C1419G	p.D473E	AATTGACCAAGGA	.	PASS	Atlas-SNP
OR8G2	26492	hgsc.bcm.edu	37	11	124096271	124096271	+	Missense_Mutation	SNP	A	A	G	rs201854907	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	201	16	175	0	0.079602	0	A|0.996;G|0.005	0.005	strong	.	.	.	.	NM_001007249	exon1	c.A874G	p.T292A	TTTTATACTATTG	.	PASS	Atlas-SNP
GAL3ST1	9514	hgsc.bcm.edu	37	22	30953295	30953295	+	Missense_Mutation	SNP	C	C	T	rs2267161	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	258	125	254	0	0.484496	0	C|0.671;T|0.329	0.329	strong	.	GAL3ST1	44	.	NM_004861	exon3	c.G85A	p.V29M	AGTACACCAGCAG	.	PASS	Atlas-SNP
FXYD5	53827	hgsc.bcm.edu	37	19	35649281	35649281	+	Silent	SNP	A	A	G	rs1128882	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	90	35	86	0	0.388889	0	A|0.828;G|0.172	0.172	strong	.	FXYD5	41	.	NM_014164	exon4	c.A177G	p.P59P	CTCTCCAACCCCA	.	PASS	Atlas-SNP
CCNT1	904	hgsc.bcm.edu	37	12	49087899	49087899	+	Silent	SNP	C	C	T	rs35678179	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	148	77	145	0	0.52027	0	C|0.984;T|0.016	0.016	strong	.	CCNT1	55	.	NM_001240	exon9	c.G1098A	p.Q366Q	ACCATCCTGTGGT	.	PASS	Atlas-SNP
MINK1	50488	hgsc.bcm.edu	37	17	4796286	4796286	+	Missense_Mutation	SNP	C	C	T	rs11556635	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	105	53	113	0	0.504762	0	C|0.313;T|0.687	0.687	strong	.	MINK1	110	.	NM_153827	exon20	c.C2324T	p.P775L	CCAAACCGGACAG	.	PASS	Atlas-SNP
KLHL10	317719	hgsc.bcm.edu	37	17	40001659	40001659	+	Silent	SNP	T	T	C	rs34933374	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91	50	73	0	0.549451	0	T|0.959;C|0.041	0.041	strong	.	KLHL10	67	.	NM_152467	exon3	c.T966C	p.T322T	TGTTACTTGTGAG	.	PASS	Atlas-SNP
ACTN1	87	hgsc.bcm.edu	37	14	69341653	69341653	+	Missense_Mutation	SNP	T	T	A	rs11557769	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	46	25	66	0	0.543478	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
CLCA1	1179	hgsc.bcm.edu	37	1	86947975	86947975	+	Silent	SNP	A	A	T	rs1321694	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	129	129	142	0	1	0	T|0.353;N|0.000	0.353	strong	.	CLCA1	109	.	NM_001285	exon5	c.A645T	p.V215V	TAAAGTAACAGGA	.	PASS	Atlas-SNP
SLC52A1	55065	hgsc.bcm.edu	37	17	4936336	4936336	+	Silent	SNP	A	A	T	rs72822610	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49	25	69	0	0.510204	0	A|0.868;T|0.132	0.132	strong	.	.	.	.	NM_017986	exon5	c.T1263A	p.L421L	GGCACCAAGCAGG	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1084362	1084362	+	Missense_Mutation	SNP	G	G	A	rs11245936	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	116	56	133	2	0.482759	0.0150376	G|0.945;A|0.055	0.055	strong	MUC2_ENST00000441003,mouth,carcinoma,0,2	MUC2	614	2	NM_002457	exon19	c.G2494A	p.G832S	TCTTCCGGCGCCA	.	scavenged	Atlas-SNP
HELB	92797	hgsc.bcm.edu	37	12	66696410	66696410	+	Silent	SNP	C	C	T	rs3741604	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	104	100	94	0	0.961538	0	C|0.620;T|0.380	0.380	strong	.	HELB	90	.	NM_033647	exon1	c.C27T	p.R9R	CCTGCGCCAACTT	.	PASS	Atlas-SNP
CALB2	794	hgsc.bcm.edu	37	16	71411636	71411636	+	Missense_Mutation	SNP	G	G	A	rs11545954	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	45	24	56	0	0.533333	0	G|0.867;A|0.133	0.133	strong	.	CALB2	46	.	NM_007088	exon4	c.G328A	p.A110T	TCCAGCGCCGAGT	.	PASS	Atlas-SNP
ZC3H6	376940	hgsc.bcm.edu	37	2	113089267	113089267	+	Silent	SNP	T	T	C	rs7601200	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	54	81	0	1	0	T|0.273;C|0.727	0.727	strong	.	ZC3H6	93	.	NM_198581	exon12	c.T2772C	p.N924N	TCAAAATACAGTG	.	PASS	Atlas-SNP
TAF1C	9013	hgsc.bcm.edu	37	16	84212928	84212928	+	Silent	SNP	G	G	A	rs3743642	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98	50	85	0	0.510204	0	G|0.867;A|0.133	0.133	strong	.	TAF1C	60	.	NM_005679	exon14	c.C2229T	p.P743P	TCTCCCGGGCTCC	.	PASS	Atlas-SNP
RARRES1	5918	hgsc.bcm.edu	37	3	158428642	158428642	+	Silent	SNP	G	G	A	rs2307064	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	318	146	368	0	0.459119	0	G|0.814;A|0.186	0.186	strong	.	RARRES1	22	.	NM_206963	exon3	c.C420T	p.T140T	ATTGATGGTTGGT	.	PASS	Atlas-SNP
GINS2	51659	hgsc.bcm.edu	37	16	85711860	85711860	+	Silent	SNP	C	C	T	rs1053328	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	173	172	156	1	0.99422	0.00641026	C|0.657;T|0.343	0.343	strong	GINS2,colon,carcinoma,-1,1	GINS2	15	1	NM_016095	exon5	c.G516A	p.T172T	GAGGTTCGTGCGG	.	PASS	Atlas-SNP
RNF213	57674	hgsc.bcm.edu	37	17	78337584	78337584	+	Missense_Mutation	SNP	A	A	G	rs61740658	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	77	44	71	0	0.571429	0	A|0.918;G|0.082	0.082	strong	.	RNF213	766	.	NM_001256071	exon41	c.A11744G	p.E3915G	TCAGGGAAGTCAG	.	PASS	Atlas-SNP
TMIGD2	126259	hgsc.bcm.edu	37	19	4294623	4294623	+	Missense_Mutation	SNP	C	C	A	rs58237134	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60	30	45	0	0.5	0	C|0.806;A|0.194	0.194	strong	.	TMIGD2	38	.	NM_144615	exon4	c.G503T	p.W168L	GCACCCCACACGA	.	PASS	Atlas-SNP
STK31	56164	hgsc.bcm.edu	37	7	23757162	23757162	+	Missense_Mutation	SNP	G	G	C	rs6945306	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	162	40	224	0	0.246914	0	G|0.742;C|0.258	0.258	strong	.	STK31	175	.	NM_031414	exon4	c.G213C	p.Q71H	CCCCCAGGCCAGT	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	108	81	102	0	0.75	0	A|0.675;G|0.325	0.325	strong	.	ALMS1	384	.	NM_015120	exon10	c.A8567G	p.N2856S	GAGTAAACAGATC	.	PASS	Atlas-SNP
TGFBI	7045	hgsc.bcm.edu	37	5	135392426	135392426	+	Silent	SNP	T	T	C	rs4669	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	205	100	178	0	0.487805	0	T|0.599;C|0.401	0.401	strong	.	TGFBI	76	.	NM_000358	exon12	c.T1620C	p.F540F	AGTCTTTGCTCCC	.	PASS	Atlas-SNP
MYH13	8735	hgsc.bcm.edu	37	17	10231417	10231417	+	Silent	SNP	C	C	T	rs2277644	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	45	90	0	0.523256	0	C|0.729;T|0.271	0.271	strong	.	MYH13	533	.	NM_003802	exon22	c.G2457A	p.Q819Q	GTTGTACTGGATG	.	PASS	Atlas-SNP
SEMA4D	10507	hgsc.bcm.edu	37	9	91978783	91978783	+	Silent	SNP	G	G	A	rs45515192	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	25	44	0	0.531915	0	G|0.883;A|0.117	0.117	strong	.	SEMA4D	81	.	NM_001142287	exon19	c.C1965T	p.P655P	GCCATCGGGCAGT	.	PASS	Atlas-SNP
NGFR	4804	hgsc.bcm.edu	37	17	47588000	47588000	+	Silent	SNP	C	C	T	rs11466155	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	132	63	153	0	0.477273	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
AP3B1	8546	hgsc.bcm.edu	37	5	77473165	77473165	+	Silent	SNP	A	A	G	rs4532349	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	99	37	100	0	0.373737	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
C16orf46	123775	hgsc.bcm.edu	37	16	81095091	81095091	+	Missense_Mutation	SNP	A	A	G	rs7198494	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	199	95	197	0	0.477387	0	A|0.792;G|0.208	0.208	strong	.	C16orf46	57	.	NM_001100873	exon3	c.T863C	p.I288T	AGGGATATCTGGG	.	PASS	Atlas-SNP
PPL	5493	hgsc.bcm.edu	37	16	4934549	4934549	+	Silent	SNP	G	G	A	rs1049208	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	32	55	0	0.516129	0	G|0.589;A|0.411	0.411	strong	.	PPL	168	.	NM_002705	exon22	c.C4107T	p.S1369S	AAAGGCGCTCGCC	.	PASS	Atlas-SNP
AEN	64782	hgsc.bcm.edu	37	15	89169614	89169614	+	Silent	SNP	A	A	G	rs3743476	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57	26	48	0	0.45614	0	A|0.763;G|0.237	0.237	strong	.	AEN	29	.	NM_022767	exon2	c.A174G	p.E58E	TCCAGAACCAGGG	.	PASS	Atlas-SNP
PNPLA5	150379	hgsc.bcm.edu	37	22	44287629	44287629	+	Silent	SNP	G	G	A	rs74445350	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	38	20	45	0	0.526316	0	G|0.878;A|0.122	0.122	strong	.	PNPLA5	46	.	NM_138814	exon1	c.C132T	p.R44R	GTAGATGCGGCGG	.	PASS	Atlas-SNP
CD83	9308	hgsc.bcm.edu	37	6	14118297	14118297	+	Splice_Site	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	32	10	29	0	0.3125	0	.	.	none	.	CD83	23	.	NM_001040280	exon2	c.153+1G>A	.	GTCAAGGTAGGTG	.	PASS	Atlas-SNP
LRPPRC	10128	hgsc.bcm.edu	37	2	44161960	44161960	+	Silent	SNP	T	T	C	rs4494798	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	111	111	123	0	1	0	T|0.988;C|0.012	0.012	strong	.	LRPPRC	105	.	NM_133259	exon24	c.A2562G	p.V854V	TGGTAATACTTTA	.	PASS	Atlas-SNP
BAD	572	hgsc.bcm.edu	37	11	64039175	64039175	+	Silent	SNP	G	G	A	rs2286615	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	29	83	0	0.460317	0	G|0.905;A|0.095	0.095	strong	BAD,NS,carcinoma,0,1	BAD	8	1	NM_032989	exon3	c.C288T	p.R96R	GCGCGAGCGGCCC	.	PASS	Atlas-SNP
CCDC168	643677	hgsc.bcm.edu	37	13	103410914	103410914	+	Missense_Mutation	SNP	A	A	T	rs12855785	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	41	27	76	0	0.658537	0	A|0.627;T|0.373	0.373	strong	.	.	.	.	NM_001146197	exon2	c.T244A	p.C82S	TGGGGCAACTGTC	.	PASS	Atlas-SNP
SPRY3	10251	hgsc.bcm.edu	37	X	155004280	155004280	+	Silent	SNP	A	A	G	rs306888	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94	66	112	0	0.702128	0	A|0.771;G|0.229	0.229	strong	.	SPRY3	52	.	NM_005840	exon2	c.A747G	p.Q249Q	GTGCCAACAGGGC	.	PASS	Atlas-SNP
INPP5A	3632	hgsc.bcm.edu	37	10	134459388	134459388	+	Missense_Mutation	SNP	A	A	G	rs1133400	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	37	19	38	0	0.513514	0	A|0.804;G|0.196	0.196	strong	.	INPP5A	77	.	NM_005539	exon3	c.A134G	p.K45R	CACACAAGCCGCA	.	PASS	Atlas-SNP
NOP9	161424	hgsc.bcm.edu	37	14	24771172	24771172	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	58	11	75	0	0.189655	0	.	.	none	.	.	.	.	NM_174913	exon4	c.G810A	p.V270V	CACAGTGTTTATC	.	PASS	Atlas-SNP
SIGLEC10	89790	hgsc.bcm.edu	37	19	51919302	51919302	+	Missense_Mutation	SNP	T	T	C	rs201376644	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	13	66	0	0.171053	0	T|0.998;C|0.002	0.002	strong	SIGLEC12_ENST00000439889,rectum,carcinoma,0,2	SIGLEC10	112	2	NM_001171157	exon5	c.A874G	p.N292D	CTCTGTTCTGCAG	.	PASS	Atlas-SNP
NRD1	4898	hgsc.bcm.edu	37	1	52266350	52266350	+	Silent	SNP	C	C	T	rs2273198	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	123	65	128	0	0.528455	0	C|0.946;T|0.054	0.054	strong	.	NRD1	89	.	NM_002525	exon23	c.G2523A	p.L841L	CTGAAACAGTAGC	.	PASS	Atlas-SNP
HCN2	610	hgsc.bcm.edu	37	19	605171	605171	+	Silent	SNP	T	T	C	rs12981860	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	75	88	0	0.986842	0	T|0.381;C|0.619	0.619	strong	.	HCN2	36	.	NM_001194	exon3	c.T1167C	p.P389P	GGTGCCTATGCTG	.	PASS	Atlas-SNP
IFT88	8100	hgsc.bcm.edu	37	13	21189941	21189941	+	Missense_Mutation	SNP	G	G	A	rs2442455	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	26	67	0	0.481481	0	G|0.837;A|0.163	0.163	strong	.	IFT88	83	.	NM_175605	exon16	c.G1149A	p.M383I	AGCCATGGCAGAA	.	PASS	Atlas-SNP
TRIM5	85363	hgsc.bcm.edu	37	11	5701001	5701001	+	Missense_Mutation	SNP	C	C	T	rs10838525	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	56	31	70	0	0.553571	0	C|0.763;T|0.237	0.237	strong	TRIM5_ENST00000380034,NS,carcinoma,0,1	TRIM5	111	1	NM_033093	exon2	c.G407A	p.R136Q	TACTCCCGGGCAA	.	PASS	Atlas-SNP
TMEM175	84286	hgsc.bcm.edu	37	4	944210	944210	+	Missense_Mutation	SNP	A	A	C	rs34884217	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	179	176	197	1	0.98324	0.00507614	A|0.930;C|0.070	0.070	strong	.	TMEM175	44	.	NM_032326	exon4	c.A194C	p.Q65P	TCCAGCAGTTCGA	.	PASS	Atlas-SNP
AVL9	23080	hgsc.bcm.edu	37	7	32613020	32613020	+	Silent	SNP	A	A	G	rs1993050	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	52	86	0	1	0	A|0.420;G|0.580	0.580	strong	AVL9,NS,carcinoma,0,1	AVL9	66	1	NM_015060	exon12	c.A1560G	p.T520T	TGCCACACTGCAA	.	PASS	Atlas-SNP
DUSP2	1844	hgsc.bcm.edu	37	2	96810556	96810556	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	9	92	0	0.118421	0	.	.	none	DUSP2,NS,carcinoma,+2,1	DUSP2	20	1	NM_004418	exon2	c.C454T	p.P152S	TTGGCGGCAGCGC	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29910759	29910759	+	Missense_Mutation	SNP	T	T	C	rs1071742	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	120	108	189	2	0.9	0.010582	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	.	scavenged	Atlas-SNP
PHF15	23338	hgsc.bcm.edu	37	5	133887780	133887780	+	Silent	SNP	G	G	A	rs12163993	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	279	125	244	1	0.448029	0.00409836	G|0.879;A|0.121	0.121	strong	.	PHF15	60	.	NM_015288	exon4	c.G192A	p.P64P	GATCCCGGACTCA	.	PASS	Atlas-SNP
GAPVD1	26130	hgsc.bcm.edu	37	9	128069703	128069703	+	Silent	SNP	C	C	A	rs13299973	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	28	52	0	0.424242	0	A|0.046;C|0.954;G|0.000	0.046	strong	.	GAPVD1	124	.	NM_015635	exon5	c.C1128A	p.A376A	TGTTGCCGCTTTC	.	PASS	Atlas-SNP
PLEKHA7	144100	hgsc.bcm.edu	37	11	16812397	16812397	+	Silent	SNP	G	G	A	rs35142528	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	104	46	98	0	0.442308	0	G|0.926;A|0.074	0.074	strong	.	PLEKHA7	120	.	NM_175058	exon21	c.C3000T	p.P1000P	TAGGGAGGGCTGG	.	PASS	Atlas-SNP
HFM1	164045	hgsc.bcm.edu	37	1	91784887	91784887	+	Silent	SNP	G	G	A	rs10493845	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	173	78	188	0	0.450867	0	G|0.749;A|0.251	0.251	strong	HFM1,NS,carcinoma,0,1	HFM1	188	1	NM_001017975	exon24	c.C2643T	p.T881T	CTTTGCGGTATCT	.	PASS	Atlas-SNP
TWF2	11344	hgsc.bcm.edu	37	3	52263967	52263967	+	Silent	SNP	G	G	A	rs34038856	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	18	43	0	0.382979	0	G|0.968;A|0.032	0.032	strong	.	TWF2	33	.	NM_007284	exon7	c.C729T	p.H243H	ATGGGTGTGCTTG	.	PASS	Atlas-SNP
JAG1	182	hgsc.bcm.edu	37	20	10622501	10622501	+	Missense_Mutation	SNP	G	G	C	rs35761929	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	123	59	125	0	0.479675	0	G|0.949;C|0.051	0.051	strong	.	JAG1	213	.	NM_000214	exon22	c.C2612G	p.P871R	CCATCTGGTATCA	.	PASS	Atlas-SNP
ACACB	32	hgsc.bcm.edu	37	12	109605730	109605730	+	Silent	SNP	C	C	T	rs4766516	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	43	95	0	0.581081	0	C|0.805;T|0.195	0.195	strong	.	ACACB	330	.	NM_001093	exon3	c.C816T	p.A272A	TGCCGCCGTGAAG	.	PASS	Atlas-SNP
PDE6C	5146	hgsc.bcm.edu	37	10	95372764	95372764	+	Silent	SNP	C	C	T	rs12781149	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	34	16	39	0	0.470588	0	C|0.939;T|0.061	0.061	strong	.	PDE6C	97	.	NM_006204	exon1	c.C282T	p.D94D	GGCTGACCGCTGC	.	PASS	Atlas-SNP
APCS	325	hgsc.bcm.edu	37	1	159558150	159558150	+	Silent	SNP	G	G	A	rs28383572	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	28	71	0	0.528302	0	G|0.984;A|0.016	0.016	strong	.	APCS	48	.	NM_001639	exon2	c.G324A	p.P108P	GTTCCCGGCTCCA	.	PASS	Atlas-SNP
HDAC10	83933	hgsc.bcm.edu	37	22	50684415	50684415	+	Missense_Mutation	SNP	T	T	C	rs11553697	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60	30	74	0	0.5	0	T|0.978;C|0.022	0.022	strong	.	HDAC10	29	.	NM_032019	exon18	c.A1757G	p.Q586R	GGGCCCTGCAGGC	.	PASS	Atlas-SNP
COL4A2	1284	hgsc.bcm.edu	37	13	111155779	111155779	+	Silent	SNP	G	G	A	rs4773199	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	56	19	78	0	0.339286	0	G|0.834;A|0.166	0.166	strong	COL4A2,NS,carcinoma,0,1	COL4A2	178	1	NM_001846	exon43	c.G4089A	p.A1363A	TGGGGCGGTGGGC	.	PASS	Atlas-SNP
DGKE	8526	hgsc.bcm.edu	37	17	54912339	54912339	+	Silent	SNP	G	G	A	rs1048159	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	59	59	60	0	1	0	G|0.882;A|0.118	0.118	strong	DGKE,NS,carcinoma,+2,1	DGKE	47	1	NM_003647	exon2	c.G183A	p.G61G	GCACGGGTGGCGC	.	PASS	Atlas-SNP
MANSC4	100287284	hgsc.bcm.edu	37	12	27916206	27916206	+	Missense_Mutation	SNP	G	G	A	rs11049125	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	241	98	246	0	0.406639	0	G|0.869;A|0.131	0.131	strong	.	MANSC4	9	.	NM_001146221	exon3	c.C488T	p.T163M	TTTATCGTGGTGG	.	PASS	Atlas-SNP
NUP54	53371	hgsc.bcm.edu	37	4	77053834	77053834	+	Missense_Mutation	SNP	T	T	C	rs61750814	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	161	160	189	0	0.993789	0	T|0.836;C|0.164	0.164	strong	.	NUP54	48	.	NM_017426	exon6	c.A749G	p.N250S	GTACCATTTGGCG	.	PASS	Atlas-SNP
WDR43	23160	hgsc.bcm.edu	37	2	29169612	29169612	+	Silent	SNP	T	T	C	rs3087649	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	24	13	19	0	0.541667	0	T|0.251;C|0.749	0.749	strong	.	WDR43	38	.	NM_015131	exon18	c.T2001C	p.D667D	TTCTGATTTAGAT	.	PASS	Atlas-SNP
CYP3A4	1576	hgsc.bcm.edu	37	7	99358595	99358595	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	261	110	287	1	0.421456	0.00348432	.	.	none	.	CYP3A4	56	.	NM_017460	exon12	c.G1263A	p.K421K	GTTCTTCTTGCTG	.	PASS	Atlas-SNP
PRRC2B	84726	hgsc.bcm.edu	37	9	134350458	134350458	+	Missense_Mutation	SNP	C	C	T	rs10751478	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	19	19	53	0	1	0	C|0.231;G|0.000;T|0.769	0.769	strong	.	PRRC2B	266	.	NM_013318	exon15	c.C2942T	p.P981L	AGAGCCCCACGGC	.	PASS	Atlas-SNP
OR1S1	219959	hgsc.bcm.edu	37	11	57982832	57982832	+	Missense_Mutation	SNP	T	T	A	rs61739243	byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	75	139	0	1	0	T|0.703;A|0.297	0.297	strong	OR1S1,NS,carcinoma,0,1	OR1S1	139	1	NM_001004458	exon1	c.T616A	p.L206M	GATACATTGATCA	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	108	55	106	0	0.509259	0	A|0.429;G|0.571	0.571	strong	.	PKD1L2	361	.	NM_001076780	exon1	c.T59C	p.V20A	GGCTTAACAGTGG	.	PASS	Atlas-SNP
BDNF	627	hgsc.bcm.edu	37	11	27679916	27679916	+	Missense_Mutation	SNP	C	C	T	rs6265	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94	43	75	0	0.457447	0	C|0.815;T|0.185	0.185	strong	.	BDNF	63	.	NM_001143810	exon3	c.G442A	p.V148M	CTATCACGTGTTC	.	PASS	Atlas-SNP
QSOX1	5768	hgsc.bcm.edu	37	1	180159657	180159657	+	Silent	SNP	C	C	T	rs1050154	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	40	78	0	0.493827	0	C|0.864;T|0.136	0.136	strong	.	QSOX1	79	.	NM_002826	exon10	c.C1230T	p.L410L	GGTCCTCTTCCAC	.	PASS	Atlas-SNP
FAM71F2	346653	hgsc.bcm.edu	37	7	128315882	128315882	+	Missense_Mutation	SNP	C	C	A	rs17169357	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	33	18	29	0	0.545455	0	C|0.664;A|0.335	0.335	strong	.	FAM71F2	19	.	NM_001012454	exon2	c.C334A	p.P112T	AGCACACCTGGTG	.	PASS	Atlas-SNP
LAMA1	284217	hgsc.bcm.edu	37	18	6997818	6997818	+	Missense_Mutation	SNP	A	A	C	rs12961939	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	24	43	0	0.45283	0	A|0.790;C|0.210	0.210	strong	.	LAMA1	458	.	NM_005559	exon33	c.T4729G	p.S1577A	TCAGAGAAAGAAC	.	PASS	Atlas-SNP
OR13C9	286362	hgsc.bcm.edu	37	9	107380177	107380177	+	Silent	SNP	A	A	G	rs1813819	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	223	83	294	0	0.372197	0	A|0.694;G|0.306	0.306	strong	.	OR13C9	42	.	NM_001001956	exon1	c.T309C	p.L103L	CAAGCCAAGGAAC	.	PASS	Atlas-SNP
FGD2	221472	hgsc.bcm.edu	37	6	36995222	36995222	+	Silent	SNP	G	G	A	rs2274587	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	128	94	131	0	0.734375	0	G|0.824;A|0.175	0.175	strong	.	FGD2	65	.	NM_173558	exon15	c.G1623A	p.T541T	AGCCACGCCTGAC	.	PASS	Atlas-SNP
FUT3	2525	hgsc.bcm.edu	37	19	5844343	5844343	+	Missense_Mutation	SNP	C	C	T	rs3745635	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	113	41	105	0	0.362832	0	C|0.902;T|0.098	0.098	strong	.	FUT3	30	.	NM_001097640	exon3	c.G508A	p.G170S	GCCAGCCGTAGGG	.	PASS	Atlas-SNP
RECQL5	9400	hgsc.bcm.edu	37	17	73625286	73625286	+	Silent	SNP	G	G	A	rs820190	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	70	33	83	0	0.471429	0	G|0.746;A|0.254	0.254	strong	.	RECQL5	77	.	NM_004259	exon16	c.C2217T	p.S739S	AAGGGAGCTGCCC	.	PASS	Atlas-SNP
PRRG4	79056	hgsc.bcm.edu	37	11	32874919	32874919	+	Missense_Mutation	SNP	C	C	A	rs34139105	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	26	57	0	0.412698	0	C|0.927;A|0.073	0.073	strong	PRRG4,NS,carcinoma,+1,1	PRRG4	15	1	NM_024081	exon6	c.C527A	p.P176Q	TGTCTCCATTGCC	.	PASS	Atlas-SNP
NELL1	4745	hgsc.bcm.edu	37	11	21392487	21392487	+	Silent	SNP	C	C	T	rs4151056	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	10	72	0	0.212766	0	C|0.868;T|0.132	0.132	strong	.	NELL1	179	.	NM_006157	exon15	c.C1638T	p.C546C	CCACTGCGAGAAA	.	PASS	Atlas-SNP
RTP4	64108	hgsc.bcm.edu	37	3	187088656	187088656	+	Missense_Mutation	SNP	C	C	T	rs1047584	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	190	91	136	0	0.478947	0	C|0.802;T|0.198	0.198	strong	.	RTP4	20	.	NM_022147	exon2	c.C236T	p.T79I	ACTGGACATCCCA	.	PASS	Atlas-SNP
COL22A1	169044	hgsc.bcm.edu	37	8	139642974	139642974	+	Silent	SNP	T	T	C	rs4131277	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57	23	63	0	0.403509	0	T|0.780;C|0.220	0.220	strong	.	COL22A1	390	.	NM_152888	exon50	c.A3627G	p.A1209A	AGCTCCTGCAATT	.	PASS	Atlas-SNP
OR5P2	120065	hgsc.bcm.edu	37	11	7817856	7817856	+	Missense_Mutation	SNP	C	C	T	rs78460198	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	142	142	161	1	1	0.00621118	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
AMPD3	272	hgsc.bcm.edu	37	11	10521764	10521764	+	Silent	SNP	T	T	C	rs3741041	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	121	53	130	0	0.438017	0	T|0.653;C|0.347	0.347	strong	.	AMPD3	68	.	NM_000480	exon11	c.T1716C	p.Y572Y	CATGTATGCCAAC	.	PASS	Atlas-SNP
WDTC1	23038	hgsc.bcm.edu	37	1	27631526	27631526	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	58	33	42	0	0.568965	0	.	.	none	.	WDTC1	69	.	NM_001276252	exon15	c.G1678A	p.G560S	GACGATGGCTCCT	.	PASS	Atlas-SNP
RNASE11	122651	hgsc.bcm.edu	37	14	21052259	21052259	+	Silent	SNP	T	T	C	rs1429539	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	194	92	224	1	0.474227	0.00446429	T|0.613;C|0.387	0.387	strong	.	RNASE11	44	.	NM_145250	exon3	c.A375G	p.T125T	CACTTCTGTGGAG	.	PASS	Atlas-SNP
ZCCHC14	23174	hgsc.bcm.edu	37	16	87451273	87451273	+	Silent	SNP	G	G	T	rs56283442	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	12	7	18	0	0.583333	0	G|0.859;T|0.141	0.141	strong	.	ZCCHC14	87	.	NM_015144	exon8	c.C765A	p.S255S	GGCGGCGGAGCCG	.	PASS	Atlas-SNP
EHMT1	79813	hgsc.bcm.edu	37	9	140638416	140638416	+	Silent	SNP	G	G	A	rs1129767	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	22	11	42	0	0.5	0	G|0.862;A|0.138	0.138	strong	EHMT1_ENST00000460843,colon,carcinoma,+1,2	EHMT1	196	2	NM_001145527	exon6	c.G1044A	p.S348S	GGACTCGGATGAG	.	PASS	Atlas-SNP
BRCA2	675	hgsc.bcm.edu	37	13	32929232	32929232	+	Silent	SNP	A	A	G	rs1799955	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	84	77	0	1	0	A|0.772;G|0.228	0.228	strong	.	BRCA2	812	.	NM_000059	exon14	c.A7242G	p.S2414S	TAAATCACATTTT	.	PASS	Atlas-SNP
FMO2	2327	hgsc.bcm.edu	37	1	171174531	171174531	+	Missense_Mutation	SNP	A	A	G	rs2020863	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	108	107	106	0	0.990741	0	A|0.884;G|0.116	0.116	strong	FMO2,NS,carcinoma,0,1	FMO2	66	1	NM_001460	exon7	c.A941G	p.E314G	TCTTTGAGGATGG	.	PASS	Atlas-SNP
NDRG4	65009	hgsc.bcm.edu	37	16	58542901	58542901	+	Silent	SNP	G	G	A	rs867583	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	65	28	65	0	0.430769	0	G|0.696;A|0.304	0.304	strong	.	NDRG4	29	.	NM_001130487	exon13	c.G921A	p.T307T	CACTACGACCTTC	.	PASS	Atlas-SNP
WFDC1	58189	hgsc.bcm.edu	37	16	84360533	84360533	+	Missense_Mutation	SNP	A	A	G	rs12933084	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	40	62	0	0.533333	0	A|0.701;G|0.299	0.299	strong	.	WFDC1	17	.	NM_021197	exon6	c.A650G	p.K217R	AACAGAAGCACTT	.	PASS	Atlas-SNP
DDX5	1655	hgsc.bcm.edu	37	17	62496670	62496670	+	Missense_Mutation	SNP	A	A	C	rs1140409	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	135	54	128	0	0.4	0	A|0.953;C|0.047	0.047	strong	.	DDX5	101	.	NM_004396	exon12	c.T1438G	p.S480A	TACCTGAACCTCT	.	PASS	Atlas-SNP
EVA1C	59271	hgsc.bcm.edu	37	21	33887131	33887131	+	Silent	SNP	G	G	A	rs1129157	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55	55	27	0	1	0	G|0.575;A|0.425	0.425	strong	.	.	.	.	NM_058187	exon8	c.G957A	p.P319P	CCACCCGGAGAGA	.	PASS	Atlas-SNP
CCT2	10576	hgsc.bcm.edu	37	12	69986788	69986788	+	Silent	SNP	A	A	G	rs1043434	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	43	18	68	0	0.418605	0	A|0.800;G|0.200	0.200	strong	.	CCT2	49	.	NM_006431	exon9	c.A783G	p.T261T	CTCTACAGCAAAG	.	PASS	Atlas-SNP
KLHL38	340359	hgsc.bcm.edu	37	8	124664113	124664113	+	Missense_Mutation	SNP	T	T	A	rs11784175	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51	23	78	0	0.45098	0	T|0.899;A|0.101	0.101	strong	KLHL38,NS,carcinoma,0,1	KLHL38	81	1	NM_001081675	exon1	c.A1054T	p.N352Y	AGACATTGTGACT	.	PASS	Atlas-SNP
ZBTB46	140685	hgsc.bcm.edu	37	20	62378364	62378364	+	Silent	SNP	C	C	T	rs12625387	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	28	16	43	0	0.571429	0	C|0.724;T|0.276	0.276	strong	ZBTB46,rectum,carcinoma,0,1	ZBTB46	72	1	NM_025224	exon5	c.G1689A	p.A563A	GTCGTCCGCCAAC	.	PASS	Atlas-SNP
EMILIN3	90187	hgsc.bcm.edu	37	20	39991144	39991144	+	Silent	SNP	A	A	G	rs41307177	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	35	13	40	0	0.371429	0	A|0.888;G|0.112	0.112	strong	EMILIN3,rectum,carcinoma,0,1	EMILIN3	63	1	NM_052846	exon4	c.T1065C	p.L355L	GCCATCAAGGCTC	.	PASS	Atlas-SNP
SPTBN5	51332	hgsc.bcm.edu	37	15	42159290	42159290	+	Missense_Mutation	SNP	C	C	T	rs2290553	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	30	19	56	0	0.633333	0	C|0.858;T|0.142	0.142	strong	.	SPTBN5	171	.	NM_016642	exon36	c.G6242A	p.R2081Q	GGGCGCCGGAGCG	.	PASS	Atlas-SNP
QRICH2	84074	hgsc.bcm.edu	37	17	74287389	74287389	+	Missense_Mutation	SNP	T	T	C	rs2279053	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	99	48	113	0	0.484848	0	T|0.545;C|0.455	0.455	strong	.	QRICH2	143	.	NM_032134	exon4	c.A2921G	p.H974R	ATTCCATGTCGGT	.	PASS	Atlas-SNP
LPA	4018	hgsc.bcm.edu	37	6	161007496	161007496	+	Missense_Mutation	SNP	G	G	C	rs7765781	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49	17	63	0	0.346939	0	G|0.582;C|0.418	0.418	strong	.	LPA	237	.	NM_005577	exon26	c.C4114G	p.L1372V	AAGGAAGCTCTGT	.	PASS	Atlas-SNP
OBSL1	23363	hgsc.bcm.edu	37	2	220431631	220431631	+	Silent	SNP	G	G	T	rs1043537	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	128	67	169	0	0.523438	0	T|0.187;G|0.813;C|0.000	0.187	strong	.	OBSL1	120	.	NM_001173431	exon5	c.C2055A	p.A685A	CTTGACGGCATGC	.	PASS	Atlas-SNP
GPR148	344561	hgsc.bcm.edu	37	2	131486765	131486765	+	Missense_Mutation	SNP	C	C	G	rs80008074	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	122	38	159	0	0.311475	0	C|0.932;G|0.068	0.068	strong	.	GPR148	54	.	NM_207364	exon1	c.C41G	p.A14G	CTACAGCTTGGCC	.	PASS	Atlas-SNP
TRERF1	55809	hgsc.bcm.edu	37	6	42232475	42232475	+	Silent	SNP	G	G	A	rs2295274	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	16	90	0	0.183908	0	G|0.848;A|0.152	0.152	strong	.	TRERF1	124	.	NM_033502	exon7	c.C1602T	p.H534H	TCCCCCGTGGGAC	.	PASS	Atlas-SNP
CCHCR1	54535	hgsc.bcm.edu	37	6	31122500	31122500	+	Missense_Mutation	SNP	G	G	A	rs130065	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60	50	56	0	0.833333	0	G|0.836;A|0.164	0.164	strong	.	CCHCR1	68	.	NM_001105564	exon4	c.C574T	p.R192W	CCAGCCGCCGCAG	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	22	10	50	0	0.454545	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
ANO7	50636	hgsc.bcm.edu	37	2	242129487	242129487	+	Silent	SNP	G	G	T	rs11695874	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	124	41	128	0	0.330645	0	G|0.805;T|0.195	0.195	strong	.	ANO7	136	.	NM_001001666	exon2	c.G171T	p.R57R	GCTGCGGCGACGG	.	PASS	Atlas-SNP
GDF3	9573	hgsc.bcm.edu	37	12	7848202	7848202	+	Silent	SNP	G	G	C	rs17727707	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79	35	65	0	0.443038	0	G|0.951;C|0.049	0.049	strong	.	GDF3	68	.	NM_020634	exon1	c.C123G	p.P41P	CTTCTGGGGTGAA	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1093066	1093066	+	Missense_Mutation	SNP	C	C	A	rs56365200	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	32	4	23	1	0.125	0.0434783	.	.	weak	MUC2_ENST00000441003,caecum,carcinoma,0,4	MUC2	614	4	NM_002457	exon30	c.C4885A	p.P1629T	CCAACCCCAACAG	.	scavenged	Atlas-SNP
FCAR	2204	hgsc.bcm.edu	37	19	55396913	55396913	+	Missense_Mutation	SNP	G	G	A	rs11666735	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	45	18	57	0	0.4	0	G|0.933;A|0.067	0.067	strong	.	FCAR	110	.	NM_133279	exon3	c.G337A	p.D113N	TACAGTGACACCC	.	PASS	Atlas-SNP
GABRR2	2570	hgsc.bcm.edu	37	6	89981413	89981413	+	Silent	SNP	T	T	C	rs282117	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	59	58	74	0	0.983051	0	T|0.334;C|0.666	0.666	strong	GABRR2,NS,carcinoma,0,1	GABRR2	41	1	NM_002043	exon3	c.A249G	p.V83V	CACCTGTACGTCC	.	PASS	Atlas-SNP
ZNF682	91120	hgsc.bcm.edu	37	19	20117685	20117685	+	Missense_Mutation	SNP	G	G	A	rs2075090	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	29	38	0	0.54717	0	G|0.895;A|0.105	0.105	strong	.	ZNF682	51	.	NM_033196	exon4	c.C626T	p.T209I	TTAAAGGTTTTGC	.	PASS	Atlas-SNP
OR2L3	391192	hgsc.bcm.edu	37	1	248224587	248224587	+	Missense_Mutation	SNP	A	A	G	rs61525219	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	228	12	347	2	0.0526316	0.00576369	.	.	weak	OR2L3,NS,carcinoma,-1,1	OR2L3	97	1	NM_001004687	exon1	c.A604G	p.T202A	TTGAGCACCACCA	.	scavenged	Atlas-SNP
RNF17	56163	hgsc.bcm.edu	37	13	25428002	25428002	+	Missense_Mutation	SNP	C	C	A	rs3783082	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	21	11	26	0	0.52381	0	C|0.876;A|0.124	0.124	strong	.	RNF17	259	.	NM_031277	exon25	c.C3330A	p.N1110K	TAATAACTTAGAT	.	PASS	Atlas-SNP
DTD2	112487	hgsc.bcm.edu	37	14	31926584	31926584	+	Missense_Mutation	SNP	G	G	A	rs3087952		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85	8	90	5	0.0941176	0.0555556	.	.	weak	C14orf126,third_ventricle,glioma,0,2	.	.	2	NM_080664	exon1	c.C16T	p.R6W	GAATCCGGCTACC	.	scavenged	Atlas-SNP
MMP14	4323	hgsc.bcm.edu	37	14	23312554	23312554	+	Silent	SNP	C	C	G	rs2236302	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	28	50	0	0.444444	0	C|0.833;G|0.167	0.167	strong	.	MMP14	40	.	NM_004995	exon5	c.C777G	p.P259P	GGCACCCTTTTAC	.	PASS	Atlas-SNP
SLFN11	91607	hgsc.bcm.edu	37	17	33680127	33680127	+	Missense_Mutation	SNP	T	T	C	rs143643982	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	26	43	0	0.553191	0	T|0.999;C|0.001	0.001	strong	.	SLFN11	112	.	NM_152270	exon5	c.A1954G	p.K652E	AAGTTTTCCGGGT	.	PASS	Atlas-SNP
FAF2	23197	hgsc.bcm.edu	37	5	175926010	175926010	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55	22	43	0	0.4	0	.	.	none	.	FAF2	38	.	NM_014613	exon9	c.G935A	p.R312Q	AGAAACGGGAGGA	.	PASS	Atlas-SNP
C17orf107	100130311	hgsc.bcm.edu	37	17	4803711	4803711	+	Nonsense_Mutation	SNP	G	G	A	rs35400274	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	32	16	41	0	0.5	0	G|0.791;A|0.209	0.209	strong	.	C17orf107	8	.	NM_001145536	exon3	c.G456A	p.W152X	AGCATGGCTATGC	.	PASS	Atlas-SNP
CRB2	286204	hgsc.bcm.edu	37	9	126132919	126132919	+	Silent	SNP	G	G	A	rs33984675	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	41	41	39	0	1	0	G|0.766;A|0.234	0.234	strong	.	CRB2	86	.	NM_173689	exon7	c.G1587A	p.A529A	TCTAGCGACCCTG	.	PASS	Atlas-SNP
LIG4	3981	hgsc.bcm.edu	37	13	108861913	108861913	+	Silent	SNP	A	A	G	rs1805386	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	89	67	126	0	0.752809	0	A|0.870;G|0.130	0.130	strong	.	LIG4	91	.	NM_206937	exon3	c.T1704C	p.D568D	ATACATATCACTG	.	PASS	Atlas-SNP
GEMIN5	25929	hgsc.bcm.edu	37	5	154307070	154307070	+	Missense_Mutation	SNP	G	G	C	rs35522740	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	140	64	118	0	0.457143	0	G|0.979;C|0.021	0.021	strong	.	GEMIN5	120	.	NM_015465	exon7	c.C955G	p.R319G	ATTTCCGTCTCCA	.	PASS	Atlas-SNP
CCDC15	80071	hgsc.bcm.edu	37	11	124908352	124908352	+	Missense_Mutation	SNP	T	T	C	rs7107487	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	129	110	140	0	0.852713	0	T|0.779;C|0.221	0.221	strong	.	CCDC15	134	.	NM_025004	exon14	c.T2437C	p.C813R	CAAGAATGTTATG	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179598228	179598228	+	Silent	SNP	A	A	G	rs12993099	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	30	18	45	0	0.6	0	A|0.957;G|0.043	0.043	strong	.	TTN	18412	.	NM_001267550	exon54	c.T15792C	p.I5264I	TCGCTCAATGATT	.	PASS	Atlas-SNP
KRT6A	3853	hgsc.bcm.edu	37	12	52886478	52886478	+	Silent	SNP	T	T	C	rs376545	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	223	77	214	0	0.345291	0	T|0.615;C|0.385	0.385	strong	.	KRT6A	89	.	NM_005554	exon1	c.A495G	p.E165E	GATCTGTTCACGC	.	PASS	Atlas-SNP
CARD8	22900	hgsc.bcm.edu	37	19	48715196	48715196	+	Missense_Mutation	SNP	T	T	C	rs34632751	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	139	57	150	0	0.410072	0	T|0.983;C|0.017	0.017	strong	.	CARD8	53	.	NM_001184900	exon11	c.A1385G	p.Q462R	CTGGCTTGGAGTT	.	PASS	Atlas-SNP
SSRP1	6749	hgsc.bcm.edu	37	11	57102096	57102096	+	Silent	SNP	A	A	G	rs2230649	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	43	16	56	0	0.372093	0	A|0.799;G|0.201	0.201	strong	.	SSRP1	75	.	NM_003146	exon3	c.T81C	p.R27R	GCCCTGACGGCTC	.	PASS	Atlas-SNP
CSMD1	64478	hgsc.bcm.edu	37	8	3253868	3253868	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	97	28	61	0	0.28866	0	.	.	none	.	CSMD1	1469	.	NM_033225	exon17	c.T2441A	p.V814D	TCTCTGACCTCCA	.	PASS	Atlas-SNP
SYCE1	93426	hgsc.bcm.edu	37	10	135370633	135370633	+	Silent	SNP	C	C	T	rs8181356	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	119	55	130	0	0.462185	0	C|0.889;T|0.111	0.111	strong	SYCE1_ENST00000343131,NS,carcinoma,0,2	SYCE1	81	2	NM_001143763	exon7	c.G402A	p.K134K	TCTCTCCTTGCAC	.	PASS	Atlas-SNP
KLHL5	51088	hgsc.bcm.edu	37	4	39116911	39116911	+	Silent	SNP	T	T	C	rs3733276	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	126	63	94	0	0.5	0	T|0.472;C|0.528	0.528	strong	.	KLHL5	75	.	NM_015990	exon10	c.T2172C	p.T724T	TAATACTGTGGAG	.	PASS	Atlas-SNP
MAP3K1	4214	hgsc.bcm.edu	37	5	56178111	56178111	+	Silent	SNP	A	A	G	rs3822625	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	102	51	78	0	0.5	0	A|0.910;G|0.090	0.090	strong	.	MAP3K1	355	.	NM_005921	exon14	c.A3084G	p.Q1028Q	TCTACAATTCCAC	.	PASS	Atlas-SNP
SERPINH1	871	hgsc.bcm.edu	37	11	75282882	75282882	+	Silent	SNP	G	G	A	rs585821	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	36	6	48	0	0.166667	0	G|0.662;A|0.338	0.338	strong	.	SERPINH1	33	.	NM_001235	exon5	c.G1011A	p.L337L	CGACTTGTCACGC	.	PASS	Atlas-SNP
PRSS58	136541	hgsc.bcm.edu	37	7	141955390	141955390	+	Silent	SNP	C	C	T	rs145731516	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	109	47	101	0	0.431193	0	C|0.994;T|0.006	0.006	strong	.	PRSS58	41	.	NM_001001317	exon3	c.G144A	p.P48P	CCAAAGCGGGTGG	.	PASS	Atlas-SNP
CTNND1	1500	hgsc.bcm.edu	37	11	57563991	57563991	+	Silent	SNP	C	C	T	rs10896644	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	114	62	93	0	0.54386	0	C|0.728;T|0.272	0.272	strong	.	CTNND1	203	.	NM_001085461	exon6	c.C483T	p.D161D	ACCAGACGGGTTG	.	PASS	Atlas-SNP
PRDM6	93166	hgsc.bcm.edu	37	5	122435627	122435627	+	Missense_Mutation	SNP	G	G	A	rs1008058	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	171	86	132	0	0.502924	0	G|0.784;A|0.216	0.216	strong	.	PRDM6	26	.	NM_001136239	exon3	c.G871A	p.A291T	GCAGGCGCCGTGA	.	PASS	Atlas-SNP
MTHFD1	4522	hgsc.bcm.edu	37	14	64908845	64908845	+	Missense_Mutation	SNP	G	G	A	rs2236225	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82	81	95	0	0.987805	0	G|0.641;N|0.000	.	strong	.	MTHFD1	61	.	NM_005956	exon20	c.G1958A	p.R653Q	CAGACCGGATCGC	.	PASS	Atlas-SNP
ITGAM	3684	hgsc.bcm.edu	37	16	31336719	31336719	+	Silent	SNP	G	G	A	rs1143682	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	62	66	1	0.925373	0.0151515	G|0.631;A|0.369	0.369	strong	ITGAM,NS,carcinoma,0,3	ITGAM	137	3	NM_001145808	exon20	c.G2502A	p.T834T	GTCCACGCTCCAG	.	scavenged	Atlas-SNP
TRPA1	8989	hgsc.bcm.edu	37	8	72987638	72987638	+	Missense_Mutation	SNP	G	G	A	rs13268757	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	18	7	16	0	0.388889	0	G|0.872;A|0.128	0.128	strong	.	TRPA1	256	.	NM_007332	exon1	c.C7T	p.R3C	GGCTGCGCTTCAT	.	PASS	Atlas-SNP
ZNF253	56242	hgsc.bcm.edu	37	19	20002439	20002439	+	Missense_Mutation	SNP	G	G	T	rs75543118	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57	27	71	0	0.473684	0	G|0.945;T|0.055	0.055	strong	.	ZNF253	99	.	NM_021047	exon4	c.G383T	p.G128V	AAGGAGGTTATAA	.	PASS	Atlas-SNP
LYRM7	90624	hgsc.bcm.edu	37	5	130515811	130515811	+	Silent	SNP	G	G	A	rs113642581	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48	23	54	0	0.479167	0	A|0.027;C|0.000;G|0.973	0.027	strong	.	LYRM7	7	.	NM_181705	exon2	c.G42A	p.L14L	AACACTGCACAGG	.	PASS	Atlas-SNP
TBP	6908	hgsc.bcm.edu	37	6	170871052	170871052	+	Silent	SNP	G	G	A	rs112083427	byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	37	13	44	1	0.351351	0.0227273	G|0.500;A|0.500	0.500	strong	TBP,NS,carcinoma,0,5	TBP	58	5	NM_003194	exon3	c.G228A	p.Q76Q	ACAGCAGCAGCAG	.	scavenged	Atlas-SNP
DENND3	22898	hgsc.bcm.edu	37	8	142200467	142200467	+	Silent	SNP	G	G	A	rs1045303	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57	28	84	0	0.491228	0	A|0.299;C|0.000;G|0.700	0.299	strong	.	DENND3	127	.	NM_014957	exon20	c.G3090A	p.P1030P	GCTGCCGCGAGGT	.	PASS	Atlas-SNP
APOBR	55911	hgsc.bcm.edu	37	16	28506428	28506428	+	Silent	SNP	C	C	T	rs151233	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	32	15	25	0	0.46875	0	C|0.894;T|0.106	0.106	strong	.	APOBR	89	.	NM_018690	exon2	c.C66T	p.L22L	TTCCCTCGGCACC	.	PASS	Atlas-SNP
ADAMTS13	11093	hgsc.bcm.edu	37	9	136304497	136304497	+	Silent	SNP	A	A	G	rs3124768	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83	32	104	0	0.385542	0	A|0.531;G|0.469	0.469	strong	.	ADAMTS13	113	.	NM_139027	exon15	c.A1716G	p.T572T	TGTCACATTTCTG	.	PASS	Atlas-SNP
CH25H	9023	hgsc.bcm.edu	37	10	90966393	90966393	+	Silent	SNP	G	G	A	rs17382301	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	89	47	91	0	0.52809	0	G|0.910;A|0.090	0.090	strong	CH25H,NS,carcinoma,0,1	CH25H	19	1	NM_003956	exon1	c.C657T	p.N219N	AGGGAAGTTGTAG	.	PASS	Atlas-SNP
LRRK1	79705	hgsc.bcm.edu	37	15	101606889	101606889	+	Missense_Mutation	SNP	G	G	A	rs2959197	bycluster;by2hit2allele;byhapmap;alternate_allele	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	124	62	122	0	0.5	0	.	.	alt	.	LRRK1	310	.	NM_024652	exon33	c.G5813A	p.G1938D	ATTCTGGCGCCCA	.	PASS	Atlas-SNP
CCDC168	643677	hgsc.bcm.edu	37	13	103402522	103402522	+	Silent	SNP	C	C	T	rs9300760	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91	91	148	1	1	0.00675676	C|0.316;N|0.001	.	strong	.	.	.	.	NM_001146197	exon4	c.G525A	p.T175T	TAGACACGTTTCC	.	PASS	Atlas-SNP
LGI2	55203	hgsc.bcm.edu	37	4	25005193	25005193	+	Silent	SNP	G	G	A	rs2232028	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	108	108	143	0	1	0	G|0.332;A|0.668	0.668	strong	.	LGI2	62	.	NM_018176	exon8	c.C1518T	p.Y506Y	CTGCACGTAAATC	.	PASS	Atlas-SNP
OR7A10	390892	hgsc.bcm.edu	37	19	14952301	14952301	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100	49	88	0	0.49	0	.	.	none	.	OR7A10	33	.	NM_001005190	exon1	c.T389G	p.L130R	TAGTGCAGAGGGT	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	136	136	90	0	1	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
KANK1	23189	hgsc.bcm.edu	37	9	712060	712060	+	Missense_Mutation	SNP	G	G	C	rs4465020	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	95	41	78	0	0.431579	0	G|0.734;C|0.266	0.266	strong	KANK1_ENST00000382303,NS,carcinoma,0,2	KANK1	231	2	NM_001256876	exon7	c.G1294C	p.E432Q	CTTGTTGAGATGA	.	PASS	Atlas-SNP
NRD1	4898	hgsc.bcm.edu	37	1	52290984	52290984	+	Silent	SNP	T	T	G	rs11205896	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	191	75	200	0	0.39267	0	T|0.532;G|0.468	0.468	strong	.	NRD1	89	.	NM_002525	exon8	c.A1215C	p.G405G	AGGATGTCCAGGT	.	PASS	Atlas-SNP
WDPCP	51057	hgsc.bcm.edu	37	2	63401820	63401820	+	Missense_Mutation	SNP	T	T	C	rs61734468	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	125	50	125	0	0.4	0	T|0.993;C|0.007	0.007	strong	.	WDPCP	79	.	NM_015910	exon15	c.A2063G	p.N688S	GAGCCATTCAGTA	.	PASS	Atlas-SNP
DDX11	1663	hgsc.bcm.edu	37	12	31256517	31256517	+	Missense_Mutation	SNP	C	C	T	rs140335402	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69	33	75	0	0.478261	0	C|0.931;T|0.069	0.069	strong	DDX11_ENST00000407793,NS,haematopoietic_neoplasm,0,2	DDX11	188	2	NM_030653	exon26	c.C2543T	p.A848V	GCAGGGCCATCAG	.	PASS	Atlas-SNP
EDA2R	60401	hgsc.bcm.edu	37	X	65824986	65824986	+	Missense_Mutation	SNP	C	C	T	rs1385699	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	120	119	98	0	0.991667	0	C|0.436;0|0.005	.	strong	.	EDA2R	30	.	NM_001242310	exon2	c.G170A	p.R57K	TGACATCTGTGGT	.	PASS	Atlas-SNP
MTMR2	8898	hgsc.bcm.edu	37	11	95657111	95657111	+	Missense_Mutation	SNP	T	T	G	rs3824874	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	224	26	215	0	0.116071	0	G|0.251;N|0.000	0.251	strong	.	MTMR2	79	.	NM_016156	exon1	c.A8C	p.K3T	GAGCTCTTCTCCA	.	PASS	Atlas-SNP
GABRQ	55879	hgsc.bcm.edu	37	X	151821277	151821277	+	Missense_Mutation	SNP	T	T	A	rs3810651	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	118	79	89	0	0.669492	0	0|0.046;A|0.417	0.417	strong	.	GABRQ	131	.	NM_018558	exon9	c.T1432A	p.F478I	AGTATTTTTCCTA	.	PASS	Atlas-SNP
CCDC38	120935	hgsc.bcm.edu	37	12	96312686	96312686	+	Missense_Mutation	SNP	C	C	A	rs12368787	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93	43	125	0	0.462366	0	C|0.915;A|0.085	0.085	strong	.	CCDC38	45	.	NM_182496	exon3	c.G106T	p.V36F	CTTTGACAAGAAA	.	PASS	Atlas-SNP
AMER3	205147	hgsc.bcm.edu	37	2	131520945	131520945	+	Missense_Mutation	SNP	C	C	G	rs72854996	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	30	9	59	0	0.3	0	C|0.945;G|0.055	0.055	strong	.	.	.	.	NM_152698	exon2	c.C1300G	p.L434V	GGTCCTCTTGGCC	.	PASS	Atlas-SNP
ELOVL2	54898	hgsc.bcm.edu	37	6	10989942	10989942	+	Silent	SNP	G	G	A	rs12195587	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94	80	92	0	0.851064	0	G|0.898;A|0.102	0.102	strong	.	ELOVL2	40	.	NM_017770	exon7	c.C759T	p.Y253Y	CTGAACGTAAAAA	.	PASS	Atlas-SNP
FAT2	2196	hgsc.bcm.edu	37	5	150908813	150908813	+	Missense_Mutation	SNP	G	G	A	rs2304024	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	90	41	97	0	0.455556	0	G|0.858;N|0.001	.	strong	.	FAT2	465	.	NM_001447	exon14	c.C9952T	p.R3318W	GGGGCCGGTGTTC	.	PASS	Atlas-SNP
LOXHD1	125336	hgsc.bcm.edu	37	18	44065109	44065109	+	Missense_Mutation	SNP	C	C	T	rs373848470		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60	30	58	0	0.5	0	.	.	weak	.	LOXHD1	367	.	NM_144612	exon38	c.G5869A	p.E1957K	CGATCTCGTAGGC	.	PASS	Atlas-SNP
TMEM143	55260	hgsc.bcm.edu	37	19	48836673	48836673	+	Silent	SNP	G	G	T	rs3826828	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	39	17	24	0	0.435897	0	G|0.645;T|0.355	0.355	strong	.	TMEM143	29	.	NM_018273	exon8	c.C1183A	p.R395R	CCGACCGGAGCCA	.	PASS	Atlas-SNP
CALCR	799	hgsc.bcm.edu	37	7	93055753	93055753	+	Missense_Mutation	SNP	A	A	G	rs1801197	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	124	57	127	1	0.459677	0.00787402	A|0.561;G|0.439	0.439	strong	CALCR_ENST00000359558,NS,adenoma,0,2	CALCR	200	2	NM_001164737	exon16	c.T1442C	p.L481P	TTCCTCAGCTCCT	.	scavenged	Atlas-SNP
TAS2R20	259295	hgsc.bcm.edu	37	12	11150240	11150240	+	Missense_Mutation	SNP	T	T	C	rs7135018	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	32	77	0	0.484848	0	T|0.779;C|0.221	0.221	strong	.	TAS2R20	17	.	NM_176889	exon1	c.A235G	p.K79E	TTACTTTTAAATT	.	PASS	Atlas-SNP
PITPNM3	83394	hgsc.bcm.edu	37	17	6441376	6441376	+	Missense_Mutation	SNP	G	G	A	rs28493751	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	200	110	165	0	0.55	0	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	.	PASS	Atlas-SNP
PARP4	143	hgsc.bcm.edu	37	13	25052261	25052261	+	Silent	SNP	C	C	T	rs4770696	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	56	27	56	0	0.482143	0	C|0.494;T|0.506	0.506	strong	PARP4,mouth,carcinoma,-1,1	PARP4	142	1	NM_006437	exon13	c.G1602A	p.S534S	TGTTTGCGAAACT	.	PASS	Atlas-SNP
PHLDB1	23187	hgsc.bcm.edu	37	11	118502121	118502121	+	Silent	SNP	A	A	G	rs17614795	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	29	6	31	0	0.206897	0	A|0.975;G|0.025	0.025	strong	.	PHLDB1	103	.	NM_001144758	exon7	c.A2025G	p.L675L	ACGCCTATGGGAG	.	PASS	Atlas-SNP
NT5C2	22978	hgsc.bcm.edu	37	10	104849468	104849468	+	Silent	SNP	G	G	A	rs3740387	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	254	129	219	0	0.507874	0	G|0.600;A|0.400	0.400	strong	.	NT5C2	41	.	NM_012229	exon19	c.C1647T	p.D549D	ATCTTCGTCATGG	.	PASS	Atlas-SNP
DNAI1	27019	hgsc.bcm.edu	37	9	34500821	34500821	+	Missense_Mutation	SNP	G	G	A	rs11793196	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	25	60	0	0.403226	0	G|0.812;A|0.188	0.188	strong	.	DNAI1	72	.	NM_012144	exon11	c.G1003A	p.V335I	CTGTCCGTCACTG	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228434395	228434395	+	Silent	SNP	T	T	C	rs7517088	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	124	56	156	1	0.451613	0.00641026	T|0.373;C|0.627	0.627	strong	OBSCN_ENST00000359599,NS,carcinoma,0,1	OBSCN	2142	1	NM_001271223	exon14	c.T4200C	p.A1400A	AGAGGCTGCGGGC	.	scavenged	Atlas-SNP
SERBP1	26135	hgsc.bcm.edu	37	1	67895779	67895779	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110	39	127	0	0.354545	0	.	.	none	.	SERBP1	31	.	NM_001018067	exon1	c.C205T	p.Q69X	GCAGCTGTTTGCC	.	PASS	Atlas-SNP
FSTL5	56884	hgsc.bcm.edu	37	4	162307060	162307060	+	Silent	SNP	G	G	T	rs17040984	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	180	80	213	0	0.444444	0	G|0.805;T|0.195	0.195	strong	FSTL5,NS,carcinoma,+2,1	FSTL5	207	1	NM_020116	exon16	c.C2383A	p.R795R	TTTTCCGGTTCCA	.	PASS	Atlas-SNP
KCNJ18	100134444	hgsc.bcm.edu	37	17	21318912	21318912	+	Silent	SNP	C	C	A	rs35011501	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	180	19	236	0	0.105556	0	C|0.733;A|0.267	0.267	strong	.	.	.	.	NM_001194958	exon3	c.C258A	p.I86I	GCTCATCTTCTCG	.	PASS	Atlas-SNP
COL9A3	1299	hgsc.bcm.edu	37	20	61452556	61452556	+	Silent	SNP	G	G	A	rs149690829	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51	27	61	0	0.529412	0	G|1.000;A|0.000	0.000	strong	.	COL9A3	70	.	NM_001853	exon6	c.G333A	p.P111P	GGGGCCGCCCGGG	.	PASS	Atlas-SNP
ADAMTS12	81792	hgsc.bcm.edu	37	5	33614391	33614391	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	104	10	111	0	0.0961538	0	.	.	none	.	ADAMTS12	464	.	NM_030955	exon16	c.T2479A	p.F827I	GCCAGAAGTACAT	.	PASS	Atlas-SNP
KIAA1328	57536	hgsc.bcm.edu	37	18	34647176	34647176	+	Silent	SNP	T	T	C	rs3747895	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	127	62	129	0	0.488189	0	T|0.749;C|0.251	0.251	strong	.	KIAA1328	39	.	NM_020776	exon7	c.T900C	p.P300P	TAAGCCTACTCCT	.	PASS	Atlas-SNP
CACNA1C	775	hgsc.bcm.edu	37	12	2224449	2224449	+	Missense_Mutation	SNP	G	G	A	rs34534613	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	34	17	34	0	0.5	0	G|0.997;A|0.003	0.003	strong	.	CACNA1C	1023	.	NM_001129831	exon2	c.G109A	p.G37R	GCAGCGGGGCTGG	.	PASS	Atlas-SNP
GSDMA	284110	hgsc.bcm.edu	37	17	38121993	38121993	+	Missense_Mutation	SNP	G	G	A	rs3894194	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44	42	60	0	0.954545	0	G|0.576;T|0.004	.	strong	.	GSDMA	26	.	NM_178171	exon2	c.G53A	p.R18Q	ACCCTCGAGGGGA	.	PASS	Atlas-SNP
CCDC18	343099	hgsc.bcm.edu	37	1	93676478	93676478	+	Missense_Mutation	SNP	A	A	C	rs76148185	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	132	62	145	0	0.469697	0	A|0.982;C|0.018	0.018	strong	.	CCDC18	93	.	NM_206886	exon10	c.A1329C	p.E443D	TTCGGAATTGAGG	.	PASS	Atlas-SNP
SLCO4C1	353189	hgsc.bcm.edu	37	5	101631790	101631790	+	Silent	SNP	T	T	G	rs10479190	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73	29	91	0	0.39726	0	T|0.830;G|0.170	0.170	strong	.	SLCO4C1	113	.	NM_180991	exon1	c.A177C	p.P59P	TGGCTCTGGTGAC	.	PASS	Atlas-SNP
C4orf17	84103	hgsc.bcm.edu	37	4	100443800	100443800	+	Missense_Mutation	SNP	G	G	A	rs17029087	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	97	50	79	0	0.515464	0	G|0.780;A|0.220	0.220	strong	.	C4orf17	42	.	NM_032149	exon3	c.G271A	p.E91K	GTCCAGGAGAGCC	.	PASS	Atlas-SNP
SLC22A15	55356	hgsc.bcm.edu	37	1	116577849	116577849	+	Missense_Mutation	SNP	C	C	T	rs201564754	by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	247	64	245	0	0.259109	0	C|1.000;T|0.000	0.000	strong	.	SLC22A15	65	.	NM_018420	exon7	c.C986T	p.A329V	TGAGTGCGGGTGA	.	PASS	Atlas-SNP
DIP2A	23181	hgsc.bcm.edu	37	21	47971585	47971585	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	95	32	66	0	0.336842	0	.	.	none	.	DIP2A	332	.	NM_015151	exon24	c.G2878T	p.A960S	CTGGTTGCTGGGA	.	PASS	Atlas-SNP
PXMP4	11264	hgsc.bcm.edu	37	20	32295541	32295541	+	Missense_Mutation	SNP	C	C	T	rs910397	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	129	68	142	0	0.527132	0	C|0.421;N|0.000	.	strong	.	PXMP4	20	.	NM_007238	exon4	c.G610A	p.V204I	TATAGACGAGGAA	.	PASS	Atlas-SNP
OBSL1	23363	hgsc.bcm.edu	37	2	220432014	220432014	+	Silent	SNP	G	G	A	rs61732787	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98	47	91	0	0.479592	0	G|0.816;A|0.184	0.184	strong	.	OBSL1	120	.	NM_001173431	exon4	c.C1818T	p.F606F	ACCGTGGAACACC	.	PASS	Atlas-SNP
CCDC136	64753	hgsc.bcm.edu	37	7	128455916	128455916	+	Silent	SNP	G	G	A	rs2270590	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	65	33	58	0	0.507692	0	G|0.609;A|0.391	0.391	strong	.	CCDC136	170	.	NM_022742	exon16	c.G3294A	p.E1098E	GGAGGAGGATGAC	.	PASS	Atlas-SNP
RAG2	5897	hgsc.bcm.edu	37	11	36615697	36615697	+	Missense_Mutation	SNP	C	C	T	rs150762709	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	30	54	0	0.422535	0	C|0.997;T|0.003	0.003	strong	RAG2,NS,carcinoma,+2,2	RAG2	92	2	NM_001243785	exon3	c.G22A	p.V8I	TACTGACTGTTAC	.	PASS	Atlas-SNP
PPP1R26	9858	hgsc.bcm.edu	37	9	138376972	138376972	+	Missense_Mutation	SNP	A	A	G	rs3928777	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	34	23	36	0	0.676471	0	A|0.724;G|0.276	0.276	strong	.	.	.	.	NM_014811	exon4	c.A616G	p.K206E	TCCAGCAAGGACC	.	PASS	Atlas-SNP
TENM1	10178	hgsc.bcm.edu	37	X	123526031	123526031	+	Silent	SNP	T	T	C	rs2076165	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	122	35	78	0	0.286885	0	0|0.003;C|0.153	0.153	strong	.	.	.	.	NM_001163278	exon28	c.A5559G	p.S1853S	CGAAGGTGAATAT	.	PASS	Atlas-SNP
TACC2	10579	hgsc.bcm.edu	37	10	123846288	123846288	+	Missense_Mutation	SNP	G	G	A	rs4752642	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	37	81	0	0.430233	0	G|0.754;A|0.246	0.246	strong	.	TACC2	271	.	NM_206862	exon4	c.G4273A	p.A1425T	GCCCTGGCCACAC	.	PASS	Atlas-SNP
KIAA0753	9851	hgsc.bcm.edu	37	17	6515387	6515387	+	Missense_Mutation	SNP	A	A	G	rs2289642	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	175	87	154	0	0.497143	0	A|0.342;G|0.658	0.658	strong	.	KIAA0753	63	.	NM_014804	exon8	c.T1397C	p.L466P	TCTTCCAGAACTA	.	PASS	Atlas-SNP
KIF1A	547	hgsc.bcm.edu	37	2	241710437	241710437	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	15	45	0	0.238095	0	.	.	none	.	KIF1A	152	.	NM_001244008	exon15	c.A1292G	p.E431G	ATGCGCTCGTGGA	.	PASS	Atlas-SNP
KIAA1324	57535	hgsc.bcm.edu	37	1	109704525	109704525	+	Missense_Mutation	SNP	C	C	T	rs74920406	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	122	55	126	0	0.45082	0	C|0.977;T|0.023	0.023	strong	.	KIAA1324	77	.	NM_020775	exon2	c.C163T	p.H55Y	GAGTACCACTATG	.	PASS	Atlas-SNP
OR5P2	120065	hgsc.bcm.edu	37	11	7818151	7818151	+	Silent	SNP	G	G	A	rs73406606	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	35	35	51	0	1	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
SPATC1	375686	hgsc.bcm.edu	37	8	145095768	145095768	+	Missense_Mutation	SNP	C	C	T	rs150277218	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	30	58	0	0.46875	0	C|0.999;T|0.001	0.001	strong	.	SPATC1	77	.	NM_001134374	exon3	c.C1066T	p.H356Y	ACCACCCACATCG	.	PASS	Atlas-SNP
SNAPC4	6621	hgsc.bcm.edu	37	9	139273288	139273288	+	Silent	SNP	C	C	T	rs3829112	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	158	156	180	0	0.987342	0	C|0.845;T|0.155	0.155	strong	.	SNAPC4	82	.	NM_003086	exon21	c.G2991A	p.E997E	TGTGCCCTCGGCC	.	PASS	Atlas-SNP
GABRA2	2555	hgsc.bcm.edu	37	4	46252540	46252540	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	212	7	172	0	0.0330189	0	.	.	none	GABRA2,caecum,carcinoma,+1,2	GABRA2	134	2	NM_000807	exon10	c.G1141A	p.D381N	CTGGATCTTTTGA	.	scavenged	Atlas-SNP
TXNDC2	84203	hgsc.bcm.edu	37	18	9887877	9887877	+	Silent	SNP	G	G	A	rs34362649	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	117	54	124	0	0.461538	0	G|0.960;A|0.040	0.040	strong	.	TXNDC2	168	.	NM_001098529	exon2	c.G1401A	p.G467G	GGCCGGGGAGAGG	.	PASS	Atlas-SNP
SPPL2C	162540	hgsc.bcm.edu	37	17	43924231	43924231	+	Silent	SNP	G	G	A	rs12373140	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	39	39	39	0	1	0	C|0.852;T|0.148	.	strong	.	.	.	.	NM_175882	exon1	c.G1959A	p.Q653Q	TGCCCAGGCCCAG	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	30	18	45	0	0.6	0	A|0.874;G|0.126	0.126	strong	.	USP8	90	.	NM_001128610	exon14	c.A2215G	p.T739A	ACTCCAACAGTTA	.	PASS	Atlas-SNP
CXorf58	254158	hgsc.bcm.edu	37	X	23933912	23933912	+	Splice_Site	SNP	G	G	A	rs62584865	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110	40	77	0	0.363636	0	G|0.991;A|0.009	0.009	strong	.	CXorf58	53	.	NM_001169574	exon4	c.311+1G>A	.	ATTCAGGTAATGT	.	PASS	Atlas-SNP
ERN2	10595	hgsc.bcm.edu	37	16	23711925	23711925	+	Missense_Mutation	SNP	C	C	G	rs26764	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	107	107	101	0	1	0	C|0.619;G|0.381	0.381	strong	.	ERN2	131	.	NM_033266	exon13	c.G1604C	p.S535T	CTCCGGCTGGCCC	.	PASS	Atlas-SNP
ATP2C2	9914	hgsc.bcm.edu	37	16	84474484	84474484	+	Missense_Mutation	SNP	G	G	A	rs2303853	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82	40	100	0	0.487805	0	G|0.951;A|0.049	0.049	strong	.	ATP2C2	75	.	NM_014861	exon14	c.G1231A	p.G411S	TATGACGGTCAAG	.	PASS	Atlas-SNP
TRMT10C	54931	hgsc.bcm.edu	37	3	101283792	101283792	+	Missense_Mutation	SNP	C	C	G	rs3762735	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	78	39	108	0	0.5	0	C|0.864;G|0.136	0.136	strong	.	.	.	.	NM_017819	exon2	c.C167G	p.P56R	GTACACCCCCTTC	.	PASS	Atlas-SNP
VWA7	80737	hgsc.bcm.edu	37	6	31733466	31733466	+	Missense_Mutation	SNP	T	T	C	rs3101017	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91	80	73	0	0.879121	0	T|0.956;C|0.044	0.044	strong	.	.	.	.	NM_025258	exon17	c.A2581G	p.T861A	CTTGAGTCACCAA	.	PASS	Atlas-SNP
TTC23	64927	hgsc.bcm.edu	37	15	99762052	99762052	+	Silent	SNP	A	A	G	rs76007555	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	41	90	0	0.546667	0	A|0.932;G|0.068	0.068	strong	.	TTC23	33	.	NM_001040657	exon4	c.T198C	p.H66H	AAGCTCATGGACG	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	42	42	43	2	1	0.0465116	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	.	scavenged	Atlas-SNP
OR2T29	343563	hgsc.bcm.edu	37	1	248722777	248722777	+	Missense_Mutation	SNP	T	T	A	rs77589892	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	908	253	599	0	0.278634	0	T|0.770;A|0.230	0.230	strong	.	OR2T29	8	.	NM_001004694	exon1	c.A16T	p.R6W	CCATCCTGGTGAT	.	PASS	Atlas-SNP
SAGE1	55511	hgsc.bcm.edu	37	X	134991078	134991078	+	Silent	SNP	A	A	G	rs5974570	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	123	36	94	0	0.292683	0	A|0.806;G|0.194	0.194	strong	.	SAGE1	160	.	NM_018666	exon13	c.A1497G	p.Q499Q	ACCCCAAACTGAT	.	PASS	Atlas-SNP
WDR67	93594	hgsc.bcm.edu	37	8	124121798	124121798	+	Silent	SNP	A	A	G	rs16897969	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	96	56	75	0	0.583333	0	A|0.694;G|0.306	0.306	strong	.	WDR67	97	.	NM_001145088	exon10	c.A1374G	p.A458A	TGTGGCATTTCTC	.	PASS	Atlas-SNP
ELF1	1997	hgsc.bcm.edu	37	13	41517985	41517985	+	Silent	SNP	A	A	G	rs3764056	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	288	179	201	1	0.621528	0.00497512	A|0.521;G|0.479	0.479	strong	.	ELF1	65	.	NM_172373	exon6	c.T606C	p.D202D	CTTTCCATCTTTG	.	PASS	Atlas-SNP
SPARCL1	8404	hgsc.bcm.edu	37	4	88401616	88401616	+	Silent	SNP	A	A	G	rs9933	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94	42	93	0	0.446809	0	G|0.689;C|0.000;A|0.310	0.689	strong	.	SPARCL1	59	.	NM_004684	exon9	c.T1725C	p.D575D	GAGAAGATCAATG	.	PASS	Atlas-SNP
RANBP17	64901	hgsc.bcm.edu	37	5	170338066	170338066	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	171	41	143	0	0.239766	0	.	.	none	.	RANBP17	108	.	NM_022897	exon7	c.T688G	p.F230V	TTTGACTTCATTG	.	PASS	Atlas-SNP
HLA-C	3107	hgsc.bcm.edu	37	6	31239407	31239407	+	Missense_Mutation	SNP	G	G	T	rs17408553	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	175	21	161	0	0.12	0	T|0.398;G|0.602	0.398	strong	.	HLA-C	92	.	NM_002117	exon2	c.C312A	p.N104K	GCGCAGGTTCCGC	.	PASS	Atlas-SNP
RCOR3	55758	hgsc.bcm.edu	37	1	211451467	211451467	+	Silent	SNP	T	T	C	rs11577985	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	33	59	0	0.492537	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
SYNGR4	23546	hgsc.bcm.edu	37	19	48869178	48869178	+	Missense_Mutation	SNP	C	C	T	rs919804	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	34	11	29	0	0.323529	0	C|0.953;T|0.047	0.047	strong	.	SYNGR4	31	.	NM_012451	exon2	c.C79T	p.R27W	ATCACGCGGGTCT	.	PASS	Atlas-SNP
MXRA5	25878	hgsc.bcm.edu	37	X	3240343	3240343	+	Missense_Mutation	SNP	G	G	A	rs1635246	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	192	190	147	0	0.989583	0	G|0.441;A|0.559	0.559	strong	.	MXRA5	815	.	NM_015419	exon5	c.C3383T	p.A1128V	GTTGTTGCTGTTG	.	PASS	Atlas-SNP
ZNF417	147687	hgsc.bcm.edu	37	19	58420152	58420152	+	Silent	SNP	C	C	A	rs17845779	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	142	48	215	0	0.338028	0	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
THRAP3	9967	hgsc.bcm.edu	37	1	36752433	36752433	+	Missense_Mutation	SNP	C	C	T	rs6425977	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	115	110	115	1	0.956522	0.00869565	C|0.211;T|0.789	0.789	strong	.	THRAP3	93	.	NM_005119	exon4	c.C602T	p.A201V	ATGAGGCCAAGGA	.	PASS	Atlas-SNP
PRRC2A	7916	hgsc.bcm.edu	37	6	31603046	31603046	+	Silent	SNP	C	C	T	rs139053368	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	105	19	114	0	0.180952	0	C|0.999;T|0.001	0.001	strong	.	PRRC2A	152	.	NM_004638	exon22	c.C5298T	p.D1766D	TAGTGACAAGGTC	.	PASS	Atlas-SNP
COL8A1	1295	hgsc.bcm.edu	37	3	99513830	99513830	+	Missense_Mutation	SNP	G	G	A	rs139380413	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	39	20	50	0	0.512821	0	G|0.999;A|0.001	0.001	strong	.	COL8A1	68	.	NM_001850	exon5	c.G1085A	p.R362Q	GTGACCGGGGCAT	.	PASS	Atlas-SNP
NLRP13	126204	hgsc.bcm.edu	37	19	56443519	56443519	+	Silent	SNP	C	C	T	rs12610617	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93	48	68	0	0.516129	0	C|0.928;T|0.072	0.072	strong	NLRP13,colon,carcinoma,-1,1	NLRP13	220	1	NM_176810	exon1	c.G159A	p.P53P	GATACGCGGGAAG	.	PASS	Atlas-SNP
TM4SF20	79853	hgsc.bcm.edu	37	2	228230945	228230945	+	Missense_Mutation	SNP	G	G	A	rs76547437	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	141	72	153	1	0.510638	0.00653595	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	.	scavenged	Atlas-SNP
RCN3	57333	hgsc.bcm.edu	37	19	50045916	50045916	+	Silent	SNP	T	T	C	rs34459162	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91	42	62	0	0.461538	0	T|0.891;C|0.109	0.109	strong	.	RCN3	28	.	NM_020650	exon6	c.T786C	p.D262D	CCTGGATGGGAGT	.	PASS	Atlas-SNP
TARM1	441864	hgsc.bcm.edu	37	19	54578105	54578105	+	Missense_Mutation	SNP	C	C	T	rs80087697	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	41	52	0	0.476744	0	C|0.950;T|0.050	0.050	strong	TARM1,NS,carcinoma,0,1	TARM1	10	1	NM_001135686	exon3	c.G332A	p.R111H	TCACTGCGCTGTG	.	PASS	Atlas-SNP
BTBD10	84280	hgsc.bcm.edu	37	11	13443250	13443250	+	Silent	SNP	C	C	T	rs3789325	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	92	39	81	0	0.423913	0	C|0.866;T|0.134	0.134	strong	.	BTBD10	43	.	NM_032320	exon3	c.G237A	p.T79T	AGACTCCGTTCTT	.	PASS	Atlas-SNP
ANKRD17	26057	hgsc.bcm.edu	37	4	73956736	73956736	+	Silent	SNP	G	G	A	rs6855349	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	130	64	144	0	0.492308	0	G|0.639;A|0.361	0.361	strong	.	ANKRD17	214	.	NM_032217	exon29	c.C6609T	p.L2203L	GACACTGAGGACT	.	PASS	Atlas-SNP
ZRANB2	9406	hgsc.bcm.edu	37	1	71536574	71536574	+	Missense_Mutation	SNP	G	G	C	rs11583800	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55	16	39	0	0.290909	0	G|0.937;C|0.063	0.063	strong	.	ZRANB2	75	.	NM_203350	exon7	c.C619G	p.R207G	AAGATCGAGACTT	.	PASS	Atlas-SNP
SMOC1	64093	hgsc.bcm.edu	37	14	70477508	70477508	+	Silent	SNP	C	C	T	rs3825739	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	87	74	0	1	0	C|0.825;T|0.175	0.175	strong	SMOC1,colon,carcinoma,+1,1	SMOC1	61	1	NM_001034852	exon8	c.C702T	p.A234A	GAGTGCCCTGGAA	.	PASS	Atlas-SNP
MAPT	4137	hgsc.bcm.edu	37	17	44060775	44060775	+	Missense_Mutation	SNP	C	C	T	rs63750417	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	53	40	0	0.981481	0	C|0.552;A|0.040	.	strong	.	MAPT	135	.	NM_001123066	exon6	c.C605T	p.P202L	GGCCGCCGCTGAA	.	PASS	Atlas-SNP
NBPF3	84224	hgsc.bcm.edu	37	1	21795388	21795388	+	Missense_Mutation	SNP	A	A	G	rs1827293	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	113	55	105	1	0.486726	0.00952381	A|0.554;G|0.446	0.446	strong	NBPF3,NS,carcinoma,0,1	NBPF3	55	1	NM_001256416	exon3	c.C341G	p.A114G	ATAATTACGGTAA	.	scavenged	Atlas-SNP
C3orf18	51161	hgsc.bcm.edu	37	3	50598396	50598396	+	Silent	SNP	G	G	A	rs41291736	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	90	41	114	0	0.455556	0	G|0.908;A|0.092	0.092	strong	.	C3orf18	12	.	NM_016210	exon5	c.C360T	p.D120D	GGCGGCGTCCCGC	.	PASS	Atlas-SNP
ZFAND4	93550	hgsc.bcm.edu	37	10	46143958	46143958	+	Missense_Mutation	SNP	T	T	G	rs17854567	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48	25	79	0	0.520833	0	T|0.909;G|0.091	0.091	strong	.	.	.	.	NM_001128324	exon5	c.A353C	p.K118T	GCCATCTTCCTAA	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	30	75	0	0.447761	0	G|0.832;A|0.168	0.168	strong	.	PEAR1	118	.	NM_001080471	exon21	c.G2654A	p.R885H	GCAGCCGCCTGGA	.	PASS	Atlas-SNP
NOC3L	64318	hgsc.bcm.edu	37	10	96114835	96114835	+	Missense_Mutation	SNP	G	G	A	rs12572897	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	106	53	123	0	0.5	0	G|0.847;A|0.153	0.153	strong	.	NOC3L	67	.	NM_022451	exon6	c.C581T	p.P194L	TGAATAGGATCTT	.	PASS	Atlas-SNP
TNFRSF13B	23495	hgsc.bcm.edu	37	17	16843666	16843666	+	Missense_Mutation	SNP	C	C	T	rs104894649	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	32	46	0	0.52459	0	C|0.999;T|0.001	0.001	strong	.	TNFRSF13B	34	.	NM_012452	exon4	c.G605A	p.R202H	CTTTGACGGGGCC	.	PASS	Atlas-SNP
GAS2	2620	hgsc.bcm.edu	37	11	22696451	22696451	+	Silent	SNP	A	A	G	rs922571	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	58	57	82	1	0.982759	0.0121951	A|0.457;G|0.543	0.543	strong	GAS2,NS,carcinoma,0,1	GAS2	46	1	NM_177553	exon2	c.A36G	p.G12G	CAGTGGACCTGGC	.	scavenged	Atlas-SNP
BOD1	91272	hgsc.bcm.edu	37	5	173036394	173036394	+	Missense_Mutation	SNP	C	C	T	rs72822197	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	216	33	161	0	0.152778	0	C|0.946;T|0.054	0.054	strong	.	BOD1	15	.	NM_138369	exon3	c.G406A	p.V136M	CCACCACCTGAGA	.	PASS	Atlas-SNP
MACF1	23499	hgsc.bcm.edu	37	1	39838174	39838174	+	Silent	SNP	T	T	C	rs80197726	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	159	98	159	0	0.616352	0	T|0.945;C|0.055	0.055	strong	.	MACF1	909	.	NM_012090	exon48	c.T6933C	p.S2311S	GGCAAGTAAGGGA	.	PASS	Atlas-SNP
CHD1L	9557	hgsc.bcm.edu	37	1	146766122	146766122	+	Silent	SNP	C	C	G	rs45563244	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	101	53	53	0	0.524752	0	C|0.980;G|0.020	0.020	strong	.	CHD1L	72	.	NM_004284	exon22	c.C2538G	p.A846A	ACATGCCACGAAA	.	PASS	Atlas-SNP
CDH3	1001	hgsc.bcm.edu	37	16	68719113	68719113	+	Missense_Mutation	SNP	G	G	A	rs34494880	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	40	38	40	0	0.95	0	G|0.953;A|0.047	0.047	strong	.	CDH3	68	.	NM_001793	exon11	c.G1430A	p.R477H	GCTACCGCATCCT	.	PASS	Atlas-SNP
IGSF9B	22997	hgsc.bcm.edu	37	11	133815981	133815981	+	Silent	SNP	C	C	G	rs10894768	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	156	25	98	0	0.160256	0	C|0.633;G|0.367	0.367	strong	.	IGSF9B	290	.	NM_014987	exon2	c.G237C	p.P79P	GTGCGGCGGGTAG	.	PASS	Atlas-SNP
CUTA	51596	hgsc.bcm.edu	37	6	33384473	33384473	+	Missense_Mutation	SNP	C	C	T	rs41267649	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	173	142	183	0	0.820809	0	C|0.986;T|0.014	0.014	strong	.	CUTA	5	.	NM_001014433	exon6	c.G551A	p.R184H	ACCTGGCGCACCC	.	PASS	Atlas-SNP
RIN2	54453	hgsc.bcm.edu	37	20	19937289	19937289	+	Silent	SNP	C	C	T	rs368413043		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	33	55	0	0.5	0	.	.	weak	.	RIN2	126	.	NM_001242581	exon4	c.C336T	p.S112S	CTATTCCGAGGAA	.	PASS	Atlas-SNP
PION	54103	hgsc.bcm.edu	37	7	76984572	76984572	+	Silent	SNP	G	G	A	rs2037753	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	77	37	89	0	0.480519	0	G|0.528;A|0.472	0.472	strong	.	PION	74	.	NM_017439	exon16	c.C1296T	p.C432C	GAGCGCGCAGTGC	.	PASS	Atlas-SNP
GNB4	59345	hgsc.bcm.edu	37	3	179137273	179137273	+	Silent	SNP	A	A	G	rs1362650	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	120	119	128	0	0.991667	0	A|0.538;G|0.462	0.462	strong	.	GNB4	37	.	NM_021629	exon4	c.T117C	p.S39S	ACCCACAGAGTCC	.	PASS	Atlas-SNP
KIAA1984	84960	hgsc.bcm.edu	37	9	139694521	139694521	+	Missense_Mutation	SNP	T	T	G	rs4546744	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	21	11	40	0	0.52381	0	T|0.772;G|0.228	0.228	strong	KIAA1984,NS,carcinoma,0,1	KIAA1984	39	1	NM_001039374	exon4	c.T338G	p.L113R	TCCACCTGGTGCG	.	PASS	Atlas-SNP
PLCG2	5336	hgsc.bcm.edu	37	16	81971403	81971403	+	Silent	SNP	T	T	C	rs1071644	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55	55	56	0	1	0	C|0.387;N|0.000	0.387	strong	.	PLCG2	276	.	NM_002661	exon28	c.T3093C	p.N1031N	TCTCAATGGGCGC	.	PASS	Atlas-SNP
KCNU1	157855	hgsc.bcm.edu	37	8	36664917	36664917	+	Missense_Mutation	SNP	G	G	A	rs180964986	by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73	18	100	0	0.246575	0	G|1.000;A|0.000	0.000	strong	KCNU1,NS,carcinoma,0,1	KCNU1	359	1	NM_001031836	exon6	c.G605A	p.R202H	CCTTGCGCCTGCT	.	PASS	Atlas-SNP
UBR2	23304	hgsc.bcm.edu	37	6	42613298	42613298	+	Silent	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	20	45	0	0.425532	0	.	.	none	.	UBR2	134	.	NM_015255	exon21	c.T2379C	p.H793H	GGCTCATAGTGAA	.	PASS	Atlas-SNP
CMYA5	202333	hgsc.bcm.edu	37	5	79028726	79028726	+	Missense_Mutation	SNP	A	A	G	rs13158477	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	119	53	120	0	0.445378	0	A|0.895;G|0.105	0.105	strong	.	CMYA5	643	.	NM_153610	exon2	c.A4138G	p.I1380V	TCTCTTATCACTC	.	PASS	Atlas-SNP
KLF11	8462	hgsc.bcm.edu	37	2	10186419	10186419	+	Missense_Mutation	SNP	A	A	G	rs35927125	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	112	55	133	0	0.491071	0	T|0.000;G|0.084;A|0.916	0.084	strong	.	KLF11	45	.	NM_003597	exon2	c.A185G	p.Q62R	GATCCCAGAAAGG	.	PASS	Atlas-SNP
BTNL9	153579	hgsc.bcm.edu	37	5	180472513	180472513	+	Silent	SNP	A	A	G	rs6894087	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	63	51	0	1	0	A|0.458;G|0.542	0.542	strong	.	BTNL9	58	.	NM_152547	exon2	c.A24G	p.P8P	CTCCCCAGACTCC	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1092692	1092692	+	Missense_Mutation	SNP	C	C	T	rs199884046		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	301	23	300	0	0.076412	0	.	.	weak	.	MUC2	614	.	NM_002457	exon30	c.C4511T	p.T1504M	CTCCAACGACTAC	.	PASS	Atlas-SNP
BTC	685	hgsc.bcm.edu	37	4	75675841	75675841	+	Missense_Mutation	SNP	A	A	T	rs11938093	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	204	100	214	0	0.490196	0	A|0.755;T|0.245	0.245	strong	.	BTC	23	.	NM_001729	exon4	c.T370A	p.L124M	CTATCAAACAAAT	.	PASS	Atlas-SNP
ABP1	26	hgsc.bcm.edu	37	7	150554887	150554887	+	Silent	SNP	G	G	A	rs2071514	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80	38	71	0	0.475	0	G|0.717;A|0.283	0.283	strong	ABP1,NS,carcinoma,+1,2	ABP1	92	2	NM_001091	exon2	c.G1329A	p.A443A	CTATGCGGGGCTG	.	PASS	Atlas-SNP
HNMT	3176	hgsc.bcm.edu	37	2	138759649	138759649	+	Missense_Mutation	SNP	C	C	T	rs11558538	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	134	41	187	0	0.30597	0	C|0.931;T|0.069	0.069	strong	.	HNMT	42	.	NM_006895	exon4	c.C314T	p.T105I	CCAAGACATCGAA	.	PASS	Atlas-SNP
ESRP1	54845	hgsc.bcm.edu	37	8	95680229	95680229	+	Silent	SNP	C	C	T	rs1549466	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91	48	123	0	0.527473	0	C|0.648;T|0.352	0.352	strong	ESRP1_ENST00000433389,NS,carcinoma,+2,2	ESRP1	148	2	NM_001122827	exon10	c.C984T	p.V328V	CATTGTCCGCATG	.	PASS	Atlas-SNP
SRRM5	100170229	hgsc.bcm.edu	37	19	44117052	44117052	+	Missense_Mutation	SNP	C	C	T	rs77545563	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	89	51	82	0	0.573034	0	C|0.977;T|0.023	0.023	strong	.	SRRM5	38	.	NM_001145641	exon1	c.C779T	p.T260I	GCCCCACTGAAAT	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1090343	1090343	+	Silent	SNP	T	T	C	rs12221966	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	117	49	100	0	0.418803	0	T|0.916;C|0.084	0.084	strong	.	MUC2	614	.	NM_002457	exon27	c.T3639C	p.C1213C	CGTGTGTACCAAC	.	PASS	Atlas-SNP
TMPRSS3	64699	hgsc.bcm.edu	37	21	43805637	43805637	+	Silent	SNP	C	C	T	rs2839501	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82	42	82	0	0.512195	0	C|0.505;A|0.004	.	strong	TMPRSS3,colon,carcinoma,0,1	TMPRSS3	40	1	NM_001256317	exon6	c.G453A	p.V151V	TGAACTCACATAG	.	PASS	Atlas-SNP
ATAD2	29028	hgsc.bcm.edu	37	8	124357253	124357253	+	Silent	SNP	G	G	A	rs16898247	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91	40	69	0	0.43956	0	G|0.843;A|0.157	0.157	strong	ATAD2,NS,carcinoma,-2,1	ATAD2	160	1	NM_014109	exon19	c.C2589T	p.H863H	CCACACGTGGATA	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	124	51	130	0	0.41129	0	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	.	PASS	Atlas-SNP
HOXA9	3205	hgsc.bcm.edu	37	7	27204732	27204732	+	Silent	SNP	C	C	A	rs35355140	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	18	15	14	0	0.833333	0	C|0.937;A|0.063	0.063	strong	HOXA9,right_upper_lobe,carcinoma,-1,3	HOXA9	20	3	NM_152739	exon1	c.G345T	p.T115T	ACCGGGCGTGGGC	.	PASS	Atlas-SNP
DND1	373863	hgsc.bcm.edu	37	5	140050926	140050926	+	Silent	SNP	G	G	A	rs62384220	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	683	158	320	0	0.231332	0	G|0.970;A|0.030	0.030	strong	DND1,NS,carcinoma,0,1	DND1	15	1	NM_194249	exon4	c.C1014T	p.N338N	CAGGAGGTTGGCC	.	PASS	Atlas-SNP
SLC35G5	83650	hgsc.bcm.edu	37	8	11189601	11189601	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69	6	108	0	0.0869565	0	.	.	none	AMAC1L2,NS,carcinoma,-1,1	.	.	1	NM_054028	exon1	c.G986T	p.S329I	ACCTCAGCTGTGA	.	scavenged	Atlas-SNP
NUP205	23165	hgsc.bcm.edu	37	7	135279315	135279315	+	Silent	SNP	A	A	C	rs7800214	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98	37	95	0	0.377551	0	A|0.596;C|0.404	0.404	strong	NUP205,colon,carcinoma,0,1	NUP205	198	1	NM_015135	exon13	c.A1851C	p.A617A	CTTGGCACTCTGT	.	PASS	Atlas-SNP
EFHD1	80303	hgsc.bcm.edu	37	2	233537125	233537125	+	Missense_Mutation	SNP	A	A	G	rs11550699	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110	46	127	0	0.418182	0	A|0.685;G|0.315	0.315	strong	.	EFHD1	28	.	NM_025202	exon3	c.A557G	p.K186R	GTGTCAAAGGTGC	.	PASS	Atlas-SNP
COL2A1	1280	hgsc.bcm.edu	37	12	48375568	48375568	+	Silent	SNP	A	A	G	rs1635553	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	84	96	0	1	0	A|0.519;G|0.481	0.481	strong	COL2A1_ENST00000380518,NS,carcinoma,0,2	COL2A1	368	2	NM_001844	exon36	c.T2400C	p.N800N	CTCGCCATTAGCA	.	PASS	Atlas-SNP
PTCHD1	139411	hgsc.bcm.edu	37	X	23398214	23398214	+	Silent	SNP	T	T	C	rs5926304	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	59	59	40	0	1	0	T|0.313;C|0.687	0.687	strong	.	PTCHD1	213	.	NM_173495	exon2	c.T858C	p.C286C	CCTGTGTTGCTCT	.	PASS	Atlas-SNP
CHPF2	54480	hgsc.bcm.edu	37	7	150931268	150931268	+	Silent	SNP	C	C	G	rs2608293	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	104	104	102	0	1	0	C|0.584;G|0.416	0.416	strong	.	CHPF2	52	.	NM_019015	exon1	c.C171G	p.S57S	AGATTCCAGAGCT	.	PASS	Atlas-SNP
METTL21A	151194	hgsc.bcm.edu	37	2	208477956	208477956	+	Silent	SNP	C	C	T	rs2709416	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83	27	96	0	0.325301	0	C|0.146;T|0.854	0.854	strong	.	METTL21A	24	.	NM_145280	exon4	c.G471A	p.Q157Q	CAGTGTCTGAAGA	.	PASS	Atlas-SNP
DBC1	1620	hgsc.bcm.edu	37	9	121929575	121929575	+	Silent	SNP	T	T	C	rs28453	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	125	53	123	0	0.424	0	T|0.797;C|0.203	0.203	strong	.	DBC1	194	.	NM_014618	exon8	c.A2073G	p.S691S	CATCACTGACGAA	.	PASS	Atlas-SNP
TRAK2	66008	hgsc.bcm.edu	37	2	202245423	202245423	+	Missense_Mutation	SNP	A	A	T	rs34594680	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	106	55	125	0	0.518868	0	A|0.935;T|0.065	0.065	strong	.	TRAK2	62	.	NM_015049	exon16	c.T2588A	p.I863N	GGACCAATTTCTG	.	PASS	Atlas-SNP
CDHR2	54825	hgsc.bcm.edu	37	5	176017455	176017455	+	Missense_Mutation	SNP	C	C	T	rs2291442	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	104	44	90	1	0.423077	0.0111111	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	.	scavenged	Atlas-SNP
ZBTB24	9841	hgsc.bcm.edu	37	6	109796673	109796673	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	4	82	0	0.0540541	0	.	.	none	.	ZBTB24	64	.	NM_014797	exon5	c.C1217T	p.P406L	CATTCCGGTAATG	.	PASS	Atlas-SNP
KCNJ18	100134444	hgsc.bcm.edu	37	17	21318773	21318773	+	Missense_Mutation	SNP	G	G	A	rs3752034	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	116	41	124	0	0.353448	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
TAS2R20	259295	hgsc.bcm.edu	37	12	11149711	11149711	+	Missense_Mutation	SNP	C	C	A	rs10845279	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	122	47	139	0	0.385246	0	C|0.671;A|0.329	0.329	strong	TAS2R20,colon,carcinoma,0,1	TAS2R20	17	1	NM_176889	exon1	c.G764T	p.R255L	TTTGGTCGCATCT	.	PASS	Atlas-SNP
DNAH7	56171	hgsc.bcm.edu	37	2	196825256	196825256	+	Silent	SNP	G	G	C	rs115124743	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	128	80	106	0	0.625	0	G|0.969;C|0.031	0.031	strong	.	DNAH7	512	.	NM_018897	exon18	c.C2619G	p.V873V	AGAGGAGACTGTG	.	PASS	Atlas-SNP
PLEC	5339	hgsc.bcm.edu	37	8	144996029	144996029	+	Missense_Mutation	SNP	A	A	G	rs7833924	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	29	15	53	1	0.517241	0.0188679	A|0.560;G|0.440	0.440	strong	PLEC_ENST00000436759,NS,carcinoma,0,9	PLEC	1144	9	NM_201380	exon32	c.T8371C	p.S2791P	GAGCTGACACCTT	.	scavenged	Atlas-SNP
BAI2	576	hgsc.bcm.edu	37	1	32196647	32196647	+	Silent	SNP	C	C	G	rs909001	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	50	50	70	0	1	0	C|0.675;G|0.325	0.325	strong	.	BAI2	128	.	NM_001703	exon29	c.G4134C	p.P1378P	CCCCTCCGGCCGG	.	PASS	Atlas-SNP
DHX58	79132	hgsc.bcm.edu	37	17	40257055	40257055	+	Missense_Mutation	SNP	T	T	C	rs34016093	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	34	23	24	0	0.676471	0	T|0.965;C|0.035	0.035	strong	.	DHX58	39	.	NM_024119	exon10	c.A1382G	p.N461S	ATTTCATTGGTCA	.	PASS	Atlas-SNP
WDR73	84942	hgsc.bcm.edu	37	15	85189464	85189464	+	Silent	SNP	T	T	G	rs2271431	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	34	15	21	0	0.441176	0	T|0.830;G|0.170	0.170	strong	.	WDR73	15	.	NM_032856	exon6	c.A468C	p.R156R	CAGACTTCGGAGC	.	PASS	Atlas-SNP
MANSC4	100287284	hgsc.bcm.edu	37	12	27916224	27916224	+	Missense_Mutation	SNP	A	A	G	rs11049126	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	238	99	236	0	0.415966	0	A|0.859;G|0.141	0.141	strong	.	MANSC4	9	.	NM_001146221	exon3	c.T470C	p.L157S	TTATCTAAATTCA	.	PASS	Atlas-SNP
VIL1	7429	hgsc.bcm.edu	37	2	219313993	219313993	+	Silent	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	101	48	119	0	0.475248	0	.	.	none	.	VIL1	65	.	NM_007127	exon20	c.A2418C	p.P806P	GACTCCAGCTGCC	.	PASS	Atlas-SNP
NOTCH4	4855	hgsc.bcm.edu	37	6	32190406	32190406	+	Silent	SNP	A	A	G	rs443198	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	149	148	146	0	0.993289	0	A|0.576;G|0.424	0.424	strong	.	NOTCH4	201	.	NM_004557	exon3	c.T333C	p.G111G	TCTCTCACCAGTG	.	PASS	Atlas-SNP
EPPK1	83481	hgsc.bcm.edu	37	8	144943223	144943223	+	Missense_Mutation	SNP	T	T	C	rs139952490	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	50	20	36	0	0.4	0	T|0.995;C|0.005	0.005	strong	.	EPPK1	199	.	NM_031308	exon1	c.A4199G	p.N1400S	AACTTGTTGTCCT	.	PASS	Atlas-SNP
POM121L12	285877	hgsc.bcm.edu	37	7	53103554	53103554	+	Missense_Mutation	SNP	C	C	G	rs11238247	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	29	28	60	0	0.965517	0	C|0.588;G|0.412	0.412	strong	.	POM121L12	146	.	NM_182595	exon1	c.C190G	p.Q64E	CATATTCAGTACT	.	PASS	Atlas-SNP
DLGAP2	9228	hgsc.bcm.edu	37	8	1616640	1616640	+	Silent	SNP	G	G	A	rs4565482	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	129	67	117	0	0.51938	0	G|0.894;A|0.106	0.106	strong	DLGAP2_ENST00000356067,NS,carcinoma,0,5	DLGAP2	292	5	NM_004745	exon6	c.G1716A	p.P572P	GTCCCCGTGGCCC	.	PASS	Atlas-SNP
ACVR1C	130399	hgsc.bcm.edu	37	2	158412701	158412701	+	Missense_Mutation	SNP	T	T	G	rs55920843	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	134	33	146	0	0.246269	0	T|0.993;G|0.007	0.007	strong	.	ACVR1C	85	.	NM_145259	exon3	c.A448C	p.N150H	CCACATTTGGTCT	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	66	77	2	1	0.025974	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	.	scavenged	Atlas-SNP
KCNK5	8645	hgsc.bcm.edu	37	6	39159379	39159379	+	Missense_Mutation	SNP	G	G	A	rs150380866	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	52	56	0	0.83871	0	G|0.997;A|0.003	0.003	strong	.	KCNK5	57	.	NM_003740	exon5	c.C787T	p.R263W	CCTTCCGTCGCCG	.	PASS	Atlas-SNP
DSPP	1834	hgsc.bcm.edu	37	4	88537444	88537444	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	112	13	142	1	0.116071	0.00704225	.	.	none	DSPP,NS,carcinoma,0,1	DSPP	174	1	NM_014208	exon5	c.C3630T	p.S1210S	TGACAGCAGTGAC	.	scavenged	Atlas-SNP
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32497917	32497917	+	Missense_Mutation	SNP	C	C	A	rs71549220	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	109	19	144	0	0.174312	0	C|0.956;A|0.044	0.044	strong	HLA-DRB5,NS,carcinoma,0,1	HLA-DRB5	31	1	NM_002125	exon1	c.G85T	p.A29S	CCCCAGCCAAAGC	.	scavenged	Atlas-SNP
SLC38A6	145389	hgsc.bcm.edu	37	14	61448049	61448049	+	Silent	SNP	C	C	G	rs17097938	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49	24	52	0	0.489796	0	C|0.968;G|0.032	0.032	strong	.	SLC38A6	87	.	NM_153811	exon1	c.C54G	p.V18V	CTCTGTCCAGCAG	.	PASS	Atlas-SNP
LANCL3	347404	hgsc.bcm.edu	37	X	37527659	37527659	+	Missense_Mutation	SNP	T	T	C	rs28503960	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	163	36	105	0	0.220859	0	T|0.847;C|0.153	0.153	strong	.	LANCL3	42	.	NM_198511	exon5	c.T1142C	p.L381P	ATCTGCTGTATAC	.	PASS	Atlas-SNP
BFAR	51283	hgsc.bcm.edu	37	16	14742400	14742400	+	Missense_Mutation	SNP	T	T	G	rs11546303	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	127	64	139	1	0.503937	0.00719424	T|0.708;G|0.292	0.292	strong	BFAR,colon,carcinoma,0,1	BFAR	38	1	NM_016561	exon3	c.T419G	p.M140R	AGCAGATGGGAGG	.	scavenged	Atlas-SNP
UNC79	57578	hgsc.bcm.edu	37	14	94088369	94088369	+	Missense_Mutation	SNP	T	T	C	rs28670114	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79	38	91	0	0.481013	0	T|0.833;C|0.167	0.167	strong	.	UNC79	366	.	NM_020818	exon30	c.T4259C	p.V1420A	CGCCGGTAAAGCC	.	PASS	Atlas-SNP
STAG3	10734	hgsc.bcm.edu	37	7	99799845	99799845	+	Silent	SNP	T	T	A	rs1043915	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68	37	81	0	0.544118	0	T|0.679;A|0.321	0.321	strong	.	STAG3	121	.	NM_012447	exon24	c.T2445A	p.I815I	GATGATTGTTGGG	.	PASS	Atlas-SNP
MTFR1	9650	hgsc.bcm.edu	37	8	66620359	66620359	+	Silent	SNP	G	G	A	rs13274205	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	15	8	25	0	0.533333	0	G|0.693;A|0.307	0.307	strong	.	MTFR1	26	.	NM_001145839	exon7	c.G1046A	p.X349X	GGAGGTGATACAG	.	PASS	Atlas-SNP
KIF1B	23095	hgsc.bcm.edu	37	1	10342522	10342522	+	Silent	SNP	G	G	A	rs17034660	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100	56	106	0	0.56	0	G|0.962;A|0.038	0.038	strong	.	KIF1B	242	.	NM_183416	exon13	c.G1227A	p.T409T	CTTGACGTCTGTG	.	PASS	Atlas-SNP
SLCO2A1	6578	hgsc.bcm.edu	37	3	133670073	133670073	+	Silent	SNP	T	T	C	rs6767412	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	58	29	67	0	0.5	0	T|0.773;C|0.227	0.227	strong	SLCO2A1,NS,carcinoma,0,1	SLCO2A1	72	1	NM_005630	exon6	c.A840G	p.R280R	CATTGCTCGAGGG	.	PASS	Atlas-SNP
ARHGAP4	393	hgsc.bcm.edu	37	X	153176254	153176254	+	Silent	SNP	A	A	G	rs2070097	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	15	31	0	0.283019	0	A|0.354;G|0.646	0.646	strong	.	ARHGAP4	103	.	NM_001164741	exon16	c.T1836C	p.H612H	CAGGTCATGGGCA	.	PASS	Atlas-SNP
ULK4	54986	hgsc.bcm.edu	37	3	41877414	41877414	+	Missense_Mutation	SNP	T	T	C	rs3774372	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	188	87	233	0	0.462766	0	T|0.818;C|0.182	0.182	strong	.	ULK4	150	.	NM_017886	exon18	c.A1706G	p.K569R	TTTAATTTGCTGT	.	PASS	Atlas-SNP
TSKU	25987	hgsc.bcm.edu	37	11	76506888	76506888	+	Silent	SNP	G	G	A	rs11546727	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	95	15	87	0	0.157895	0	G|0.939;A|0.061	0.061	strong	TSKU,right_lower_lobe,carcinoma,+1,1	TSKU	26	1	NM_015516	exon2	c.G228A	p.S76S	TGAGTCGGTGTTG	.	PASS	Atlas-SNP
PDDC1	347862	hgsc.bcm.edu	37	11	772490	772490	+	Silent	SNP	G	G	A	rs12224894	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	53	60	0	0.981481	0	G|0.633;A|0.367	0.367	strong	.	PDDC1	16	.	NM_182612	exon5	c.C387T	p.A129A	CAGGGCGGCGACA	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	136	91	91	0	0.669118	0	0|0.015;A|0.479	0.479	strong	.	GPR112	459	.	NM_153834	exon6	c.C3638A	p.T1213N	ATGAGACCACACC	.	PASS	Atlas-SNP
SNX5	27131	hgsc.bcm.edu	37	20	17933265	17933265	+	Missense_Mutation	SNP	C	C	T	rs145056868	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55	30	77	0	0.545455	0	C|1.000;T|0.000	0.000	strong	.	SNX5	38	.	NM_014426	exon5	c.G479A	p.R160H	AAGTTGCGATCTT	.	PASS	Atlas-SNP
WDR81	124997	hgsc.bcm.edu	37	17	1639458	1639458	+	Silent	SNP	A	A	G	rs11549259	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	32	51	0	0.477612	0	A|0.293;G|0.707	0.707	strong	WDR81_ENST00000437219,NS,carcinoma,0,3	WDR81	180	3	NM_001163809	exon9	c.A5451G	p.T1817T	CCGCACAGGCCTG	.	PASS	Atlas-SNP
RYR2	6262	hgsc.bcm.edu	37	1	237814783	237814783	+	Silent	SNP	C	C	T	rs684923	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	165	68	184	0	0.412121	0	C|0.455;T|0.545	0.545	strong	.	RYR2	1273	.	NM_001035	exon51	c.C7806T	p.H2602H	TGAACACGCAAAG	.	PASS	Atlas-SNP
POLE	5426	hgsc.bcm.edu	37	12	133236000	133236000	+	Silent	SNP	C	C	T	rs5744857	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	86	106	0	1	0	C|0.443;T|0.557	0.557	strong	POLE_ENST00000320574,caecum,carcinoma,-1,2	POLE	416	2	NM_006231	exon26	c.G3156A	p.T1052T	GATGGACGTAGAC	.	PASS	Atlas-SNP
ACAP3	116983	hgsc.bcm.edu	37	1	1229538	1229538	+	Silent	SNP	C	C	T	rs148138514	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	43	13	62	0	0.302326	0	C|0.993;T|0.007	0.007	strong	.	ACAP3	87	.	NM_030649	exon22	c.G2181A	p.A727A	CACGTCCGCTCCG	.	PASS	Atlas-SNP
INPP4B	8821	hgsc.bcm.edu	37	4	143067054	143067054	+	Silent	SNP	G	G	A	rs35390852	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	168	88	139	0	0.52381	0	G|0.911;A|0.089	0.089	strong	.	INPP4B	132	.	NM_003866	exon19	c.C1659T	p.G553G	GTTGCCGCCACTG	.	PASS	Atlas-SNP
SLC4A5	57835	hgsc.bcm.edu	37	2	74450058	74450058	+	Missense_Mutation	SNP	C	C	T	rs36081793	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82	47	104	0	0.573171	0	C|0.977;T|0.023	0.023	strong	.	SLC4A5	215	.	NM_021196	exon25	c.G3316A	p.V1106I	TTATAACCGAGGG	.	PASS	Atlas-SNP
MAT2A	4144	hgsc.bcm.edu	37	2	85769711	85769711	+	Silent	SNP	C	C	G	rs1078004	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	119	93	161	0	0.781513	0	C|0.483;G|0.517	0.517	strong	MAT2A,NS,carcinoma,0,1	MAT2A	23	1	NM_005911	exon7	c.C792G	p.R264R	TGGACGCAAAATC	.	PASS	Atlas-SNP
NUP210	23225	hgsc.bcm.edu	37	3	13421150	13421150	+	Missense_Mutation	SNP	C	C	T	rs7628051	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	140	62	139	0	0.442857	0	C|0.416;T|0.584	0.584	strong	.	NUP210	182	.	NM_024923	exon7	c.G889A	p.A297T	GCCGGGCTGGGTC	.	PASS	Atlas-SNP
NIPAL2	79815	hgsc.bcm.edu	37	8	99208190	99208190	+	Silent	SNP	A	A	C	rs3779721	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	96	48	121	0	0.5	0	A|0.642;C|0.358	0.358	strong	.	NIPAL2	23	.	NM_024759	exon9	c.T924G	p.T308T	AAATACAGTGAGA	.	PASS	Atlas-SNP
MRPL37	51253	hgsc.bcm.edu	37	1	54683856	54683856	+	Silent	SNP	C	C	G	rs15921	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	141	57	151	1	0.404255	0.00662252	C|0.704;G|0.296	0.296	strong	MRPL37,NS,carcinoma,0,2	MRPL37	36	2	NM_016491	exon7	c.C1206G	p.G402G	TGTTGGCCCAGTT	.	scavenged	Atlas-SNP
NARR	0	hgsc.bcm.edu	37	17	27044004	27044004	+	Missense_Mutation	SNP	C	C	T	rs11545699	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	20	10	42	0	0.5	0	C|0.983;T|0.017	0.017	strong	.	.	.	.	NM_001256281	exon2	c.G505A	p.E169K	CTCCTTCCTCAGG	.	PASS	Atlas-SNP
SPACA7	122258	hgsc.bcm.edu	37	13	113052388	113052388	+	Silent	SNP	A	A	G	rs2296895	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	53	90	0	0.791045	0	A|0.363;G|0.637	0.637	strong	SPACA7,NS,adenoma,0,1	SPACA7	36	1	NM_145248	exon3	c.A177G	p.L59L	GATTTTAGATCTG	.	PASS	Atlas-SNP
DISP1	84976	hgsc.bcm.edu	37	1	223176275	223176275	+	Silent	SNP	G	G	A	rs61738819	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	134	71	136	0	0.529851	0	G|0.899;A|0.101	0.101	strong	.	DISP1	145	.	NM_032890	exon10	c.G1536A	p.V512V	CATTGTGATTGTC	.	PASS	Atlas-SNP
BTN3A2	11118	hgsc.bcm.edu	37	6	26370707	26370707	+	Silent	SNP	T	T	C	rs9379862	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	156	23	131	0	0.147436	0	T|0.752;C|0.248	0.248	strong	.	BTN3A2	44	.	NM_001197246	exon3	c.T591C	p.D197D	TGCAGATGGAGTG	.	PASS	Atlas-SNP
TRIOBP	11078	hgsc.bcm.edu	37	22	38120429	38120429	+	Silent	SNP	T	T	C	rs6000868	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	171	13	154	1	0.0760234	0.00649351	T|0.625;C|0.375	0.375	strong	TRIOBP_ENST00000344404,colon,carcinoma,0,1	TRIOBP	262	1	NM_001039141	exon7	c.T1866C	p.D622D	ACGAGATAACCCC	.	scavenged	Atlas-SNP
PCSK5	5125	hgsc.bcm.edu	37	9	78936492	78936492	+	Missense_Mutation	SNP	A	A	G	rs1110223	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	34	21	35	0	0.617647	0	A|0.687;G|0.313	0.313	strong	.	PCSK5	329	.	NM_001190482	exon30	c.A3958G	p.K1320E	GCTGTGAAGGGGG	.	PASS	Atlas-SNP
PYGB	5834	hgsc.bcm.edu	37	20	25264814	25264814	+	Silent	SNP	T	T	C	rs2227892	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93	38	98	0	0.408602	0	T|0.523;C|0.477	0.477	strong	.	PYGB	84	.	NM_002862	exon14	c.T1695C	p.D565D	GTTCGATGTGCAT	.	PASS	Atlas-SNP
KANSL1	284058	hgsc.bcm.edu	37	17	44249096	44249096	+	Silent	SNP	A	A	C	rs17662889	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	30	44	0	0.47619	0	A|0.888;C|0.112	0.112	strong	.	.	.	.	NM_001193466	exon2	c.T414G	p.L138L	GGTTCTAAGATTT	.	PASS	Atlas-SNP
HRNR	388697	hgsc.bcm.edu	37	1	152191051	152191051	+	Silent	SNP	G	G	A	rs74868796	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	119	53	102	0	0.445378	0	G|0.942;A|0.058	0.058	strong	.	HRNR	403	.	NM_001009931	exon3	c.C3054T	p.S1018S	CTGCCCGGAACCA	.	PASS	Atlas-SNP
NFATC1	4772	hgsc.bcm.edu	37	18	77170477	77170477	+	Missense_Mutation	SNP	C	C	A	rs1051978	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	70	41	71	0	0.585714	0	C|0.931;A|0.069	0.069	strong	.	NFATC1	105	.	NM_172390	exon2	c.C202A	p.P68T	CCGGCCCCGTGCC	.	PASS	Atlas-SNP
ZNF331	55422	hgsc.bcm.edu	37	19	54080144	54080144	+	Silent	SNP	A	A	G	rs8109631	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82	52	81	1	0.634146	0.0123457	A|0.243;G|0.757	0.757	strong	ZNF331,NS,carcinoma,0,1	ZNF331	66	1	NM_001253801	exon5	c.A330G	p.R110R	CAAAAGACCTGCT	.	scavenged	Atlas-SNP
ZNF211	10520	hgsc.bcm.edu	37	19	58152361	58152361	+	Silent	SNP	T	T	A	rs3746219	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	104	52	129	0	0.5	0	T|0.805;A|0.195	0.195	strong	.	ZNF211	78	.	NM_001265597	exon5	c.T702A	p.T234T	GGACACTGCCTCG	.	PASS	Atlas-SNP
GLT6D1	360203	hgsc.bcm.edu	37	9	138516128	138516128	+	Missense_Mutation	SNP	C	C	T	rs61739510	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	27	62	0	0.442623	0	C|0.947;T|0.053	0.053	strong	.	GLT6D1	56	.	NM_182974	exon5	c.G646A	p.A216T	TGCAAGCTGCTGA	.	PASS	Atlas-SNP
KRTAP5-5	439915	hgsc.bcm.edu	37	11	1651150	1651150	+	Missense_Mutation	SNP	G	G	A	rs201376522	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55	38	56	0	0.690909	0	.	.	weak	KRTAP5-5,right_upper_lobe,carcinoma,-1,2	KRTAP5-5	86	2	NM_001001480	exon1	c.G80A	p.G27D	GCTCCGGCTGTGG	.	PASS	Atlas-SNP
NPAP1	23742	hgsc.bcm.edu	37	15	24922208	24922208	+	Silent	SNP	C	C	G	rs12905237	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	45	17	51	0	0.377778	0	C|0.867;G|0.133	0.133	strong	.	.	.	.	NM_018958	exon1	c.C1194G	p.A398A	GCCTGCCCCTTCT	.	PASS	Atlas-SNP
SORL1	6653	hgsc.bcm.edu	37	11	121460846	121460846	+	Silent	SNP	C	C	T	rs2276412	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	129	21	96	0	0.162791	0	C|0.924;T|0.076	0.076	strong	.	SORL1	218	.	NM_003105	exon30	c.C4176T	p.N1392N	GGAGAACGACTGT	.	PASS	Atlas-SNP
CHAF1A	10036	hgsc.bcm.edu	37	19	4409756	4409756	+	Silent	SNP	A	A	G	rs2230636	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	27	9	23	0	0.333333	0	A|0.809;G|0.191	0.191	strong	.	CHAF1A	69	.	NM_005483	exon3	c.A960G	p.R320R	CCGCAGAGTGAGT	.	PASS	Atlas-SNP
CPN2	1370	hgsc.bcm.edu	37	3	194062519	194062519	+	Missense_Mutation	SNP	C	C	T	rs3732477	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	97	42	86	0	0.43299	0	C|0.653;T|0.347	0.347	strong	.	CPN2	56	.	NM_001080513	exon2	c.G913A	p.A305T	CCTCAGCGACAGT	.	PASS	Atlas-SNP
APOL5	80831	hgsc.bcm.edu	37	22	36123083	36123083	+	Missense_Mutation	SNP	C	C	T	rs2076672	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	32	18	25	0	0.5625	0	C|0.812;T|0.188	0.188	strong	.	APOL5	45	.	NM_030642	exon3	c.C968T	p.T323M	CAAGGACGGAGAC	.	PASS	Atlas-SNP
MCF2	4168	hgsc.bcm.edu	37	X	138679712	138679712	+	Silent	SNP	T	T	A	rs1051619	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	199	48	152	0	0.241206	0	T|0.720;0|0.003	.	strong	.	MCF2	432	.	NM_001171876	exon22	c.A2190T	p.G730G	AGCAGATCCTTCA	.	PASS	Atlas-SNP
DOCK7	85440	hgsc.bcm.edu	37	1	62960101	62960101	+	Silent	SNP	A	A	G	rs10889335	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	105	61	120	0	0.580952	0	A|0.670;G|0.330	0.330	strong	.	DOCK7	184	.	NM_001271999	exon40	c.T5035C	p.L1679L	AGGTCAATCGCAG	.	PASS	Atlas-SNP
ARMCX1	51309	hgsc.bcm.edu	37	X	100808222	100808222	+	Silent	SNP	C	C	T	rs1044275	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	59	13	47	0	0.220339	0	C|0.948;T|0.052	0.052	strong	.	ARMCX1	67	.	NM_016608	exon4	c.C309T	p.G103G	AGGTGGCCTAGAG	.	PASS	Atlas-SNP
TNFRSF4	7293	hgsc.bcm.edu	37	1	1148445	1148445	+	Silent	SNP	G	G	A	rs34160451	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	134	62	143	0	0.462687	0	G|0.988;A|0.012	0.012	strong	.	TNFRSF4	12	.	NM_003327	exon3	c.C297T	p.C99C	GGCCGTGCACAGC	.	PASS	Atlas-SNP
RC3H2	54542	hgsc.bcm.edu	37	9	125618080	125618080	+	Silent	SNP	T	T	G	rs7033878	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68	26	67	0	0.382353	0	T|0.932;G|0.068	0.068	strong	.	RC3H2	150	.	NM_018835	exon14	c.A2532C	p.I844I	GGAGCCTATGGTG	.	PASS	Atlas-SNP
KIAA1143	57456	hgsc.bcm.edu	37	3	44794881	44794881	+	Missense_Mutation	SNP	A	A	C	rs3853404	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94	38	80	0	0.404255	0	A|1.000;|0.000	.	weak	.	KIAA1143	10	.	NM_020696	exon3	c.T417G	p.I139M	ATTTTTAATTTGT	.	PASS	Atlas-SNP
PYDC2	152138	hgsc.bcm.edu	37	3	191179193	191179193	+	Missense_Mutation	SNP	A	A	G	rs293833	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	105	42	103	0	0.4	0	A|0.344;G|0.656	0.656	strong	.	PYDC2	24	.	NM_001083308	exon1	c.A242G	p.Q81R	TGAATCAAACGCA	.	PASS	Atlas-SNP
IL23R	149233	hgsc.bcm.edu	37	1	67633812	67633812	+	Missense_Mutation	SNP	G	G	T	rs1884444	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	122	122	139	0	1	0	G|0.477;T|0.523	0.523	strong	.	IL23R	52	.	NM_144701	exon2	c.G9T	p.Q3H	GAATCAGGTCACT	.	PASS	Atlas-SNP
DYNLRB2	83657	hgsc.bcm.edu	37	16	80583497	80583497	+	Silent	SNP	C	C	T	rs11866734	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85	42	84	0	0.494118	0	C|0.779;T|0.221	0.221	strong	DYNLRB2,NS,carcinoma,0,3	DYNLRB2	17	3	NM_130897	exon3	c.C196T	p.L66L	AACGACCTGACTT	.	PASS	Atlas-SNP
CELSR1	9620	hgsc.bcm.edu	37	22	46761565	46761565	+	Silent	SNP	G	G	C	rs34184256	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	29	103	0	0.333333	0	G|0.992;C|0.008	0.008	strong	.	CELSR1	242	.	NM_014246	exon31	c.C8322G	p.L2774L	CACGCCGAGCTTC	.	PASS	Atlas-SNP
NEB	4703	hgsc.bcm.edu	37	2	152427080	152427080	+	Silent	SNP	C	C	A	rs140688592	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	107	15	133	0	0.140187	0	C|0.995;A|0.005	0.005	strong	.	NEB	1697	.	NM_001271208	exon108	c.G17049T	p.A5683A	ACAGCCCGCCTTC	.	PASS	Atlas-SNP
KAL1	3730	hgsc.bcm.edu	37	X	8503641	8503641	+	Silent	SNP	G	G	A	rs809446	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	237	236	137	0	0.995781	0	G|0.471;0|0.003	.	strong	.	KAL1	78	.	NM_000216	exon12	c.C1833T	p.I611I	AGGCAGGATCTGG	.	PASS	Atlas-SNP
C1orf86	199990	hgsc.bcm.edu	37	1	2125172	2125172	+	Missense_Mutation	SNP	G	G	A	rs1058411	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	18	7	22	0	0.388889	0	G|0.825;A|0.175	0.175	strong	.	C1orf86	20	.	NM_001256946	exon3	c.C376T	p.P126S	TGCAGGGATCAGG	.	PASS	Atlas-SNP
POLRMT	5442	hgsc.bcm.edu	37	19	617614	617614	+	Silent	SNP	G	G	A	rs41551212	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	27	18	19	0	0.666667	0	G|0.881;A|0.119	0.119	strong	.	POLRMT	91	.	NM_005035	exon19	c.C3537T	p.I1179I	CTGCAGGATGGGC	.	PASS	Atlas-SNP
EPHB6	2051	hgsc.bcm.edu	37	7	142561786	142561786	+	Silent	SNP	T	T	C	rs56300555	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	143	73	171	0	0.51049	0	T|0.990;C|0.010	0.010	strong	.	EPHB6	168	.	NM_004445	exon7	c.T228C	p.H76H	ATGTCATGTGGCA	.	PASS	Atlas-SNP
DUS1L	64118	hgsc.bcm.edu	37	17	80020812	80020812	+	Silent	SNP	C	C	T	rs11542332	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	22	41	0	0.468085	0	C|0.901;T|0.099	0.099	strong	DUS1L,colon,carcinoma,-1,1	DUS1L	25	1	NM_022156	exon5	c.G435A	p.T145T	TTTGCACGTGACA	.	PASS	Atlas-SNP
PYGL	5836	hgsc.bcm.edu	37	14	51387782	51387782	+	Missense_Mutation	SNP	C	C	T	rs946616	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	101	42	110	0	0.415842	0	C|0.897;T|0.103	0.103	strong	.	PYGL	77	.	NM_002863	exon6	c.G664A	p.V222I	CCAGGACCACCTG	.	PASS	Atlas-SNP
LYST	1130	hgsc.bcm.edu	37	1	235971763	235971763	+	Silent	SNP	A	A	G	rs3768066	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	108	66	134	0	0.611111	0	A|0.898;G|0.102	0.102	strong	.	LYST	370	.	NM_000081	exon5	c.T2355C	p.L785L	GGATTTAAGCAGG	.	PASS	Atlas-SNP
DNAH8	1769	hgsc.bcm.edu	37	6	38883000	38883000	+	Silent	SNP	C	C	T	rs150857304	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	103	79	89	0	0.76699	0	C|0.998;T|0.002	0.002	strong	.	DNAH8	1239	.	NM_001206927	exon68	c.C9987T	p.S3329S	AGTAAGCGCTCAG	.	PASS	Atlas-SNP
PDE6C	5146	hgsc.bcm.edu	37	10	95395364	95395364	+	Silent	SNP	C	C	G	rs3737228	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80	36	109	0	0.45	0	C|0.752;G|0.248	0.248	strong	.	PDE6C	97	.	NM_006204	exon10	c.C1380G	p.T460T	CCAAACCAAAGCC	.	PASS	Atlas-SNP
AGL	178	hgsc.bcm.edu	37	1	100358103	100358103	+	Missense_Mutation	SNP	C	C	T	rs3753494	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	109	53	100	0	0.486239	0	C|0.869;T|0.131	0.131	strong	.	AGL	137	.	NM_000644	exon24	c.C3199T	p.P1067S	GATGTACCTTATA	.	PASS	Atlas-SNP
BIVM-ERCC5	0	hgsc.bcm.edu	37	13	103460019	103460019	+	Silent	SNP	G	G	A	rs111947510	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	21	89	0	0.318182	0	G|0.991;A|0.009	0.009	strong	.	.	.	.	NM_001204425	exon1	c.G402A	p.L134L	CAGCCTGGGCAAG	.	PASS	Atlas-SNP
UPF2	26019	hgsc.bcm.edu	37	10	12043790	12043790	+	Silent	SNP	T	T	G	rs11595168	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	131	70	107	0	0.534351	0	T|0.947;G|0.053	0.053	strong	.	UPF2	111	.	NM_080599	exon6	c.A1539C	p.S513S	GGGACTTGATACC	.	PASS	Atlas-SNP
SEMA5B	54437	hgsc.bcm.edu	37	3	122645277	122645277	+	Silent	SNP	C	C	T	rs2276777	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85	41	67	0	0.482353	0	C|0.925;T|0.075	0.075	strong	SEMA5B_ENST00000451055,NS,carcinoma,0,2	SEMA5B	303	2	NM_001256347	exon9	c.G1260A	p.P420P	CTGCTCCGGCAAG	.	PASS	Atlas-SNP
MUC1	4582	hgsc.bcm.edu	37	1	155162067	155162067	+	Silent	SNP	C	C	T	rs4072037	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	101	41	98	0	0.405941	0	C|0.385;T|0.615	0.615	strong	MUC1_ENST00000368395,caecum,carcinoma,-1,3	MUC1	94	3	NM_001204286	exon2	c.G93A	p.T31T	AGAACCCGTAACA	.	PASS	Atlas-SNP
PGD	5226	hgsc.bcm.edu	37	1	10479791	10479791	+	Silent	SNP	G	G	A	rs41274480	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83	45	71	0	0.542169	0	A|0.035;C|0.000;G|0.965	0.035	strong	.	PGD	39	.	NM_002631	exon13	c.G1437A	p.S479S	ATCCTCGTCATAC	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	177	177	210	0	1	0	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
PON2	5445	hgsc.bcm.edu	37	7	95034775	95034775	+	Missense_Mutation	SNP	G	G	C	rs7493	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	149	78	146	0	0.52349	0	G|0.747;C|0.253	0.253	strong	.	PON2	32	.	NM_000305	exon9	c.C932G	p.S311C	TTCTCAGATAGAA	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	58	58	43	0	1	0	T|0.672;C|0.328	0.328	strong	.	METTL21B	16	.	NM_015433	exon3	c.T558C	p.H186H	GGAGCATGGGACA	.	PASS	Atlas-SNP
DAP3	7818	hgsc.bcm.edu	37	1	155699118	155699118	+	Silent	SNP	T	T	C	rs4933	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	129	62	140	0	0.48062	0	A|0.000;C|0.066;G|0.000;T|0.934	0.066	strong	.	DAP3	46	.	NM_033657	exon9	c.T804C	p.L268L	TGCTCTTTGGGGA	.	PASS	Atlas-SNP
POTEC	388468	hgsc.bcm.edu	37	18	14543098	14543098	+	Silent	SNP	C	C	T	rs11873462	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	278	119	244	1	0.428058	0.00409836	C|0.744;T|0.256	0.256	strong	.	POTEC	129	.	NM_001137671	exon1	c.G48A	p.K16K	GAATGGCTTCTTC	.	PASS	Atlas-SNP
PLEC	5339	hgsc.bcm.edu	37	8	144992862	144992862	+	Silent	SNP	A	A	G	rs7819099	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55	31	76	2	0.563636	0.0263158	A|0.555;G|0.445	0.445	strong	PLEC_ENST00000436759,NS,carcinoma,0,3	PLEC	1144	3	NM_201380	exon32	c.T11538C	p.A3846A	CTTGAGAGCCTGG	.	scavenged	Atlas-SNP
CCDC88B	283234	hgsc.bcm.edu	37	11	64109208	64109208	+	Silent	SNP	G	G	C	rs61735121	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110	58	133	0	0.527273	0	G|0.980;C|0.020	0.020	strong	.	CCDC88B	89	.	NM_032251	exon7	c.G669C	p.G223G	CCTGGGGGCCCAG	.	PASS	Atlas-SNP
OTOGL	283310	hgsc.bcm.edu	37	12	80747209	80747209	+	Missense_Mutation	SNP	C	C	G	rs7312569	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98	58	85	0	0.591837	0	C|0.844;G|0.156	0.156	strong	.	OTOGL	235	.	NM_173591	exon45	c.C5485G	p.L1829V	TTGAATCTAAGAG	.	PASS	Atlas-SNP
APOBEC3H	164668	hgsc.bcm.edu	37	22	39496336	39496336	+	Missense_Mutation	SNP	G	G	T	rs139293	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110	55	131	0	0.5	0	A|0.000;G|0.804;T|0.196	0.196	strong	.	APOBEC3H	28	.	NM_001166003	exon2	c.G53T	p.R18L	AGCGCCGCCTCAG	.	PASS	Atlas-SNP
PRDM9	56979	hgsc.bcm.edu	37	5	23527469	23527469	+	Missense_Mutation	SNP	C	C	A	rs112501567	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	41	13	76	2	0.317073	0.0263158	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
SERBP1	26135	hgsc.bcm.edu	37	1	67895758	67895758	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	149	50	169	0	0.33557	0	.	.	none	.	SERBP1	31	.	NM_001018067	exon1	c.A226C	p.K76Q	GGTCTTTCTGGGA	.	PASS	Atlas-SNP
SLC36A3	285641	hgsc.bcm.edu	37	5	150666962	150666962	+	Missense_Mutation	SNP	G	G	A	rs12520516	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	122	65	125	0	0.532787	0	G|0.909;A|0.091	0.091	strong	SLC36A3,NS,carcinoma,0,1	SLC36A3	54	1	NM_001145017	exon7	c.C676T	p.P226S	GGATGGGGGTCAG	.	PASS	Atlas-SNP
SLC1A1	6505	hgsc.bcm.edu	37	9	4564432	4564432	+	Silent	SNP	G	G	A	rs2228622	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	115	115	111	0	1	0	G|0.657;A|0.343	0.343	strong	.	SLC1A1	43	.	NM_004170	exon4	c.G414A	p.T138T	CAGTACGGTGGAT	.	PASS	Atlas-SNP
SLC6A5	9152	hgsc.bcm.edu	37	11	20648364	20648364	+	Missense_Mutation	SNP	G	G	C	rs3740870	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80	35	73	0	0.4375	0	G|0.895;C|0.105	0.105	strong	SLC6A5,caecum,carcinoma,0,1	SLC6A5	151	1	NM_004211	exon8	c.G1371C	p.K457N	ACCCAAGTGGGAG	.	PASS	Atlas-SNP
PNLDC1	154197	hgsc.bcm.edu	37	6	160225012	160225012	+	Silent	SNP	T	T	G	rs35435543	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	203	202	208	0	0.995074	0	T|0.564;G|0.436	0.436	strong	.	PNLDC1	66	.	NM_173516	exon5	c.T231G	p.S77S	CCATTCTTGTAAC	.	PASS	Atlas-SNP
CARHSP1	23589	hgsc.bcm.edu	37	16	8953030	8953030	+	Silent	SNP	C	C	T	rs2231706	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	141	63	124	0	0.446809	0	C|0.989;T|0.011	0.011	strong	.	CARHSP1	12	.	NM_001042476	exon2	c.G156A	p.S52S	TCACGCCGAGAAG	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98	98	87	0	1	0	A|0.601;G|0.399	0.399	strong	.	CR1	354	.	NM_000651	exon37	c.A6193G	p.I2065V	GAGATCATCAGAT	.	PASS	Atlas-SNP
MLPH	79083	hgsc.bcm.edu	37	2	238443226	238443226	+	Missense_Mutation	SNP	A	A	G	rs2292884	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	131	57	136	0	0.435115	0	A|0.644;G|0.356	0.356	strong	.	MLPH	41	.	NM_024101	exon9	c.A1040G	p.H347R	ATAAGCATATTTC	.	PASS	Atlas-SNP
INTS1	26173	hgsc.bcm.edu	37	7	1542814	1542814	+	Silent	SNP	T	T	C	rs3752715	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	163	99	134	0	0.607362	0	T|0.412;C|0.588	0.588	strong	INTS1,colon,carcinoma,-1,1	INTS1	145	1	NM_001080453	exon3	c.A72G	p.P24P	GTCTCCTGGGGGA	.	PASS	Atlas-SNP
GATA2	2624	hgsc.bcm.edu	37	3	128204641	128204641	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	102	31	94	0	0.303922	0	.	.	none	.	GATA2	122	.	NM_001145662	exon3	c.C800A	p.P267H	CCTCCGGGGTGGA	.	PASS	Atlas-SNP
C11orf1	64776	hgsc.bcm.edu	37	11	111754574	111754574	+	Silent	SNP	A	A	C	rs1045282	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	56	45	48	0	0.803571	0	A|0.734;C|0.266	0.266	strong	.	C11orf1	15	.	NM_022761	exon4	c.A423C	p.S141S	AAAGTCAACTTAC	.	PASS	Atlas-SNP
TRIM9	114088	hgsc.bcm.edu	37	14	51446216	51446216	+	Missense_Mutation	SNP	T	T	G	rs2275462	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	90	46	87	0	0.511111	0	T|0.451;G|0.549	0.549	strong	TRIM9_ENST00000338969,NS,carcinoma,-2,2	TRIM9	188	2	NM_015163	exon9	c.A1959C	p.L653F	TCTATTTAAGTCG	.	PASS	Atlas-SNP
MAT2B	27430	hgsc.bcm.edu	37	5	162940999	162940999	+	Silent	SNP	A	A	G	rs11546512	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	33	67	0	0.532258	0	A|0.889;G|0.111	0.111	strong	.	MAT2B	42	.	NM_013283	exon4	c.A525G	p.L175L	CAATCTAGGTAAG	.	PASS	Atlas-SNP
B3GNTL1	146712	hgsc.bcm.edu	37	17	80904844	80904844	+	Missense_Mutation	SNP	C	C	T	rs7225887	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44	21	85	0	0.477273	0	C|0.840;T|0.160	0.160	strong	B3GNTL1,NS,carcinoma,+2,1	B3GNTL1	40	1	NM_001009905	exon12	c.G1021A	p.A341T	CAAAGGCGCCCCC	.	PASS	Atlas-SNP
SLC44A3	126969	hgsc.bcm.edu	37	1	95330440	95330440	+	Silent	SNP	C	C	T	rs142406496	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	99	51	83	0	0.515152	0	C|0.996;T|0.004	0.004	strong	.	SLC44A3	109	.	NM_001114106	exon11	c.C1380T	p.N460N	GCAAAACGCACTG	.	PASS	Atlas-SNP
ANKRD26	22852	hgsc.bcm.edu	37	10	27381349	27381349	+	Silent	SNP	T	T	C	rs2297145	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	39	39	46	0	1	0	T|0.691;C|0.309	0.309	strong	.	ANKRD26	179	.	NM_014915	exon4	c.A624G	p.V208V	CTTATCTACTGCA	.	PASS	Atlas-SNP
PROC	5624	hgsc.bcm.edu	37	2	128178900	128178900	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	127	47	202	0	0.370079	0	.	.	none	PROC,colon,carcinoma,-1,1	PROC	31	1	NM_000312	exon3	c.C112T	p.R38W	GTGCTGCGGATCC	.	PASS	Atlas-SNP
BCDIN3D	144233	hgsc.bcm.edu	37	12	50232496	50232496	+	Silent	SNP	T	T	C	rs17260403	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48	21	61	0	0.4375	0	T|0.938;C|0.062	0.062	strong	.	BCDIN3D	20	.	NM_181708	exon2	c.A537G	p.L179L	CTCCCATAGGCCA	.	PASS	Atlas-SNP
HHLA2	11148	hgsc.bcm.edu	37	3	108095365	108095365	+	Silent	SNP	G	G	A	rs2124736	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	42	22	48	0	0.52381	0	G|0.881;A|0.119	0.119	strong	.	HHLA2	95	.	NM_007072	exon9	c.G1185A	p.E395E	TGGTGAGCGCTGT	.	PASS	Atlas-SNP
ELP3	55140	hgsc.bcm.edu	37	8	27957438	27957438	+	Silent	SNP	C	C	T	rs200001470	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	65	27	60	0	0.415385	0	C|1.000;T|0.000	0.000	strong	.	ELP3	36	.	NM_018091	exon3	c.C213T	p.V71V	CAAGGTCTTGATG	.	PASS	Atlas-SNP
DFNA5	1687	hgsc.bcm.edu	37	7	24758795	24758795	+	Silent	SNP	T	T	C	rs876305	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	45	13	46	0	0.288889	0	T|0.394;C|0.606	0.606	strong	.	DFNA5	51	.	NM_001127453	exon4	c.A447G	p.E149E	CCTTCCTTCCAGC	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	20	9	26	0	0.45	0	C|0.641;T|0.359	0.359	strong	.	MLF1IP	33	.	NM_024629	exon1	c.G46A	p.G16S	CTTACCCCTCAGA	.	PASS	Atlas-SNP
BTN3A2	11118	hgsc.bcm.edu	37	6	26370748	26370748	+	Missense_Mutation	SNP	G	G	A	rs35183513	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	163	26	140	0	0.159509	0	G|0.877;A|0.123	0.123	strong	.	BTN3A2	44	.	NM_001197246	exon3	c.G632A	p.R211K	TCATGAGAGGCGG	.	PASS	Atlas-SNP
OR10A5	144124	hgsc.bcm.edu	37	11	6867462	6867462	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	186	5	207	1	0.0268817	0.00483092	.	.	none	OR10A5,NS,carcinoma,0,3	OR10A5	48	3	NM_178168	exon1	c.G549A	p.P183P	CAGCCCGCCTGTG	.	scavenged	Atlas-SNP
GIMAP2	26157	hgsc.bcm.edu	37	7	150389856	150389856	+	Missense_Mutation	SNP	A	A	G	rs2075078	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	139	79	141	0	0.568345	0	A|0.741;G|0.259	0.259	strong	.	GIMAP2	39	.	NM_015660	exon3	c.A482G	p.H161R	ACATGCACGACTC	.	PASS	Atlas-SNP
MAEL	84944	hgsc.bcm.edu	37	1	166958601	166958601	+	Silent	SNP	T	T	C	rs2296837	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68	29	49	0	0.426471	0	T|0.682;G|0.000;C|0.317;A|0.000	0.317	strong	.	MAEL	95	.	NM_032858	exon1	c.T12C	p.R4R	GAACCGTAAGGCC	.	PASS	Atlas-SNP
DNMBP	23268	hgsc.bcm.edu	37	10	101639877	101639877	+	Missense_Mutation	SNP	A	A	C	rs11190305	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	252	103	257	1	0.40873	0.00389105	A|0.708;C|0.292	0.292	strong	.	DNMBP	173	.	NM_015221	exon16	c.T4239G	p.C1413W	TTGGTCACATTCT	.	PASS	Atlas-SNP
OR5A1	219982	hgsc.bcm.edu	37	11	59211421	59211421	+	Silent	SNP	C	C	T	rs17591107	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	248	127	258	1	0.512097	0.00387597	C|0.815;T|0.185	0.185	strong	OR5A1,NS,adenoma,0,1	OR5A1	72	1	NM_001004728	exon1	c.C780T	p.F260F	CCTTTTCGTGTAC	.	PASS	Atlas-SNP
PARVB	29780	hgsc.bcm.edu	37	22	44495953	44495953	+	Missense_Mutation	SNP	A	A	G	rs56194750	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	35	79	0	0.530303	0	A|0.997;G|0.003	0.003	strong	.	PARVB	44	.	NM_001003828	exon4	c.A322G	p.M108V	CGCACGATGATTG	.	PASS	Atlas-SNP
CRHR1	1394	hgsc.bcm.edu	37	17	43910507	43910507	+	Silent	SNP	C	C	T	rs16940674	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	67	64	0	1	0	C|0.860;T|0.140	0.140	strong	.	CRHR1	48	.	NM_001145146	exon10	c.C861T	p.C287C	TAGGTGCTGGTTT	.	PASS	Atlas-SNP
SLC22A25	387601	hgsc.bcm.edu	37	11	62951221	62951221	+	Missense_Mutation	SNP	C	C	G	rs11231397	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	126	46	138	0	0.365079	0	C|0.621;G|0.379	0.379	strong	.	SLC22A25	87	.	NM_199352	exon5	c.G899C	p.R300T	GCTTTTCTAAGTT	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1081074	1081074	+	Missense_Mutation	SNP	T	T	C	rs41411848	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	82	119	0	0.97619	0	T|0.714;C|0.286	0.286	strong	.	MUC2	614	.	NM_002457	exon11	c.T1370C	p.V457A	TGCAGGTGGTGGT	.	PASS	Atlas-SNP
RGS11	8786	hgsc.bcm.edu	37	16	320992	320992	+	Nonsense_Mutation	SNP	C	C	A	rs61759901	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	70	24	62	0	0.342857	0	C|0.996;A|0.004	0.004	strong	.	RGS11	29	.	NM_183337	exon13	c.G970T	p.E324X	TGAACTCCTTTCC	.	PASS	Atlas-SNP
RAP1GAP2	23108	hgsc.bcm.edu	37	17	2929674	2929674	+	Silent	SNP	T	T	C	rs12941934	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	168	80	150	2	0.47619	0.0133333	T|0.421;C|0.579	0.579	strong	RAP1GAP2_ENST00000254695,NS,lymphoid_neoplasm,0,2	RAP1GAP2	90	2	NM_015085	exon21	c.T1896C	p.R632R	CGGCCGTGCCATC	.	scavenged	Atlas-SNP
RNF152	220441	hgsc.bcm.edu	37	18	59483202	59483202	+	Silent	SNP	G	G	C	rs4538107	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	140	64	153	0	0.457143	0	G|0.959;C|0.041	0.041	strong	.	RNF152	37	.	NM_173557	exon2	c.C495G	p.T165T	CGACCAGGTGGAG	.	PASS	Atlas-SNP
XCR1	2829	hgsc.bcm.edu	37	3	46063329	46063329	+	Silent	SNP	T	T	C	rs2230322	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	107	49	138	0	0.457944	0	T|0.794;C|0.206	0.206	strong	.	XCR1	51	.	NM_001024644	exon2	c.A111G	p.L37L	GCAGTATAGGACA	.	PASS	Atlas-SNP
ZBTB21	49854	hgsc.bcm.edu	37	21	43413651	43413651	+	Missense_Mutation	SNP	T	T	C	rs871545	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	347	118	320	0	0.340058	0	T|0.878;C|0.122	0.122	strong	ZNF295,NS,carcinoma,+1,1	.	.	1	NM_001098402	exon3	c.A554G	p.N185S	TTGGTATTGGCCT	.	PASS	Atlas-SNP
PAG1	55824	hgsc.bcm.edu	37	8	81905397	81905397	+	Silent	SNP	A	A	G	rs2016465	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	32	17	33	0	0.53125	0	A|0.513;G|0.487	0.487	strong	.	PAG1	39	.	NM_018440	exon4	c.T66C	p.A22A	GACAGCAGCCAGA	.	PASS	Atlas-SNP
KCNA1	3736	hgsc.bcm.edu	37	12	5021228	5021228	+	Silent	SNP	T	T	C	rs1048500	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	34	65	0	0.53125	0	T|0.498;C|0.502	0.502	strong	KCNA1,colon,carcinoma,0,1	KCNA1	112	1	NM_000217	exon2	c.T684C	p.C228C	GCTGTGTATCATC	.	PASS	Atlas-SNP
RLF	6018	hgsc.bcm.edu	37	1	40705726	40705726	+	Missense_Mutation	SNP	A	A	T	rs10889205	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	124	71	104	0	0.572581	0	A|0.804;T|0.196	0.196	strong	RLF,NS,carcinoma,0,1	RLF	152	1	NM_012421	exon8	c.A5352T	p.E1784D	GAAAGAAGATGAT	.	PASS	Atlas-SNP
AACS	65985	hgsc.bcm.edu	37	12	125561151	125561151	+	Missense_Mutation	SNP	A	A	G	rs11549081	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	29	71	0	0.460317	0	A|0.803;G|0.197	0.197	strong	.	AACS	59	.	NM_023928	exon3	c.A352G	p.I118V	CTTTACATTGCAA	.	PASS	Atlas-SNP
KRT14	3861	hgsc.bcm.edu	37	17	39743081	39743081	+	Silent	SNP	G	G	A	rs11551759	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	17	9	34	0	0.529412	0	G|0.355;A|0.645	0.645	strong	.	KRT14	65	.	NM_000526	exon1	c.C6T	p.T2T	GCAGGTGGTCATG	.	PASS	Atlas-SNP
CCL3	6348	hgsc.bcm.edu	37	17	34416537	34416537	+	Silent	SNP	G	G	A	rs1130371	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	266	262	247	1	0.984962	0.00404858	G|0.795;A|0.205	0.205	strong	.	CCL3	8	.	NM_002983	exon2	c.C180T	p.P60P	GACACCGGGCTTG	.	PASS	Atlas-SNP
PCDHB16	57717	hgsc.bcm.edu	37	5	140563586	140563586	+	Silent	SNP	C	C	T	rs61745655	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	56	43	70	0	0.767857	0	C|0.937;T|0.063	0.063	strong	PCDHB16,NS,carcinoma,+2,1	PCDHB16	159	1	NM_020957	exon1	c.C1452T	p.A484A	CAACGCCCAGGTC	.	scavenged	Atlas-SNP
SULF2	55959	hgsc.bcm.edu	37	20	46365636	46365636	+	Missense_Mutation	SNP	C	C	T	rs56218501	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	174	84	181	1	0.482759	0.00552486	C|0.856;G|0.000;T|0.144	0.144	strong	SULF2,colon,carcinoma,+2,3	SULF2	131	3	NM_001161841	exon3	c.G226A	p.A76T	AGTGCGCCCCGCC	.	scavenged	Atlas-SNP
MATN3	4148	hgsc.bcm.edu	37	2	20205680	20205680	+	Silent	SNP	C	C	T	rs28401180	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	101	40	101	0	0.39604	0	C|0.513;T|0.487	0.487	strong	.	MATN3	28	.	NM_002381	exon2	c.G615A	p.E205E	CGCCACCTCATTC	.	PASS	Atlas-SNP
CLEC10A	10462	hgsc.bcm.edu	37	17	6981397	6981397	+	Missense_Mutation	SNP	A	A	G	rs90951	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	41	84	0	0.471264	0	A|0.467;G|0.532	0.532	strong	.	CLEC10A	40	.	NM_182906	exon3	c.T103C	p.C35R	CAGAGCAGAGACG	.	PASS	Atlas-SNP
AKAP11	11215	hgsc.bcm.edu	37	13	42872866	42872866	+	Missense_Mutation	SNP	A	A	G	rs75739749	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	201	134	103	0	0.666667	0	A|1.000;G|0.000	0.000	strong	.	AKAP11	146	.	NM_016248	exon7	c.A549G	p.I183M	ATCCATAGAGGAT	.	PASS	Atlas-SNP
FSCB	84075	hgsc.bcm.edu	37	14	44975511	44975511	+	Missense_Mutation	SNP	G	G	A	rs45478391	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	99	48	121	0	0.484848	0	G|0.852;A|0.148	0.148	strong	.	FSCB	173	.	NM_032135	exon1	c.C680T	p.P227L	AGTACCGGGGGAC	.	PASS	Atlas-SNP
SPTBN5	51332	hgsc.bcm.edu	37	15	42168400	42168400	+	Missense_Mutation	SNP	C	C	T	rs2290559	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57	56	61	0	0.982456	0	C|0.835;T|0.165	0.165	strong	.	SPTBN5	171	.	NM_016642	exon21	c.G3929A	p.R1310H	TTTCTGCGCGCTC	.	PASS	Atlas-SNP
ANPEP	290	hgsc.bcm.edu	37	15	90335788	90335788	+	Missense_Mutation	SNP	C	C	T	rs25651	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	95	43	87	0	0.452632	0	C|0.642;T|0.358	0.358	strong	.	ANPEP	124	.	NM_001150	exon17	c.G2255A	p.S752N	ACCTCGCTGTACC	.	PASS	Atlas-SNP
TRIOBP	11078	hgsc.bcm.edu	37	22	38164106	38164106	+	Silent	SNP	C	C	T	rs4821708	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	96	51	105	0	0.53125	0	C|0.739;T|0.261	0.261	strong	TRIOBP_ENST00000344404,NS,carcinoma,0,1	TRIOBP	262	1	NM_001039141	exon19	c.C6498T	p.Y2166Y	GGCCTACCAGGAA	.	PASS	Atlas-SNP
TIAM1	7074	hgsc.bcm.edu	37	21	32493031	32493031	+	Silent	SNP	A	A	G	rs762194	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	56	32	43	0	0.571429	0	A|0.482;G|0.518	0.518	strong	.	TIAM1	522	.	NM_003253	exon29	c.T4431C	p.G1477G	GTCCCCACCACCG	.	PASS	Atlas-SNP
NKTR	4820	hgsc.bcm.edu	37	3	42662976	42662976	+	Silent	SNP	A	A	C	rs35419602	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	78	29	67	0	0.371795	0	A|0.988;C|0.012	0.012	strong	.	NKTR	116	.	NM_005385	exon6	c.A342C	p.R114R	AAATCGAGGGAAA	.	PASS	Atlas-SNP
TGFBI	7045	hgsc.bcm.edu	37	5	135391374	135391374	+	Silent	SNP	C	C	T	rs1133170	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	45	25	54	0	0.555556	0	C|0.738;T|0.262	0.262	strong	TGFBI,NS,carcinoma,+2,1	TGFBI	76	1	NM_000358	exon11	c.C1416T	p.L472L	GAGCCTCTGCATT	.	PASS	Atlas-SNP
EIF4A3	9775	hgsc.bcm.edu	37	17	78113832	78113832	+	Silent	SNP	G	G	A	rs2241886	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	20	42	0	0.425532	0	G|0.864;A|0.136	0.136	strong	EIF4A3,NS,adenoma,0,1	EIF4A3	35	1	NM_014740	exon5	c.C480T	p.V160V	GCCCGCGACAACA	.	PASS	Atlas-SNP
C19orf21	126353	hgsc.bcm.edu	37	19	757241	757241	+	Missense_Mutation	SNP	G	G	A	rs45477999	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	88	32	81	0	0.363636	0	G|0.989;A|0.011	0.011	strong	C19orf21,caecum,carcinoma,0,1	C19orf21	56	1	NM_173481	exon2	c.G295A	p.A99T	CTGGGCGCCAGGG	.	PASS	Atlas-SNP
SLC44A3	126969	hgsc.bcm.edu	37	1	95294089	95294089	+	Silent	SNP	T	T	C	rs2640065	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93	48	69	0	0.516129	0	T|0.790;C|0.210	0.210	strong	SLC44A3,NS,carcinoma,0,1	SLC44A3	109	1	NM_001114106	exon5	c.T456C	p.Y152Y	CAACTATACCCAC	.	PASS	Atlas-SNP
C12orf4	57102	hgsc.bcm.edu	37	12	4627414	4627414	+	Silent	SNP	C	C	T	rs35924298	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	78	42	49	0	0.538462	0	C|0.922;T|0.078	0.078	strong	.	C12orf4	58	.	NM_020374	exon8	c.G843A	p.Q281Q	CTTCAACTGGGCT	.	PASS	Atlas-SNP
KRT6B	3854	hgsc.bcm.edu	37	12	52844243	52844243	+	Silent	SNP	A	A	G	rs28414881	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	226	44	208	7	0.19469	0.0336538	A|0.959;G|0.041	0.041	strong	KRT6B,NS,carcinoma,-1,1	KRT6B	90	1	NM_005555	exon2	c.T702C	p.R234R	GTCCAGACGACCC	.	scavenged	Atlas-SNP
FAM83F	113828	hgsc.bcm.edu	37	22	40417820	40417820	+	Missense_Mutation	SNP	A	A	G	rs5995794	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	28	28	38	0	1	0	A|0.766;G|0.234	0.234	strong	FAM83F,NS,carcinoma,0,1	FAM83F	29	1	NM_138435	exon4	c.A1306G	p.R436G	CCCGCCAGGCGCT	.	PASS	Atlas-SNP
LRIG1	26018	hgsc.bcm.edu	37	3	66433676	66433676	+	Silent	SNP	A	A	G	rs900171	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	97	58	88	0	0.597938	0	A|0.361;G|0.639	0.639	strong	.	LRIG1	138	.	NM_015541	exon15	c.T2221C	p.L741L	GGGTCAAGTGGTG	.	PASS	Atlas-SNP
GCAT	23464	hgsc.bcm.edu	37	22	38205989	38205989	+	Missense_Mutation	SNP	T	T	C	rs2285178	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	121	58	93	0	0.479339	0	T|0.723;C|0.277	0.277	strong	.	GCAT	27	.	NM_001171690	exon2	c.T230C	p.L77S	TGCCCTTGCCCCA	.	PASS	Atlas-SNP
KIAA0754	643314	hgsc.bcm.edu	37	1	39878815	39878815	+	Missense_Mutation	SNP	A	A	G	rs1746842	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	35	104	0	0.472973	0	A|0.949;G|0.051	0.051	strong	.	KIAA0754	93	.	NM_015038	exon1	c.A2878G	p.I960V	TTAGCTATTACAG	.	PASS	Atlas-SNP
TACR2	6865	hgsc.bcm.edu	37	10	71164655	71164655	+	Missense_Mutation	SNP	C	C	T	rs2229170	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83	44	67	0	0.53012	0	C|0.868;T|0.132	0.132	strong	.	TACR2	37	.	NM_001057	exon5	c.G1124A	p.R375H	TGGGGACGCCCCG	.	PASS	Atlas-SNP
RNF5	6048	hgsc.bcm.edu	37	6	32148031	32148031	+	Silent	SNP	A	A	G	rs1062070	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44	40	58	0	0.909091	0	A|0.860;G|0.140	0.140	strong	.	RNF5	16	.	NM_006913	exon6	c.A471G	p.P157P	TCACCCAGCCTCC	.	PASS	Atlas-SNP
BTNL8	79908	hgsc.bcm.edu	37	5	180376974	180376974	+	Missense_Mutation	SNP	T	T	G	rs77335601		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51	41	112	0	0.803922	0	T|1.000;|0.000	.	weak	.	BTNL8	114	.	NM_001040462	exon8	c.T933G	p.H311Q	AACCCATAGAAAA	.	PASS	Atlas-SNP
H1FNT	341567	hgsc.bcm.edu	37	12	48723784	48723784	+	Missense_Mutation	SNP	C	C	T	rs2291483	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	58	24	44	0	0.413793	0	C|0.772;T|0.228	0.228	strong	H1FNT,NS,carcinoma,0,1	H1FNT	30	1	NM_181788	exon1	c.C710T	p.S237F	GAAGCTCCAAGCC	.	PASS	Atlas-SNP
NOSTRIN	115677	hgsc.bcm.edu	37	2	169721381	169721381	+	Silent	SNP	A	A	G	rs3931	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	56	22	55	0	0.392857	0	A|0.757;G|0.243	0.243	strong	.	NOSTRIN	68	.	NM_001171631	exon21	c.A1593G	p.G531G	AGGAGGATGGTGG	.	PASS	Atlas-SNP
GOLGB1	2804	hgsc.bcm.edu	37	3	121415610	121415610	+	Missense_Mutation	SNP	G	G	A	rs33988592	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	279	129	261	0	0.462366	0	G|0.780;A|0.220	0.220	strong	.	GOLGB1	319	.	NM_001256486	exon13	c.C3760T	p.P1254S	TGCTTGGGAGTTT	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228433217	228433217	+	Silent	SNP	A	A	G	rs2487384	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	191	105	150	0	0.549738	0	A|0.366;G|0.634	0.634	strong	.	OBSCN	2142	.	NM_001271223	exon13	c.A3861G	p.T1287T	CCAGACAGAGGTG	.	PASS	Atlas-SNP
CYP4Z1	199974	hgsc.bcm.edu	37	1	47571905	47571905	+	Silent	SNP	C	C	T	rs28463559	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	275	105	315	1	0.381818	0.0031746	C|0.568;T|0.432	0.432	strong	.	CYP4Z1	43	.	NM_178134	exon9	c.C1173T	p.T391T	CATCACCTTTCCA	.	PASS	Atlas-SNP
GNB1L	54584	hgsc.bcm.edu	37	22	19789541	19789541	+	Missense_Mutation	SNP	A	A	C	rs2073770	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	34	57	0	0.53125	0	A|0.844;C|0.156	0.156	strong	.	GNB1L	34	.	NM_053004	exon7	c.T715G	p.W239G	GCTGCCAGTCCAG	.	PASS	Atlas-SNP
DTNB	1838	hgsc.bcm.edu	37	2	25655772	25655772	+	Silent	SNP	T	T	C	rs7583475	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	45	22	37	0	0.488889	0	T|0.743;C|0.257	0.257	strong	.	DTNB	43	.	NM_021907	exon14	c.A1440G	p.A480A	CAGCTCTGCCAGC	.	PASS	Atlas-SNP
CDH23	64072	hgsc.bcm.edu	37	10	73558952	73558952	+	Missense_Mutation	SNP	C	C	T	rs4747195	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68	31	78	1	0.455882	0.0128205	C|0.668;T|0.332	0.332	strong	CDH23,NS,carcinoma,0,1	CDH23	365	1	NM_022124	exon49	c.C7139T	p.P2380L	GGTCCCCGCCCCG	.	scavenged	Atlas-SNP
PRR18	285800	hgsc.bcm.edu	37	6	166721211	166721211	+	Silent	SNP	G	G	T	rs13204594	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	18	18	14	0	1	0	G|0.224;T|0.776	0.776	strong	PRR18,NS,lymphoid_neoplasm,0,1	PRR18	4	1	NM_175922	exon1	c.C420A	p.T140T	CTCGGGGGTGAGA	.	PASS	Atlas-SNP
COL24A1	255631	hgsc.bcm.edu	37	1	86488270	86488270	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	166	16	148	0	0.0963855	0	.	.	none	.	COL24A1	202	.	NM_152890	exon17	c.A2153C	p.E718A	CCTTGTTCACCCT	.	PASS	Atlas-SNP
B3GNT5	84002	hgsc.bcm.edu	37	3	182987591	182987591	+	Missense_Mutation	SNP	G	G	A	rs115825683	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	26	69	0	0.412698	0	G|0.994;A|0.006	0.006	strong	.	B3GNT5	26	.	NM_032047	exon2	c.G5A	p.R2K	ATATGAGAATGTT	.	PASS	Atlas-SNP
GALR1	2587	hgsc.bcm.edu	37	18	74980601	74980601	+	Missense_Mutation	SNP	A	A	T	rs77169818	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82	36	77	0	0.439024	0	A|0.965;T|0.035	0.035	strong	.	GALR1	53	.	NM_001480	exon3	c.A793T	p.I265F	CACCACATCATCC	.	PASS	Atlas-SNP
SPATA13	221178	hgsc.bcm.edu	37	13	24797913	24797913	+	Silent	SNP	C	C	T	rs1220546	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	21	66	0	0.388889	0	C|0.720;T|0.280	0.280	strong	.	SPATA13	92	.	NM_001166271	exon2	c.C846T	p.D282D	CCATGACGCACGG	.	PASS	Atlas-SNP
C5orf42	65250	hgsc.bcm.edu	37	5	37196028	37196028	+	Missense_Mutation	SNP	C	C	T	rs72736758	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	216	93	210	0	0.430556	0	C|0.972;T|0.028	0.028	strong	.	C5orf42	422	.	NM_023073	exon21	c.G3743A	p.G1248D	GCGATACCTCCTT	.	PASS	Atlas-SNP
MRGPRX4	117196	hgsc.bcm.edu	37	11	18194944	18194944	+	Silent	SNP	T	T	A	rs11024531	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	132	59	121	0	0.44697	0	T|0.760;A|0.240	0.240	strong	.	MRGPRX4	68	.	NM_054032	exon1	c.T141A	p.V47V	CGCGGTTGTGCTC	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	267	132	230	0	0.494382	0	A|0.607;C|0.000;G|0.393	0.393	strong	.	IFITM2	21	.	NM_006435	exon2	c.A361G	p.I121V	CTGCTCATCATCA	.	PASS	Atlas-SNP
C1orf114	57821	hgsc.bcm.edu	37	1	169390957	169390957	+	Missense_Mutation	SNP	A	A	T	rs35107735	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	162	161	132	0	0.993827	0	A|0.752;T|0.248	0.248	strong	.	C1orf114	67	.	NM_021179	exon3	c.T712A	p.F238I	GCAAAAACCCCTG	.	PASS	Atlas-SNP
SGPL1	8879	hgsc.bcm.edu	37	10	72629567	72629567	+	Silent	SNP	C	C	T	rs827249	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	163	77	147	0	0.472393	0	C|0.943;T|0.057	0.057	strong	.	SGPL1	37	.	NM_003901	exon9	c.C723T	p.A241A	AAGTGCCCATGCT	.	PASS	Atlas-SNP
LYRM2	57226	hgsc.bcm.edu	37	6	90347511	90347511	+	Missense_Mutation	SNP	T	T	C	rs34012596	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	182	98	206	0	0.538462	0	T|0.844;C|0.156	0.156	strong	.	LYRM2	6	.	NM_020466	exon2	c.A136G	p.K46E	AATCTTTCAGGTA	.	PASS	Atlas-SNP
FAM211B	388886	hgsc.bcm.edu	37	22	24982254	24982254	+	Missense_Mutation	SNP	G	G	A	rs41277319	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	133	68	139	0	0.511278	0	G|0.983;A|0.017	0.017	strong	.	.	.	.	NM_207644	exon4	c.C548T	p.A183V	AGCACCGCCAGCA	.	PASS	Atlas-SNP
LILRB4	11006	hgsc.bcm.edu	37	19	55179342	55179342	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	184	6	212	0	0.0326087	0	.	.	none	LILRB4,NS,carcinoma,0,1	LILRB4	86	1	NM_006847	exon12	c.C1219T	p.P407S	GAAGCCCCCCAGG	.	scavenged	Atlas-SNP
GPD2	2820	hgsc.bcm.edu	37	2	157367399	157367399	+	Silent	SNP	G	G	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	144	107	199	1	0.743056	0.00502513	.	.	none	.	GPD2	59	.	NM_001083112	exon4	c.G366T	p.L122L	ATATCTGCAGAAG	.	PASS	Atlas-SNP
CASZ1	54897	hgsc.bcm.edu	37	1	10705018	10705018	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	40	103	0	0.493827	0	.	.	none	.	CASZ1	150	.	NM_001079843	exon18	c.A3824G	p.N1275S	AAGCCATTGGCTG	.	PASS	Atlas-SNP
ARL13A	392509	hgsc.bcm.edu	37	X	100242536	100242536	+	Missense_Mutation	SNP	C	C	T	rs41307262	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	39	28	29	0	0.717949	0	C|0.866;T|0.134	0.134	strong	.	ARL13A	7	.	NM_001162490	exon6	c.C644T	p.S215L	GATGCTCATCACA	.	PASS	Atlas-SNP
VCX3B	425054	hgsc.bcm.edu	37	X	8434346	8434346	+	Silent	SNP	G	G	A	rs808146	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	450	135	326	0	0.3	0	.	.	weak	.	VCX3B	34	.	NM_001001888	exon3	c.G663A	p.E221E	GGTGGAGGAACCA	.	PASS	Atlas-SNP
RAG1	5896	hgsc.bcm.edu	37	11	36595600	36595600	+	Missense_Mutation	SNP	A	A	G	rs3740955	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	59	35	58	0	0.59322	0	A|0.471;G|0.529	0.529	strong	.	RAG1	151	.	NM_000448	exon2	c.A746G	p.H249R	GTCAGCACAAGAG	.	PASS	Atlas-SNP
CD1D	912	hgsc.bcm.edu	37	1	158151974	158151974	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	198	7	231	0	0.0353535	0	.	.	none	CD1D,NS,carcinoma,0,2	CD1D	60	2	NM_001766	exon4	c.T481G	p.L161V	GTAAACTTGGCCA	.	scavenged	Atlas-SNP
MT1A	4489	hgsc.bcm.edu	37	16	56673828	56673828	+	Missense_Mutation	SNP	A	A	G	rs8052394	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	23	30	0	0.425926	0	A|0.853;G|0.147	0.147	strong	.	MT1A	4	.	NM_005946	exon3	c.A152G	p.K51R	TCTGCAAAGGGGC	.	PASS	Atlas-SNP
YBX1	4904	hgsc.bcm.edu	37	1	43149084	43149084	+	Silent	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	104	28	104	0	0.269231	0	.	.	none	.	YBX1	49	.	NM_004559	exon2	c.T177C	p.V59V	GAAGGTTTTGGGA	.	PASS	Atlas-SNP
NUP210	23225	hgsc.bcm.edu	37	3	13395579	13395579	+	Missense_Mutation	SNP	C	C	A	rs2280084	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	139	75	121	0	0.539568	0	C|0.358;A|0.642	0.642	strong	NUP210,NS,carcinoma,0,1	NUP210	182	1	NM_024923	exon17	c.G2357T	p.R786L	TCCAGCCGGGGGT	.	PASS	Atlas-SNP
EXPH5	23086	hgsc.bcm.edu	37	11	108384661	108384661	+	Missense_Mutation	SNP	C	C	A	rs12146448	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	77	59	53	0	0.766234	0	C|0.975;A|0.025	0.025	strong	.	EXPH5	193	.	NM_015065	exon6	c.G1573T	p.V525F	AAGAAACATTATG	.	PASS	Atlas-SNP
PRDM5	11107	hgsc.bcm.edu	37	4	121706201	121706201	+	Silent	SNP	A	A	G	rs12499000	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	27	12	41	0	0.444444	0	A|0.807;G|0.193	0.193	strong	PRDM5,NS,carcinoma,0,1	PRDM5	76	1	NM_018699	exon11	c.T1234C	p.L412L	GGAACAAAGCTTT	.	PASS	Atlas-SNP
TMC4	147798	hgsc.bcm.edu	37	19	54664752	54664752	+	Silent	SNP	A	A	C	rs36656	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	28	47	0	0.518519	0	A|0.558;C|0.442	0.442	strong	.	TMC4	89	.	NM_001145303	exon13	c.T1854G	p.L618L	ACCACAAAGCTTA	.	PASS	Atlas-SNP
AKAP3	10566	hgsc.bcm.edu	37	12	4735922	4735922	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	112	30	98	0	0.267857	0	.	.	none	.	AKAP3	212	.	NM_006422	exon4	c.G2146C	p.E716Q	AGCACTCATATAA	.	PASS	Atlas-SNP
TOPORS	10210	hgsc.bcm.edu	37	9	32542204	32542204	+	Silent	SNP	A	A	G	rs10971019	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	333	166	301	1	0.498498	0.00332226	A|0.836;G|0.164	0.164	strong	.	TOPORS	127	.	NM_005802	exon3	c.T2319C	p.S773S	GTTACTAGACAGG	.	PASS	Atlas-SNP
DEFB110	245913	hgsc.bcm.edu	37	6	49986738	49986738	+	Silent	SNP	C	C	T	rs115648436	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	132	65	159	0	0.492424	0	C|0.991;T|0.009	0.009	strong	.	DEFB110	5	.	NM_001037497	exon2	c.G156A	p.R52R	AGCAATCCTAATT	.	PASS	Atlas-SNP
USP6NL	9712	hgsc.bcm.edu	37	10	11505743	11505743	+	Missense_Mutation	SNP	G	G	A	rs113611342	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	23	16	22	0	0.695652	0	G|0.986;A|0.014	0.014	strong	.	USP6NL	57	.	NM_001080491	exon14	c.C1235T	p.P412L	GGGCTCGGCCGGC	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	107	61	87	0	0.570093	0	A|0.792;T|0.208	0.208	strong	.	CCDC13	71	.	NM_144719	exon13	c.T1639A	p.S547T	TCTCTGACACTTG	.	PASS	Atlas-SNP
THBS1	7057	hgsc.bcm.edu	37	15	39885301	39885301	+	Silent	SNP	T	T	C	rs2228263	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	92	44	93	0	0.478261	0	T|0.841;C|0.159	0.159	strong	.	THBS1	106	.	NM_003246	exon18	c.T2868C	p.D956D	GACCGATTTCCGC	.	PASS	Atlas-SNP
MMP20	9313	hgsc.bcm.edu	37	11	102495998	102495998	+	Missense_Mutation	SNP	T	T	G	rs2245803	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82	15	44	0	0.182927	0	T|0.342;G|0.658	0.658	strong	.	MMP20	52	.	NM_004771	exon1	c.A53C	p.K18T	GAAAACTTCAAAG	.	PASS	Atlas-SNP
FAM178B	51252	hgsc.bcm.edu	37	2	97559759	97559759	+	Silent	SNP	G	G	A	rs11677797	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73	37	70	0	0.506849	0	G|0.745;A|0.255	0.255	strong	.	FAM178B	35	.	NM_001122646	exon14	c.C1680T	p.L560L	CCTCATGAGGCCC	.	PASS	Atlas-SNP
FANK1	92565	hgsc.bcm.edu	37	10	127585221	127585221	+	Nonsense_Mutation	SNP	C	C	T	rs202109621		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	31	4	39	0	0.129032	0	.	.	weak	.	FANK1	46	.	NM_145235	exon1	c.C10T	p.Q4X	GAGCCCCAGAGTA	.	PASS	Atlas-SNP
PWP1	11137	hgsc.bcm.edu	37	12	108096769	108096769	+	Missense_Mutation	SNP	G	G	C	rs11547907	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57	57	57	0	1	0	G|0.964;C|0.036	0.036	strong	.	PWP1	43	.	NM_007062	exon9	c.G864C	p.L288F	GTCCTTGGGGAAA	.	PASS	Atlas-SNP
ARNT	405	hgsc.bcm.edu	37	1	150789884	150789884	+	Missense_Mutation	SNP	C	C	T	rs1805133	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	117	67	123	0	0.57265	0	C|0.994;T|0.006	0.006	strong	.	ARNT	68	.	NM_001668	exon16	c.G1531A	p.D511N	CCATGTCCAATTC	.	PASS	Atlas-SNP
MYOM2	9172	hgsc.bcm.edu	37	8	2005883	2005883	+	Missense_Mutation	SNP	C	C	T	rs17064618	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	37	89	0	0.486842	0	C|0.929;T|0.071	0.071	strong	.	MYOM2	251	.	NM_003970	exon5	c.C545T	p.T182M	TTCCCACGCCCGT	.	PASS	Atlas-SNP
SETMAR	6419	hgsc.bcm.edu	37	3	4354697	4354697	+	Missense_Mutation	SNP	G	G	A	rs6801634	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	126	51	125	0	0.404762	0	G|0.871;A|0.129	0.129	strong	.	SETMAR	30	.	NM_001243723	exon2	c.G272A	p.R91H	GTCTCCGCCATGG	.	PASS	Atlas-SNP
REM1	28954	hgsc.bcm.edu	37	20	30070239	30070239	+	Silent	SNP	C	C	A	rs2233832	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	27	64	0	0.409091	0	C|0.886;A|0.114	0.114	strong	.	REM1	54	.	NM_014012	exon4	c.C573A	p.I191I	CATCATCCTCGTG	.	PASS	Atlas-SNP
POTEB	339010	hgsc.bcm.edu	37	15	21071492	21071492	+	Missense_Mutation	SNP	G	G	T	rs2664992		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	156	104	154	42	0.666667	0.272727	.	.	weak	ENSG00000230031,NS,carcinoid-endocrine_tumour,0,1	POTEB	22	1	NM_207355	exon1	c.C119A	p.T40K	TTGCTCGTGCCGC	.	scavenged	Atlas-SNP
AIM1	202	hgsc.bcm.edu	37	6	106967778	106967778	+	Missense_Mutation	SNP	T	T	C	rs3747787	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	150	67	151	0	0.446667	0	T|0.805;C|0.195	0.195	strong	.	AIM1	161	.	NM_001624	exon2	c.T1471C	p.C491R	TTCCCATGCACTG	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1092891	1092891	+	Silent	SNP	C	C	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	41	4	39	0	0.097561	0	.	.	none	MUC2_ENST00000441003,NS,carcinoma,0,2	MUC2	614	2	NM_002457	exon30	c.C4710A	p.T1570T	GGTGACCCCAACC	.	PASS	Atlas-SNP
ATP8B3	148229	hgsc.bcm.edu	37	19	1806667	1806667	+	Missense_Mutation	SNP	C	C	T	rs45574836	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	70	37	83	0	0.528571	0	C|0.941;T|0.059	0.059	strong	.	ATP8B3	108	.	NM_138813	exon7	c.G637A	p.A213T	TGATGGCTCTGTC	.	PASS	Atlas-SNP
BIVM-ERCC5	0	hgsc.bcm.edu	37	13	103504517	103504517	+	Silent	SNP	T	T	C	rs1047768	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	75	108	0	1	0	T|0.449;C|0.551	0.551	strong	.	.	.	.	NM_001204425	exon10	c.T1500C	p.H500H	TCGCCATGGGAAC	.	PASS	Atlas-SNP
IBSP	3381	hgsc.bcm.edu	37	4	88732763	88732763	+	Missense_Mutation	SNP	A	A	G	rs17013181	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	50	50	37	0	1	0	A|0.733;G|0.267	0.267	strong	.	IBSP	53	.	NM_004967	exon7	c.A655G	p.R219G	ACCGGAAGGCAGG	.	PASS	Atlas-SNP
C1orf127	148345	hgsc.bcm.edu	37	1	11009679	11009679	+	Splice_Site	SNP	G	G	A	rs1281013	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51	29	56	0	0.568627	0	G|0.907;A|0.093	0.093	strong	.	C1orf127	134	.	NM_001170754	exon12	c.1290+2C>T	.	AGACGTGCTTTGG	.	PASS	Atlas-SNP
DMBT1	1755	hgsc.bcm.edu	37	10	124339378	124339378	+	Missense_Mutation	SNP	A	A	G	rs1969620	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68	38	73	0	0.558824	0	A|0.909;G|0.091	0.091	strong	.	DMBT1	677	.	NM_007329	exon10	c.A964G	p.N322D	ACCCACAACTGTG	.	PASS	Atlas-SNP
HNRNPCL1	343069	hgsc.bcm.edu	37	1	12907633	12907633	+	Silent	SNP	G	G	A	rs75660350	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	156	45	108	0	0.288462	0	G|0.950;A|0.050	0.050	strong	.	HNRNPCL1	68	.	NM_001013631	exon2	c.C510T	p.S170S	AGACTTGGAAGAT	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	115	113	101	0	0.982609	0	T|0.574;A|0.426	0.426	strong	.	WDR93	63	.	NM_020212	exon2	c.T197A	p.L66H	TGAACCTTCTGTT	.	PASS	Atlas-SNP
ADAMTS14	140766	hgsc.bcm.edu	37	10	72520254	72520254	+	Missense_Mutation	SNP	C	C	T	rs61736607	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	43	25	40	0	0.581395	0	C|0.944;T|0.056	0.056	strong	.	ADAMTS14	148	.	NM_139155	exon22	c.C3326T	p.P1109L	CAGACCCTGGCCC	.	PASS	Atlas-SNP
TBATA	219793	hgsc.bcm.edu	37	10	72537086	72537086	+	Silent	SNP	C	C	T	rs4747099	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	33	16	38	0	0.484848	0	C|0.940;T|0.060	0.060	strong	.	.	.	.	NM_152710	exon7	c.G513A	p.E171E	CTTCTGCTCCTTC	.	PASS	Atlas-SNP
EP400	57634	hgsc.bcm.edu	37	12	132547093	132547093	+	Silent	SNP	A	A	G	rs28513925	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83	24	66	1	0.289157	0.0151515	A|0.500;G|0.500	0.500	weak	EP400,NS,carcinoma,0,15	EP400	370	15	NM_015409	exon47	c.A8181G	p.Q2727Q	GCAACAACAGCAG	.	scavenged	Atlas-SNP
LCT	3938	hgsc.bcm.edu	37	2	136574968	136574968	+	Silent	SNP	G	G	C	rs35093754	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	35	15	59	0	0.428571	0	G|0.950;C|0.050	0.050	strong	.	LCT	309	.	NM_002299	exon6	c.C1650G	p.G550G	GCCATAGCCTGCG	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	18	14	31	0	0.777778	0	G|0.539;A|0.461	0.461	strong	.	TGM5	88	.	NM_201631	exon5	c.C660T	p.Y220Y	GCTGACGTAGACG	.	PASS	Atlas-SNP
APOL6	80830	hgsc.bcm.edu	37	22	36055406	36055406	+	Silent	SNP	A	A	C	rs34014315	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80	55	72	0	0.6875	0	A|0.965;C|0.035	0.035	strong	.	APOL6	26	.	NM_030641	exon3	c.A795C	p.T265T	AAGGACAAAGTTT	.	PASS	Atlas-SNP
LIG4	3981	hgsc.bcm.edu	37	13	108861048	108861048	+	Missense_Mutation	SNP	C	C	T	rs2232642	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79	21	107	0	0.265823	0	C|0.958;T|0.042	0.042	strong	.	LIG4	91	.	NM_206937	exon3	c.G2569A	p.A857T	CCTCAGCTAAACA	.	PASS	Atlas-SNP
PIWIL4	143689	hgsc.bcm.edu	37	11	94322352	94322352	+	Missense_Mutation	SNP	A	A	T	rs11020845	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	175	29	156	0	0.165714	0	A|0.793;T|0.207	0.207	strong	.	PIWIL4	70	.	NM_152431	exon8	c.A980T	p.Q327L	CCTTTCAGAAGCG	.	PASS	Atlas-SNP
IKBKE	9641	hgsc.bcm.edu	37	1	206669465	206669465	+	Missense_Mutation	SNP	C	C	T	rs3748022	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	135	57	120	0	0.422222	0	C|0.844;T|0.156	0.156	strong	IKBKE,NS,adenoma,0,1	IKBKE	77	1	NM_014002	exon22	c.C2138T	p.P713L	CAGCACCTCCTGA	.	PASS	Atlas-SNP
ITGAE	3682	hgsc.bcm.edu	37	17	3661052	3661052	+	Missense_Mutation	SNP	G	G	A	rs71366574	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	108	53	108	0	0.490741	0	G|0.979;A|0.021	0.021	strong	.	ITGAE	96	.	NM_002208	exon9	c.C968T	p.T323M	ACTGTCGTAAGGT	.	PASS	Atlas-SNP
TTLL2	83887	hgsc.bcm.edu	37	6	167753691	167753691	+	Silent	SNP	C	C	T	rs877653	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	90	89	73	0	0.988889	0	C|0.724;T|0.276	0.276	strong	.	TTLL2	82	.	NM_031949	exon3	c.C303T	p.S101S	GCAAAGCGTCCTC	.	PASS	Atlas-SNP
AGBL3	340351	hgsc.bcm.edu	37	7	134678253	134678253	+	Missense_Mutation	SNP	T	T	A	rs2348049	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	140	53	134	0	0.378571	0	T|0.760;A|0.240	0.240	strong	.	AGBL3	45	.	NM_178563	exon4	c.T134A	p.F45Y	ACTCTTTTGGTGA	.	PASS	Atlas-SNP
SVIL	6840	hgsc.bcm.edu	37	10	29783908	29783908	+	Missense_Mutation	SNP	A	A	G	rs78773460	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	128	29	110	0	0.226562	0	A|0.500;G|0.500	0.500	strong	SVIL,NS,carcinoma,0,2	SVIL	226	2	NM_021738	exon20	c.T3776C	p.M1259T	AACTGCATATCTG	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179436020	179436020	+	Missense_Mutation	SNP	G	G	A	rs744426	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	92	37	113	0	0.402174	0	G|0.817;N|0.001	.	strong	TTN_ENST00000359218,brain,glioma,+1,10	TTN	18412	10	NM_001267550	exon326	c.C74839T	p.R24947C	CCTTGCGTTCTAG	.	PASS	Atlas-SNP
TFG	10342	hgsc.bcm.edu	37	3	100467018	100467018	+	Silent	SNP	T	T	C	rs11353	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	180	180	205	1	1	0.00487805	T|0.339;C|0.661	0.661	strong	.	TFG	42	.	NM_006070	exon8	c.T846C	p.P282P	TGGACCTCAACAA	.	PASS	Atlas-SNP
CCDC168	643677	hgsc.bcm.edu	37	13	103394716	103394716	+	Silent	SNP	T	T	C	rs9585987	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	18	18	55	0	1	0	T|0.305;C|0.695	0.695	strong	.	.	.	.	NM_001146197	exon4	c.A8331G	p.T2777T	AATAGATGTGTAG	.	PASS	Atlas-SNP
PAK7	57144	hgsc.bcm.edu	37	20	9520133	9520133	+	Silent	SNP	G	G	A	rs6039495	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98	61	121	0	0.622449	0	G|0.962;A|0.038	0.038	strong	.	PAK7	194	.	NM_177990	exon10	c.C2136T	p.L712L	TCTCATGAGGGGG	.	PASS	Atlas-SNP
ATF4	468	hgsc.bcm.edu	37	22	39917561	39917561	+	Silent	SNP	C	C	T	rs375843215		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100	45	112	0	0.45	0	.	.	weak	.	ATF4	27	.	NM_001675	exon1	c.C111T	p.Y37Y	TGATTACCTGGAG	.	PASS	Atlas-SNP
C1orf127	148345	hgsc.bcm.edu	37	1	11008102	11008102	+	Missense_Mutation	SNP	G	G	A	rs1281018	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	37	64	0	0.521127	0	G|0.914;A|0.086	0.086	strong	.	C1orf127	134	.	NM_001170754	exon12	c.C2090T	p.A697V	AGGGGCGCTGCCA	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	86	62	0	0.988506	0	A|0.461;G|0.539	0.539	strong	.	MMP3	60	.	NM_002422	exon8	c.T1086C	p.A362A	TCTGATAGCCCAG	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	145	69	127	0	0.475862	0	G|0.474;A|0.526	0.526	strong	.	MB	7	.	NM_203377	exon3	c.C204T	p.T68T	GAGCACGGTGGCA	.	PASS	Atlas-SNP
KRTAP16-1	100505753	hgsc.bcm.edu	37	17	39465038	39465038	+	Silent	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	118	35	125	0	0.29661	0	.	.	none	.	KRTAP16-1	12	.	NM_001146182	exon1	c.T468C	p.P156P	AATAGCAGGCTCA	.	PASS	Atlas-SNP
TNRC18	84629	hgsc.bcm.edu	37	7	5391702	5391702	+	Missense_Mutation	SNP	C	C	G	rs3801048	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	121	40	97	0	0.330579	0	C|0.797;G|0.203	0.203	strong	.	TNRC18	311	.	NM_001080495	exon17	c.G5218C	p.E1740Q	GGAATTCTTCGTC	.	PASS	Atlas-SNP
SIX4	51804	hgsc.bcm.edu	37	14	61180336	61180336	+	Missense_Mutation	SNP	C	C	T	rs112624131	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	141	61	131	0	0.432624	0	C|0.991;T|0.009	0.009	strong	SIX4,NS,carcinoma,0,1	SIX4	69	1	NM_017420	exon3	c.G2135A	p.R712H	ACCAAACGATGTT	.	PASS	Atlas-SNP
MFF	56947	hgsc.bcm.edu	37	2	228221725	228221725	+	Silent	SNP	A	A	G	rs74713223	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	25	10	29	0	0.4	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
DEPDC5	9681	hgsc.bcm.edu	37	22	32194581	32194581	+	Silent	SNP	A	A	G	rs16989495	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	46	21	75	0	0.456522	0	A|0.965;G|0.035	0.035	strong	.	DEPDC5	266	.	NM_001242897	exon14	c.A885G	p.Q295Q	TCCTCAAGGAGAT	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	41	121	0	0.476744	0	G|0.716;A|0.284	0.284	strong	.	MTOR	327	.	NM_004958	exon39	c.C5553T	p.S1851S	GGCCTCGCTCTCA	.	PASS	Atlas-SNP
ALMS1	7840	hgsc.bcm.edu	37	2	73676965	73676965	+	Missense_Mutation	SNP	G	G	A	rs201074268	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	42	64	0	0.688525	0	G|0.998;A|0.002	0.002	strong	.	ALMS1	384	.	NM_015120	exon8	c.G3308A	p.G1103D	AGCCTGGTATTTT	.	PASS	Atlas-SNP
OSBPL9	114883	hgsc.bcm.edu	37	1	52231560	52231560	+	Missense_Mutation	SNP	C	C	T	rs61739207	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	274	127	270	0	0.463504	0	C|0.994;T|0.006	0.006	strong	.	OSBPL9	192	.	NM_148909	exon12	c.C875T	p.T292I	CAAATACAGTCCC	.	PASS	Atlas-SNP
MAN2B2	23324	hgsc.bcm.edu	37	4	6596360	6596360	+	Missense_Mutation	SNP	G	G	A	rs2301795	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	46	81	0	0.547619	0	G|0.522;A|0.478	0.478	strong	.	MAN2B2	80	.	NM_015274	exon7	c.G958A	p.V320M	GTCTCGGTGCAGT	.	PASS	Atlas-SNP
SEH1L	81929	hgsc.bcm.edu	37	18	12951878	12951878	+	Missense_Mutation	SNP	G	G	A	rs117978838	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	20	71	0	0.377358	0	G|0.988;A|0.012	0.012	strong	SEH1L,NS,carcinoma,0,1	SEH1L	33	1	NM_001013437	exon2	c.G136A	p.D46N	AGTGGTGATTGGC	.	PASS	Atlas-SNP
HMCN1	83872	hgsc.bcm.edu	37	1	186050417	186050417	+	Missense_Mutation	SNP	A	A	G	rs10798035	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	29	101	0	0.333333	0	A|0.425;G|0.575	0.575	strong	HMCN1,NS,carcinoma,0,2	HMCN1	797	2	NM_031935	exon56	c.A8678G	p.E2893G	TGATAGAGTGTTT	.	PASS	Atlas-SNP
THUMPD3	25917	hgsc.bcm.edu	37	3	9422210	9422210	+	Silent	SNP	T	T	C	rs2596916	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	105	105	91	0	1	0	T|0.410;C|0.590	0.590	strong	.	THUMPD3	46	.	NM_001114092	exon7	c.T1032C	p.C344C	TGACTGTTTCCAT	.	PASS	Atlas-SNP
FAM111A	63901	hgsc.bcm.edu	37	11	58920492	58920492	+	Missense_Mutation	SNP	C	C	G	rs116918730	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	34	57	0	0.459459	0	C|0.966;G|0.034	0.034	strong	.	FAM111A	57	.	NM_001142520	exon5	c.C1351G	p.Q451E	GGACAACAAGTAC	.	PASS	Atlas-SNP
LOXHD1	125336	hgsc.bcm.edu	37	18	44057673	44057673	+	Missense_Mutation	SNP	C	C	T	rs74316327	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85	34	103	0	0.4	0	C|0.959;T|0.041	0.041	strong	LOXHD1_ENST00000398722,NS,carcinoma,-1,4	LOXHD1	367	4	NM_144612	exon40	c.G6398A	p.R2133H	AGGTTGCGCATTT	.	PASS	Atlas-SNP
TAS2R14	50840	hgsc.bcm.edu	37	12	11091693	11091693	+	Silent	SNP	T	T	A	rs7138535	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	36	61	0	0.48	0	T|0.766;A|0.234	0.234	strong	.	TAS2R14	26	.	NM_023922	exon1	c.A114T	p.G38G	CTTTCTTCCCTTG	.	PASS	Atlas-SNP
RNF213	57674	hgsc.bcm.edu	37	17	78346870	78346870	+	Missense_Mutation	SNP	C	C	A	rs62077764	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68	41	65	0	0.602941	0	C|0.953;A|0.047	0.047	strong	.	RNF213	766	.	NM_001256071	exon49	c.C12847A	p.L4283I	CGGAAGCTCAGCA	.	PASS	Atlas-SNP
PLEC	5339	hgsc.bcm.edu	37	8	144991176	144991176	+	Silent	SNP	T	T	C	rs6558405	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	58	24	58	0	0.413793	0	T|0.548;C|0.452	0.452	strong	.	PLEC	1144	.	NM_201380	exon32	c.A13224G	p.S4408S	GGGGTCTGACCAG	.	PASS	Atlas-SNP
CNTN2	6900	hgsc.bcm.edu	37	1	205031116	205031116	+	Missense_Mutation	SNP	C	C	T	rs2229866	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	59	33	69	0	0.559322	0	C|0.586;T|0.414	0.414	strong	.	CNTN2	116	.	NM_005076	exon9	c.C1097T	p.P366L	GGGAGCCTCTGGC	.	PASS	Atlas-SNP
C4orf26	152816	hgsc.bcm.edu	37	4	76489345	76489345	+	Missense_Mutation	SNP	C	C	T	rs2306175	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72	37	57	0	0.513889	0	C|0.741;T|0.259	0.259	strong	C4orf26,NS,carcinoma,0,1	C4orf26	24	1	NM_001206981	exon3	c.C133T	p.L45F	TTACGCCTCCTGG	.	PASS	Atlas-SNP
SLC22A18AS	5003	hgsc.bcm.edu	37	11	2909507	2909507	+	Missense_Mutation	SNP	G	G	A	rs146094810	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60	33	49	0	0.55	0	G|0.998;A|0.002	0.002	strong	.	SLC22A18AS	7	.	NM_007105	exon4	c.C665T	p.P222L	GGGTTGGGGGGGC	.	PASS	Atlas-SNP
EPHX1	2052	hgsc.bcm.edu	37	1	226033030	226033030	+	Silent	SNP	G	G	C	rs4149230	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	34	17	36	0	0.5	0	G|0.955;C|0.045	0.045	strong	.	EPHX1	57	.	NM_001136018	exon9	c.G1350C	p.S450S	CCTGTCGGTGCTG	.	PASS	Atlas-SNP
PRAMEF2	65122	hgsc.bcm.edu	37	1	12919111	12919111	+	Missense_Mutation	SNP	G	G	A	rs9728577	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	160	48	115	0	0.3	0	G|0.953;A|0.047	0.047	strong	.	PRAMEF2	85	.	NM_023014	exon2	c.G247A	p.E83K	TTGCTGGAAGGGC	.	PASS	Atlas-SNP
GCOM1	145781	hgsc.bcm.edu	37	15	57918069	57918069	+	Silent	SNP	A	A	G	rs2069133	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	102	48	130	0	0.470588	0	A|0.516;G|0.484	0.484	strong	.	GCOM1	66	.	NM_001018090	exon5	c.A504G	p.A168A	CTTGGCATCAGAT	.	PASS	Atlas-SNP
ITIH1	3697	hgsc.bcm.edu	37	3	52820403	52820403	+	Silent	SNP	C	C	T	rs142797927	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	170	87	173	0	0.511765	0	C|1.000;T|0.000	0.000	strong	ITIH1,caecum,carcinoma,0,1	ITIH1	108	1	NM_002215	exon13	c.C1686T	p.V562V	CCACGTCGAGCGC	.	PASS	Atlas-SNP
UBC	7316	hgsc.bcm.edu	37	12	125397061	125397061	+	Silent	SNP	G	G	A	rs17840844	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	262	206	278	1	0.78626	0.00359712	G|0.625;A|0.375	0.375	strong	UBC,NS,carcinoma,-2,1	UBC	79	1	NM_021009	exon2	c.C1257T	p.D419D	CTGCTGGTCAGGA	.	scavenged	Atlas-SNP
ZNF180	7733	hgsc.bcm.edu	37	19	44981883	44981883	+	Missense_Mutation	SNP	C	C	G	rs1897820	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	106	106	126	0	1	0	C|0.530;G|0.470	0.470	strong	.	ZNF180	103	.	NM_013256	exon5	c.G815C	p.C272S	CCATAGCATTTAT	.	PASS	Atlas-SNP
CDH17	1015	hgsc.bcm.edu	37	8	95161102	95161102	+	Silent	SNP	G	G	A	rs35792427	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	92	34	69	0	0.369565	0	G|0.892;A|0.108	0.108	strong	.	CDH17	119	.	NM_004063	exon14	c.C1797T	p.S599S	TGAATAGCTTCAT	.	PASS	Atlas-SNP
SGK1	6446	hgsc.bcm.edu	37	6	134495169	134495169	+	Missense_Mutation	SNP	G	G	A	rs141028225	alternate_allele	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72	21	80	0	0.291667	0	G|1.000;C|0.000	.	alt	.	SGK1	387	.	NM_001143676	exon5	c.C487T	p.L163F	TCATAAGCTCAGG	.	PASS	Atlas-SNP
NUP88	4927	hgsc.bcm.edu	37	17	5294976	5294976	+	Silent	SNP	T	T	A	rs14231	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	25	76	0	0.462963	0	T|0.571;A|0.429	0.429	strong	.	NUP88	47	.	NM_002532	exon10	c.A1389T	p.P463P	TGGAGCTGGCTGC	.	PASS	Atlas-SNP
KIF16B	55614	hgsc.bcm.edu	37	20	16493533	16493533	+	Silent	SNP	T	T	C	rs6135775	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	45	31	47	0	0.688889	0	T|0.759;C|0.241	0.241	strong	.	KIF16B	305	.	NM_001199865	exon5	c.A384G	p.G128G	GAAGAGTCCTTCA	.	PASS	Atlas-SNP
NCAPD2	9918	hgsc.bcm.edu	37	12	6630996	6630996	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	21	70	0	0.318182	0	.	.	none	NCAPD2,NS,carcinoma,0,1	NCAPD2	99	1	NM_014865	exon15	c.C1747T	p.R583W	AATCCCCGGGAGT	.	PASS	Atlas-SNP
ADH4	127	hgsc.bcm.edu	37	4	100052733	100052733	+	Silent	SNP	C	C	A	rs1126670	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	150	149	158	0	0.993333	0	C|0.217;A|0.783	0.783	strong	ADH4,NS,carcinoma,-1,1	ADH4	35	1	NM_000670	exon6	c.G765T	p.P255P	CTGGATCGGTTTA	.	PASS	Atlas-SNP
OR2T29	343563	hgsc.bcm.edu	37	1	248722671	248722671	+	Missense_Mutation	SNP	T	T	A	rs9439338	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	467	175	372	0	0.374732	0	T|0.250;A|0.750	0.750	weak	.	OR2T29	8	.	NM_001004694	exon1	c.A122T	p.K41M	AACGCCTTCAGGA	.	PASS	Atlas-SNP
C15orf52	388115	hgsc.bcm.edu	37	15	40633138	40633138	+	Silent	SNP	A	A	T	rs4924455	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	78	61	109	0	0.782051	0	A|0.762;T|0.238	0.238	strong	.	C15orf52	47	.	NM_207380	exon1	c.T15A	p.A5A	CTGCTCAGCACAC	.	PASS	Atlas-SNP
SKA3	221150	hgsc.bcm.edu	37	13	21746637	21746637	+	Missense_Mutation	SNP	C	C	T	rs11546983	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	88	42	99	0	0.477273	0	C|0.980;T|0.020	0.020	strong	.	SKA3	76	.	NM_145061	exon3	c.G172A	p.V58I	TATTAACATCATC	.	PASS	Atlas-SNP
CCDC137	339230	hgsc.bcm.edu	37	17	79637367	79637367	+	Missense_Mutation	SNP	C	C	G	rs7226091	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79	32	76	0	0.405063	0	C|0.754;G|0.245	0.245	strong	CCDC137,NS,carcinoma,0,2	CCDC137	27	2	NM_199287	exon3	c.C381G	p.H127Q	TATCCACCGCATG	.	PASS	Atlas-SNP
APOBEC3H	164668	hgsc.bcm.edu	37	22	39497404	39497404	+	Missense_Mutation	SNP	G	G	C	rs139297	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	90	89	97	0	0.988889	0	G|0.456;C|0.544	0.544	strong	.	APOBEC3H	28	.	NM_001166003	exon3	c.G313C	p.G105R	AACCTGGGCATCT	.	PASS	Atlas-SNP
ASGR2	433	hgsc.bcm.edu	37	17	7012077	7012077	+	Silent	SNP	C	C	T	rs2304979	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	133	60	175	0	0.451128	0	C|0.777;T|0.223	0.223	strong	ASGR2,NS,carcinoma,-2,2	ASGR2	38	2	NM_080912	exon3	c.G255A	p.G85G	CTGGCCCCCGTGA	.	PASS	Atlas-SNP
NCR1	9437	hgsc.bcm.edu	37	19	55420801	55420801	+	Silent	SNP	C	C	A	rs3765013	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	31	15	32	0	0.483871	0	C|0.604;A|0.396	0.396	strong	.	NCR1	60	.	NM_001145458	exon4	c.C553A	p.R185R	GCCCACCGAGGGA	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	122	56	115	0	0.459016	0	C|0.693;T|0.307	0.307	strong	.	TMX4	39	.	NM_021156	exon8	c.G907A	p.G303R	CCTCTCCTGGGGG	.	PASS	Atlas-SNP
SBF1	6305	hgsc.bcm.edu	37	22	50894987	50894987	+	Silent	SNP	G	G	A	rs79468232	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	45	20	60	0	0.444444	0	G|0.963;A|0.037	0.037	strong	.	SBF1	211	.	NM_002972	exon30	c.C4020T	p.P1340P	CGGGTCGGGAGGG	.	PASS	Atlas-SNP
POLD1	5424	hgsc.bcm.edu	37	19	50909765	50909765	+	Silent	SNP	C	C	T	rs2230245	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	104	53	89	0	0.509615	0	C|0.925;T|0.075	0.075	strong	POLD1_ENST00000440232,colon,carcinoma,0,2	POLD1	174	2	NM_002691	exon12	c.C1485T	p.T495T	CATCACCGACCTG	.	PASS	Atlas-SNP
ABCA13	154664	hgsc.bcm.edu	37	7	48312084	48312084	+	Missense_Mutation	SNP	G	G	C	rs78575608	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	120	26	164	0	0.216667	0	G|0.974;C|0.026	0.026	strong	.	ABCA13	1192	.	NM_152701	exon17	c.G2821C	p.V941L	CAAGAAGTTGATA	.	PASS	Atlas-SNP
ITPKB	3707	hgsc.bcm.edu	37	1	226924642	226924642	+	Missense_Mutation	SNP	C	C	T	rs3754415	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	46	23	38	0	0.5	0	C|0.795;T|0.205	0.205	strong	ITPKB_ENST00000429204,NS,carcinoma,0,1	ITPKB	158	1	NM_002221	exon2	c.G518A	p.R173H	GGCGAGCGAGCCC	.	PASS	Atlas-SNP
PTPRS	5802	hgsc.bcm.edu	37	19	5210762	5210762	+	Silent	SNP	G	G	A	rs1143699	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	92	35	76	0	0.380435	0	G|0.874;A|0.126	0.126	strong	.	PTPRS	169	.	NM_002850	exon34	c.C5289T	p.D1763D	CCAGAAGTCTTCC	.	PASS	Atlas-SNP
ACSM5	54988	hgsc.bcm.edu	37	16	20442613	20442613	+	Silent	SNP	T	T	C	rs77351186	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	125	15	96	0	0.12	0	T|0.997;C|0.003	0.003	strong	ACSM5,NS,carcinoma,0,1	ACSM5	101	1	NM_017888	exon10	c.T1278C	p.T426T	ACCCACTCGGCCC	.	PASS	Atlas-SNP
PLEC	5339	hgsc.bcm.edu	37	8	144994916	144994916	+	Missense_Mutation	SNP	C	C	T	rs35027700	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	38	65	0	0.622951	0	C|0.953;T|0.047	0.047	strong	.	PLEC	1144	.	NM_201380	exon32	c.G9484A	p.V3162I	CGATGACGTTGGC	.	PASS	Atlas-SNP
TGFA	7039	hgsc.bcm.edu	37	2	70677994	70677994	+	Silent	SNP	G	G	A	rs2166975	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	107	107	171	0	1	0	G|0.782;A|0.218	0.218	strong	TGFA,NS,lymphoid_neoplasm,0,1	TGFA	14	1	NM_003236	exon6	c.C480T	p.V160V	TCTTCAGACCACT	.	PASS	Atlas-SNP
MYPOP	339344	hgsc.bcm.edu	37	19	46394268	46394268	+	Silent	SNP	G	G	A	rs150220406	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	22	60	0	0.468085	0	G|0.988;A|0.012	0.012	strong	.	MYPOP	23	.	NM_001012643	exon3	c.C813T	p.N271N	GATGGCGTTGGCA	.	PASS	Atlas-SNP
RXFP2	122042	hgsc.bcm.edu	37	13	32360547	32360547	+	Silent	SNP	A	A	G	rs7325513	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	102	102	119	0	1	0	A|0.387;G|0.613	0.613	strong	.	RXFP2	95	.	NM_130806	exon12	c.A957G	p.E319E	AACGGAACTATCA	.	PASS	Atlas-SNP
CEACAM5	1048	hgsc.bcm.edu	37	19	42213744	42213744	+	Silent	SNP	T	T	C	rs10402825	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	165	100	151	1	0.606061	0.00662252	C|0.181;G|0.000;T|0.819	0.181	strong	CEACAM5,NS,carcinoma,+1,1	CEACAM5	84	1	NM_004363	exon2	c.T210C	p.G70G	CAAAGGTGAAAGA	.	scavenged	Atlas-SNP
TUBA3E	112714	hgsc.bcm.edu	37	2	130951584	130951584	+	Silent	SNP	T	T	C	rs7340507	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110	22	161	0	0.2	0	T|0.595;C|0.405	0.405	strong	.	TUBA3E	73	.	NM_207312	exon4	c.A831G	p.S277S	CTCAGCTGAGATG	.	PASS	Atlas-SNP
OR10G7	390265	hgsc.bcm.edu	37	11	123909671	123909671	+	Missense_Mutation	SNP	G	G	A	rs11827843	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	171	143	153	1	0.836257	0.00653595	G|0.939;A|0.061	0.061	strong	.	OR10G7	103	.	NM_001004463	exon1	c.C38T	p.T13M	AGGCCCGTGAGGA	.	PASS	Atlas-SNP
HR	55806	hgsc.bcm.edu	37	8	21984650	21984650	+	Silent	SNP	A	A	G	rs12675745	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	111	111	113	0	1	0	A|0.372;G|0.628	0.628	strong	HR,NS,carcinoma,0,1	HR	71	1	NM_018411	exon3	c.T1305C	p.F435F	GCCTGGAAAAGGG	.	PASS	Atlas-SNP
DAAM1	23002	hgsc.bcm.edu	37	14	59797373	59797373	+	Silent	SNP	G	G	A	rs28927674	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	143	64	148	0	0.447552	0	G|0.939;A|0.061	0.061	strong	DAAM1,colon,carcinoma,+1,1	DAAM1	95	1	NM_001270520	exon13	c.G1527A	p.A509A	GGTGGCGGACCTC	.	PASS	Atlas-SNP
DOCK5	80005	hgsc.bcm.edu	37	8	25159885	25159885	+	Silent	SNP	G	G	A	rs907157	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	50	24	41	0	0.48	0	G|0.698;N|0.000	.	strong	.	DOCK5	167	.	NM_024940	exon10	c.G891A	p.V297V	CCTTGTGTGCCAG	.	PASS	Atlas-SNP
PAOX	196743	hgsc.bcm.edu	37	10	135204950	135204950	+	Missense_Mutation	SNP	C	C	G	rs1046175	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	36	36	65	0	1	0	C|0.163;G|0.837	0.837	strong	PAOX_ENST00000357296,NS,carcinoma,0,2	PAOX	82	2	NM_207128	exon6	c.C1369G	p.Q457E	CAGGCCCAGGCTC	.	PASS	Atlas-SNP
PAH	5053	hgsc.bcm.edu	37	12	103246700	103246700	+	Silent	SNP	C	C	T	rs1042503	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60	31	60	0	0.516667	0	C|0.723;T|0.276	0.276	strong	.	PAH	77	.	NM_000277	exon7	c.G735A	p.V245V	GCCAGCCACAGGT	.	PASS	Atlas-SNP
SGK1	6446	hgsc.bcm.edu	37	6	134495154	134495154	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60	12	75	0	0.2	0	.	.	none	SGK1_ENST00000367858,NS,carcinoma,0,5	SGK1	387	5	NM_001143676	exon5	c.C502T	p.P168S	GAGAAGGGTTGGC	.	PASS	Atlas-SNP
CDH23	64072	hgsc.bcm.edu	37	10	73377054	73377054	+	Silent	SNP	G	G	A	rs74608315	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	96	56	96	0	0.583333	0	G|0.972;A|0.028	0.028	strong	.	CDH23	365	.	NM_052836	exon11	c.G1038A	p.P346P	TGCCCCGGAGTTC	.	PASS	Atlas-SNP
NCAPD2	9918	hgsc.bcm.edu	37	12	6639981	6639981	+	Missense_Mutation	SNP	C	C	G	rs2240871	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55	24	55	0	0.436364	0	C|0.834;G|0.166	0.166	strong	.	NCAPD2	99	.	NM_014865	exon30	c.C3962G	p.T1321S	CATCCACTGGTAC	.	PASS	Atlas-SNP
OR2F1	26211	hgsc.bcm.edu	37	7	143657473	143657473	+	Missense_Mutation	SNP	A	A	G	rs2072165	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	144	74	164	0	0.513889	0	A|0.807;G|0.193	0.193	strong	.	OR2F1	71	.	NM_012369	exon1	c.A410G	p.H137R	TCATGCATGGAGG	.	PASS	Atlas-SNP
GPR113	165082	hgsc.bcm.edu	37	2	26534112	26534112	+	Silent	SNP	G	G	A	rs77088392	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85	40	70	0	0.470588	0	G|0.985;A|0.015	0.015	strong	.	GPR113	134	.	NM_001145168	exon11	c.C2484T	p.G828G	TGGGGCGCCCAGG	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	92	54	61	0	0.586957	0	A|0.686;G|0.314	0.314	strong	.	ZNF584	31	.	NM_173548	exon4	c.A901G	p.T301A	GAGTGTACAGAAT	.	PASS	Atlas-SNP
DIS3	22894	hgsc.bcm.edu	37	13	73350079	73350079	+	Missense_Mutation	SNP	T	T	C	rs4883918	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	88	28	58	0	0.318182	0	T|0.726;C|0.274	0.274	strong	.	DIS3	103	.	NM_014953	exon5	c.A806G	p.N269S	TCTTCATTGTCGC	.	PASS	Atlas-SNP
IL6R	3570	hgsc.bcm.edu	37	1	154426970	154426970	+	Missense_Mutation	SNP	A	A	C	rs2228145	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	35	21	32	0	0.6	0	A|0.687;C|0.313;T|0.000	0.313	strong	.	IL6R	47	.	NM_000565	exon9	c.A1073C	p.D358A	TGCAAGATTCTTC	.	PASS	Atlas-SNP
KRTAP10-5	386680	hgsc.bcm.edu	37	21	45999908	45999908	+	Missense_Mutation	SNP	A	A	C	rs380585	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	124	73	94	0	0.58871	0	A|0.902;C|0.098	0.098	strong	.	KRTAP10-5	43	.	NM_198694	exon1	c.T548G	p.F183C	GGTTTGAAGCAGA	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79	79	74	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
WDR72	256764	hgsc.bcm.edu	37	15	54003091	54003091	+	Missense_Mutation	SNP	G	G	A	rs551225	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	56	56	64	0	1	0	G|0.619;A|0.381	0.381	strong	.	WDR72	177	.	NM_182758	exon9	c.C917T	p.P306L	AAATGAGGATAAA	.	PASS	Atlas-SNP
CHD1	1105	hgsc.bcm.edu	37	5	98216991	98216991	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	183	40	197	0	0.218579	0	.	.	none	.	CHD1	137	.	NM_001270	exon20	c.G2956T	p.E986X	GGGGCTCTTGTTC	.	PASS	Atlas-SNP
POU5F1	5460	hgsc.bcm.edu	37	6	31138107	31138107	+	Silent	SNP	G	G	A	rs1062630	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	44	76	0	0.721311	0	G|0.784;A|0.216	0.216	strong	POU5F1,colon,carcinoma,0,2	POU5F1	25	2	NM_002701	exon1	c.C291T	p.G97G	TGCTTCGCCCTCA	.	PASS	Atlas-SNP
SLC15A1	6564	hgsc.bcm.edu	37	13	99376181	99376181	+	Missense_Mutation	SNP	C	C	T	rs2297322	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	132	78	88	0	0.590909	0	C|0.768;T|0.232	0.232	strong	.	SLC15A1	92	.	NM_005073	exon5	c.G350A	p.S117N	GGAAGGCTGTCGG	.	PASS	Atlas-SNP
UBE4B	10277	hgsc.bcm.edu	37	1	10218439	10218439	+	Silent	SNP	T	T	C	rs2273299	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	106	43	100	0	0.40566	0	T|0.658;C|0.342	0.342	strong	UBE4B,NS,carcinoma,0,1	UBE4B	233	1	NM_001105562	exon22	c.T2952C	p.S984S	CACCAGTGAGTTT	.	PASS	Atlas-SNP
LAMA5	3911	hgsc.bcm.edu	37	20	60897488	60897488	+	Silent	SNP	G	G	A	rs2274933	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	50	26	56	0	0.52	0	G|0.817;C|0.000;A|0.183	0.183	strong	.	LAMA5	268	.	NM_005560	exon47	c.C6183T	p.F2061F	GCCATCGAAACCA	.	PASS	Atlas-SNP
CABLES2	81928	hgsc.bcm.edu	37	20	60968596	60968596	+	Silent	SNP	A	A	G	rs1570027	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	102	47	86	0	0.460784	0	A|0.785;G|0.215	0.215	strong	.	CABLES2	30	.	NM_031215	exon6	c.T780C	p.H260H	CAGGCCATGGCTG	.	PASS	Atlas-SNP
S100A7L2	645922	hgsc.bcm.edu	37	1	153410822	153410822	+	Missense_Mutation	SNP	C	C	A	rs41323044	bycluster;alternate_allele	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	113	53	109	0	0.469027	0	C|0.875;G|0.125	.	alt	.	S100A7L2	36	.	NM_001045479	exon2	c.G17T	p.G6V	AAAAAGCCTTCAG	.	PASS	Atlas-SNP
RNF213	57674	hgsc.bcm.edu	37	17	78335610	78335610	+	Silent	SNP	G	G	A	rs61741791	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83	27	110	0	0.325301	0	G|0.955;A|0.045	0.045	strong	.	RNF213	766	.	NM_001256071	exon39	c.G11277A	p.P3759P	AGAGCCGCAGCAG	.	PASS	Atlas-SNP
MGLL	11343	hgsc.bcm.edu	37	3	127413881	127413881	+	Silent	SNP	T	T	C	rs4881	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	205	92	217	0	0.44878	0	T|0.903;C|0.097	0.097	strong	.	MGLL	19	.	NM_007283	exon7	c.A753G	p.L251L	GTCACATAGGCGA	.	PASS	Atlas-SNP
ACOT2	10965	hgsc.bcm.edu	37	14	74036500	74036500	+	Missense_Mutation	SNP	C	C	T	rs146968042	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	18	14	20	0	0.777778	0	C|0.986;T|0.014	0.014	strong	.	ACOT2	24	.	NM_006821	exon1	c.C556T	p.R186W	CAGACGCGGCACG	.	PASS	Atlas-SNP
CHRD	8646	hgsc.bcm.edu	37	3	184102396	184102396	+	Silent	SNP	C	C	T	rs16858778	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	25	31	0	0.531915	0	C|0.909;T|0.091	0.091	strong	.	CHRD	149	.	NM_003741	exon13	c.C1512T	p.N504N	CCTGAACGTGGGC	.	PASS	Atlas-SNP
TMEM219	124446	hgsc.bcm.edu	37	16	29979376	29979376	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	95	7	99	0	0.0736842	0	.	.	none	.	TMEM219	10	.	NM_001083613	exon4	c.C386T	p.T129I	TTATCACAGCCAG	.	PASS	Atlas-SNP
PLA2G6	8398	hgsc.bcm.edu	37	22	38525510	38525510	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	181	2	171	0	0.0110497	0	.	.	none	PLA2G6,NS,malignant_melanoma,-1,1	PLA2G6	54	1	NM_003560	exon8	c.G1137A	p.P379P	GTCATTCGGGGTG	.	scavenged	Atlas-SNP
SPPL2C	162540	hgsc.bcm.edu	37	17	43923654	43923654	+	Missense_Mutation	SNP	G	G	C	rs12185233	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91	90	100	0	0.989011	0	G|0.509;C|0.491	0.491	strong	IMP5,NS,carcinoma,0,1	.	.	1	NM_175882	exon1	c.G1382C	p.R461P	GTTGCCGCTTTGA	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	153	152	149	1	0.993464	0.00671141	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
WNT10B	7480	hgsc.bcm.edu	37	12	49359989	49359989	+	Silent	SNP	G	G	A	rs1051886	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	31	59	0	0.584906	0	G|0.679;A|0.321	0.321	strong	.	WNT10B	41	.	NM_003394	exon5	c.C1059T	p.H353H	CACGTTGTGCCCA	.	PASS	Atlas-SNP
CR1L	1379	hgsc.bcm.edu	37	1	207851611	207851611	+	Missense_Mutation	SNP	A	A	G	rs2296158	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	147	76	145	0	0.517007	0	A|0.473;G|0.527	0.527	strong	.	CR1L	97	.	NM_175710	exon3	c.A346G	p.R116G	CAGTTCAGATCCC	.	PASS	Atlas-SNP
DNAH7	56171	hgsc.bcm.edu	37	2	196851911	196851911	+	Missense_Mutation	SNP	G	G	A	rs10931715	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	146	66	153	0	0.452055	0	G|0.453;A|0.547	0.547	strong	.	DNAH7	512	.	NM_018897	exon14	c.C1633T	p.R545C	CTAAACGAATAGT	.	PASS	Atlas-SNP
COL11A2	1302	hgsc.bcm.edu	37	6	33136310	33136310	+	Missense_Mutation	SNP	G	G	T	rs2229784	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	70	8	82	0	0.114286	0	G|0.947;T|0.053	0.053	strong	.	COL11A2	124	.	NM_080680	exon54	c.C3946A	p.P1316T	CAAGTGGCCCTGG	.	PASS	Atlas-SNP
CACNA1F	778	hgsc.bcm.edu	37	X	49061742	49061742	+	Missense_Mutation	SNP	C	C	T	rs33910054	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110	68	68	0	0.618182	0	C|0.926;T|0.074	0.074	strong	.	CACNA1F	218	.	NM_005183	exon48	c.G5789A	p.R1930H	GTCAGGCGACACG	.	PASS	Atlas-SNP
AGXT2	64902	hgsc.bcm.edu	37	5	34998877	34998877	+	Missense_Mutation	SNP	C	C	A	rs16899974	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	40	83	0	0.526316	0	C|0.795;A|0.205	0.205	strong	.	AGXT2	89	.	NM_031900	exon14	c.G1492T	p.V498L	CTTCTACTGCAAA	.	PASS	Atlas-SNP
CCDC85C	317762	hgsc.bcm.edu	37	14	100070030	100070030	+	Silent	SNP	G	G	A	rs78667152	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	13	4	13	0	0.307692	0	G|0.808;A|0.192	0.192	strong	.	CCDC85C	3	.	NM_001144995	exon1	c.C267T	p.C89C	GAGGAAGCAGCAG	.	PASS	Atlas-SNP
MLH1	4292	hgsc.bcm.edu	37	3	37053568	37053568	+	Missense_Mutation	SNP	A	A	G	rs1799977	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73	38	81	0	0.520548	0	A|0.799;G|0.201	0.201	strong	MLH1,NS,carcinoma,0,1	MLH1	226	1	NM_000249	exon8	c.A655G	p.I219V	CGCTCCATCTTTG	.	PASS	Atlas-SNP
ARFGEF2	10564	hgsc.bcm.edu	37	20	47626847	47626847	+	Silent	SNP	T	T	C	rs2295580	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93	43	72	0	0.462366	0	A|0.003;C|0.372;G|0.003;T|0.622	0.372	strong	ARFGEF2,colon,carcinoma,0,1	ARFGEF2	160	1	NM_006420	exon27	c.T3663C	p.G1221G	CTCAGGTTGGAAG	.	PASS	Atlas-SNP
GRIN2B	2904	hgsc.bcm.edu	37	12	13720043	13720043	+	Silent	SNP	G	G	A	rs3026160	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	115	52	103	0	0.452174	0	G|0.922;A|0.078	0.078	strong	.	GRIN2B	303	.	NM_000834	exon12	c.C2514T	p.C838C	GTGTTCGCAGATG	.	PASS	Atlas-SNP
KY	339855	hgsc.bcm.edu	37	3	134369716	134369716	+	Silent	SNP	C	C	A	rs13060869	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	114	54	102	0	0.473684	0	C|0.832;A|0.168	0.168	strong	.	KY	92	.	NM_178554	exon1	c.G87T	p.T29T	TGAGAGCGTACCC	.	PASS	Atlas-SNP
CHMP5	51510	hgsc.bcm.edu	37	9	33266075	33266075	+	Missense_Mutation	SNP	A	A	C	rs146626883	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73	29	72	0	0.39726	0	A|0.999;C|0.001	0.001	strong	CHMP5,rectum,carcinoma,-1,1	CHMP5	15	1	NM_016410	exon2	c.A137C	p.K46T	AGTATAAGGATCA	.	PASS	Atlas-SNP
MMP24	10893	hgsc.bcm.edu	37	20	33842284	33842284	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57	15	72	0	0.263158	0	.	.	none	.	MMP24	35	.	NM_006690	exon4	c.C544A	p.L182I	GGTGAGCTAGACA	.	PASS	Atlas-SNP
SVEP1	79987	hgsc.bcm.edu	37	9	113169631	113169631	+	Missense_Mutation	SNP	G	G	A	rs7030192	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	214	106	220	0	0.495327	0	A|0.380;G|0.620	0.380	strong	.	SVEP1	326	.	NM_153366	exon38	c.C8249T	p.A2750V	GAGCCTGCTAGAA	.	PASS	Atlas-SNP
TRIM45	80263	hgsc.bcm.edu	37	1	117660754	117660754	+	Missense_Mutation	SNP	C	C	T	rs749902	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	132	132	141	0	1	0	C|0.742;T|0.258	0.258	strong	.	TRIM45	55	.	NM_001145635	exon2	c.G1124A	p.C375Y	TGAGGACAGAAGC	.	PASS	Atlas-SNP
PPL	5493	hgsc.bcm.edu	37	16	4942099	4942099	+	Missense_Mutation	SNP	C	C	T	rs1049205	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	78	39	97	0	0.5	0	C|0.588;T|0.412	0.412	strong	PPL,NS,carcinoma,0,1	PPL	168	1	NM_002705	exon15	c.G1766A	p.R589Q	TCCACCCGGGTCC	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	125	60	102	0	0.48	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
MUC4	4585	hgsc.bcm.edu	37	3	195505822	195505822	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	7	81	2	0.0945946	0.0246914	.	.	none	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.C12629A	p.P4210H	GTGACAGGAAGAG	.	scavenged	Atlas-SNP
GALNTL6	442117	hgsc.bcm.edu	37	4	173269737	173269737	+	Silent	SNP	T	T	C	rs114177519	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	148	78	111	0	0.527027	0	T|0.994;C|0.006	0.006	strong	.	GALNTL6	102	.	NM_001034845	exon5	c.T450C	p.N150N	TCATAATGAAGGT	.	PASS	Atlas-SNP
C1orf127	148345	hgsc.bcm.edu	37	1	11008594	11008594	+	Missense_Mutation	SNP	A	A	T	rs1281016	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	159	83	126	0	0.522013	0	A|0.922;T|0.078	0.078	strong	.	C1orf127	134	.	NM_001170754	exon12	c.T1598A	p.V533D	CCTGAGACCAGAA	.	PASS	Atlas-SNP
SVIL	6840	hgsc.bcm.edu	37	10	29754535	29754535	+	Missense_Mutation	SNP	G	G	A	rs17694739	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	133	70	144	0	0.526316	0	G|0.917;A|0.083	0.083	strong	SVIL,colon,carcinoma,+1,1	SVIL	226	1	NM_021738	exon34	c.C6122T	p.A2041V	TGGGGCGCGCTGT	.	PASS	Atlas-SNP
LY6K	54742	hgsc.bcm.edu	37	8	143782044	143782044	+	Silent	SNP	A	A	G	rs2585174	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	43	43	66	0	1	0	A|0.482;G|0.518	0.518	strong	.	LY6K	23	.	NM_001160354	exon1	c.A99G	p.R33R	CCAGCGAACGGGT	.	PASS	Atlas-SNP
PARP12	64761	hgsc.bcm.edu	37	7	139734069	139734069	+	Missense_Mutation	SNP	C	C	T	rs35456446	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80	37	92	0	0.4625	0	C|0.953;T|0.047	0.047	strong	.	PARP12	59	.	NM_022750	exon8	c.G1387A	p.V463M	GAGACACGTATTT	.	PASS	Atlas-SNP
MLL4	8085	hgsc.bcm.edu	37	19	36222857	36222857	+	Missense_Mutation	SNP	C	C	T	rs16970649	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	32	95	0	0.484848	0	C|0.902;T|0.098	0.098	strong	.	MLL4	229	.	NM_014727	exon27	c.C5486T	p.P1829L	TTGTCCCTGGAGC	.	PASS	Atlas-SNP
LDHAL6B	92483	hgsc.bcm.edu	37	15	59499179	59499179	+	Missense_Mutation	SNP	G	G	A	rs3809530	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	92	31	98	0	0.336957	0	G|0.690;A|0.310	0.310	strong	.	LDHAL6B	30	.	NM_033195	exon1	c.G40A	p.V14M	CAGAGAGTGAGCT	.	PASS	Atlas-SNP
IL3RA	3563	hgsc.bcm.edu	37	X	1497644	1497644	+	Missense_Mutation	SNP	G	G	C	rs17883366	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	142	92	219	1	0.647887	0.00456621	G|0.868;C|0.132	0.132	strong	.	IL3RA	49	.	NM_002183	exon10	c.G967C	p.V323L	GTCTTCGTGATCT	.	PASS	Atlas-SNP
PDE4DIP	9659	hgsc.bcm.edu	37	1	144906508	144906508	+	Missense_Mutation	SNP	C	C	T	rs34169189	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	259	126	267	1	0.486486	0.00374532	C|0.898;T|0.102	0.102	strong	.	PDE4DIP	817	.	NM_001002811	exon14	c.G2838A	p.M946I	CACAGCCATCATG	.	PASS	Atlas-SNP
CSPP1	79848	hgsc.bcm.edu	37	8	68074137	68074137	+	Missense_Mutation	SNP	G	G	A	rs16933182	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	123	47	124	0	0.382114	0	G|0.883;A|0.117	0.117	strong	.	CSPP1	129	.	NM_024790	exon20	c.G2615A	p.R872H	TCATACGTTCCTT	.	PASS	Atlas-SNP
CST1	1469	hgsc.bcm.edu	37	20	23731494	23731494	+	Missense_Mutation	SNP	A	A	G	rs6076122	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51	51	65	0	1	0	A|0.194;G|0.806	0.806	strong	.	CST1	37	.	NM_001898	exon1	c.T10C	p.Y4H	TCAGATACTGGGC	.	PASS	Atlas-SNP
ABCG8	64241	hgsc.bcm.edu	37	2	44073405	44073405	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	109	26	115	0	0.238532	0	.	.	none	.	ABCG8	98	.	NM_022437	exon3	c.T277C	p.F93L	CTAAGCTTCAAAG	.	PASS	Atlas-SNP
AKAP8L	26993	hgsc.bcm.edu	37	19	15491357	15491357	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93	48	98	0	0.516129	0	.	.	none	.	AKAP8L	64	.	NM_014371	exon13	c.A1603G	p.I535V	TGCTGATGAGCTT	.	PASS	Atlas-SNP
DCHS2	54798	hgsc.bcm.edu	37	4	155410667	155410667	+	Missense_Mutation	SNP	G	G	A	rs55810732	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85	37	85	0	0.435294	0	G|0.837;A|0.163	0.163	strong	DCHS2_ENST00000443500,NS,carcinoma,+1,2	DCHS2	594	2	NM_001142552	exon1	c.C1841T	p.A614V	CTGATCGCACCGC	.	PASS	Atlas-SNP
STAT1	6772	hgsc.bcm.edu	37	2	191874667	191874667	+	Silent	SNP	A	A	G	rs2066802	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	126	63	134	0	0.5	0	A|0.909;G|0.091	0.091	strong	.	STAT1	93	.	NM_007315	exon3	c.T63C	p.L21L	ATCATAAAGCTGG	.	PASS	Atlas-SNP
DCAF8L2	347442	hgsc.bcm.edu	37	X	27766776	27766776	+	Silent	SNP	G	G	A	rs45553337	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	184	141	88	0	0.766304	0	G|0.816;A|0.184	0.184	strong	.	DCAF8L2	79	.	NM_001136533	exon1	c.G1764A	p.T588T	CGTGACGCAGAGA	.	PASS	Atlas-SNP
CGB2	114336	hgsc.bcm.edu	37	19	49536390	49536390	+	Missense_Mutation	SNP	C	C	A	rs78219294		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	107	30	161	10	0.280374	0.0621118	A|1.000;|0.000	1.000	weak	CGB2,NS,carcinoma,0,1	CGB2	6	1	NM_033378	exon3	c.C404A	p.A135D	TCCAGGCCTCCTC	.	scavenged	Atlas-SNP
TNNC2	7125	hgsc.bcm.edu	37	20	44452697	44452697	+	Silent	SNP	C	C	A	rs4629	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	101	43	82	0	0.425743	0	C|0.569;A|0.431	0.431	strong	.	TNNC2	12	.	NM_003279	exon5	c.G384T	p.T128T	CTCGTCCGTCACG	.	PASS	Atlas-SNP
C17orf74	201243	hgsc.bcm.edu	37	17	7330307	7330307	+	Missense_Mutation	SNP	C	C	T	rs146528431	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	41	77	0	0.672131	0	C|0.995;T|0.005	0.005	strong	.	C17orf74	56	.	NM_175734	exon3	c.C997T	p.R333W	AACGCCCGGCCTG	.	PASS	Atlas-SNP
BANK1	55024	hgsc.bcm.edu	37	4	102751076	102751076	+	Missense_Mutation	SNP	G	G	A	rs10516487	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	32	103	0	0.395062	0	G|0.748;A|0.252	0.252	strong	.	BANK1	95	.	NM_017935	exon2	c.G182A	p.R61H	TATATCGCTTGGA	.	PASS	Atlas-SNP
SPTB	6710	hgsc.bcm.edu	37	14	65216120	65216120	+	Silent	SNP	C	C	T	rs57421986	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	70	33	59	0	0.471429	0	A|0.000;C|0.891;T|0.108	0.108	strong	.	SPTB	378	.	NM_001024858	exon35	c.G6891A	p.A2297A	GCTCTGCGCCTTG	.	PASS	Atlas-SNP
PTPN3	5774	hgsc.bcm.edu	37	9	112145817	112145817	+	Silent	SNP	C	C	T	rs146869100	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79	41	82	0	0.518987	0	C|0.998;T|0.002	0.002	strong	.	PTPN3	106	.	NM_002829	exon23	c.G2268A	p.Q756Q	CCAGTACTGGTGA	.	PASS	Atlas-SNP
BTNL8	79908	hgsc.bcm.edu	37	5	180377331	180377331	+	Silent	SNP	T	T	C	rs2278689	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73	73	113	0	1	0	T|0.757;C|0.243	0.243	strong	.	BTNL8	114	.	NM_001040462	exon8	c.T1290C	p.Y430Y	TATTTATACCCTG	.	PASS	Atlas-SNP
FANCA	2175	hgsc.bcm.edu	37	16	89836323	89836323	+	Missense_Mutation	SNP	C	C	T	rs7195066	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69	31	78	0	0.449275	0	C|0.485;T|0.515	0.515	strong	FANCA,NS,carcinoma,0,1	FANCA	99	1	NM_000135	exon26	c.G2426A	p.G809D	CCAGCACCAGGTG	.	PASS	Atlas-SNP
DOCK2	1794	hgsc.bcm.edu	37	5	169483706	169483706	+	Silent	SNP	C	C	T	rs17647491	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83	34	79	0	0.409639	0	C|0.989;T|0.011	0.011	strong	.	DOCK2	389	.	NM_004946	exon43	c.C4314T	p.Y1438Y	CAACTACGTGCAA	.	PASS	Atlas-SNP
ZP3	7784	hgsc.bcm.edu	37	7	76062798	76062798	+	Missense_Mutation	SNP	G	G	A	rs74676082	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	21	13	39	0	0.619048	0	G|0.996;A|0.004	0.004	strong	.	ZP3	32	.	NM_001110354	exon4	c.G547A	p.A183T	TGGAACGCTGAGA	.	PASS	Atlas-SNP
CHMP4C	92421	hgsc.bcm.edu	37	8	82670747	82670747	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	143	5	144	0	0.034965	0	.	.	none	CHMP4C,bladder,carcinoma,0,1	CHMP4C	28	1	NM_152284	exon5	c.G670T	p.D224Y	GATGATGATATCA	.	scavenged	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9057896	9057896	+	Missense_Mutation	SNP	G	G	C	rs12984471	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	149	77	143	0	0.516779	0	G|0.760;C|0.240	0.240	strong	.	MUC16	4315	.	NM_024690	exon3	c.C29550G	p.D9850E	GGTATCGTCCACA	.	PASS	Atlas-SNP
C2CD2	25966	hgsc.bcm.edu	37	21	43327856	43327856	+	Silent	SNP	A	A	G	rs3746906	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	84	109	0	1	0	A|0.367;G|0.633	0.633	strong	.	C2CD2	47	.	NM_015500	exon9	c.T1056C	p.F352F	CTTCTTAAATAAG	.	PASS	Atlas-SNP
SHROOM2	357	hgsc.bcm.edu	37	X	9914947	9914947	+	Missense_Mutation	SNP	G	G	C	rs2073942	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73	15	39	0	0.205479	0	0|0.003;C|0.476	0.476	strong	.	SHROOM2	139	.	NM_001649	exon10	c.G4821C	p.L1607F	CTTATTGGACAGC	.	PASS	Atlas-SNP
LIPC	3990	hgsc.bcm.edu	37	15	58838010	58838010	+	Missense_Mutation	SNP	A	A	G	rs6083	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	32	57	0	0.603774	0	A|0.457;G|0.543	0.543	strong	.	LIPC	56	.	NM_000236	exon5	c.A644G	p.N215S	ATGCCAATTTTGT	.	PASS	Atlas-SNP
NKTR	4820	hgsc.bcm.edu	37	3	42679486	42679486	+	Missense_Mutation	SNP	A	A	G	rs150528581	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94	47	68	0	0.5	0	A|0.992;G|0.008	0.008	strong	NKTR,NS,carcinoma,-1,1	NKTR	116	1	NM_005385	exon13	c.A2290G	p.K764E	AGTGGGAAAAAAA	.	PASS	Atlas-SNP
NALCN	259232	hgsc.bcm.edu	37	13	101881777	101881777	+	Silent	SNP	G	G	A	rs3916906	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	32	19	47	1	0.59375	0.0212766	G|0.766;N|0.000	.	strong	NALCN,NS,carcinoma,0,1	NALCN	431	1	NM_052867	exon13	c.C1593T	p.V531V	TTCTTCGACAAAG	.	scavenged	Atlas-SNP
FCGBP	8857	hgsc.bcm.edu	37	19	40399383	40399383	+	Silent	SNP	T	T	C	rs138090709	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	187	37	191	1	0.197861	0.0052356	T|1.000;C|0.000	0.000	weak	FCGBP,NS,carcinoma,-2,2	FCGBP	416	2	NM_003890	exon13	c.A6312G	p.G2104G	GGGTGGTCCGTGG	.	scavenged	Atlas-SNP
CFH	3075	hgsc.bcm.edu	37	1	196709774	196709774	+	Missense_Mutation	SNP	G	G	T	rs1065489	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98	52	88	0	0.530612	0	G|0.828;T|0.172	0.172	strong	.	CFH	251	.	NM_000186	exon18	c.G2808T	p.E936D	ACCTGAGATTTCT	.	PASS	Atlas-SNP
KRT9	3857	hgsc.bcm.edu	37	17	39728050	39728050	+	Silent	SNP	G	G	A	rs8070680	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	155	70	128	0	0.451613	0	A|0.670;G|0.330	0.670	strong	.	KRT9	78	.	NM_000226	exon1	c.C195T	p.G65G	GCCACCGCCTCCC	.	PASS	Atlas-SNP
C20orf194	25943	hgsc.bcm.edu	37	20	3362033	3362033	+	Silent	SNP	T	T	C	rs6051818	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	66	73	0	0.985075	0	T|0.757;C|0.243	0.243	strong	.	C20orf194	83	.	NM_001009984	exon3	c.A276G	p.V92V	ATCTAGTACTTCT	.	PASS	Atlas-SNP
PUS3	83480	hgsc.bcm.edu	37	11	125764156	125764156	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	8	33	0	0.129032	0	.	.	none	.	PUS3	33	.	NM_031307	exon4	c.T970G	p.L324V	CATATAAGACTAG	.	PASS	Atlas-SNP
OR10AD1	121275	hgsc.bcm.edu	37	12	48596241	48596241	+	Missense_Mutation	SNP	A	A	G	rs11168459	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79	50	73	0	0.632911	0	A|0.772;G|0.228	0.228	strong	OR10AD1,NS,carcinoma,0,1	OR10AD1	24	1	NM_001004134	exon1	c.T835C	p.Y279H	TGGTGTACAGGAG	.	PASS	Atlas-SNP
ZNF675	171392	hgsc.bcm.edu	37	19	23837145	23837145	+	Missense_Mutation	SNP	A	A	G	rs11671053	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	59	57	66	0	0.966102	0	A|0.544;G|0.456	0.456	strong	.	ZNF675	88	.	NM_138330	exon4	c.T590C	p.V197A	AAATTCACCTTGG	.	PASS	Atlas-SNP
SOAT1	6646	hgsc.bcm.edu	37	1	179310262	179310262	+	Silent	SNP	C	C	T	rs11576517	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	157	91	204	0	0.579618	0	C|0.773;T|0.227	0.227	strong	SOAT1,NS,carcinoma,0,1	SOAT1	53	1	NM_003101	exon7	c.C597T	p.P199P	AGTTCCCTATTTT	.	PASS	Atlas-SNP
TENM1	10178	hgsc.bcm.edu	37	X	123539063	123539063	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60	25	39	0	0.416667	0	.	.	none	.	.	.	.	NM_001163278	exon27	c.T5209G	p.F1737V	TGGCAAAAGTGAC	.	PASS	Atlas-SNP
BABAM1	29086	hgsc.bcm.edu	37	19	17389704	17389704	+	Silent	SNP	G	G	A	rs8170	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	56	29	47	0	0.517857	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
TMED6	146456	hgsc.bcm.edu	37	16	69385641	69385641	+	Missense_Mutation	SNP	A	A	G	rs76116020	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48	29	45	0	0.604167	0	A|0.979;G|0.021	0.021	strong	.	TMED6	19	.	NM_144676	exon1	c.T16C	p.F6L	CCCCAAAGAGCAA	.	PASS	Atlas-SNP
BMP10	27302	hgsc.bcm.edu	37	2	69093312	69093312	+	Silent	SNP	A	A	G	rs2231344	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	208	60	319	0	0.288462	0	A|0.870;G|0.130	0.130	strong	.	BMP10	70	.	NM_014482	exon2	c.T726C	p.D242D	ACTGGTATCTATT	.	PASS	Atlas-SNP
NT5C1B	93034	hgsc.bcm.edu	37	2	18757501	18757501	+	Silent	SNP	G	G	C	rs3902946	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	296	156	313	1	0.527027	0.00319489	G|0.689;C|0.311	0.311	strong	.	NT5C1B	72	.	NM_001199087	exon9	c.C1509G	p.L503L	TTTGTCGAGCCCA	.	PASS	Atlas-SNP
METTL13	51603	hgsc.bcm.edu	37	1	171751236	171751236	+	Silent	SNP	T	T	C	rs2294720	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	39	19	63	0	0.487179	0	T|0.439;C|0.561	0.561	strong	METTL13,NS,carcinoma,0,1	METTL13	67	1	NM_015935	exon1	c.T129C	p.H43H	GCTACATAAATAT	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152275921	152275921	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	156	57	161	0	0.365385	0	.	.	none	FLG,NS,carcinoma,0,1	FLG	900	1	NM_002016	exon3	c.G11441A	p.R3814H	TCATTACGTGTTT	.	PASS	Atlas-SNP
ND4	0	hgsc.bcm.edu	37	MT	11044	11044	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	6	6	10	0	1	0	.	.	none	.	.	.	.	ENST00000361381	exon1	c.C285T	p.Y95Y	ACTCTACCTCTCT	.	PASS	Atlas-SNP
SP140	11262	hgsc.bcm.edu	37	2	231118041	231118041	+	Missense_Mutation	SNP	A	A	C	rs3820975	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	133	67	154	0	0.503759	0	A|0.867;C|0.133	0.133	strong	.	SP140	121	.	NM_007237	exon11	c.A1068C	p.L356F	TTGTTTATCTGCA	.	PASS	Atlas-SNP
A4GALT	53947	hgsc.bcm.edu	37	22	43089055	43089055	+	Silent	SNP	G	G	C	rs6002904	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	88	43	77	0	0.488636	0	G|0.332;C|0.668	0.668	strong	.	A4GALT	35	.	NM_017436	exon3	c.C903G	p.P301P	CTCCTCGGGGTTG	.	PASS	Atlas-SNP
TAS2R42	353164	hgsc.bcm.edu	37	12	11338750	11338750	+	Missense_Mutation	SNP	T	T	C	rs1451772	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	29	74	0	0.460317	0	C|0.238;N|0.001	0.238	strong	.	TAS2R42	30	.	NM_181429	exon1	c.A794G	p.Y265C	TTTATGTACTTGT	.	PASS	Atlas-SNP
GPR141	353345	hgsc.bcm.edu	37	7	37780799	37780799	+	Silent	SNP	C	C	A	rs61729279	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100	69	163	0	0.69	0	C|0.923;A|0.077	0.077	strong	.	GPR141	79	.	NM_181791	exon1	c.C804A	p.I268I	CGAAATCTTCTTG	.	PASS	Atlas-SNP
PRR3	80742	hgsc.bcm.edu	37	6	30530245	30530245	+	Silent	SNP	T	T	C	rs2074504	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60	60	79	0	1	0	T|0.274;C|0.726	0.726	strong	PRR3,NS,carcinoma,+2,1	PRR3	5	1	NM_025263	exon4	c.T540C	p.H180H	CTACCATCCAGGC	.	PASS	Atlas-SNP
TAF1L	138474	hgsc.bcm.edu	37	9	32632860	32632860	+	Silent	SNP	A	A	G	rs142256340	byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	344	181	380	1	0.526163	0.00263158	A|1.000;G|0.000	0.000	strong	.	TAF1L	382	.	NM_153809	exon1	c.T2718C	p.A906A	ATAATAAGCACAG	.	PASS	Atlas-SNP
OR2B2	81697	hgsc.bcm.edu	37	6	27879200	27879200	+	Missense_Mutation	SNP	C	C	A	rs34788973	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82	69	86	0	0.841463	0	C|0.943;A|0.057	0.057	strong	.	OR2B2	54	.	NM_033057	exon1	c.G898T	p.A300S	TAAAGGCTTCCTT	.	PASS	Atlas-SNP
STRN4	29888	hgsc.bcm.edu	37	19	47223949	47223949	+	Silent	SNP	G	G	A	rs313841	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	211	100	191	0	0.473934	0	G|0.913;N|0.000	.	strong	.	STRN4	33	.	NM_001039877	exon17	c.C2193T	p.H731H	CTCCTCGTGCTTC	.	PASS	Atlas-SNP
DNAH7	56171	hgsc.bcm.edu	37	2	196892695	196892695	+	Missense_Mutation	SNP	T	T	C	rs62203391	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100	50	106	0	0.5	0	T|0.949;C|0.051	0.051	strong	.	DNAH7	512	.	NM_018897	exon6	c.A475G	p.K159E	TGTCTTTCTCTAT	.	PASS	Atlas-SNP
SUN1	23353	hgsc.bcm.edu	37	7	897496	897496	+	Missense_Mutation	SNP	G	G	A	rs59910530	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	96	49	76	0	0.510417	0	G|0.839;A|0.161	0.161	strong	.	SUN1	157	.	NM_001130965	exon13	c.G1426A	p.E476K	ACAGTCGAGCACC	.	PASS	Atlas-SNP
SUSD5	26032	hgsc.bcm.edu	37	3	33194990	33194990	+	Missense_Mutation	SNP	C	C	A	rs6810039	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	165	165	172	0	1	0	C|0.374;A|0.626	0.626	strong	.	SUSD5	53	.	NM_015551	exon5	c.G1134T	p.E378D	AGCCCCCTCTGTC	.	PASS	Atlas-SNP
DNAH2	146754	hgsc.bcm.edu	37	17	7630505	7630505	+	Silent	SNP	T	T	C	rs11867551	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	220	106	221	1	0.481818	0.00452489	T|0.866;C|0.134	0.134	strong	.	DNAH2	498	.	NM_020877	exon3	c.T294C	p.H98H	GGAGCATGATGCC	.	PASS	Atlas-SNP
ZNF501	115560	hgsc.bcm.edu	37	3	44775962	44775962	+	Missense_Mutation	SNP	A	A	G	rs4682752	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83	46	85	0	0.554217	0	A|0.329;G|0.671	0.671	strong	.	ZNF501	27	.	NM_001258280	exon3	c.A49G	p.M17V	GTTAACATGCAGA	.	PASS	Atlas-SNP
IMMT	10989	hgsc.bcm.edu	37	2	86371883	86371883	+	Silent	SNP	T	T	C	rs8244	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	41	41	89	0	1	0	T|0.689;G|0.000;C|0.310;A|0.000	0.310	strong	IMMT,colon,carcinoma,-1,1	IMMT	65	1	NM_006839	exon15	c.A1785G	p.A595A	CTCAACTGCACTA	.	PASS	Atlas-SNP
HERC2	8924	hgsc.bcm.edu	37	15	28483809	28483809	+	Silent	SNP	G	G	A	rs149204675	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	275	5	328	3	0.0181818	0.00914634	G|0.998;A|0.002	0.002	strong	HERC2,NS,carcinoma,0,1	HERC2	501	1	NM_004667	exon24	c.C3687T	p.D1229D	CTTCCCGTCAATC	.	scavenged	Atlas-SNP
DKKL1	27120	hgsc.bcm.edu	37	19	49869051	49869051	+	Missense_Mutation	SNP	T	T	G	rs2303759	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83	42	79	0	0.506024	0	T|0.710;G|0.290	0.290	strong	.	DKKL1	23	.	NM_014419	exon4	c.T326G	p.M109R	CACAGATGACCGA	.	PASS	Atlas-SNP
FDXACB1	91893	hgsc.bcm.edu	37	11	111747297	111747297	+	Silent	SNP	A	A	G	rs7124696	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	121	105	117	0	0.867769	0	A|0.738;G|0.262	0.262	strong	.	FDXACB1	74	.	NM_138378	exon4	c.T600C	p.F200F	ACCTTCAAAAGGT	.	PASS	Atlas-SNP
ZNF600	162966	hgsc.bcm.edu	37	19	53269614	53269614	+	Silent	SNP	G	G	A	rs58262989	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	39	24	37	0	0.615385	0	G|0.962;A|0.038	0.038	strong	ZNF600,caecum,carcinoma,0,1	ZNF600	75	1	NM_198457	exon3	c.C1395T	p.T465T	CTCTCCGGTGTGA	.	PASS	Atlas-SNP
SSC5D	284297	hgsc.bcm.edu	37	19	56011279	56011279	+	Missense_Mutation	SNP	C	C	T	rs35651406	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48	26	40	0	0.541667	0	C|0.997;T|0.003	0.003	strong	.	SSC5D	65	.	NM_001195267	exon10	c.C1802T	p.A601V	AGCTGGCCACCAA	.	PASS	Atlas-SNP
DTNB	1838	hgsc.bcm.edu	37	2	25611102	25611102	+	Silent	SNP	G	G	A	rs200383554	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	36	22	45	0	0.611111	0	G|1.000;A|0.000	0.000	strong	.	DTNB	43	.	NM_021907	exon17	c.C1704T	p.V568V	TCCCCCGACTCCG	.	PASS	Atlas-SNP
TMEM200A	114801	hgsc.bcm.edu	37	6	130761804	130761804	+	Silent	SNP	C	C	T	rs12200105	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83	41	100	0	0.493976	0	C|0.743;T|0.257	0.257	strong	.	TMEM200A	108	.	NM_001258277	exon3	c.C237T	p.A79A	TATGGCCGTTCTT	.	PASS	Atlas-SNP
LIG4	3981	hgsc.bcm.edu	37	13	108862810	108862810	+	Silent	SNP	G	G	A	rs2232638	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72	14	103	0	0.194444	0	G|0.956;A|0.044	0.044	strong	.	LIG4	91	.	NM_206937	exon3	c.C807T	p.Y269Y	TTCTATGTAGAAA	.	PASS	Atlas-SNP
ZP3	7784	hgsc.bcm.edu	37	7	76062913	76062913	+	Missense_Mutation	SNP	C	C	G	rs139729790	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	59	26	74	0	0.440678	0	C|0.991;G|0.009	0.009	strong	ZP3_ENST00000394857,NS,lymphoid_neoplasm,0,2	ZP3	32	2	NM_001110354	exon4	c.C662G	p.P221R	CCACACCGACACC	.	PASS	Atlas-SNP
ZNF578	147660	hgsc.bcm.edu	37	19	53014851	53014851	+	Missense_Mutation	SNP	A	A	T	rs35720624	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	58	35	33	0	0.603448	0	A|0.992;T|0.008	0.008	strong	.	.	.	.	NM_001099694	exon6	c.A1217T	p.K406M	GTGGCAAGGCTTT	.	PASS	Atlas-SNP
JAK1	3716	hgsc.bcm.edu	37	1	65312343	65312343	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73	20	94	0	0.273973	0	.	.	none	JAK1,NS,malignant_melanoma,0,1	JAK1	209	1	NM_002227	exon14	c.G1976A	p.R659H	ACGTCGCGGACAC	.	PASS	Atlas-SNP
CYP2A13	1553	hgsc.bcm.edu	37	19	41594389	41594389	+	Missense_Mutation	SNP	G	G	T	rs71579358	alternate_allele	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	120	2	130	0	0.0166667	0	.	.	alt	CYP2A13,colon,carcinoma,-1,2	CYP2A13	90	2	NM_000766	exon1	c.G13T	p.G5W	GCCTCAGGGCTGC	.	scavenged	Atlas-SNP
ZNF354B	117608	hgsc.bcm.edu	37	5	178294060	178294060	+	Missense_Mutation	SNP	G	G	A	rs11955074	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	129	62	154	0	0.48062	0	G|0.854;A|0.146	0.146	strong	.	ZNF354B	67	.	NM_058230	exon4	c.G244A	p.V82I	TCTGGTGTCTCCT	.	PASS	Atlas-SNP
DNAH8	1769	hgsc.bcm.edu	37	6	38951998	38951998	+	Missense_Mutation	SNP	C	C	T	rs1537232	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	112	84	89	0	0.75	0	C|0.843;T|0.157	0.157	strong	.	DNAH8	1239	.	NM_001206927	exon87	c.C12968T	p.T4323M	GGAATACGGTTCG	.	PASS	Atlas-SNP
FSD1	79187	hgsc.bcm.edu	37	19	4306311	4306311	+	Silent	SNP	T	T	C	rs4807578	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48	48	51	0	1	0	T|0.402;C|0.598	0.598	strong	.	FSD1	51	.	NM_024333	exon3	c.T228C	p.R76R	CAGCCGTACCTAC	.	PASS	Atlas-SNP
OR5A1	219982	hgsc.bcm.edu	37	11	59210761	59210761	+	Silent	SNP	C	C	G	rs11605572	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	36	60	0	0.48	0	C|0.809;G|0.191	0.191	strong	OR5A1,right_upper_lobe,carcinoma,+1,1	OR5A1	72	1	NM_001004728	exon1	c.C120G	p.T40T	TCTTACCACCCTG	.	PASS	Atlas-SNP
NCOA3	8202	hgsc.bcm.edu	37	20	46279866	46279866	+	Silent	SNP	A	A	G	rs28529067	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60	31	54	0	0.516667	0	A|0.870;G|0.130	0.130	strong	NCOA3,colon,carcinoma,0,1	NCOA3	156	1	NM_181659	exon20	c.A3792G	p.Q1264Q	GCAGCAACAGCAA	.	PASS	Atlas-SNP
PTPN12	5782	hgsc.bcm.edu	37	7	77267956	77267956	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	101	47	128	0	0.465347	0	.	.	none	.	PTPN12	83	.	NM_002835	exon17	c.G2189A	p.G730D	CGGGAGGTATTCA	.	PASS	Atlas-SNP
RPAP1	26015	hgsc.bcm.edu	37	15	41813279	41813279	+	Silent	SNP	C	C	T	rs3743031	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	116	25	142	0	0.215517	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
PRDM8	56978	hgsc.bcm.edu	37	4	81124596	81124596	+	Silent	SNP	G	G	C	rs12780	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	105	56	98	0	0.533333	0	G|0.671;C|0.329	0.329	strong	PRDM8,colon,carcinoma,0,1	PRDM8	44	1	NM_001099403	exon4	c.G1980C	p.R660R	GAAGCGGCGGCGA	.	PASS	Atlas-SNP
WDFY4	57705	hgsc.bcm.edu	37	10	50025446	50025446	+	Missense_Mutation	SNP	G	G	T	rs12268007	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	40	17	42	0	0.425	0	G|0.836;T|0.164	0.164	strong	.	WDFY4	205	.	NM_020945	exon32	c.G5497T	p.A1833S	CTGGGAGCCCAAA	.	PASS	Atlas-SNP
NLRC5	84166	hgsc.bcm.edu	37	16	57060213	57060213	+	Missense_Mutation	SNP	C	C	T	rs9938543	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57	31	48	0	0.54386	0	C|0.891;T|0.109	0.109	strong	.	NLRC5	186	.	NM_032206	exon5	c.C1358T	p.P453L	ACTTGCCCACCTC	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9047267	9047267	+	Missense_Mutation	SNP	C	C	T	rs10410169	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85	46	93	0	0.541176	0	C|0.788;T|0.212	0.212	strong	.	MUC16	4315	.	NM_024690	exon5	c.G34364A	p.G11455D	GATGCACCAGGGG	.	PASS	Atlas-SNP
MATN2	4147	hgsc.bcm.edu	37	8	99045866	99045866	+	Missense_Mutation	SNP	G	G	A	rs17831160	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	109	50	90	0	0.458716	0	G|0.979;A|0.021	0.021	strong	.	MATN2	165	.	NM_002380	exon18	c.G2794A	p.V932I	GAAGAAGTAAGAA	.	PASS	Atlas-SNP
CBLB	868	hgsc.bcm.edu	37	3	105438957	105438957	+	Silent	SNP	T	T	G	rs2305036	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	147	72	150	0	0.489796	0	T|0.786;G|0.214	0.214	strong	.	CBLB	118	.	NM_170662	exon10	c.A1341C	p.L447L	CAAGTCTAGCATC	.	PASS	Atlas-SNP
PSG4	5672	hgsc.bcm.edu	37	19	43708245	43708245	+	Missense_Mutation	SNP	G	G	C	rs3170216	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	62	131	0	1	0	G|0.800;C|0.200	0.200	strong	.	PSG4	129	.	NM_002780	exon2	c.A223G	p.T75A	GGTAGAGGTATGT	.	PASS	Atlas-SNP
SIGLEC10	89790	hgsc.bcm.edu	37	19	51918135	51918135	+	Missense_Mutation	SNP	G	G	T	rs1833785	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82	44	89	0	0.536585	0	G|0.776;T|0.224	0.224	strong	.	SIGLEC10	112	.	NM_033130	exon8	c.C1558A	p.R520S	CACAGCGGAGCCT	.	PASS	Atlas-SNP
CYP3A4	1576	hgsc.bcm.edu	37	7	99358604	99358604	+	Silent	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	240	102	270	1	0.425	0.0037037	.	.	none	.	CYP3A4	56	.	NM_017460	exon12	c.A1254G	p.R418R	GCTGAATCTGGTT	.	PASS	Atlas-SNP
PRAMEF2	65122	hgsc.bcm.edu	37	1	12919872	12919872	+	Missense_Mutation	SNP	T	T	G	rs3204798	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	139	48	125	0	0.345324	0	T|0.947;G|0.053	0.053	strong	.	PRAMEF2	85	.	NM_023014	exon3	c.T612G	p.I204M	ATACATTAATAGT	.	PASS	Atlas-SNP
KBTBD12	166348	hgsc.bcm.edu	37	3	127703085	127703085	+	Silent	SNP	G	G	A	rs13100951	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	128	62	110	0	0.484375	0	G|0.771;A|0.229	0.229	strong	.	KBTBD12	41	.	NM_207335	exon5	c.G1836A	p.P612P	CCCCCCGCCTTCA	.	PASS	Atlas-SNP
ALMS1	7840	hgsc.bcm.edu	37	2	73677833	73677833	+	Silent	SNP	A	A	G	rs6546836	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	32	77	0	0.592593	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
LILRB3	11025	hgsc.bcm.edu	37	19	54724443	54724443	+	Missense_Mutation	SNP	G	G	A	rs201735825	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	39	30	46	0	0.769231	0	G|0.860;A|0.140	0.140	strong	.	LILRB3	67	.	NM_006864	exon6	c.C1213T	p.H405Y	GCAGGTGGGGGTT	.	PASS	Atlas-SNP
CHEK2	11200	hgsc.bcm.edu	37	22	29091840	29091840	+	Missense_Mutation	SNP	T	T	C	rs74751600		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	101	7	85	0	0.0693069	0	.	.	weak	CHEK2,NS,carcinoma,0,36	CHEK2	438	36	NM_001005735	exon12	c.A1246G	p.K416E	AAATCTTGGAGTG	.	scavenged	Atlas-SNP
SMARCA2	6595	hgsc.bcm.edu	37	9	2191309	2191309	+	Missense_Mutation	SNP	C	C	G	rs2296212	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	103	61	123	0	0.592233	0	C|0.831;G|0.169	0.169	strong	.	SMARCA2	313	.	NM_003070	exon33	c.C4638G	p.D1546E	AGATGACAAAGGC	.	PASS	Atlas-SNP
BEND7	222389	hgsc.bcm.edu	37	10	13481427	13481427	+	Silent	SNP	T	T	A	rs12415754	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	96	96	80	0	1	0	T|0.703;A|0.297	0.297	strong	.	BEND7	85	.	NM_152751	exon9	c.A1152T	p.S384S	CTGAGGTGAGCTC	.	PASS	Atlas-SNP
COL4A4	1286	hgsc.bcm.edu	37	2	227892619	227892619	+	Silent	SNP	C	C	T	rs2228556	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	31	15	17	0	0.483871	0	C|0.556;T|0.444	0.444	strong	.	COL4A4	215	.	NM_000092	exon42	c.G4080A	p.P1360P	CTCACCCGGAAGA	.	PASS	Atlas-SNP
DCBLD2	131566	hgsc.bcm.edu	37	3	98541116	98541116	+	Silent	SNP	G	G	A	rs828616	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	120	52	160	0	0.433333	0	G|0.593;A|0.407	0.407	strong	.	DCBLD2	62	.	NM_080927	exon6	c.C786T	p.I262I	ATAGGGGATACCT	.	PASS	Atlas-SNP
ABCA2	20	hgsc.bcm.edu	37	9	139904722	139904722	+	Silent	SNP	C	C	T	rs34125425	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	30	60	0	0.47619	0	C|0.984;T|0.016	0.016	strong	.	ABCA2	113	.	NM_212533	exon41	c.G6366A	p.A2122A	CTTGCCCGCACCG	.	PASS	Atlas-SNP
TTYH2	94015	hgsc.bcm.edu	37	17	72248512	72248512	+	Missense_Mutation	SNP	C	C	T	rs12600564	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	31	18	42	0	0.580645	0	C|0.907;T|0.093	0.093	strong	.	TTYH2	63	.	NM_032646	exon11	c.C1256T	p.T419I	TCACCACCAGGTG	.	PASS	Atlas-SNP
EPHA5	2044	hgsc.bcm.edu	37	4	66535284	66535284	+	Silent	SNP	G	G	A	rs55860557	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	131	75	144	0	0.572519	0	G|0.861;A|0.139	0.139	strong	EPHA5,brain,glioma,0,1	EPHA5	315	1	NM_004439	exon1	c.C177T	p.N59N	ACCTTCGTTGCTG	.	PASS	Atlas-SNP
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32634369	32634369	+	Missense_Mutation	SNP	C	C	A	rs1049056	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	8	5	15	0	0.625	0	C|0.811;A|0.189	0.189	strong	.	HLA-DQB1	15	.	NM_002123	exon1	c.G16T	p.A6S	GCAAAGCCTTCTT	.	PASS	Atlas-SNP
VWA8	23078	hgsc.bcm.edu	37	13	42442546	42442546	+	Missense_Mutation	SNP	A	A	G	rs3742262	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	263	186	175	0	0.707224	0	A|0.760;G|0.240	0.240	strong	.	.	.	.	NM_015058	exon10	c.T1148C	p.M383T	TTTTCCATCATCT	.	PASS	Atlas-SNP
ZNF717	100131827	hgsc.bcm.edu	37	3	75790797	75790797	+	Missense_Mutation	SNP	C	C	T	rs147946451	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	27	4	28	0	0.148148	0	C|0.753;T|0.247	0.247	strong	ZNF717,NS,malignant_melanoma,0,1	ZNF717	160	1	NM_001128223	exon3	c.G148A	p.V50M	GCATCACGTCCCT	.	scavenged	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9083174	9083174	+	Missense_Mutation	SNP	G	G	A	rs7245960	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	181	87	149	0	0.480663	0	G|0.757;A|0.243	0.243	strong	.	MUC16	4315	.	NM_024690	exon1	c.C8641T	p.P2881S	AAGTTGGGGGAGC	.	PASS	Atlas-SNP
P4HA2	8974	hgsc.bcm.edu	37	5	131539462	131539462	+	Silent	SNP	T	T	C	rs144253110	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	136	64	118	0	0.470588	0	T|0.999;C|0.001	0.001	strong	.	P4HA2	72	.	NM_001017974	exon10	c.A1230G	p.V410V	AGTCTTTACTGTT	.	PASS	Atlas-SNP
CXorf64	100130613	hgsc.bcm.edu	37	X	125954964	125954964	+	Missense_Mutation	SNP	C	C	G	rs12835991	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	89	61	67	0	0.685393	0	C|0.945;G|0.055	0.055	strong	.	.	.	.	NM_001122716	exon2	c.C343G	p.L115V	GATGCACTGGCAG	.	PASS	Atlas-SNP
LRP6	4040	hgsc.bcm.edu	37	12	12334006	12334006	+	Silent	SNP	G	G	C	rs10082834	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68	36	62	0	0.529412	0	G|0.935;C|0.065	0.065	strong	.	LRP6	170	.	NM_002336	exon6	c.C1344G	p.P448P	AGCCCGGGGTTCC	.	PASS	Atlas-SNP
FRMD3	257019	hgsc.bcm.edu	37	9	85863091	85863091	+	Silent	SNP	A	A	G	rs10114696	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	52	55	0	1	0	A|0.685;G|0.315	0.315	strong	.	FRMD3	96	.	NM_174938	exon14	c.T1536C	p.Y512Y	AATGTCATAGCTC	.	PASS	Atlas-SNP
ROS1	6098	hgsc.bcm.edu	37	6	117683821	117683821	+	Missense_Mutation	SNP	G	G	A	rs2229079	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94	42	95	0	0.446809	0	G|0.939;A|0.061	0.061	strong	.	ROS1	728	.	NM_002944	exon21	c.C3326T	p.S1109L	ATCACTGAGGGAG	.	PASS	Atlas-SNP
LTBP1	4052	hgsc.bcm.edu	37	2	33172827	33172827	+	Missense_Mutation	SNP	G	G	A	rs147166401	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	39	84	0	0.58209	0	G|0.992;A|0.008	0.008	strong	.	LTBP1	317	.	NM_206943	exon1	c.G436A	p.E146K	CCGCAGGAGACCC	.	PASS	Atlas-SNP
TOPORS	10210	hgsc.bcm.edu	37	9	32541532	32541532	+	Silent	SNP	A	A	G	rs12348918	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	113	44	113	0	0.389381	0	A|0.832;G|0.168	0.168	strong	TOPORS_ENST00000360538,NS,carcinoma,0,2	TOPORS	127	2	NM_005802	exon3	c.T2991C	p.D997D	TCTTACATCGAGA	.	PASS	Atlas-SNP
C6orf15	29113	hgsc.bcm.edu	37	6	31079371	31079371	+	Silent	SNP	C	C	G	rs2233983	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	128	18	106	0	0.140625	0	C|0.932;G|0.068	0.068	strong	.	C6orf15	29	.	NM_014070	exon2	c.G765C	p.R255R	TGGATACCGATTA	.	PASS	Atlas-SNP
ICAM5	7087	hgsc.bcm.edu	37	19	10403368	10403368	+	Missense_Mutation	SNP	G	G	A	rs2228615	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110	55	97	0	0.5	0	G|0.713;A|0.287	0.287	strong	.	ICAM5	53	.	NM_003259	exon5	c.G1042A	p.A348T	GCTGGGGCCCAAG	.	PASS	Atlas-SNP
GLRA4	441509	hgsc.bcm.edu	37	X	102974119	102974119	+	Silent	SNP	G	G	A	rs41300882	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	196	141	128	0	0.719388	0	G|0.995;A|0.005	0.005	strong	.	GLRA4	86	.	NM_001024452	exon7	c.C799T	p.L267L	TGAGTAGGCTGGG	.	PASS	Atlas-SNP
EVPLL	645027	hgsc.bcm.edu	37	17	18291559	18291559	+	Silent	SNP	T	T	C	rs9890369	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	256	138	309	0	0.539062	0	T|0.770;C|0.230	0.230	strong	EVPLL,NS,NS,+2,1	EVPLL	10	1	NM_001145127	exon10	c.T903C	p.H301H	TCCTCATTGACTC	.	PASS	Atlas-SNP
PER2	8864	hgsc.bcm.edu	37	2	239165636	239165636	+	Silent	SNP	C	C	T	rs2304670	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	30	73	0	0.4	0	C|0.913;T|0.087	0.087	strong	.	PER2	85	.	NM_022817	exon17	c.G1992A	p.A664A	GAGCGACGCCACA	.	PASS	Atlas-SNP
SERPINA6	866	hgsc.bcm.edu	37	14	94772429	94772429	+	Silent	SNP	G	G	A	rs2228543	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	90	43	86	0	0.477778	0	G|0.677;T|0.043	.	strong	SERPINA6_ENST00000341584,NS,carcinoma,-2,2	SERPINA6	102	2	NM_001756	exon4	c.C1011T	p.D337D	CTGGGCGTCCTGG	.	PASS	Atlas-SNP
CDH23	64072	hgsc.bcm.edu	37	10	73562744	73562744	+	Silent	SNP	G	G	A	rs10823849	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93	54	138	1	0.580645	0.00724638	G|0.681;A|0.319	0.319	strong	CDH23,NS,carcinoma,0,1	CDH23	365	1	NM_022124	exon52	c.G7572A	p.A2524A	GCCGGCGGGCACC	.	scavenged	Atlas-SNP
CFH	3075	hgsc.bcm.edu	37	1	196695742	196695742	+	Silent	SNP	A	A	G	rs3753396	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	128	67	146	0	0.523438	0	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
C20orf26	26074	hgsc.bcm.edu	37	20	20257958	20257958	+	Silent	SNP	C	C	T	rs2424317	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	20	60	0	0.425532	0	C|0.824;T|0.176	0.176	strong	.	C20orf26	188	.	NM_015585	exon22	c.C2652T	p.S884S	GGAGAGCGCCGTG	.	PASS	Atlas-SNP
BTBD10	84280	hgsc.bcm.edu	37	11	13441126	13441126	+	Silent	SNP	A	A	G	rs7114113	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	171	85	121	0	0.497076	0	A|0.855;G|0.145	0.145	strong	.	BTBD10	43	.	NM_032320	exon4	c.T465C	p.N155N	TTTTGCATTTTCA	.	PASS	Atlas-SNP
NDUFS2	4720	hgsc.bcm.edu	37	1	161182208	161182208	+	Missense_Mutation	SNP	C	C	G	rs11576415	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	43	20	42	0	0.465116	0	C|0.937;G|0.063	0.063	strong	NDUFS2,lymph_node,lymphoid_neoplasm,0,1	NDUFS2	33	1	NM_001166159	exon10	c.C1054G	p.P352A	AAGATGCCTCCTG	.	PASS	Atlas-SNP
TEX15	56154	hgsc.bcm.edu	37	8	30702525	30702525	+	Missense_Mutation	SNP	A	A	C	rs323344	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	123	66	128	0	0.536585	0	A|0.701;C|0.299	0.299	strong	.	TEX15	350	.	NM_031271	exon1	c.T4009G	p.L1337V	CTGATAACTGAGG	.	PASS	Atlas-SNP
SERPINB10	5273	hgsc.bcm.edu	37	18	61587067	61587067	+	Missense_Mutation	SNP	C	C	T	rs9967382	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69	38	50	0	0.550725	0	C|0.604;N|0.000	.	strong	.	SERPINB10	53	.	NM_005024	exon4	c.C418T	p.P140S	CCTCAGCCTGTTA	.	PASS	Atlas-SNP
CEP192	55125	hgsc.bcm.edu	37	18	13069782	13069782	+	Missense_Mutation	SNP	C	C	T	rs6505780	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	22	57	0	0.423077	0	C|0.258;T|0.742	0.742	strong	.	CEP192	340	.	NM_032142	exon27	c.C5101T	p.L1701F	AATCTACTCCTTA	.	PASS	Atlas-SNP
RCN3	57333	hgsc.bcm.edu	37	19	50046365	50046365	+	Silent	SNP	T	T	C	rs3187346	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	130	66	127	0	0.507692	0	T|0.895;C|0.105	0.105	strong	.	RCN3	28	.	NM_020650	exon7	c.T882C	p.D294D	CCAGGATGGGCGG	.	PASS	Atlas-SNP
WARS2	10352	hgsc.bcm.edu	37	1	119584949	119584949	+	Silent	SNP	G	G	A	rs33960696	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	121	56	133	0	0.46281	0	G|0.937;A|0.063	0.063	strong	.	WARS2	69	.	NM_015836	exon4	c.C453T	p.H151H	GCCATCGTGCTTC	.	PASS	Atlas-SNP
ZFP64	55734	hgsc.bcm.edu	37	20	50803573	50803573	+	Silent	SNP	G	G	A	rs34351592	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	70	31	68	0	0.442857	0	G|0.864;A|0.136	0.136	strong	.	ZFP64	240	.	NM_018197	exon2	c.C84T	p.P28P	GATGTCGGGAGTC	.	PASS	Atlas-SNP
RANBP2	5903	hgsc.bcm.edu	37	2	109371498	109371498	+	Silent	SNP	G	G	A	rs373469365	alternate_allele	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	276	5	241	2	0.0181159	0.00829876	.	.	alt	RANBP2_ENST00000283195,NS,carcinoma,0,2	RANBP2	488	2	NM_006267	exon16	c.G2340A	p.P780P	TACACCGTCTCCT	.	scavenged	Atlas-SNP
TUB	7275	hgsc.bcm.edu	37	11	8119298	8119298	+	Missense_Mutation	SNP	A	A	G	rs55892969	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	106	59	112	0	0.556604	0	A|0.983;G|0.017	0.017	strong	.	TUB	71	.	NM_003320	exon9	c.A1088G	p.K363R	AGAGTAAAACTTC	.	PASS	Atlas-SNP
UNC13B	10497	hgsc.bcm.edu	37	9	35399243	35399243	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	186	8	223	0	0.0430108	0	.	.	none	.	UNC13B	153	.	NM_006377	exon33	c.G3913A	p.E1305K	ACAATGGAGAGGA	.	PASS	Atlas-SNP
OR13C5	138799	hgsc.bcm.edu	37	9	107361129	107361129	+	Missense_Mutation	SNP	C	C	T	rs4117966	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	270	122	271	1	0.451852	0.00369004	C|0.726;T|0.274	0.274	strong	.	OR13C5	60	.	NM_001004482	exon1	c.G566A	p.C189Y	TCAGCACAGGCCA	.	PASS	Atlas-SNP
TXN2	25828	hgsc.bcm.edu	37	22	36872873	36872873	+	Silent	SNP	C	C	T	rs150502647	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	138	67	120	0	0.485507	0	C|0.993;T|0.007	0.007	strong	.	TXN2	15	.	NM_012473	exon3	c.G294A	p.P98P	TAACCTCGGCCCC	.	PASS	Atlas-SNP
KIAA1614	57710	hgsc.bcm.edu	37	1	180905448	180905448	+	Missense_Mutation	SNP	G	G	T	rs3795504	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	37	96	0	0.45679	0	G|0.614;T|0.386	0.386	strong	.	KIAA1614	75	.	NM_020950	exon5	c.G2403T	p.L801F	TTCCTTGTGTCCT	.	PASS	Atlas-SNP
C19orf10	56005	hgsc.bcm.edu	37	19	4670236	4670236	+	Silent	SNP	C	C	G	rs10401515	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	15	10	27	0	0.666667	0	C|0.891;G|0.109	0.109	strong	.	C19orf10	9	.	NM_019107	exon1	c.G111C	p.T37T	CGCCACCGTCGTG	.	PASS	Atlas-SNP
CHDH	55349	hgsc.bcm.edu	37	3	53856653	53856653	+	Silent	SNP	C	C	T	rs2241808	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83	39	64	0	0.46988	0	C|0.555;T|0.444	0.444	strong	CHDH,colon,carcinoma,-2,1	CHDH	34	1	NM_018397	exon4	c.G720A	p.A240A	ACAGGCCGCGCTC	.	PASS	Atlas-SNP
KDM6A	7403	hgsc.bcm.edu	37	X	44938563	44938563	+	Silent	SNP	G	G	A	rs20539	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	279	85	216	0	0.304659	0	0|0.018;A|0.156	0.156	strong	.	KDM6A	274	.	NM_021140	exon20	c.G3111A	p.Q1037Q	TGCACAGTACCAG	.	PASS	Atlas-SNP
NBEAL2	23218	hgsc.bcm.edu	37	3	47045846	47045846	+	Missense_Mutation	SNP	C	C	T	rs2305637	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	70	37	64	0	0.528571	0	C|0.844;T|0.156	0.156	strong	.	NBEAL2	267	.	NM_015175	exon37	c.C6161T	p.S2054F	GCCGCTCCCCCCA	.	PASS	Atlas-SNP
EXOG	9941	hgsc.bcm.edu	37	3	38565576	38565576	+	Missense_Mutation	SNP	G	G	T	rs1141223	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	108	39	103	0	0.361111	0	G|0.993;T|0.007	0.007	strong	.	EXOG	29	.	NM_005107	exon6	c.G830T	p.G277V	TGTCAGGACTGGT	.	PASS	Atlas-SNP
HOMER3	9454	hgsc.bcm.edu	37	19	19049194	19049194	+	Silent	SNP	G	G	A	rs11540741	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	113	49	117	0	0.433628	0	G|0.895;A|0.105	0.105	strong	.	HOMER3	19	.	NM_001145722	exon4	c.C271T	p.L91L	AGCCCAGGCCGTA	.	PASS	Atlas-SNP
SLC28A1	9154	hgsc.bcm.edu	37	15	85447431	85447431	+	Missense_Mutation	SNP	G	G	A	rs2290272	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98	49	106	0	0.5	0	G|0.674;A|0.326	0.326	strong	SLC28A1,NS,carcinoma,0,1	SLC28A1	118	1	NM_004213	exon7	c.G565A	p.V189I	GTGTTCGTCGCTC	.	PASS	Atlas-SNP
RIF1	55183	hgsc.bcm.edu	37	2	152314385	152314385	+	Silent	SNP	G	G	A	rs16830047	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	18	124	0	0.268657	0	G|0.749;A|0.251	0.251	strong	.	RIF1	244	.	NM_018151	exon24	c.G2763A	p.L921L	ATTTCTGCACAAG	.	PASS	Atlas-SNP
YBX1	4904	hgsc.bcm.edu	37	1	43166630	43166630	+	Missense_Mutation	SNP	G	G	A	rs200741644		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	122	17	119	0	0.139344	0	G|0.998;A|0.002	0.002	weak	YBX1,mouth,carcinoma,0,1	YBX1	49	1	NM_004559	exon7	c.G919A	p.D307N	GCAGCCGATCCAC	.	scavenged	Atlas-SNP
KIAA0753	9851	hgsc.bcm.edu	37	17	6513329	6513329	+	Missense_Mutation	SNP	G	G	A	rs2304977	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	203	92	190	0	0.453202	0	G|0.714;A|0.286	0.286	strong	.	KIAA0753	63	.	NM_014804	exon9	c.C1697T	p.P566L	GACGCTGGTGGGG	.	PASS	Atlas-SNP
PRKCQ	5588	hgsc.bcm.edu	37	10	6527143	6527143	+	Missense_Mutation	SNP	G	G	A	rs2236379	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	36	15	37	0	0.416667	0	G|0.675;T|0.002	.	strong	PRKCQ,NS,carcinoma,0,1	PRKCQ	113	1	NM_006257	exon10	c.C989T	p.P330L	CATGGCGGCCTTG	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	197	75	115	0	0.380711	0	A|0.246;G|0.754	0.754	strong	.	KRTAP12-3	18	.	NM_198697	exon1	c.A50G	p.H17R	GCATACACAGCCC	.	PASS	Atlas-SNP
C1orf101	257044	hgsc.bcm.edu	37	1	244715966	244715966	+	Silent	SNP	G	G	A	rs35587664	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	144	59	159	0	0.409722	0	G|0.880;A|0.120	0.120	strong	.	C1orf101	158	.	NM_173807	exon9	c.G879A	p.S293S	CTTATCGCGGGAT	.	PASS	Atlas-SNP
EPHA1	2041	hgsc.bcm.edu	37	7	143097100	143097100	+	Missense_Mutation	SNP	A	A	G	rs4725617	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	88	88	90	0	1	0	A|0.081;G|0.919	0.919	strong	.	EPHA1	193	.	NM_005232	exon4	c.T479C	p.V160A	CCAGACACAAGGT	.	PASS	Atlas-SNP
UBXN6	80700	hgsc.bcm.edu	37	19	4454083	4454083	+	Missense_Mutation	SNP	C	C	T	rs1127888	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	29	13	28	0	0.448276	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
MOV10L1	54456	hgsc.bcm.edu	37	22	50538028	50538028	+	Missense_Mutation	SNP	G	G	A	rs146380250	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	113	3	111	0	0.0265487	0	G|1.000;A|0.000	0.000	strong	MOV10L1_ENST00000540615,NS,malignant_melanoma,0,2	MOV10L1	238	2	NM_018995	exon3	c.G439A	p.E147K	GTGTGCGAAGGTA	.	scavenged	Atlas-SNP
LRRC4C	57689	hgsc.bcm.edu	37	11	40137543	40137543	+	Silent	SNP	T	T	C	rs2953310	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	149	64	146	1	0.42953	0.00684932	T|0.478;C|0.522	0.522	strong	LRRC4C,NS,carcinoma,0,1	LRRC4C	190	1	NM_001258419	exon7	c.A300G	p.R100R	CAAGTGTCTCAAG	.	scavenged	Atlas-SNP
OR10G9	219870	hgsc.bcm.edu	37	11	123893757	123893757	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	239	25	199	0	0.104603	0	.	.	none	OR10G9,NS,carcinoma,0,2	OR10G9	80	2	NM_001001953	exon1	c.C38T	p.T13M	TCCTCACGGGCCT	.	scavenged	Atlas-SNP
TAS2R43	259289	hgsc.bcm.edu	37	12	11244199	11244199	+	Missense_Mutation	SNP	C	C	G	rs201245949	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	103	12	26	0	0.116505	0	C|0.994;G|0.006	0.006	strong	.	TAS2R43	19	.	NM_176884	exon1	c.G630C	p.Q210H	ATGGAGCTGCATC	.	PASS	Atlas-SNP
MCTP1	79772	hgsc.bcm.edu	37	5	94050487	94050487	+	Silent	SNP	T	T	A	rs2636	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	47	70	0	1	0	T|0.597;N|0.000	.	strong	.	MCTP1	110	.	NM_024717	exon20	c.A2715T	p.I905I	CTTCTTTATCCTT	.	PASS	Atlas-SNP
CYP4F2	8529	hgsc.bcm.edu	37	19	15996820	15996820	+	Silent	SNP	G	G	A	rs2074900	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	101	53	78	0	0.524752	0	G|0.734;A|0.266	0.266	strong	.	CYP4F2	97	.	NM_001082	exon9	c.C1029T	p.H343H	TGCAAGGTGGTAC	.	PASS	Atlas-SNP
KRT76	51350	hgsc.bcm.edu	37	12	53165949	53165949	+	Missense_Mutation	SNP	C	C	T	rs12296548	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	136	67	176	0	0.492647	0	C|0.889;T|0.111	0.111	strong	.	KRT76	72	.	NM_015848	exon5	c.G1066A	p.E356K	GGACCTCGGCAAT	.	PASS	Atlas-SNP
SLC13A3	64849	hgsc.bcm.edu	37	20	45242269	45242269	+	Silent	SNP	G	G	C	rs2273024	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	107	50	140	0	0.46729	0	G|0.680;C|0.320	0.320	strong	.	SLC13A3	88	.	NM_022829	exon2	c.C207G	p.L69L	GGGGAAGAGGACG	.	PASS	Atlas-SNP
SPRR3	6707	hgsc.bcm.edu	37	1	152975763	152975763	+	Silent	SNP	C	C	A	rs1977734	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69	24	76	0	0.347826	0	T|0.000;C|0.476;A|0.524	0.524	strong	.	SPRR3	45	.	NM_001097589	exon2	c.C267A	p.G89G	GCCAGGCTGTACC	.	PASS	Atlas-SNP
IVL	3713	hgsc.bcm.edu	37	1	152882979	152882979	+	Missense_Mutation	SNP	C	C	T	rs17855670	by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51	8	40	0	0.156863	0	C|0.943;T|0.057	0.057	strong	IVL,colon,carcinoma,0,2	IVL	100	2	NM_005547	exon2	c.C706T	p.P236S	GAGCTCCCACAGC	.	PASS	Atlas-SNP
MYCBP2	23077	hgsc.bcm.edu	37	13	77738664	77738664	+	Silent	SNP	A	A	G	rs2274547	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	134	50	96	0	0.373134	0	A|0.832;G|0.168	0.168	strong	.	MYCBP2	1029	.	NM_015057	exon43	c.T6472C	p.L2158L	TTTCCAATTGGAT	.	PASS	Atlas-SNP
DCAF8L2	347442	hgsc.bcm.edu	37	X	27766045	27766045	+	Missense_Mutation	SNP	A	A	G	rs5926895	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	130	93	92	0	0.715385	0	A|0.784;0|0.046	.	strong	.	DCAF8L2	79	.	NM_001136533	exon1	c.A1033G	p.T345A	GTCTTCACCATTG	.	PASS	Atlas-SNP
KIF13B	23303	hgsc.bcm.edu	37	8	29033628	29033628	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	3	81	0	0.0491803	0	.	.	none	KIF13B_ENST00000524189,colon,carcinoma,+1,2	KIF13B	192	2	NM_015254	exon10	c.A902C	p.K301T	ACAAATTTATTCT	.	scavenged	Atlas-SNP
DIS3	22894	hgsc.bcm.edu	37	13	73340177	73340177	+	Missense_Mutation	SNP	G	G	A	rs35017269	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	25	15	23	0	0.6	0	G|0.989;A|0.011	0.011	strong	.	DIS3	103	.	NM_014953	exon15	c.C1903T	p.P635S	CTTCAGGAGAGGA	.	PASS	Atlas-SNP
TRIM31	11074	hgsc.bcm.edu	37	6	30078275	30078275	+	Missense_Mutation	SNP	C	C	T	rs2523989	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	130	103	157	1	0.792308	0.00636943	C|0.898;T|0.102	0.102	strong	.	TRIM31	40	.	NM_007028	exon4	c.G694A	p.V232I	AATCAACGAGCTT	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	75	87	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
ABCC4	10257	hgsc.bcm.edu	37	13	95696540	95696540	+	Silent	SNP	C	C	T	rs11568695	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	126	72	95	0	0.571429	0	C|0.950;T|0.050	0.050	strong	ABCC4_ENST00000376887,colon,carcinoma,-1,2	ABCC4	248	2	NM_005845	exon28	c.G3609A	p.A1203A	TGCCGTCGCTTCA	.	PASS	Atlas-SNP
MYH2	4620	hgsc.bcm.edu	37	17	10450816	10450816	+	Silent	SNP	T	T	C	rs12600539	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	242	119	238	1	0.491736	0.00420168	T|0.540;C|0.460	0.460	strong	MYH2,NS,carcinoma,-2,1	MYH2	390	1	NM_017534	exon4	c.A324G	p.E108E	ATAACGTTCTTTG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195505742	195505742	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	5	89	5	0.0675676	0.0561798	.	.	none	MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	NM_018406	exon2	c.C12709G	p.H4237D	TGGCGTGACCTGT	.	scavenged	Atlas-SNP
OR1S1	219959	hgsc.bcm.edu	37	11	57982620	57982620	+	Missense_Mutation	SNP	A	A	G	rs1966834	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	189	188	225	0	0.994709	0	A|0.569;G|0.431	0.431	strong	.	OR1S1	139	.	NM_001004458	exon1	c.A404G	p.H135R	ATGACCACTTTGT	.	PASS	Atlas-SNP
ANKRD30B	374860	hgsc.bcm.edu	37	18	14752601	14752601	+	Silent	SNP	A	A	G	rs200428778	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	25	58	0	0.471698	0	A|0.992;G|0.008	0.008	strong	ANKRD30B_ENST00000358984,NS,carcinoma,+2,2	ANKRD30B	237	2	NM_001145029	exon2	c.A258G	p.A86A	CCATGCAGAAGTA	.	PASS	Atlas-SNP
MAPT	4137	hgsc.bcm.edu	37	17	44067400	44067400	+	Missense_Mutation	SNP	T	T	C	rs10445337	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	65	65	66	0	1	0	T|0.856;C|0.144	0.144	strong	.	MAPT	135	.	NM_001123066	exon8	c.T1339C	p.S447P	GTCACTTCCCGAA	.	PASS	Atlas-SNP
BCAS1	8537	hgsc.bcm.edu	37	20	52573971	52573971	+	Missense_Mutation	SNP	T	T	G	rs35575210	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	181	84	178	0	0.464088	0	T|0.857;G|0.143	0.143	strong	.	BCAS1	77	.	NM_003657	exon10	c.A1416C	p.Q472H	ACTTACTTGGCAG	.	PASS	Atlas-SNP
IL3	3562	hgsc.bcm.edu	37	5	131396478	131396478	+	Missense_Mutation	SNP	C	C	T	rs40401	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	36	86	0	0.473684	0	C|0.616;N|0.000	.	strong	IL3,NS,carcinoma,0,1	IL3	28	1	NM_000588	exon1	c.C79T	p.P27S	ACAACGCCCTTGA	.	PASS	Atlas-SNP
ZNF83	55769	hgsc.bcm.edu	37	19	53117017	53117017	+	Silent	SNP	T	T	G	rs7248435	bycluster;byfrequency;byhapmap	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	18	7	43	0	0.388889	0	T|0.881;G|0.119	0.119	strong	.	ZNF83	73	.	NM_018300	exon3	c.A801C	p.G267G	GACCTTTCCACAT	.	PASS	Atlas-SNP
TBCK	93627	hgsc.bcm.edu	37	4	107156462	107156462	+	Missense_Mutation	SNP	C	C	T	rs34961213	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	27	59	0	0.442623	0	C|0.876;T|0.124	0.124	strong	.	TBCK	89	.	NM_001163436	exon15	c.G1413A	p.M471I	ACCTCTCATAAGA	.	PASS	Atlas-SNP
GOLGA6L1	283767	hgsc.bcm.edu	37	15	22743249	22743249	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	26	2	32	0	0.0769231	0	.	.	none	GOLGA6L1,caecum,carcinoma,0,1	GOLGA6L1	20	1	NM_001001413	exon8	c.T1634A	p.M545K	AGGAGATGATGCA	.	scavenged	Atlas-SNP
OR8B4	283162	hgsc.bcm.edu	37	11	124294236	124294236	+	Missense_Mutation	SNP	A	A	G	rs4057749	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	96	85	105	0	0.885417	0	A|0.720;G|0.280	0.280	strong	.	OR8B4	60	.	NM_001005196	exon1	c.T532C	p.C178R	CGTCACACAGATA	.	PASS	Atlas-SNP
NID2	22795	hgsc.bcm.edu	37	14	52520746	52520746	+	Missense_Mutation	SNP	G	G	T	rs35657569	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	99	56	76	0	0.565657	0	G|0.939;T|0.061	0.061	strong	.	NID2	201	.	NM_007361	exon4	c.C1061A	p.P354H	TCTAAAGGCTTTG	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29911271	29911271	+	Missense_Mutation	SNP	G	G	C	rs3098019	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100	54	124	0	0.54	0	C|0.644;G|0.356	0.644	strong	HLA-A,colon,carcinoma,0,1	HLA-A	89	1	NM_001242758	exon3	c.G570C	p.E190D	CGTGGAGTGGCTC	.	PASS	Atlas-SNP
AQP8	343	hgsc.bcm.edu	37	16	25239805	25239805	+	Missense_Mutation	SNP	G	G	C	rs2287798	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	34	85	0	0.515152	0	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	.	PASS	Atlas-SNP
OR52E4	390081	hgsc.bcm.edu	37	11	5906143	5906143	+	Silent	SNP	T	T	C	rs11823809	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	288	140	268	0	0.486111	0	T|0.611;C|0.389	0.389	strong	.	OR52E4	65	.	NM_001005165	exon1	c.T621C	p.Y207Y	TTCTTATATTATT	.	PASS	Atlas-SNP
KLHL40	131377	hgsc.bcm.edu	37	3	42728144	42728144	+	Missense_Mutation	SNP	A	A	G	rs6805421	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	121	121	123	0	1	0	A|0.408;G|0.592	0.592	strong	KBTBD5,colon,carcinoma,0,2	.	.	2	NM_152393	exon1	c.A1034G	p.N345S	TCTCCAACCAGGT	.	PASS	Atlas-SNP
LCTL	197021	hgsc.bcm.edu	37	15	66850362	66850362	+	Missense_Mutation	SNP	C	C	T	rs1030986	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	106	48	110	0	0.45283	0	C|0.963;T|0.037	0.037	strong	.	LCTL	73	.	NM_207338	exon7	c.G718A	p.A240T	GCCAGGCTTTGGC	.	PASS	Atlas-SNP
CBFA2T2	9139	hgsc.bcm.edu	37	20	32212690	32212690	+	Silent	SNP	C	C	T	rs3803939	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	102	43	92	0	0.421569	0	T|0.624;G|0.002;C|0.371;N|0.000;A|0.003	0.624	strong	CBFA2T2,NS,carcinoma,0,1	CBFA2T2	93	1	NM_005093	exon7	c.C840T	p.P280P	GAATCCCGGGGGC	.	PASS	Atlas-SNP
GOLGA7	51125	hgsc.bcm.edu	37	8	41355096	41355096	+	Silent	SNP	C	C	T	rs17656952	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44	21	34	0	0.477273	0	C|0.876;T|0.124	0.124	strong	.	GOLGA7	10	.	NM_001002296	exon2	c.C180T	p.L60L	GAAGCTCGGCGGC	.	PASS	Atlas-SNP
COL4A4	1286	hgsc.bcm.edu	37	2	227896976	227896976	+	Silent	SNP	C	C	T	rs10203363	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	58	21	73	0	0.362069	0	C|0.544;T|0.456	0.456	strong	.	COL4A4	215	.	NM_000092	exon39	c.G3594A	p.G1198G	AGGTGGCCCCACA	.	PASS	Atlas-SNP
CYP1B1	1545	hgsc.bcm.edu	37	2	38298203	38298203	+	Missense_Mutation	SNP	C	C	G	rs1056836	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	108	108	164	0	1	0	C|0.487;G|0.513	0.513	strong	CYP1B1,caecum,carcinoma,0,1	CYP1B1	39	1	NM_000104	exon3	c.G1294C	p.V432L	ACTTCACTGGGTC	.	PASS	Atlas-SNP
ARSG	22901	hgsc.bcm.edu	37	17	66364691	66364691	+	Missense_Mutation	SNP	C	C	G	rs1558876	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55	36	66	0	0.654545	0	C|0.673;G|0.327	0.327	strong	.	ARSG	55	.	NM_001267727	exon7	c.C707G	p.T236S	TCAGCACCAGCGG	.	PASS	Atlas-SNP
SUV39H1	6839	hgsc.bcm.edu	37	X	48558888	48558888	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94	52	86	0	0.553191	0	.	.	none	.	SUV39H1	36	.	NM_003173	exon3	c.C572T	p.T191I	CACCCACTGGAGG	.	PASS	Atlas-SNP
CEP112	201134	hgsc.bcm.edu	37	17	64023642	64023642	+	Silent	SNP	A	A	G	rs11079628	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	143	143	170	0	1	0	A|0.561;G|0.439	0.439	strong	.	CEP112	192	.	NM_001199165	exon16	c.T1633C	p.L545L	GTTTTAAATGACT	.	PASS	Atlas-SNP
PCNXL4	64430	hgsc.bcm.edu	37	14	60585131	60585131	+	Missense_Mutation	SNP	A	A	G	rs308998	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	222	220	185	0	0.990991	0	A|0.702;G|0.298	0.298	strong	.	.	.	.	NM_022495	exon6	c.A961G	p.K321E	ACAGAGAAAAAAC	.	PASS	Atlas-SNP
PLCB2	5330	hgsc.bcm.edu	37	15	40589002	40589002	+	Silent	SNP	A	A	G	rs2229691	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	33	33	48	0	1	0	A|0.697;G|0.303	0.303	strong	.	PLCB2	177	.	NM_004573	exon14	c.T1431C	p.T477T	CCCACCAGTATCC	.	PASS	Atlas-SNP
SEC22C	9117	hgsc.bcm.edu	37	3	42610374	42610374	+	Silent	SNP	A	A	G	rs2271186	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	116	50	109	0	0.431034	0	A|0.520;G|0.480	0.480	strong	.	SEC22C	27	.	NM_001201584	exon2	c.T165C	p.G55G	GTCACAACCTTCT	.	PASS	Atlas-SNP
ADAM23	8745	hgsc.bcm.edu	37	2	207459467	207459467	+	Silent	SNP	C	C	T	rs3732079	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	195	99	189	0	0.507692	0	C|0.856;G|0.000;T|0.144	0.144	strong	ADAM23,NS,carcinoma,0,1	ADAM23	239	1	NM_003812	exon23	c.C2085T	p.A695A	TGGTGCCCATGTA	.	PASS	Atlas-SNP
FDFT1	2222	hgsc.bcm.edu	37	8	11667179	11667179	+	Silent	SNP	C	C	T	rs8417	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72	37	84	0	0.513889	0	C|0.809;T|0.191	0.191	strong	.	FDFT1	25	.	NM_004462	exon3	c.C201T	p.N67N	CAGCAACGCAGTG	.	PASS	Atlas-SNP
SYNE3	161176	hgsc.bcm.edu	37	14	95918625	95918625	+	Silent	SNP	T	T	C	rs4905318	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	97	97	79	0	1	0	T|0.562;C|0.438	0.438	strong	.	SYNE3	130	.	NM_152592	exon6	c.A1233G	p.P411P	AGAGAGTGGCTTC	.	PASS	Atlas-SNP
RBM15B	29890	hgsc.bcm.edu	37	3	51430657	51430657	+	Silent	SNP	A	A	C	rs3804766	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	59	36	71	0	0.610169	0	A|0.905;C|0.095	0.095	strong	.	RBM15B	47	.	NM_013286	exon1	c.A1827C	p.S609S	CCATTCACCATAT	.	PASS	Atlas-SNP
CSDE1	7812	hgsc.bcm.edu	37	1	115272916	115272916	+	Missense_Mutation	SNP	T	T	C	rs149300730	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	108	39	100	0	0.361111	0	T|1.000;C|0.000	0.000	weak	.	CSDE1	145	.	NM_001242891	exon13	c.A1457G	p.N486S	TTAGGATTGGAAA	.	PASS	Atlas-SNP
TIMM17B	10245	hgsc.bcm.edu	37	X	48751471	48751471	+	Silent	SNP	A	A	G	rs1128363	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	89	89	80	0	1	0	A|0.307;G|0.693	0.693	strong	.	TIMM17B	15	.	NM_001167947	exon6	c.T378C	p.I126I	ACAGTCAATGGTG	.	PASS	Atlas-SNP
PIK3CG	5294	hgsc.bcm.edu	37	7	106509331	106509331	+	Missense_Mutation	SNP	C	C	A	rs17847825	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73	40	84	0	0.547945	0	C|0.912;A|0.088	0.088	strong	.	PIK3CG	279	.	NM_002649	exon2	c.C1325A	p.S442Y	CACTGTCCAGCAA	.	PASS	Atlas-SNP
TOR3A	64222	hgsc.bcm.edu	37	1	179055020	179055020	+	Silent	SNP	C	C	T	rs2296376	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55	20	73	0	0.363636	0	C|0.872;T|0.128	0.128	strong	.	TOR3A	28	.	NM_022371	exon3	c.C631T	p.L211L	GTGGACCTGTACA	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	126	54	103	0	0.428571	0	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	.	PASS	Atlas-SNP
CCDC50	152137	hgsc.bcm.edu	37	3	191093175	191093175	+	Missense_Mutation	SNP	T	T	A	rs2028574	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	28	83	0	0.41791	0	A|0.494;N|0.000	0.494	strong	.	CCDC50	39	.	NM_178335	exon6	c.T773A	p.I258N	CTAAGATTAACCA	.	PASS	Atlas-SNP
OR2L8	391190	hgsc.bcm.edu	37	1	248112794	248112794	+	Missense_Mutation	SNP	G	G	C	rs200574966		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	168	8	159	0	0.047619	0	.	.	weak	OR2L8,NS,carcinoma,0,2	OR2L8	92	2	NM_001001963	exon1	c.G635C	p.G212A	TCATTGGTATTTC	.	scavenged	Atlas-SNP
NAA15	80155	hgsc.bcm.edu	37	4	140264020	140264020	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	128	40	137	0	0.3125	0	.	.	none	.	NAA15	88	.	NM_057175	exon5	c.G443A	p.R148K	CGCAGAGAGCATC	.	PASS	Atlas-SNP
KLHL22	84861	hgsc.bcm.edu	37	22	20800835	20800835	+	Silent	SNP	A	A	G	rs8748	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	97	47	67	0	0.484536	0	A|0.853;G|0.147	0.147	strong	.	KLHL22	52	.	NM_032775	exon6	c.T1434C	p.D478D	AGGCCCATCAGCC	.	PASS	Atlas-SNP
PSG11	5680	hgsc.bcm.edu	37	19	43519324	43519324	+	Missense_Mutation	SNP	G	G	A	rs139355393	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	102	49	120	0	0.480392	0	G|1.000;A|0.000	0.000	weak	.	PSG11	57	.	NM_002785	exon4	c.C908T	p.A303V	TTACGAGCAGAGC	.	PASS	Atlas-SNP
QPCT	25797	hgsc.bcm.edu	37	2	37599963	37599963	+	Missense_Mutation	SNP	A	A	C	rs4670696	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	37	70	0	0.5	0	A|0.925;C|0.075	0.075	strong	QPCT,colon,carcinoma,0,1	QPCT	34	1	NM_012413	exon7	c.A1079C	p.H360P	ATCTTCATTTGTA	.	PASS	Atlas-SNP
IRF2BP1	26145	hgsc.bcm.edu	37	19	46387503	46387503	+	Silent	SNP	T	T	C	rs3745926	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	20	8	36	0	0.4	0	T|0.681;C|0.319	0.319	strong	.	IRF2BP1	23	.	NM_015649	exon1	c.A1530G	p.L510L	GTCTTCTAGCCGC	.	PASS	Atlas-SNP
SORBS1	10580	hgsc.bcm.edu	37	10	97106165	97106165	+	Silent	SNP	T	T	C	rs726176	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	41	25	61	0	0.609756	0	A|0.002;C|0.320	0.320	strong	.	SORBS1	185	.	NM_001034955	exon24	c.A2493G	p.L831L	TTACTTTAGTGTC	.	PASS	Atlas-SNP
SLC39A8	64116	hgsc.bcm.edu	37	4	103188709	103188709	+	Missense_Mutation	SNP	C	C	T	rs13107325	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	173	87	196	0	0.50289	0	C|0.945;T|0.055	0.055	strong	.	SLC39A8	24	.	NM_022154	exon7	c.G1171A	p.A391T	TTGGAGCGAAATT	.	PASS	Atlas-SNP
SBF2	81846	hgsc.bcm.edu	37	11	9853777	9853777	+	Missense_Mutation	SNP	G	G	C	rs12574508	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	41	66	0	0.554054	0	G|0.910;C|0.090	0.090	strong	.	SBF2	146	.	NM_030962	exon27	c.C3646G	p.Q1216E	CGGCCTGAGGGGA	.	PASS	Atlas-SNP
XIRP2	129446	hgsc.bcm.edu	37	2	168101142	168101142	+	Silent	SNP	T	T	G	rs61748633	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	31	65	0	0.469697	0	T|0.933;G|0.067	0.067	strong	XIRP2,NS,carcinoma,+1,1	XIRP2	914	1	NM_152381	exon9	c.T3240G	p.T1080T	TAAAACTGAACAA	.	PASS	Atlas-SNP
MXRA5	25878	hgsc.bcm.edu	37	X	3241791	3241791	+	Silent	SNP	G	G	A	rs1635250	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	164	164	146	0	1	0	0|0.003;A|0.487	0.487	strong	.	MXRA5	815	.	NM_015419	exon5	c.C1935T	p.D645D	ACCACTGTCACTG	.	PASS	Atlas-SNP
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32610445	32610445	+	Silent	SNP	G	G	A	rs1048381	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	145	85	84	0	0.586207	0	G|0.851;A|0.149	0.149	strong	.	HLA-DQA1	52	.	NM_002122	exon4	c.G672A	p.G224G	CCTGGGGTTGTCT	.	PASS	Atlas-SNP
EFCAB13	124989	hgsc.bcm.edu	37	17	45425287	45425287	+	Nonsense_Mutation	SNP	C	C	T	rs71377306	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	42	69	0	0.552632	0	C|0.948;T|0.052	0.052	strong	.	.	.	.	NM_152347	exon9	c.C631T	p.R211X	GAAATGCGACAGG	.	PASS	Atlas-SNP
PLXNA4	91584	hgsc.bcm.edu	37	7	132192295	132192295	+	Silent	SNP	G	G	A	rs156961	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	70	31	60	0	0.442857	0	G|0.594;A|0.406	0.406	strong	.	PLXNA4	873	.	NM_001105543	exon2	c.C1158T	p.L386L	CACCTTGAGCCAG	.	PASS	Atlas-SNP
HSPG2	3339	hgsc.bcm.edu	37	1	22181895	22181895	+	Missense_Mutation	SNP	C	C	T	rs2229475	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	140	77	146	0	0.55	0	C|0.966;T|0.034	0.034	strong	.	HSPG2	311	.	NM_005529	exon47	c.G5899A	p.V1967I	CGTGGACCTGGGT	.	PASS	Atlas-SNP
C17orf82	388407	hgsc.bcm.edu	37	17	59489707	59489707	+	Missense_Mutation	SNP	C	C	T	rs77617620	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	56	33	70	1	0.589286	0.0142857	C|0.968;T|0.032	0.032	strong	C17orf82_ENST00000335108,NS,carcinoma,0,2	C17orf82	16	2	NM_203425	exon1	c.C371T	p.A124V	GAGGCGCATATCT	.	scavenged	Atlas-SNP
UHRF2	115426	hgsc.bcm.edu	37	9	6413515	6413515	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	77	14	87	0	0.181818	0	.	.	none	UHRF2,NS,carcinoma,-1,1	UHRF2	50	1	NM_152896	exon1	c.G25C	p.D9H	ACCATTGATGGCT	.	PASS	Atlas-SNP
FAM83H	286077	hgsc.bcm.edu	37	8	144808953	144808953	+	Missense_Mutation	SNP	G	G	T	rs200179667	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	22	62	0	0.468085	0	G|0.999;T|0.001	0.001	strong	.	FAM83H	68	.	NM_198488	exon5	c.C2678A	p.P893Q	GTAGTTGGACTTC	.	PASS	Atlas-SNP
TOP1MT	116447	hgsc.bcm.edu	37	8	144403449	144403449	+	Silent	SNP	G	G	A	rs61631623	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	30	75	0	0.447761	0	G|0.866;A|0.134	0.134	strong	.	TOP1MT	63	.	NM_052963	exon8	c.C1068T	p.G356G	TTGGCAGCCATCG	.	PASS	Atlas-SNP
ART5	116969	hgsc.bcm.edu	37	11	3660238	3660238	+	Missense_Mutation	SNP	G	G	A	rs142998376	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73	33	83	0	0.452055	0	G|0.998;A|0.002	0.002	strong	.	ART5	38	.	NM_053017	exon3	c.C815T	p.A272V	CCTGGCGCAGACA	.	PASS	Atlas-SNP
ZNF544	27300	hgsc.bcm.edu	37	19	58774094	58774094	+	Missense_Mutation	SNP	C	C	T	rs34914886	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	28	16	47	0	0.571429	0	C|0.989;T|0.011	0.011	strong	.	ZNF544	57	.	NM_014480	exon7	c.C2122T	p.R708W	CATCGGCGGACAC	.	PASS	Atlas-SNP
PPP1R15A	23645	hgsc.bcm.edu	37	19	49377424	49377424	+	Missense_Mutation	SNP	G	G	A	rs11541192	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	107	59	94	0	0.551402	0	G|0.811;A|0.189	0.189	strong	.	PPP1R15A	48	.	NM_014330	exon2	c.G934A	p.G312S	GAGGAGGGTGAGG	.	PASS	Atlas-SNP
COL6A3	1293	hgsc.bcm.edu	37	2	238249630	238249630	+	Silent	SNP	C	C	T	rs4433949	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	151	150	174	0	0.993378	0	C|0.625;T|0.375	0.375	strong	.	COL6A3	608	.	NM_004369	exon38	c.G7929A	p.A2643A	CAGGTACGCTATG	.	PASS	Atlas-SNP
PSG5	5673	hgsc.bcm.edu	37	19	43680269	43680269	+	Missense_Mutation	SNP	G	G	C	rs55992450		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	16	16	34	0	1	0	.	.	weak	.	PSG5	58	.	NM_002781	exon3	c.C462G	p.N154K	TGAGTTGTTGATG	.	PASS	Atlas-SNP
CEP152	22995	hgsc.bcm.edu	37	15	49048705	49048705	+	Missense_Mutation	SNP	G	G	C	rs16961560	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	34	20	42	0	0.588235	0	G|0.933;C|0.067	0.067	strong	.	CEP152	145	.	NM_014985	exon20	c.C2740G	p.L914V	TTTCAAGCTCACT	.	PASS	Atlas-SNP
PPP6R2	9701	hgsc.bcm.edu	37	22	50882338	50882338	+	Missense_Mutation	SNP	G	G	A	rs56269507	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	128	63	118	0	0.492188	0	G|0.984;A|0.016	0.016	strong	.	PPP6R2	71	.	NM_001242898	exon23	c.G2623A	p.A875T	TGCCCCGCGCCAA	.	PASS	Atlas-SNP
OR4L1	122742	hgsc.bcm.edu	37	14	20529019	20529019	+	Silent	SNP	C	C	T	rs1959629	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72	37	61	0	0.513889	0	C|0.617;T|0.383	0.383	strong	.	OR4L1	98	.	NM_001004717	exon1	c.C816T	p.A272A	TCTTGCCGTATTT	.	PASS	Atlas-SNP
SAMD11	148398	hgsc.bcm.edu	37	1	878314	878314	+	Silent	SNP	G	G	C	rs142558220	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	77	29	96	0	0.376623	0	G|0.952;C|0.048	0.048	strong	SAMD11,NS,carcinoma,0,1	SAMD11	34	1	NM_152486	exon11	c.G1440C	p.G480G	TGTTGGGTGCAGG	.	PASS	Atlas-SNP
DHX34	9704	hgsc.bcm.edu	37	19	47858526	47858526	+	Silent	SNP	C	C	T	rs138629177		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	105	53	122	0	0.504762	0	C|1.000;T|0.000	0.000	weak	.	DHX34	98	.	NM_014681	exon3	c.C936T	p.A312A	GTCGGCCACCATC	.	PASS	Atlas-SNP
MRPS34	65993	hgsc.bcm.edu	37	16	1823024	1823024	+	Missense_Mutation	SNP	G	G	T	rs11552431	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	13	5	10	0	0.384615	0	G|0.846;T|0.154	0.154	strong	.	MRPS34	7	.	NM_023936	exon1	c.C97A	p.L33I	CGTAGAGCTGGGA	.	PASS	Atlas-SNP
XRRA1	143570	hgsc.bcm.edu	37	11	74559446	74559446	+	Missense_Mutation	SNP	G	G	C	rs4944960	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	84	89	0	1	0	G|0.659;C|0.341	0.341	strong	.	XRRA1	46	.	NM_182969	exon15	c.C1418G	p.T473R	GTTGTCGTCATGC	.	PASS	Atlas-SNP
DLX3	1747	hgsc.bcm.edu	37	17	48070878	48070878	+	Silent	SNP	C	C	T	rs2303466	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	75	65	0	1	0	C|0.804;T|0.196	0.196	strong	.	DLX3	28	.	NM_005220	exon2	c.G402A	p.T134T	GTAGATCGTACGC	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1080391	1080391	+	Missense_Mutation	SNP	G	G	A	rs41521547	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91	45	118	0	0.494505	0	G|0.947;A|0.053	0.053	strong	.	MUC2	614	.	NM_002457	exon8	c.G1111A	p.E371K	GACTGCGAGCAGT	.	PASS	Atlas-SNP
BCL9	607	hgsc.bcm.edu	37	1	147090956	147090956	+	Missense_Mutation	SNP	C	C	T	rs61751616	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	46	23	25	0	0.5	0	C|0.990;T|0.010	0.010	strong	.	BCL9	150	.	NM_004326	exon8	c.C995T	p.P332L	CCCCTCCGCCTCC	.	PASS	Atlas-SNP
FAM83F	113828	hgsc.bcm.edu	37	22	40417780	40417780	+	Silent	SNP	C	C	T	rs5995793	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	61	62	0	1	0	C|0.719;T|0.281	0.281	strong	.	FAM83F	29	.	NM_138435	exon4	c.C1266T	p.N422N	CCGAAACGGCATG	.	PASS	Atlas-SNP
HYOU1	10525	hgsc.bcm.edu	37	11	118919206	118919206	+	Silent	SNP	T	T	C	rs568922	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	56	42	66	0	0.75	0	T|0.207;C|0.793	0.793	strong	HYOU1,caecum,carcinoma,-1,1	HYOU1	88	1	NM_006389	exon19	c.A2235G	p.A745A	TATGAATGCTTCC	.	PASS	Atlas-SNP
FCRL1	115350	hgsc.bcm.edu	37	1	157771880	157771880	+	Silent	SNP	C	C	T	rs4971154	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	135	72	141	0	0.533333	0	C|0.596;T|0.404	0.404	strong	FCRL1,NS,carcinoma,-1,1	FCRL1	164	1	NM_001159397	exon5	c.G711A	p.P237P	CAGGATCGGAGGA	.	PASS	Atlas-SNP
TAS2R43	259289	hgsc.bcm.edu	37	12	11244725	11244725	+	Missense_Mutation	SNP	C	C	G	rs68157013	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	116	108	16	0	0.931035	0	C|0.597;G|0.403	0.403	strong	TAS2R46_ENST00000422992,NS,carcinoma,0,4	TAS2R43	19	4	NM_176884	exon1	c.G104C	p.W35S	TTGAACCACTCAA	.	PASS	Atlas-SNP
KRTAP27-1	643812	hgsc.bcm.edu	37	21	31709723	31709723	+	Silent	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	230	45	157	0	0.195652	0	.	.	none	.	KRTAP27-1	53	.	NM_001077711	exon1	c.T264G	p.T88T	GGAGTAAGTAGTT	.	PASS	Atlas-SNP
FUCA2	2519	hgsc.bcm.edu	37	6	143825104	143825104	+	Missense_Mutation	SNP	G	G	T	rs11155297	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	130	65	112	0	0.5	0	G|0.844;T|0.156	0.156	strong	FUCA2,colon,carcinoma,0,1	FUCA2	28	1	NM_032020	exon3	c.C698A	p.A233E	TCCGGTGCTCCTC	.	PASS	Atlas-SNP
TRIM31	11074	hgsc.bcm.edu	37	6	30078330	30078330	+	Silent	SNP	C	C	T	rs2239529	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	127	98	122	0	0.771654	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
CDH23	64072	hgsc.bcm.edu	37	10	73434906	73434906	+	Missense_Mutation	SNP	G	G	A	rs10999947	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	27	50	0	0.428571	0	G|0.725;A|0.275	0.275	strong	.	CDH23	365	.	NM_022124	exon14	c.G1487A	p.S496N	AAGTCAGCTACTT	.	PASS	Atlas-SNP
DNAH12	201625	hgsc.bcm.edu	37	3	57528503	57528503	+	Missense_Mutation	SNP	A	A	G	rs9311651	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80	35	79	0	0.4375	0	A|0.760;G|0.240	0.240	strong	.	DNAH12	182	.	NM_198564	exon2	c.T95C	p.V32A	GTATCAACGCCTA	.	PASS	Atlas-SNP
WISP1	8840	hgsc.bcm.edu	37	8	134239770	134239770	+	Missense_Mutation	SNP	T	T	C	rs3739261	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	142	69	132	0	0.485915	0	T|0.682;C|0.318	0.318	strong	.	WISP1	64	.	NM_001204869	exon3	c.T466C	p.X156Q	GGACAATAGGTGC	.	PASS	Atlas-SNP
SCAMP4	113178	hgsc.bcm.edu	37	19	1918193	1918193	+	Silent	SNP	G	G	A	rs144595321	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	154	66	149	0	0.428571	0	G|0.993;A|0.007	0.007	strong	.	SCAMP4	7	.	NM_079834	exon4	c.G204A	p.G68G	CTCGGGGACCAAC	.	PASS	Atlas-SNP
DOCK2	1794	hgsc.bcm.edu	37	5	169504743	169504743	+	Silent	SNP	T	T	C	rs1045168	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79	33	85	2	0.417722	0.0235294	A|0.000;C|0.311;T|0.689	0.311	strong	DOCK2,NS,carcinoma,0,3	DOCK2	389	3	NM_004946	exon48	c.T4896C	p.R1632R	GGGCCGTCCCAGG	.	scavenged	Atlas-SNP
ARHGAP23	57636	hgsc.bcm.edu	37	17	36628191	36628191	+	Missense_Mutation	SNP	G	G	A	rs199655106	byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	106	19	84	1	0.179245	0.0119048	G|0.986;A|0.014	0.014	strong	ARHGAP23,NS,carcinoma,0,1	ARHGAP23	48	1	NM_001199417	exon11	c.G2062A	p.D688N	TTCAGCGATATCA	.	scavenged	Atlas-SNP
GTF3C1	2975	hgsc.bcm.edu	37	16	27474910	27474910	+	Missense_Mutation	SNP	A	A	G	rs12919017	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	38	20	26	0	0.526316	0	A|0.904;G|0.096	0.096	strong	.	GTF3C1	210	.	NM_001520	exon35	c.T5876C	p.F1959S	TCTGTGAACCCTG	.	PASS	Atlas-SNP
LHX3	8022	hgsc.bcm.edu	37	9	139092571	139092571	+	Silent	SNP	C	C	T	rs33998096	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100	52	115	0	0.52	0	C|0.990;T|0.010	0.010	strong	.	LHX3	23	.	NM_014564	exon2	c.G123A	p.Q41Q	GATGTGCTGGTCA	.	PASS	Atlas-SNP
MRPS35	60488	hgsc.bcm.edu	37	12	27867727	27867727	+	Missense_Mutation	SNP	G	G	A	rs1127787	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	78	39	47	0	0.5	0	G|0.873;A|0.127	0.127	strong	.	MRPS35	26	.	NM_001190864	exon2	c.G127A	p.G43R	ACACCCGGAAATG	.	PASS	Atlas-SNP
TMPRSS11F	389208	hgsc.bcm.edu	37	4	68995529	68995529	+	Missense_Mutation	SNP	C	C	T	rs10030708	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	105	105	114	0	1	0	C|0.674;T|0.326	0.326	strong	.	TMPRSS11F	79	.	NM_207407	exon1	c.G10A	p.A4T	CTTACGCGTACAT	.	PASS	Atlas-SNP
ZNF79	7633	hgsc.bcm.edu	37	9	130197414	130197414	+	Missense_Mutation	SNP	A	A	G	rs4504745	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	125	58	130	0	0.464	0	A|0.413;G|0.587	0.587	strong	.	ZNF79	47	.	NM_007135	exon3	c.A151G	p.R51G	CAGGAAAGGTGGA	.	PASS	Atlas-SNP
TENM4	26011	hgsc.bcm.edu	37	11	78399121	78399121	+	Silent	SNP	G	G	A	rs1792148	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	113	19	99	0	0.168142	0	G|0.864;A|0.136	0.136	strong	ODZ4_ENST00000278550,colon,carcinoma,-2,1	.	.	1	NM_001098816	exon29	c.C5238T	p.G1746G	GAAGGCGCCTGAG	.	PASS	Atlas-SNP
KIAA0146	23514	hgsc.bcm.edu	37	8	48612997	48612997	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	103	10	119	0	0.0970874	0	.	.	none	.	KIAA0146	64	.	NM_001080394	exon12	c.T1718A	p.L573Q	ACACCCTGTGGCC	.	PASS	Atlas-SNP
P2RY4	5030	hgsc.bcm.edu	37	X	69478942	69478942	+	Missense_Mutation	SNP	T	T	G	rs1152187	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	105	81	63	0	0.771429	0	0|0.003;G|0.369	0.369	strong	.	P2RY4	39	.	NM_002565	exon1	c.A533C	p.N178T	CCTTTGTTGCTGG	.	PASS	Atlas-SNP
PPP1R26	9858	hgsc.bcm.edu	37	9	138377433	138377433	+	Silent	SNP	G	G	A	rs3827827	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79	44	92	0	0.556962	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
DNHD1	144132	hgsc.bcm.edu	37	11	6578788	6578788	+	Missense_Mutation	SNP	C	C	T	rs111982303	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	38	71	0	0.612903	0	C|0.988;T|0.012	0.012	strong	.	DNHD1	198	.	NM_144666	exon25	c.C8263T	p.P2755S	ATAGGACCAGTAA	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	29	23	19	0	0.793103	0	G|0.697;N|0.000	.	strong	.	C11orf82	71	.	NM_145018	exon6	c.G1380T	p.R460S	CAGCAGGTTATCT	.	PASS	Atlas-SNP
MRPL28	10573	hgsc.bcm.edu	37	16	419154	419154	+	Silent	SNP	G	G	A	rs1802752	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	134	61	150	0	0.455224	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
DPY19L3	147991	hgsc.bcm.edu	37	19	32973077	32973077	+	Silent	SNP	C	C	T	rs7253039	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98	52	87	0	0.530612	0	C|0.821;T|0.179	0.179	strong	.	DPY19L3	70	.	NM_001172774	exon19	c.C2082T	p.Y694Y	TCCCTACGTGGCC	.	PASS	Atlas-SNP
C17orf70	80233	hgsc.bcm.edu	37	17	79517729	79517729	+	Missense_Mutation	SNP	G	G	A	rs62076033	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79	36	83	0	0.455696	0	G|0.997;A|0.003	0.003	strong	.	C17orf70	79	.	NM_025161	exon3	c.C791T	p.A264V	CCAGGGGCTGACC	.	PASS	Atlas-SNP
PPP2R1B	5519	hgsc.bcm.edu	37	11	111637053	111637053	+	Silent	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	35	17	25	0	0.485714	0	.	.	none	.	PPP2R1B	44	.	NM_001177562	exon1	c.A33G	p.P11P	TGCTCCTGGGCCG	.	PASS	Atlas-SNP
MYO9A	4649	hgsc.bcm.edu	37	15	72189925	72189925	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	192	52	229	0	0.270833	0	.	.	none	.	MYO9A	203	.	NM_006901	exon25	c.G4919A	p.R1640H	GAAATGCGATTAT	.	PASS	Atlas-SNP
MFSD10	10227	hgsc.bcm.edu	37	4	2935527	2935527	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	149	114	181	0	0.765101	0	.	.	none	.	MFSD10	22	.	NM_001120	exon1	c.C124A	p.L42M	GCAGCAGCAGCGT	.	PASS	Atlas-SNP
SMAD7	4092	hgsc.bcm.edu	37	18	46468946	46468946	+	Missense_Mutation	SNP	G	G	A	rs3764482	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44	26	38	0	0.590909	0	G|0.884;A|0.116	0.116	strong	.	SMAD7	22	.	NM_001190823	exon1	c.C83T	p.S28F	AGGGGAGAGAAAG	.	PASS	Atlas-SNP
OR2T4	127074	hgsc.bcm.edu	37	1	248525060	248525060	+	Missense_Mutation	SNP	T	T	A	rs28491677	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	533	11	559	0	0.0206379	0	T|0.787;A|0.213	0.213	strong	OR2T4,NS,carcinoma,-1,1	OR2T4	126	1	NM_001004696	exon1	c.T178A	p.C60S	CTACTTTGTGTGG	.	scavenged	Atlas-SNP
PARVG	64098	hgsc.bcm.edu	37	22	44594584	44594584	+	Silent	SNP	C	C	G	rs139152	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	134	72	160	0	0.537313	0	C|0.712;G|0.288	0.288	strong	.	PARVG	41	.	NM_001137606	exon12	c.C795G	p.P265P	CACTCCCAACTCT	.	PASS	Atlas-SNP
CHD2	1106	hgsc.bcm.edu	37	15	93536197	93536197	+	Silent	SNP	C	C	T	rs2272457	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	43	40	56	0	0.930233	0	C|0.770;T|0.230	0.230	strong	.	CHD2	280	.	NM_001271	exon28	c.C3564T	p.Y1188Y	GGAATACGAAGAG	.	PASS	Atlas-SNP
PIGZ	80235	hgsc.bcm.edu	37	3	196674916	196674916	+	Silent	SNP	A	A	C	rs1147240	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51	51	42	0	1	0	A|0.479;C|0.521	0.521	strong	.	PIGZ	34	.	NM_025163	exon3	c.T852G	p.A284A	GGATGTAGCGGGG	.	PASS	Atlas-SNP
TRIM69	140691	hgsc.bcm.edu	37	15	45048651	45048651	+	Missense_Mutation	SNP	C	C	T	rs3759880	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	28	21	53	0	0.75	0	C|0.866;N|0.000	.	strong	.	TRIM69	47	.	NM_182985	exon3	c.C569T	p.A190V	CTATTGCTGCTCA	.	PASS	Atlas-SNP
ANPEP	290	hgsc.bcm.edu	37	15	90335534	90335534	+	Silent	SNP	G	G	A	rs25652	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	162	88	135	0	0.54321	0	T|0.000;G|0.749;A|0.251	0.251	strong	.	ANPEP	124	.	NM_001150	exon18	c.C2385T	p.T795T	GTAGACGGTGGAC	.	PASS	Atlas-SNP
UTP20	27340	hgsc.bcm.edu	37	12	101779435	101779435	+	Silent	SNP	T	T	C	rs149160478		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	95	49	97	0	0.515789	0	T|1.000;C|0.000	0.000	weak	.	UTP20	222	.	NM_014503	exon61	c.T8131C	p.L2711L	TTCTCATTAGCCT	.	PASS	Atlas-SNP
SIRPG	55423	hgsc.bcm.edu	37	20	1610894	1610894	+	Silent	SNP	G	G	A	rs3746721	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49	22	46	0	0.44898	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
FSHR	2492	hgsc.bcm.edu	37	2	49189921	49189921	+	Missense_Mutation	SNP	C	C	T	rs6166	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	92	92	89	0	1	0	C|0.421;T|0.579	0.579	strong	.	FSHR	164	.	NM_000145	exon10	c.G2039A	p.S680N	GAACCACTGGTGA	.	PASS	Atlas-SNP
DIS3L	115752	hgsc.bcm.edu	37	15	66612965	66612965	+	Silent	SNP	T	T	C	rs17851970	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	118	69	128	0	0.584746	0	T|0.806;C|0.194	0.194	strong	.	DIS3L	175	.	NM_001143688	exon9	c.T1221C	p.N407N	TCCAAATGGACAT	.	PASS	Atlas-SNP
PHC1	1911	hgsc.bcm.edu	37	12	9086898	9086898	+	Missense_Mutation	SNP	A	A	G	rs1049925	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55	16	62	0	0.290909	0	A|0.630;G|0.370	0.370	strong	.	PHC1	67	.	NM_004426	exon10	c.A2077G	p.T693A	GCTAATACTCCAA	.	PASS	Atlas-SNP
SGK1	6446	hgsc.bcm.edu	37	6	134495674	134495674	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	45	7	71	0	0.155556	0	.	.	none	.	SGK1	387	.	NM_001143676	exon4	c.G412A	p.A138T	TATTGGCAATCTT	.	PASS	Atlas-SNP
PCDHA12	56137	hgsc.bcm.edu	37	5	140255356	140255356	+	Missense_Mutation	SNP	C	C	T	rs182160950	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57	28	61	0	0.491228	0	C|0.998;T|0.002	0.002	strong	PCDHA12,colon,carcinoma,0,1	PCDHA12	196	1	NM_018903	exon1	c.C299T	p.A100V	GGAGCGCGGAGTG	.	scavenged	Atlas-SNP
ADAM30	11085	hgsc.bcm.edu	37	1	120437718	120437718	+	Silent	SNP	G	G	A	rs2793823	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	65	30	64	0	0.461538	0	G|0.719;A|0.280	0.280	strong	.	ADAM30	88	.	NM_021794	exon1	c.C1242T	p.D414D	ACCACAGTCACAT	.	PASS	Atlas-SNP
SCARF1	8578	hgsc.bcm.edu	37	17	1542153	1542153	+	Silent	SNP	G	G	A	rs2272012	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	148	66	132	0	0.445946	0	G|0.403;A|0.597	0.597	strong	.	SCARF1	46	.	NM_145350	exon8	c.C1311T	p.G437G	GGCAAGGCCCAGG	.	PASS	Atlas-SNP
TMEM204	79652	hgsc.bcm.edu	37	16	1591962	1591962	+	Silent	SNP	G	G	A	rs2076443	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	45	25	77	1	0.555556	0.012987	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	.	scavenged	Atlas-SNP
LAMC2	3918	hgsc.bcm.edu	37	1	183192304	183192304	+	Silent	SNP	T	T	G	rs1047980	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110	49	118	0	0.445455	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
ABCC4	10257	hgsc.bcm.edu	37	13	95858996	95858996	+	Silent	SNP	T	T	C	rs2274406	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	53	52	0	1	0	T|0.463;C|0.537	0.537	strong	ABCC4_ENST00000376887,NS,carcinoma,0,1	ABCC4	248	1	NM_005845	exon8	c.A951G	p.R317R	CATCCCTCTGAGG	.	PASS	Atlas-SNP
HS1BP3	64342	hgsc.bcm.edu	37	2	20838318	20838318	+	Silent	SNP	G	G	A	rs3796064	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	235	118	253	0	0.502128	0	G|0.702;A|0.298	0.298	strong	.	HS1BP3	33	.	NM_022460	exon4	c.C501T	p.F167F	AAAGTCGAAAGCC	.	PASS	Atlas-SNP
TREML2	79865	hgsc.bcm.edu	37	6	41166063	41166063	+	Missense_Mutation	SNP	C	C	A	rs147506354	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72	59	75	0	0.819444	0	C|0.998;A|0.002	0.002	strong	.	TREML2	41	.	NM_024807	exon2	c.G160T	p.V54F	ACCAAACCTTGCC	.	PASS	Atlas-SNP
PRSS1	5644	hgsc.bcm.edu	37	7	142460313	142460313	+	Silent	SNP	T	T	C	rs6666	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	276	97	351	0	0.351449	0	T|0.437;C|0.563	0.563	strong	.	PRSS1	68	.	NM_002769	exon4	c.T486C	p.D162D	CCTGGATGCTCCT	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	88	88	72	0	1	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
CHIA	27159	hgsc.bcm.edu	37	1	111857951	111857951	+	Missense_Mutation	SNP	A	A	G	rs61756687	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	92	43	83	0	0.467391	0	A|0.900;G|0.100	0.100	strong	.	CHIA	115	.	NM_201653	exon6	c.A374G	p.K125R	TCATCAAATTCCT	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85	85	96	0	1	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
RXFP2	122042	hgsc.bcm.edu	37	13	32367033	32367033	+	Missense_Mutation	SNP	C	C	G	rs138951290	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	138	67	114	0	0.485507	0	C|0.999;G|0.001	0.001	strong	RXFP2,NS,carcinoma,0,1	RXFP2	95	1	NM_130806	exon16	c.C1594G	p.R532G	AACATTCGACCTG	.	PASS	Atlas-SNP
NLRC5	84166	hgsc.bcm.edu	37	16	57068107	57068107	+	Silent	SNP	C	C	T	rs3995817	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	36	75	0	0.507042	0	C|0.834;T|0.166	0.166	strong	.	NLRC5	186	.	NM_032206	exon12	c.C2571T	p.H857H	GGTCCACGATGCG	.	PASS	Atlas-SNP
CCL23	6368	hgsc.bcm.edu	37	17	34341398	34341398	+	Silent	SNP	A	A	G	rs61737011	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	130	76	114	0	0.584615	0	A|0.979;G|0.021	0.021	strong	.	CCL23	17	.	NM_005064	exon2	c.T112C	p.L38L	TTTCCAATGGAAG	.	PASS	Atlas-SNP
NOP58	51602	hgsc.bcm.edu	37	2	203157538	203157538	+	Silent	SNP	A	A	G	rs16839032	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	132	66	116	0	0.5	0	A|0.989;G|0.011	0.011	strong	NOP58,NS,carcinoma,0,1	NOP58	41	1	NM_015934	exon9	c.A819G	p.E273E	CTATGAATATCTA	.	PASS	Atlas-SNP
FAM5B	57795	hgsc.bcm.edu	37	1	177247854	177247854	+	Missense_Mutation	SNP	C	C	G	rs3176443	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	96	45	104	0	0.46875	0	C|0.730;G|0.270	0.270	strong	.	FAM5B	191	.	NM_021165	exon7	c.C1168G	p.L390V	CGGATCCTACGCC	.	PASS	Atlas-SNP
TEX38	374973	hgsc.bcm.edu	37	1	47139103	47139103	+	Missense_Mutation	SNP	C	C	T	rs1025806	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	20	32	0	0.384615	0	C|0.719;T|0.281	0.281	strong	ATPAF1-AS1_ENST00000569393,colon,carcinoma,0,2	.	.	2	NM_001145474	exon2	c.C596T	p.A199V	TCAATGCCAAGCC	.	PASS	Atlas-SNP
MED13L	23389	hgsc.bcm.edu	37	12	116446445	116446445	+	Silent	SNP	C	C	T	rs3741768	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	144	71	165	0	0.493056	0	C|0.855;T|0.145	0.145	strong	.	MED13L	193	.	NM_015335	exon10	c.G1773A	p.Q591Q	AGACAACTGCTGG	.	PASS	Atlas-SNP
TESK2	10420	hgsc.bcm.edu	37	1	45810923	45810923	+	Silent	SNP	G	G	A	rs3893383	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	22	61	0	0.468085	0	G|0.838;A|0.161	0.161	strong	.	TESK2	60	.	NM_007170	exon11	c.C1305T	p.P435P	AGTTCCGGGCCCT	.	PASS	Atlas-SNP
ACTN4	81	hgsc.bcm.edu	37	19	39196736	39196736	+	Silent	SNP	G	G	A	rs11553600	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79	43	59	0	0.544304	0	G|0.852;A|0.148	0.148	strong	ACTN4,NS,carcinoma,+1,1	ACTN4	69	1	NM_004924	exon5	c.G537A	p.P179P	AGCCCCGTATAAG	.	PASS	Atlas-SNP
ARHGEF18	23370	hgsc.bcm.edu	37	19	7524855	7524855	+	Silent	SNP	C	C	T	rs2287915	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	20	101	0	0.298507	0	C|0.775;T|0.225	0.225	strong	.	ARHGEF18	129	.	NM_001130955	exon10	c.C1863T	p.R621R	GGCCCGCGCCACG	.	PASS	Atlas-SNP
DOT1L	84444	hgsc.bcm.edu	37	19	2217023	2217023	+	Silent	SNP	C	C	T	rs141523228	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83	33	85	0	0.39759	0	C|0.981;T|0.019	0.019	strong	.	DOT1L	205	.	NM_032482	exon21	c.C2478T	p.S826S	GCTGAGCCCTCAG	.	PASS	Atlas-SNP
BSN	8927	hgsc.bcm.edu	37	3	49701298	49701298	+	Missense_Mutation	SNP	G	G	A	rs2005557	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	203	90	205	0	0.44335	0	G|0.472;A|0.528	0.528	strong	BSN,NS,adenoma,0,1	BSN	272	1	NM_003458	exon8	c.G11587A	p.A3863T	CAGCCAGCACCAG	.	PASS	Atlas-SNP
RABGGTB	5876	hgsc.bcm.edu	37	1	76260248	76260248	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	78	20	72	0	0.25641	0	.	.	none	.	RABGGTB	37	.	NM_004582	exon9	c.A909C	p.E303D	GGGAGAAGAACAG	.	PASS	Atlas-SNP
SWT1	54823	hgsc.bcm.edu	37	1	185143721	185143721	+	Missense_Mutation	SNP	A	A	G	rs10489579	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	114	51	138	0	0.447368	0	G|0.396;N|0.000	0.396	strong	.	SWT1	88	.	NM_017673	exon5	c.A442G	p.I148V	CATGGAATTAAAA	.	PASS	Atlas-SNP
UBQLNL	143630	hgsc.bcm.edu	37	11	5537045	5537045	+	Silent	SNP	T	T	G	rs872751	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	104	66	121	0	0.634615	0	T|0.688;G|0.312	0.312	strong	.	UBQLNL	74	.	NM_145053	exon1	c.A627C	p.P209P	AACTTCTGGGTTC	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1081141	1081141	+	Silent	SNP	C	C	T	rs41375149	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	43	101	0	0.511905	0	C|0.939;T|0.061	0.061	strong	.	MUC2	614	.	NM_002457	exon11	c.C1437T	p.T479T	CGTGACCGGTGAG	.	PASS	Atlas-SNP
ZNF30	90075	hgsc.bcm.edu	37	19	35434448	35434448	+	Missense_Mutation	SNP	A	A	G	rs62122088	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	38	84	0	0.452381	0	A|0.892;G|0.108	0.108	strong	.	ZNF30	44	.	NM_001099438	exon5	c.A581G	p.K194R	TTGTTAAGCATGG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195510011	195510011	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	6	65	0	0.0909091	0	.	.	none	.	MUC4	1505	.	NM_018406	exon2	c.G8440A	p.A2814T	AGGTGGCGTGACC	.	PASS	Atlas-SNP
CD163L1	283316	hgsc.bcm.edu	37	12	7528471	7528471	+	Silent	SNP	G	G	A	rs7306824	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	58	26	91	0	0.448276	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
FHAD1	114827	hgsc.bcm.edu	37	1	15708540	15708540	+	Missense_Mutation	SNP	A	A	G	rs1010294	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	209	100	226	0	0.478469	0	T|0.004;G|0.400	0.400	strong	.	FHAD1	78	.	NM_052929	exon30	c.A3973G	p.I1325V	GTGTCCATTGAGA	.	PASS	Atlas-SNP
ZNF83	55769	hgsc.bcm.edu	37	19	53116940	53116940	+	Missense_Mutation	SNP	T	T	A	rs75857698	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	33	10	55	0	0.30303	0	T|0.867;A|0.133	0.133	strong	.	ZNF83	73	.	NM_018300	exon3	c.A878T	p.E293V	CCACACTCATTAC	.	PASS	Atlas-SNP
DDX4	54514	hgsc.bcm.edu	37	5	55082474	55082474	+	Silent	SNP	C	C	T	rs957459	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	164	77	151	0	0.469512	0	C|0.565;T|0.435	0.435	strong	.	DDX4	194	.	NM_024415	exon14	c.C993T	p.C331C	GGCTTGCGCTCAA	.	PASS	Atlas-SNP
TNF	7124	hgsc.bcm.edu	37	6	31543607	31543607	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	43	7	71	0	0.162791	0	.	.	none	.	TNF	15	.	NM_000594	exon1	c.G89A	p.C30Y	GGCGGTGCTTGTT	.	PASS	Atlas-SNP
TRPM1	4308	hgsc.bcm.edu	37	15	31330313	31330313	+	Silent	SNP	A	A	G	rs12913672	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72	35	57	0	0.486111	0	A|0.799;G|0.201	0.201	strong	.	TRPM1	183	.	NM_001252020	exon18	c.T2424C	p.Y808Y	ATCATCATATGTG	.	PASS	Atlas-SNP
DNAJC30	84277	hgsc.bcm.edu	37	7	73097654	73097654	+	Missense_Mutation	SNP	C	C	T	rs1128349	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	29	29	33	0	1	0	C|0.641;T|0.359	0.359	strong	.	DNAJC30	12	.	NM_032317	exon1	c.G100A	p.G34R	TCGCTCCTAGGCC	.	PASS	Atlas-SNP
PADI6	353238	hgsc.bcm.edu	37	1	17715015	17715015	+	Missense_Mutation	SNP	C	C	G	rs200922673	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	109	55	108	0	0.504587	0	.	.	weak	PADI6,colon,carcinoma,0,1	PADI6	51	1	NM_207421	exon7	c.C819G	p.I273M	CCTCATCTCCTAC	.	PASS	Atlas-SNP
SLC6A12	6539	hgsc.bcm.edu	37	12	319111	319111	+	Silent	SNP	T	T	C	rs526690	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	87	113	0	1	0	T|0.434;C|0.566	0.566	strong	.	SLC6A12	60	.	NM_001122848	exon3	c.A42G	p.A14A	GGAGACTGCAGGA	.	PASS	Atlas-SNP
WDR44	54521	hgsc.bcm.edu	37	X	117521338	117521338	+	Silent	SNP	G	G	A	rs17318100	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	223	144	190	0	0.64574	0	0|0.003;A|0.146	0.146	strong	.	WDR44	188	.	NM_001184965	exon3	c.G147A	p.E49E	AAATGAGTCCCCT	.	PASS	Atlas-SNP
GEMIN4	50628	hgsc.bcm.edu	37	17	649232	649232	+	Missense_Mutation	SNP	C	C	T	rs3744741	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	26	20	38	0	0.769231	0	C|0.765;T|0.235	0.235	strong	.	GEMIN4	116	.	NM_015721	exon2	c.G2051A	p.R684Q	TCCTCTCGGCACG	.	PASS	Atlas-SNP
OR5B17	219965	hgsc.bcm.edu	37	11	58126305	58126305	+	Missense_Mutation	SNP	A	A	T	rs4939208	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	171	170	175	0	0.994152	0	A|0.322;T|0.678	0.678	strong	.	OR5B17	64	.	NM_001005489	exon1	c.T238A	p.L80I	CAGTTAAAACCTT	.	PASS	Atlas-SNP
SAGE1	55511	hgsc.bcm.edu	37	X	134978425	134978425	+	Silent	SNP	G	G	A	rs5930805	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	253	70	147	0	0.27668	0	G|0.792;A|0.208	0.208	strong	.	SAGE1	160	.	NM_018666	exon2	c.G24A	p.T8T	TCAAACGAGTCAA	.	PASS	Atlas-SNP
CATSPERD	257062	hgsc.bcm.edu	37	19	5778517	5778517	+	Missense_Mutation	SNP	A	A	T	rs2305925	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	165	77	192	0	0.466667	0	A|0.755;T|0.245	0.245	strong	.	.	.	.	NM_152784	exon22	c.A2227T	p.T743S	TACAAGACCCCCA	.	PASS	Atlas-SNP
IL25	64806	hgsc.bcm.edu	37	14	23844979	23844979	+	Silent	SNP	C	C	A	rs79877597	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	175	71	162	0	0.405714	0	A|0.271;C|0.727;T|0.002	0.271	strong	IL25,NS,carcinoma,0,1	IL25	21	1	NM_022789	exon2	c.C424A	p.R142R	TTCTACCGGCGGC	.	PASS	Atlas-SNP
PRSS55	203074	hgsc.bcm.edu	37	8	10396054	10396054	+	Silent	SNP	A	A	C	rs6601483	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	139	137	103	0	0.985611	0	A|0.358;C|0.642	0.642	strong	.	PRSS55	67	.	NM_198464	exon5	c.A810C	p.I270I	CATCATAAGCTGG	.	PASS	Atlas-SNP
HBE1	3046	hgsc.bcm.edu	37	11	5289816	5289816	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	6	49	0	0.111111	0	.	.	none	.	HBE1	42	.	NM_005330	exon3	c.C327T	p.N109N	CATCACGTTACCC	.	PASS	Atlas-SNP
MIPEP	4285	hgsc.bcm.edu	37	13	24436475	24436475	+	Missense_Mutation	SNP	C	C	T	rs11551114	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	181	95	175	1	0.524862	0.00571429	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	.	scavenged	Atlas-SNP
TXLNG	55787	hgsc.bcm.edu	37	X	16847765	16847765	+	Missense_Mutation	SNP	A	A	G	rs5969783	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	112	24	95	0	0.214286	0	A|0.979;G|0.021	0.021	strong	.	TXLNG	40	.	NM_018360	exon5	c.A736G	p.I246V	TTCCAGATTACCT	.	PASS	Atlas-SNP
HMHB1	57824	hgsc.bcm.edu	37	5	143200053	143200053	+	Missense_Mutation	SNP	C	C	T	rs161557	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	119	118	155	0	0.991597	0	C|0.720;T|0.280	0.280	strong	.	HMHB1	3	.	NM_021182	exon2	c.C46T	p.H16Y	TCTCTGCATGTTT	.	PASS	Atlas-SNP
HUNK	30811	hgsc.bcm.edu	37	21	33371123	33371123	+	Missense_Mutation	SNP	C	C	T	rs10775648	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	111	67	87	0	0.603604	0	C|0.807;T|0.193	0.193	strong	.	HUNK	74	.	NM_014586	exon11	c.C1771T	p.R591C	TTGGCTCGCAGAA	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	30	14	33	0	0.466667	0	A|0.808;G|0.192	0.192	strong	.	.	.	.	NM_018182	exon4	c.T1413C	p.L471L	CATGGCAAGGTCC	.	PASS	Atlas-SNP
LYZL2	119180	hgsc.bcm.edu	37	10	30901756	30901756	+	Silent	SNP	G	G	A	rs9954	bycluster;byfrequency;bysubmitter;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	135	47	131	0	0.348148	0	G|0.517;A|0.483	0.483	strong	LYZL2,NS,carcinoma,-2,1	LYZL2	33	1	NM_183058	exon4	c.C510T	p.N170N	CCAATAGTTCATT	.	PASS	Atlas-SNP
DPH1	1801	hgsc.bcm.edu	37	17	1943888	1943888	+	Silent	SNP	T	T	C	rs2236375	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	129	63	153	0	0.488372	0	T|0.175;C|0.825	0.825	strong	.	DPH1	32	.	NM_001383	exon9	c.T1011C	p.P337P	ACTTCCTGAGGTG	.	PASS	Atlas-SNP
DUS3L	56931	hgsc.bcm.edu	37	19	5786815	5786815	+	Silent	SNP	G	G	A	rs10811	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	95	46	99	0	0.484211	0	G|0.770;A|0.230	0.230	strong	.	DUS3L	42	.	NM_020175	exon9	c.C1431T	p.A477A	CCAGTCGGCTAGC	.	PASS	Atlas-SNP
PNMAL1	55228	hgsc.bcm.edu	37	19	46973981	46973981	+	Silent	SNP	G	G	A	rs4803960	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51	30	51	0	0.588235	0	G|0.732;A|0.268	0.268	strong	.	PNMAL1	87	.	NM_018215	exon2	c.C312T	p.A104A	AAACTCGGCATCC	.	PASS	Atlas-SNP
BTG2	7832	hgsc.bcm.edu	37	1	203274836	203274836	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110	30	125	0	0.272727	0	.	.	none	.	BTG2	16	.	NM_006763	exon1	c.G102A	p.R34R	GCAGAGGCTTAAG	.	PASS	Atlas-SNP
TPCN2	219931	hgsc.bcm.edu	37	11	68840160	68840160	+	Missense_Mutation	SNP	A	A	G	rs3750965	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	104	79	105	2	0.759615	0.0190476	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	.	scavenged	Atlas-SNP
SRP72	6731	hgsc.bcm.edu	37	4	57333822	57333822	+	Silent	SNP	G	G	T	rs12513091	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79	38	88	0	0.481013	0	A|0.000;C|0.000;G|0.800;T|0.199	0.199	strong	SRP72,NS,carcinoma,0,1	SRP72	59	1	NM_006947	exon1	c.G21T	p.G7G	CAGCGGGGGGGTG	.	PASS	Atlas-SNP
TRIM31	11074	hgsc.bcm.edu	37	6	30080496	30080496	+	Silent	SNP	G	G	A	rs2844793	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	104	87	113	0	0.836538	0	G|0.893;A|0.107	0.107	strong	.	TRIM31	40	.	NM_007028	exon2	c.C87T	p.I29I	ACAGTCGATGGTG	.	PASS	Atlas-SNP
MRO	83876	hgsc.bcm.edu	37	18	48331524	48331524	+	Silent	SNP	G	G	A	rs2586776	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	128	52	119	1	0.40625	0.00840336	G|0.541;A|0.459	0.459	strong	MRO_ENST00000436348,colon,carcinoma,0,2	MRO	36	2	NM_001127175	exon4	c.C471T	p.D157D	ACTTACGTCATCT	.	scavenged	Atlas-SNP
KBTBD8	84541	hgsc.bcm.edu	37	3	67054649	67054649	+	Missense_Mutation	SNP	T	T	C	rs13096789	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	111	110	121	0	0.990991	0	C|0.097;N|0.000	0.097	strong	.	KBTBD8	101	.	NM_032505	exon3	c.T1258C	p.C420R	GAGAATTGTTGGA	.	PASS	Atlas-SNP
C10orf11	83938	hgsc.bcm.edu	37	10	77807027	77807027	+	Silent	SNP	T	T	C	rs1898071	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98	44	78	0	0.44898	0	T|0.608;C|0.392	0.392	strong	.	C10orf11	19	.	NM_032024	exon3	c.T280C	p.L94L	GTCAGCTTGGAAA	.	PASS	Atlas-SNP
POLRMT	5442	hgsc.bcm.edu	37	19	621070	621070	+	Silent	SNP	G	G	A	rs77809401	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	29	58	0	0.439394	0	G|0.849;A|0.151	0.151	strong	.	POLRMT	91	.	NM_005035	exon10	c.C2628T	p.D876D	GGGTTGGTCCGCG	.	PASS	Atlas-SNP
ST13	6767	hgsc.bcm.edu	37	22	41223190	41223190	+	Missense_Mutation	SNP	C	C	T	rs710193	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	15	7	13	0	0.466667	0	C|0.940;T|0.060	0.060	strong	.	ST13	16	.	NM_003932	exon11	c.G891A	p.M297I	TCCAGGCATTCCT	.	PASS	Atlas-SNP
EFCAB7	84455	hgsc.bcm.edu	37	1	63997633	63997633	+	Silent	SNP	A	A	T	rs9804078	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	130	50	134	0	0.384615	0	A|0.815;T|0.185	0.185	strong	EFCAB7,colon,carcinoma,+1,1	EFCAB7	45	1	NM_032437	exon3	c.A330T	p.S110S	AAAATCATTTAAG	.	PASS	Atlas-SNP
OR10K2	391107	hgsc.bcm.edu	37	1	158390501	158390501	+	Silent	SNP	G	G	A	rs34616883	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	193	91	186	0	0.471503	0	G|0.643;A|0.357	0.357	strong	OR10K2,NS,carcinoma,0,1	OR10K2	69	1	NM_001004476	exon1	c.C156T	p.D52D	GGCCCTGTCCAGG	.	PASS	Atlas-SNP
NSL1	25936	hgsc.bcm.edu	37	1	212965095	212965095	+	Missense_Mutation	SNP	G	G	A	rs17856201	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	34	57	0	0.539683	0	G|0.841;A|0.159	0.159	strong	.	NSL1	24	.	NM_015471	exon1	c.C11T	p.S4F	TCAGGAGACCCCG	.	PASS	Atlas-SNP
BCL2A1	597	hgsc.bcm.edu	37	15	80260014	80260014	+	Silent	SNP	T	T	C	rs8026803	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	26	114	0	0.366197	0	T|0.622;C|0.378	0.378	strong	.	BCL2A1	28	.	NM_001114735	exon2	c.A441G	p.T147T	CATAGGTGTGTGA	.	PASS	Atlas-SNP
NUDC	10726	hgsc.bcm.edu	37	1	27268110	27268110	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	105	6	84	0	0.0571429	0	.	.	none	.	NUDC	15	.	NM_006600	exon3	c.A322C	p.T108P	GAGCTAACTGATG	.	PASS	Atlas-SNP
NUDT16	131870	hgsc.bcm.edu	37	3	131102053	131102053	+	Silent	SNP	A	A	G	rs11549806	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	45	66	0	0.6	0	A|0.956;G|0.044	0.044	strong	.	NUDT16	10	.	NM_152395	exon3	c.A456G	p.V152V	TGGTGTAGGAGGC	.	PASS	Atlas-SNP
ZNF853	54753	hgsc.bcm.edu	37	7	6656897	6656897	+	Missense_Mutation	SNP	A	A	G	rs1806552	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	29	12	32	0	0.413793	0	A|0.289;G|0.711	0.711	strong	ZNF853_ENST00000457543,NS,carcinoma,+1,2	ZNF853	32	2	NM_017560	exon2	c.A89G	p.Q30R	AACTTCAATGTCT	.	PASS	Atlas-SNP
MMP10	4319	hgsc.bcm.edu	37	11	102650246	102650246	+	Silent	SNP	G	G	A	rs17860949	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	89	60	108	0	0.674157	0	G|0.872;A|0.128	0.128	strong	.	MMP10	44	.	NM_002425	exon2	c.C336T	p.H112H	TGTAAGGTGGGTT	.	PASS	Atlas-SNP
MARVELD3	91862	hgsc.bcm.edu	37	16	71674882	71674882	+	Silent	SNP	C	C	G	rs2303225	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	173	90	178	0	0.520231	0	C|0.647;G|0.353	0.353	strong	.	MARVELD3	63	.	NM_001017967	exon3	c.C1185G	p.P395P	ACAGCCCGGAAGT	.	PASS	Atlas-SNP
EFCAB7	84455	hgsc.bcm.edu	37	1	64011657	64011657	+	Missense_Mutation	SNP	A	A	G	rs41313264	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	170	75	164	0	0.441176	0	A|0.993;G|0.007	0.007	strong	.	EFCAB7	45	.	NM_032437	exon7	c.A875G	p.Y292C	ATCAGTACAGGAT	.	PASS	Atlas-SNP
HPSE2	60495	hgsc.bcm.edu	37	10	100481475	100481475	+	Missense_Mutation	SNP	C	C	T	rs142102360	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	21	61	0	0.403846	0	C|0.997;T|0.003	0.003	strong	.	HPSE2	203	.	NM_001166246	exon5	c.G895A	p.A299T	AGCTGGCTCTGGA	.	PASS	Atlas-SNP
STOML1	9399	hgsc.bcm.edu	37	15	74277666	74277666	+	Silent	SNP	C	C	T	rs34353835	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	34	77	0	0.507463	0	C|0.980;T|0.020	0.020	strong	.	STOML1	22	.	NM_001256672	exon5	c.G783A	p.P261P	TGGCCCCGGGGAC	.	PASS	Atlas-SNP
SNX29	92017	hgsc.bcm.edu	37	16	12662420	12662420	+	Silent	SNP	C	C	T	rs2288423	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	21	21	30	0	1	0	C|0.684;T|0.316	0.316	strong	.	SNX29	60	.	NM_032167	exon21	c.C2376T	p.F792F	CCGCTTCCCCAAA	.	PASS	Atlas-SNP
NPAS2	4862	hgsc.bcm.edu	37	2	101606810	101606810	+	Silent	SNP	G	G	A	rs1053091	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	108	43	105	0	0.398148	0	G|0.989;A|0.011	0.011	strong	.	NPAS2	88	.	NM_002518	exon18	c.G1920A	p.A640A	AGCTGCGCTCCCG	.	PASS	Atlas-SNP
COL2A1	1280	hgsc.bcm.edu	37	12	48379731	48379731	+	Silent	SNP	G	G	T	rs41317925	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73	31	78	0	0.424658	0	G|0.990;T|0.010	0.010	strong	COL2A1_ENST00000380518,colon,carcinoma,-1,2	COL2A1	368	2	NM_001844	exon24	c.C1545A	p.R515R	GAAACCGCGGTTG	.	PASS	Atlas-SNP
SPPL2C	162540	hgsc.bcm.edu	37	17	43923934	43923934	+	Silent	SNP	T	T	C	rs11079725	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	39	39	48	0	1	0	T|0.854;C|0.146	0.146	strong	.	.	.	.	NM_175882	exon1	c.T1662C	p.D554D	AGCAGATGCCCAC	.	PASS	Atlas-SNP
CSNK2A3	283106	hgsc.bcm.edu	37	11	11374269	11374269	+	Missense_Mutation	SNP	A	A	G	rs41334347	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83	82	113	0	0.987952	0	A|0.875;G|0.125	0.125	weak	.	.	.	.	NM_001256686	exon1	c.T398C	p.I133T	AATCGAATATCAT	.	PASS	Atlas-SNP
CARD8	22900	hgsc.bcm.edu	37	19	48737764	48737764	+	Silent	SNP	A	A	G	rs2288876	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80	37	72	0	0.4625	0	A|0.758;G|0.242	0.242	strong	.	CARD8	53	.	NM_001184900	exon3	c.T246C	p.L82L	GTCACAAAGGGTC	.	PASS	Atlas-SNP
LCAT	3931	hgsc.bcm.edu	37	16	67976320	67976320	+	Missense_Mutation	SNP	A	A	T	rs4986970	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	114	64	126	0	0.561404	0	A|0.983;T|0.017	0.017	strong	.	LCAT	31	.	NM_000229	exon5	c.T694A	p.S232T	CAAGAGAGATGAA	.	PASS	Atlas-SNP
OR2L2	26246	hgsc.bcm.edu	37	1	248202344	248202344	+	Missense_Mutation	SNP	G	G	C	rs6658141	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	122	62	104	0	0.508197	0	G|0.650;C|0.350	0.350	strong	.	OR2L2	115	.	NM_001004686	exon1	c.G775C	p.V259L	ACCTATGTACGTC	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1264940	1264940	+	Missense_Mutation	SNP	C	C	G	rs71469858	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	298	16	304	0	0.0536913	0	C|0.500;G|0.500	0.500	weak	MUC5B,NS,carcinoma,0,2	MUC5B	473	2	NM_002458	exon31	c.C6830G	p.T2277R	ACACCACGGCCAC	.	scavenged	Atlas-SNP
RALGDS	5900	hgsc.bcm.edu	37	9	135985796	135985796	+	Silent	SNP	C	C	T	rs3761824	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	41	15	54	0	0.365854	0	C|0.754;T|0.246	0.246	strong	.	RALGDS	75	.	NM_006266	exon3	c.G375A	p.V125V	GTGCTCCACCAGC	.	PASS	Atlas-SNP
COX3	5742	hgsc.bcm.edu	37	MT	9932	9932	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	8	8	4	0	1	0	.	.	none	.	.	.	.	ENST00000362079	exon1	c.G726A	p.W242W	ATACTGGCATTTT	.	PASS	Atlas-SNP
C1orf131	128061	hgsc.bcm.edu	37	1	231376806	231376806	+	Missense_Mutation	SNP	G	G	C	rs2274067	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	103	56	136	0	0.543689	0	G|0.919;C|0.081	0.081	strong	.	C1orf131	30	.	NM_152379	exon1	c.C82G	p.L28V	CAAGAAGTGTCGG	.	PASS	Atlas-SNP
LIPK	643414	hgsc.bcm.edu	37	10	90503075	90503075	+	Silent	SNP	T	T	C	rs390152	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	56	29	62	1	0.517857	0.016129	T|0.754;C|0.246	0.246	strong	LIPK_ENST00000404190,colon,carcinoma,0,2	LIPK	50	2	NM_001080518	exon8	c.T957C	p.H319H	CTTCCATCAGGTA	.	scavenged	Atlas-SNP
SLC4A9	83697	hgsc.bcm.edu	37	5	139745154	139745154	+	Silent	SNP	T	T	C	rs6860077	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	242	241	227	0	0.995868	0	T|0.282;C|0.718	0.718	strong	.	SLC4A9	125	.	NM_001258428	exon12	c.T1773C	p.I591I	CGACATTGTAAGC	.	PASS	Atlas-SNP
CERS6	253782	hgsc.bcm.edu	37	2	169312974	169312974	+	Missense_Mutation	SNP	G	G	A	rs4496303	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72	36	75	0	0.5	0	A|0.008;G|0.990;T|0.002	0.008	strong	.	.	.	.	NM_001256126	exon1	c.G16A	p.A6T	ATCTTAGCCTGGT	.	PASS	Atlas-SNP
MASTL	84930	hgsc.bcm.edu	37	10	27462061	27462061	+	Silent	SNP	G	G	A	rs41282228	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	31	52	0	0.469697	0	G|0.989;A|0.011	0.011	strong	.	MASTL	81	.	NM_001172303	exon9	c.G2139A	p.Q713Q	AAATCAGATCAAG	.	PASS	Atlas-SNP
DMGDH	29958	hgsc.bcm.edu	37	5	78324352	78324352	+	Missense_Mutation	SNP	A	A	G	rs1805074	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110	57	101	0	0.518182	0	A|0.674;G|0.326	0.326	strong	.	DMGDH	88	.	NM_013391	exon12	c.T1936C	p.S646P	CTTCAGAGGTCAG	.	PASS	Atlas-SNP
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32629963	32629963	+	Missense_Mutation	SNP	C	C	T	rs1049100	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	40	18	29	0	0.45	0	C|0.816;T|0.184	0.184	strong	.	HLA-DQB1	15	.	NM_002123	exon3	c.G442A	p.V148I	AGCAGACCAGCAG	.	PASS	Atlas-SNP
LAMC2	3918	hgsc.bcm.edu	37	1	183206573	183206573	+	Silent	SNP	G	G	A	rs1047981	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	235	121	272	2	0.514894	0.00735294	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	.	scavenged	Atlas-SNP
MAEL	84944	hgsc.bcm.edu	37	1	166958710	166958710	+	Missense_Mutation	SNP	T	T	G	rs11578336	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	21	48	0	0.396226	0	T|0.743;G|0.257	0.257	strong	MAEL,NS,carcinoma,0,1	MAEL	95	1	NM_032858	exon1	c.T121G	p.S41A	TGCTCCTCAGACT	.	PASS	Atlas-SNP
DNMBP	23268	hgsc.bcm.edu	37	10	101645498	101645498	+	Silent	SNP	T	T	C	rs2490763	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	142	140	119	0	0.985915	0	T|0.492;C|0.508	0.508	strong	.	DNMBP	173	.	NM_015221	exon14	c.A3744G	p.P1248P	CTCAAATGGCTTC	.	PASS	Atlas-SNP
TSR1	55720	hgsc.bcm.edu	37	17	2238675	2238675	+	Silent	SNP	A	A	G	rs61743762	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57	28	68	0	0.491228	0	A|0.974;G|0.026	0.026	strong	.	TSR1	57	.	NM_018128	exon4	c.T435C	p.V145V	TAACACAACGTGC	.	PASS	Atlas-SNP
SETX	23064	hgsc.bcm.edu	37	9	135205006	135205006	+	Missense_Mutation	SNP	G	G	C	rs882709	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	117	35	142	0	0.299145	0	G|0.828;C|0.172	0.172	strong	.	SETX	234	.	NM_015046	exon10	c.C1979G	p.A660G	TTATCTGCTTTGA	.	PASS	Atlas-SNP
SLC7A4	6545	hgsc.bcm.edu	37	22	21385843	21385843	+	Silent	SNP	G	G	A	rs2072549	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	46	25	37	0	0.543478	0	G|0.789;A|0.211	0.211	strong	.	SLC7A4	50	.	NM_004173	exon2	c.C259T	p.L87L	AGCATAGGGCTGC	.	PASS	Atlas-SNP
BCL10	8915	hgsc.bcm.edu	37	1	85742012	85742012	+	Silent	SNP	G	G	C	rs11576939	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	126	57	133	0	0.452381	0	G|0.735;C|0.265	0.265	strong	.	BCL10	39	.	NM_003921	exon1	c.C24G	p.L8L	CTCGGTGAGGGAC	.	PASS	Atlas-SNP
MMP20	9313	hgsc.bcm.edu	37	11	102477377	102477377	+	Missense_Mutation	SNP	G	G	T	rs1784424	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	131	21	122	0	0.160305	0	G|0.598;T|0.402	0.402	strong	.	MMP20	52	.	NM_004771	exon6	c.C842A	p.T281N	GGCAGAGTGGGCT	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	23	93	0	0.348485	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
MAN2A2	4122	hgsc.bcm.edu	37	15	91459475	91459475	+	Missense_Mutation	SNP	G	G	A	rs12909056	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	31	12	35	0	0.387097	0	G|0.859;A|0.141	0.141	strong	.	MAN2A2	99	.	NM_006122	exon19	c.G2983A	p.V995M	CGAACCGTGGGCA	.	PASS	Atlas-SNP
PDILT	204474	hgsc.bcm.edu	37	16	20410547	20410547	+	Missense_Mutation	SNP	C	C	T	rs9926580	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	35	59	0	0.432099	0	C|0.673;T|0.327	0.327	strong	.	PDILT	120	.	NM_174924	exon2	c.G76A	p.A26T	CACCGGCGTTAAC	.	PASS	Atlas-SNP
ERCC6	2074	hgsc.bcm.edu	37	10	50740876	50740876	+	Silent	SNP	G	G	C	rs2228524	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55	55	45	0	1	0	G|0.381;C|0.619	0.619	strong	.	ERCC6	162	.	NM_000124	exon2	c.G135G	p.T45T	AAAGGAGAGGTAC	.	PASS	Atlas-SNP
ZSCAN12	9753	hgsc.bcm.edu	37	6	28366151	28366151	+	Missense_Mutation	SNP	A	A	G	rs2232423	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	208	158	240	0	0.759615	0	A|0.959;G|0.041	0.041	strong	.	ZSCAN12	35	.	NM_001163391	exon2	c.T32C	p.M11T	TGGTCCATGTGGG	.	PASS	Atlas-SNP
NCKAP5	344148	hgsc.bcm.edu	37	2	133489601	133489601	+	Silent	SNP	A	A	G	rs56284623	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	22	94	0	0.349206	0	A|0.822;G|0.178	0.178	strong	.	NCKAP5	322	.	NM_207363	exon17	c.T5152C	p.L1718L	TGTCCAATGTTCT	.	PASS	Atlas-SNP
MS4A14	84689	hgsc.bcm.edu	37	11	60184191	60184191	+	Missense_Mutation	SNP	G	G	A	rs3825020	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	65	34	52	0	0.523077	0	G|0.445;A|0.555	0.555	strong	.	MS4A14	120	.	NM_001261828	exon6	c.G1849A	p.G617R	AAAGATGGACAAG	.	PASS	Atlas-SNP
RPA4	29935	hgsc.bcm.edu	37	X	96139406	96139406	+	Missense_Mutation	SNP	G	G	A	rs2642219	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82	22	68	0	0.268293	0	G|0.556;0|0.014	.	strong	.	RPA4	29	.	NM_013347	exon1	c.G97A	p.A33T	ACTCCTGCTATTA	.	PASS	Atlas-SNP
OR4L1	122742	hgsc.bcm.edu	37	14	20528362	20528362	+	Silent	SNP	A	A	G	rs1958717	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	303	129	362	0	0.425743	0	A|0.530;G|0.470	0.470	strong	.	OR4L1	98	.	NM_001004717	exon1	c.A159G	p.S53S	TAGGTCAACCCTT	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	46	18	53	0	0.391304	0	G|0.607;C|0.393	0.393	strong	.	MUC4	1505	.	NM_018406	exon7	c.C13506G	p.N4502K	CACCGGGTTGCCT	.	PASS	Atlas-SNP
NEFH	4744	hgsc.bcm.edu	37	22	29885473	29885473	+	Missense_Mutation	SNP	C	C	T	rs5763269	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	25	13	27	0	0.52	0	C|0.815;T|0.185	0.185	strong	.	NEFH	178	.	NM_021076	exon4	c.C1844T	p.P615L	AGTCACCGGCTGA	.	PASS	Atlas-SNP
SLC51A	200931	hgsc.bcm.edu	37	3	195956827	195956827	+	Silent	SNP	T	T	C	rs17852687	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	36	99	0	0.418605	0	T|0.544;C|0.456	0.456	strong	.	.	.	.	NM_152672	exon7	c.T675C	p.L225L	TTTCCTTGGCGTG	.	PASS	Atlas-SNP
C11orf24	53838	hgsc.bcm.edu	37	11	68030173	68030173	+	Missense_Mutation	SNP	C	C	A	rs3802746	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	161	159	211	1	0.987578	0.00473934	T|0.000;C|0.709;A|0.291	0.291	strong	.	C11orf24	35	.	NM_022338	exon4	c.G290T	p.G97V	GCTGCACCTCCTG	.	PASS	Atlas-SNP
TCHP	84260	hgsc.bcm.edu	37	12	110340852	110340852	+	Silent	SNP	G	G	A	rs11539159	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	107	52	108	0	0.485981	0	G|0.883;A|0.117	0.117	strong	.	TCHP	45	.	NM_001143852	exon2	c.G21A	p.P7P	GCTGCCGTCCTAC	.	PASS	Atlas-SNP
TUBGCP3	10426	hgsc.bcm.edu	37	13	113140350	113140350	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	150	101	154	0	0.673333	0	.	.	none	.	TUBGCP3	74	.	NM_006322	exon22	c.G2681A	p.R894H	GACACACGGAGCC	.	PASS	Atlas-SNP
GDF9	2661	hgsc.bcm.edu	37	5	132200000	132200000	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100	13	95	0	0.13	0	.	.	none	.	GDF9	50	.	NM_005260	exon1	c.T226G	p.S76A	TAGGTGACCCACC	.	PASS	Atlas-SNP
APOL5	80831	hgsc.bcm.edu	37	22	36122517	36122517	+	Silent	SNP	T	T	C	rs17723764	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	114	54	82	0	0.473684	0	C|0.262;N|0.000	0.262	strong	.	APOL5	45	.	NM_030642	exon3	c.T402C	p.L134L	GTTGCTTACCAAG	.	PASS	Atlas-SNP
HIST1H2BF	8343	hgsc.bcm.edu	37	6	26200083	26200083	+	Silent	SNP	A	A	G	rs1059486	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	45	36	57	0	0.8	0	A|0.469;G|0.531	0.531	strong	.	HIST1H2BF	25	.	NM_003522	exon1	c.A297G	p.V99V	GGCCGTACGCCTG	.	PASS	Atlas-SNP
YME1L1	10730	hgsc.bcm.edu	37	10	27436566	27436566	+	Missense_Mutation	SNP	T	T	C	rs62622019	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	262	129	260	0	0.492366	0	T|0.948;C|0.052	0.052	strong	.	YME1L1	71	.	NM_139312	exon3	c.A200G	p.N67S	ACAATGTTAAGCT	.	PASS	Atlas-SNP
SPARCL1	8404	hgsc.bcm.edu	37	4	88416223	88416223	+	Silent	SNP	A	A	G	rs8342	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	243	109	264	1	0.44856	0.00378788	A|0.308;G|0.692	0.692	strong	.	SPARCL1	59	.	NM_004684	exon3	c.T111C	p.P37P	GTTGTCAGGTGCT	.	PASS	Atlas-SNP
CDRT1	374286	hgsc.bcm.edu	37	17	15510888	15510888	+	Missense_Mutation	SNP	G	G	A	rs62070401	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	157	76	159	0	0.484076	0	G|0.754;A|0.246	0.246	strong	.	CDRT1	83	.	NM_006382	exon6	c.C1232T	p.T411M	ACCTACGTGTCAG	.	PASS	Atlas-SNP
C19orf55	148137	hgsc.bcm.edu	37	19	36258721	36258721	+	Missense_Mutation	SNP	C	C	T	rs73592448	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	46	21	64	0	0.456522	0	C|0.916;T|0.084	0.084	strong	.	C19orf55	39	.	NM_001039887	exon9	c.C974T	p.A325V	TGAAAGCCAAGGC	.	PASS	Atlas-SNP
DNAJA4	55466	hgsc.bcm.edu	37	15	78565495	78565495	+	Silent	SNP	G	G	A	rs74978019	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	255	113	234	1	0.443137	0.0042735	G|0.997;A|0.003	0.003	strong	DNAJA4_ENST00000446172,NS,carcinoma,+1,2	DNAJA4	63	2	NM_018602	exon4	c.G459A	p.T153T	AGTCACGAAGAAA	.	PASS	Atlas-SNP
OR2T33	391195	hgsc.bcm.edu	37	1	248436721	248436721	+	Silent	SNP	A	A	G	rs74363422	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	770	89	609	4	0.115584	0.00656814	A|0.999;G|0.001	0.001	weak	OR2T33,NS,carcinoma,-1,1	OR2T33	133	1	NM_001004695	exon1	c.T396C	p.T132T	CATGAGAGTGGGA	.	scavenged	Atlas-SNP
HNRNPCL1	343069	hgsc.bcm.edu	37	1	12907762	12907762	+	Silent	SNP	T	T	C	rs57026768	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	188	35	150	0	0.18617	0	T|0.966;C|0.034	0.034	strong	HNRNPCL1,NS,carcinoma,0,2	HNRNPCL1	68	2	NM_001013631	exon2	c.A381G	p.P127P	ACGTGCTGGGAAA	.	PASS	Atlas-SNP
CASS4	57091	hgsc.bcm.edu	37	20	55012318	55012318	+	Silent	SNP	G	G	A	rs911159	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	26	90	0	0.346667	0	G|0.864;A|0.136	0.136	strong	.	CASS4	121	.	NM_020356	exon2	c.G135A	p.V45V	ACACGTGCCAGAA	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	149	116	126	0	0.778524	0	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	.	PASS	Atlas-SNP
SNX5	27131	hgsc.bcm.edu	37	20	17949050	17949050	+	Silent	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	16	114	2	0.253968	0.0175439	.	.	none	SNX5,NS,lymphoid_neoplasm,+2,1	SNX5	38	1	NM_014426	exon1	c.T19C	p.L7L	GCAGCAACTCGGG	.	scavenged	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9056989	9056989	+	Missense_Mutation	SNP	C	C	G	rs4804381	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94	44	88	0	0.468085	0	C|0.780;G|0.220	0.220	strong	.	MUC16	4315	.	NM_024690	exon3	c.G30457C	p.E10153Q	TGGTCTCAAAATT	.	PASS	Atlas-SNP
BBS12	166379	hgsc.bcm.edu	37	4	123664427	123664427	+	Silent	SNP	G	G	C	rs13135766	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	83	135	0	0.988095	0	G|0.853;C|0.147	0.147	strong	.	BBS12	63	.	NM_001178007	exon3	c.G1380C	p.V460V	ACAAGTGAATGAA	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9049339	9049339	+	Silent	SNP	C	C	G	rs11883220	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	144	141	148	1	0.979167	0.00675676	C|0.572;G|0.428;T|0.001	0.428	strong	.	MUC16	4315	.	NM_024690	exon5	c.G32292C	p.T10764T	GGCTATCGTCTTT	.	PASS	Atlas-SNP
TNRC6C	57690	hgsc.bcm.edu	37	17	76093866	76093866	+	Silent	SNP	T	T	C	rs2290906	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	30	51	0	0.576923	0	T|0.737;C|0.263	0.263	strong	.	TNRC6C	173	.	NM_001142640	exon18	c.T4338C	p.S1446S	GCCTTCTTCGAGT	.	PASS	Atlas-SNP
VWDE	221806	hgsc.bcm.edu	37	7	12433390	12433390	+	Missense_Mutation	SNP	G	G	A	rs139605380	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	29	76	0	0.54717	0	G|0.993;A|0.007	0.007	strong	.	VWDE	123	.	NM_001135924	exon2	c.C73T	p.P25S	CCCCAGGAGAGCA	.	PASS	Atlas-SNP
CPO	130749	hgsc.bcm.edu	37	2	207825656	207825656	+	Silent	SNP	A	A	T	rs13397039	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	101	56	134	0	0.554455	0	A|0.570;T|0.430	0.430	strong	.	CPO	42	.	NM_173077	exon6	c.A564T	p.A188A	CAATGCATCTTGG	.	PASS	Atlas-SNP
LCE1F	353137	hgsc.bcm.edu	37	1	152749091	152749091	+	Missense_Mutation	SNP	C	C	T	rs41268480	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	59	27	65	0	0.457627	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
CARD8	22900	hgsc.bcm.edu	37	19	48715153	48715153	+	Silent	SNP	T	T	C	rs3745718	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	162	90	178	0	0.555556	0	T|0.588;C|0.412	0.412	strong	CARD8_ENST00000391898,colon,carcinoma,0,1	CARD8	53	1	NM_001184900	exon11	c.A1428G	p.Q476Q	ATTGTCTTGGAGA	.	PASS	Atlas-SNP
PSG5	5673	hgsc.bcm.edu	37	19	43690506	43690506	+	Missense_Mutation	SNP	G	G	C	rs8107936	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	12	12	28	0	1	0	G|0.373;C|0.627	0.627	strong	PSG5,rectum,carcinoma,0,1	PSG5	58	1	NM_002781	exon1	c.C52G	p.L18V	GCAGGAGCCCCTT	.	PASS	Atlas-SNP
IFT74	80173	hgsc.bcm.edu	37	9	27062721	27062721	+	Missense_Mutation	SNP	C	C	T	rs3429	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	134	65	115	0	0.485075	0	C|0.900;T|0.100	0.100	strong	.	IFT74	46	.	NM_001099222	exon20	c.C1790T	p.T597I	ATAGCACCAGCGG	.	PASS	Atlas-SNP
RSL1D1	26156	hgsc.bcm.edu	37	16	11933666	11933666	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	173	3	174	0	0.017341	0	.	.	none	RSL1D1,NS,NS,0,1	RSL1D1	40	1	NM_015659	exon8	c.G1032A	p.G344G	TTTCTTCCCATGC	.	scavenged	Atlas-SNP
KRT28	162605	hgsc.bcm.edu	37	17	38950272	38950272	+	Silent	SNP	T	T	C	rs2250671	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	90	89	129	0	0.988889	0	T|0.373;C|0.627	0.627	strong	.	KRT28	65	.	NM_181535	exon6	c.A1005G	p.T335T	GGTCTCTGTCAAG	.	PASS	Atlas-SNP
FAM86C1	55199	hgsc.bcm.edu	37	11	71507205	71507205	+	Missense_Mutation	SNP	C	C	T	rs71459604		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	133	13	160	0	0.0977444	0	C|0.500;T|0.500	0.500	weak	FAM86C1_ENST00000426628,NS,carcinoma,0,2	FAM86C1	27	2	NM_018172	exon4	c.C404T	p.P135L	CACCACCGAGCTA	.	scavenged	Atlas-SNP
LRRC55	219527	hgsc.bcm.edu	37	11	56954846	56954846	+	Silent	SNP	C	C	T	rs716745	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	127	126	129	1	0.992126	0.00775194	C|0.718;T|0.282	0.282	strong	.	LRRC55	52	.	NM_001005210	exon2	c.C918T	p.F306F	TGCGTTCGTGGGC	.	PASS	Atlas-SNP
MATN2	4147	hgsc.bcm.edu	37	8	98954108	98954108	+	Silent	SNP	G	G	T	rs35407519	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	250	108	259	0	0.432	0	G|0.905;T|0.095	0.095	strong	.	MATN2	165	.	NM_002380	exon4	c.G816T	p.S272S	CAACTCGGATCAG	.	PASS	Atlas-SNP
DOCK10	55619	hgsc.bcm.edu	37	2	225750861	225750861	+	Silent	SNP	C	C	T	rs2304336	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	27	43	0	0.364865	0	C|0.784;T|0.216	0.216	strong	DOCK10,colon,carcinoma,-1,1	DOCK10	308	1	NM_014689	exon6	c.G531A	p.A177A	TCCTCCCGCTCCT	.	PASS	Atlas-SNP
BAI3	577	hgsc.bcm.edu	37	6	69348966	69348966	+	Silent	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	43	9	36	0	0.209302	0	.	.	none	BAI3,NS,carcinoma,+1,1	BAI3	451	1	NM_001704	exon3	c.A399C	p.V133V	TCGAGTATTTCCA	.	scavenged	Atlas-SNP
UAP1L1	91373	hgsc.bcm.edu	37	9	139972672	139972672	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44	24	73	0	0.545455	0	.	.	none	.	UAP1L1	46	.	NM_207309	exon2	c.G460A	p.G154S	CTGGCCGGTGAGC	.	PASS	Atlas-SNP
SOS2	6655	hgsc.bcm.edu	37	14	50616878	50616878	+	Silent	SNP	G	G	A	rs2229869	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	170	81	176	0	0.476471	0	G|0.426;A|0.574	0.574	strong	.	SOS2	195	.	NM_006939	exon14	c.C2232T	p.N744N	TACTCCGTTTGCC	.	PASS	Atlas-SNP
OR10K1	391109	hgsc.bcm.edu	37	1	158435928	158435928	+	Missense_Mutation	SNP	G	G	A	rs41273489	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	274	147	275	1	0.536496	0.00363636	G|0.931;A|0.069	0.069	strong	.	OR10K1	80	.	NM_001004473	exon1	c.G577A	p.G193S	CACTCCGGCTTCA	.	PASS	Atlas-SNP
WDR66	144406	hgsc.bcm.edu	37	12	122405912	122405912	+	Missense_Mutation	SNP	G	G	T	rs1169081	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	45	25	39	0	0.555556	0	G|0.708;T|0.292	0.292	strong	.	WDR66	143	.	NM_001178003	exon17	c.G2608T	p.V870L	TTCTAGGTGGGAC	.	PASS	Atlas-SNP
SEPT12	124404	hgsc.bcm.edu	37	16	4833970	4833970	+	Silent	SNP	C	C	T	rs759991	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	80	106	0	0.952381	0	C|0.728;T|0.272	0.272	strong	SEPT12,NS,carcinoma,0,1	SEPT12	40	1	NM_144605	exon5	c.G474A	p.V158V	GCAGTGCACCCGG	.	PASS	Atlas-SNP
ACAP1	9744	hgsc.bcm.edu	37	17	7254315	7254315	+	Missense_Mutation	SNP	G	G	A	rs35985803	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73	38	70	0	0.520548	0	G|0.944;A|0.056	0.056	strong	.	ACAP1	66	.	NM_014716	exon21	c.G2119A	p.A707T	GGGCAGGCAGGTA	.	PASS	Atlas-SNP
VCAN	1462	hgsc.bcm.edu	37	5	82815408	82815408	+	Missense_Mutation	SNP	G	G	A	rs2287926	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	137	78	158	0	0.569343	0	G|0.819;A|0.181	0.181	strong	.	VCAN	498	.	NM_004385	exon7	c.G1283A	p.G428D	CTACTGGCAGTAC	.	PASS	Atlas-SNP
IKBKAP	8518	hgsc.bcm.edu	37	9	111668652	111668652	+	Missense_Mutation	SNP	C	C	T	rs838827	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	124	60	136	0	0.483871	0	C|0.924;T|0.076	0.076	strong	.	IKBKAP	122	.	NM_003640	exon14	c.G1574A	p.R525Q	ACAGACCGGGGGC	.	PASS	Atlas-SNP
NPHP4	261734	hgsc.bcm.edu	37	1	5965381	5965381	+	Silent	SNP	C	C	T	rs12120967	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	148	146	145	0	0.986486	0	C|0.908;T|0.092	0.092	strong	.	NPHP4	119	.	NM_015102	exon15	c.G1926A	p.E642E	CACCATCTCGTTG	.	PASS	Atlas-SNP
SRA1	10011	hgsc.bcm.edu	37	5	139936760	139936760	+	Nonsense_Mutation	SNP	G	G	T	rs250426	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	103	96	106	0	0.932039	0	A|0.000;G|0.374;T|0.626	0.626	strong	.	SRA1	24	.	NM_001253764	exon1	c.C278A	p.S93X	TGCGGCGACCCTC	.	PASS	Atlas-SNP
SUSD5	26032	hgsc.bcm.edu	37	3	33195309	33195309	+	Missense_Mutation	SNP	A	A	G	rs61743461	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68	32	55	0	0.470588	0	A|0.820;G|0.180	0.180	strong	.	SUSD5	53	.	NM_015551	exon5	c.T815C	p.L272S	CCAGGCAAGCCTG	.	PASS	Atlas-SNP
FAM135B	51059	hgsc.bcm.edu	37	8	139144914	139144914	+	Silent	SNP	G	G	A	rs2280848	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	152	87	157	0	0.572368	0	G|0.930;A|0.070	0.070	strong	.	FAM135B	423	.	NM_015912	exon20	c.C4143T	p.A1381A	GTGAGCGGCTCGG	.	PASS	Atlas-SNP
OR10J1	26476	hgsc.bcm.edu	37	1	159410258	159410258	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	226	69	229	0	0.30531	0	.	.	none	OR10J1,NS,carcinoma,0,1	OR10J1	118	1	NM_012351	exon1	c.A710C	p.K237T	TCCTCAAGATTGC	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	58	29	43	0	0.5	0	C|0.325;N|0.000	0.325	strong	.	PTPRB	676	.	NM_001109754	exon5	c.A1033G	p.S345G	GCAAGCTGGTTGA	.	PASS	Atlas-SNP
MON2	23041	hgsc.bcm.edu	37	12	62928633	62928633	+	Missense_Mutation	SNP	G	G	A	rs10219555	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	36	11	27	0	0.305556	0	G|0.641;A|0.359	0.359	strong	.	MON2	160	.	NM_015026	exon13	c.G1642A	p.A548T	AGTAGGGCTGTTT	.	PASS	Atlas-SNP
UMODL1	89766	hgsc.bcm.edu	37	21	43543193	43543193	+	Missense_Mutation	SNP	G	G	A	rs150611312	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	22	51	1	0.293333	0.0196078	G|0.993;A|0.007	0.007	strong	UMODL1_ENST00000408989,NS,haematopoietic_neoplasm,0,2	UMODL1	186	2	NM_173568	exon16	c.G3464A	p.S1155N	ACGTGAGCCACAG	.	scavenged	Atlas-SNP
SGK1	6446	hgsc.bcm.edu	37	6	134494655	134494655	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85	16	81	0	0.188235	0	.	.	none	.	SGK1	387	.	NM_001143676	exon6	c.C563T	p.A188V	GGTTTAGCATGAG	.	PASS	Atlas-SNP
RGS12	6002	hgsc.bcm.edu	37	4	3417845	3417845	+	Silent	SNP	G	G	C	rs3213507	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73	20	130	0	0.273973	0	G|0.669;C|0.331	0.331	strong	.	RGS12	128	.	NM_002926	exon7	c.G2424C	p.L808L	GCAGCTGCAGGTA	.	PASS	Atlas-SNP
LRRC16B	90668	hgsc.bcm.edu	37	14	24534916	24534916	+	Missense_Mutation	SNP	G	G	T	rs79328356	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	33	68	0	0.515625	0	G|0.958;T|0.042	0.042	strong	LRRC16B,NS,carcinoma,+1,1	LRRC16B	120	1	NM_138360	exon34	c.G3482T	p.G1161V	TTCCCGGGTTGGA	.	PASS	Atlas-SNP
MAML1	9794	hgsc.bcm.edu	37	5	179201847	179201847	+	Missense_Mutation	SNP	G	G	A	rs6895902	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	22	76	0	0.34375	0	G|0.733;A|0.267	0.267	strong	MAML1,brain,glioma,0,1	MAML1	118	1	NM_014757	exon5	c.G3020A	p.S1007N	GGATGAGTGATTT	.	PASS	Atlas-SNP
IL1RN	3557	hgsc.bcm.edu	37	2	113890304	113890304	+	Silent	SNP	T	T	C	rs315952	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	49	128	0	0.604938	0	T|0.641;C|0.359	0.359	strong	.	IL1RN	30	.	NM_173841	exon6	c.T399C	p.S133S	AGACAGTGGCCCC	.	PASS	Atlas-SNP
STAG3	10734	hgsc.bcm.edu	37	7	99796146	99796146	+	Silent	SNP	A	A	C	rs3735241	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	252	128	220	0	0.507937	0	C|0.482;N|0.000	0.482	strong	.	STAG3	121	.	NM_012447	exon13	c.A1293C	p.P431P	CTACCCAGTTGTG	.	PASS	Atlas-SNP
APOC4	346	hgsc.bcm.edu	37	19	45448465	45448465	+	Missense_Mutation	SNP	T	T	G	rs5167	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	65	65	64	0	1	0	G|0.427;N|0.000	0.427	strong	.	APOC4	6	.	NM_001646	exon3	c.T287G	p.L96R	GTCCGCTCACCAA	.	PASS	Atlas-SNP
PSD4	23550	hgsc.bcm.edu	37	2	113940681	113940681	+	Silent	SNP	T	T	C	rs3748914	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48	47	70	0	0.979167	0	C|0.529;N|0.000	0.529	strong	PSD4,NS,carcinoma,0,1	PSD4	74	1	NM_012455	exon2	c.T648C	p.S216S	CAGCAGTGAGCCT	.	PASS	Atlas-SNP
CCDC168	643677	hgsc.bcm.edu	37	13	103391634	103391634	+	Missense_Mutation	SNP	C	C	T	rs7322112	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	53	94	0	1	0	C|0.324;T|0.676	0.676	strong	.	.	.	.	NM_001146197	exon4	c.G11413A	p.V3805I	CCATTACATCTTT	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179650701	179650701	+	Silent	SNP	C	C	T	rs6715406	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	115	53	115	0	0.46087	0	C|0.722;T|0.278	0.278	strong	.	TTN	18412	.	NM_001267550	exon14	c.G2244A	p.E748E	GGGAGGCTCAGCT	.	PASS	Atlas-SNP
KLB	152831	hgsc.bcm.edu	37	4	39448586	39448586	+	Missense_Mutation	SNP	C	C	T	rs35372803	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	22	11	31	0	0.5	0	C|0.969;T|0.031	0.031	strong	.	KLB	95	.	NM_175737	exon4	c.C2240T	p.A747V	ACTGGGCGGAACC	.	PASS	Atlas-SNP
GRIN3B	116444	hgsc.bcm.edu	37	19	1004740	1004740	+	Missense_Mutation	SNP	T	T	C	rs2240157	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	26	26	31	0	1	0	T|0.304;C|0.696	0.696	strong	.	GRIN3B	46	.	NM_138690	exon3	c.T1240C	p.W414R	CAGGTCTGGCCCA	.	PASS	Atlas-SNP
KRT14	3861	hgsc.bcm.edu	37	17	39742718	39742718	+	Silent	SNP	A	A	G	rs61729648	byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	38	71	0	0.575758	0	A|0.554;G|0.446	0.446	strong	.	KRT14	65	.	NM_000526	exon1	c.T369C	p.N123N	GCGGTCATTGAGG	.	PASS	Atlas-SNP
CD101	9398	hgsc.bcm.edu	37	1	117560818	117560818	+	Silent	SNP	A	A	G	rs3736908	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	38	83	0	0.44186	0	A|0.738;G|0.262	0.262	strong	.	CD101	95	.	NM_001256109	exon6	c.A1653G	p.Q551Q	GCCGCAAGTGATG	.	PASS	Atlas-SNP
CSNK1A1	1452	hgsc.bcm.edu	37	5	148904609	148904609	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	261	18	212	0	0.0689655	0	.	.	none	.	CSNK1A1	63	.	NM_001025105	exon3	c.A356T	p.Q119L	CATACCTGGTCAG	.	PASS	Atlas-SNP
OR2AG2	338755	hgsc.bcm.edu	37	11	6790028	6790028	+	Missense_Mutation	SNP	C	C	G	rs10839616	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	108	61	112	1	0.564815	0.00892857	C|0.737;G|0.263	0.263	strong	OR2AG2,right_upper_lobe,carcinoma,-1,1	OR2AG2	55	1	NM_001004490	exon1	c.G161C	p.R54P	TGGAGCCGGGCTT	.	scavenged	Atlas-SNP
TMEM17	200728	hgsc.bcm.edu	37	2	62729653	62729653	+	Silent	SNP	A	A	G	rs6713096	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	36	17	63	0	0.472222	0	A|0.922;G|0.078	0.078	strong	.	TMEM17	19	.	NM_198276	exon3	c.T237C	p.I79I	GATCACAATGAAT	.	PASS	Atlas-SNP
BIN3	55909	hgsc.bcm.edu	37	8	22526559	22526559	+	Silent	SNP	G	G	A	rs11550509	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	33	50	0	0.492537	0	G|0.877;A|0.123	0.123	strong	.	BIN3	16	.	NM_018688	exon1	c.C6T	p.S2S	TCACCAGCTCATG	.	PASS	Atlas-SNP
COL4A4	1286	hgsc.bcm.edu	37	2	227872182	227872182	+	Silent	SNP	G	G	A	rs2228557	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98	50	114	0	0.510204	0	G|0.540;A|0.460	0.460	strong	.	COL4A4	215	.	NM_000092	exon48	c.C4932T	p.F1644F	ATTTGCGAAAAAG	.	PASS	Atlas-SNP
PLEC	5339	hgsc.bcm.edu	37	8	144994212	144994212	+	Silent	SNP	A	A	T	rs34644439	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	32	57	0	0.592593	0	A|0.938;T|0.062	0.062	strong	PLEC_ENST00000436759,NS,carcinoma,0,3	PLEC	1144	3	NM_201380	exon32	c.T10188A	p.S3396S	GTACTCAGAGCTG	.	PASS	Atlas-SNP
SENP6	26054	hgsc.bcm.edu	37	6	76344431	76344431	+	Missense_Mutation	SNP	C	C	T	rs17414086	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	50	48	65	0	0.96	0	C|0.803;N|0.000	.	strong	.	SENP6	189	.	NM_001100409	exon5	c.C362T	p.T121M	AAAATACGCAAAA	.	PASS	Atlas-SNP
ARL11	115761	hgsc.bcm.edu	37	13	50205025	50205025	+	Missense_Mutation	SNP	T	T	C	rs3803185	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	107	66	73	0	0.616822	0	T|0.660;C|0.340	0.340	strong	.	ARL11	26	.	NM_138450	exon2	c.T442C	p.C148R	GACCACTGCTGGG	.	PASS	Atlas-SNP
COBL	23242	hgsc.bcm.edu	37	7	51094269	51094269	+	Missense_Mutation	SNP	G	G	A	rs61737954	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	30	56	0	0.454545	0	G|0.947;A|0.053	0.053	strong	.	COBL	167	.	NM_015198	exon11	c.C3478T	p.H1160Y	CGCTGTGCCCGCG	.	PASS	Atlas-SNP
SYT2	127833	hgsc.bcm.edu	37	1	202565948	202565948	+	Silent	SNP	G	G	A	rs504261	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	52	57	0	1	0	G|0.655;A|0.345	0.345	strong	.	SYT2	51	.	NM_177402	exon9	c.C1197T	p.I399I	CTGGGCGATGGGC	.	PASS	Atlas-SNP
ZCCHC9	84240	hgsc.bcm.edu	37	5	80600619	80600619	+	Missense_Mutation	SNP	C	C	G	rs16878594	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	108	64	121	0	0.592593	0	C|0.916;G|0.084	0.084	strong	.	ZCCHC9	26	.	NM_001131036	exon2	c.C43G	p.P15A	AAGAGACCCTTGC	.	PASS	Atlas-SNP
LPIN3	64900	hgsc.bcm.edu	37	20	39986085	39986085	+	Missense_Mutation	SNP	A	A	C	rs12625565	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48	23	45	0	0.479167	0	A|0.667;C|0.333	0.333	strong	.	LPIN3	69	.	NM_022896	exon16	c.A2037C	p.Q679H	AATCCAACTGTGA	.	PASS	Atlas-SNP
PSG6	5675	hgsc.bcm.edu	37	19	43420451	43420451	+	Missense_Mutation	SNP	G	G	C	rs3198831	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	133	63	153	0	0.473684	0	G|0.625;C|0.375	0.375	strong	.	PSG6	89	.	NM_001031850	exon2	c.C253G	p.H85D	GACCGTGTACTAC	.	PASS	Atlas-SNP
CCDC157	550631	hgsc.bcm.edu	37	22	30766698	30766698	+	Silent	SNP	G	G	A	rs141091935	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	115	52	102	0	0.452174	0	G|0.996;A|0.004	0.004	strong	.	CCDC157	86	.	NM_001017437	exon5	c.G804A	p.P268P	ACTGCCGGCTGCC	.	PASS	Atlas-SNP
MLPH	79083	hgsc.bcm.edu	37	2	238449007	238449007	+	Missense_Mutation	SNP	T	T	C	rs3817362	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	42	80	0	0.518519	0	T|0.643;C|0.357	0.357	strong	.	MLPH	41	.	NM_024101	exon10	c.T1121C	p.V374A	CTGGAGTGCGCAC	.	PASS	Atlas-SNP
ZDHHC11	79844	hgsc.bcm.edu	37	5	825286	825286	+	Missense_Mutation	SNP	G	G	T	rs2335585	bycluster;byfrequency;bysubmitter;byhapmap	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	129	14	94	0	0.108527	0	G|0.985;T|0.015	0.015	strong	ZDHHC11_ENST00000424784,NS,carcinoma,0,2	ZDHHC11	97	2	NM_024786	exon8	c.C1016A	p.T339K	CGTGCCGTCGAAT	.	PASS	Atlas-SNP
CYP2C9	1559	hgsc.bcm.edu	37	10	96702047	96702047	+	Missense_Mutation	SNP	C	C	T	rs41400645		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	131	59	149	0	0.450382	0	C|1.000;|0.000	.	weak	.	CYP2C9	82	.	NM_000771	exon3	c.C430T	p.R144C	GAGGACCGTGTTC	.	PASS	Atlas-SNP
STRN3	29966	hgsc.bcm.edu	37	14	31404490	31404490	+	Silent	SNP	A	A	C	rs149753992		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80	37	77	0	0.4625	0	A|1.000;C|0.000	0.000	weak	.	STRN3	117	.	NM_001083893	exon7	c.T867G	p.A289A	GTCAGCAGCTAAA	.	PASS	Atlas-SNP
BBOX1	8424	hgsc.bcm.edu	37	11	27114788	27114788	+	Silent	SNP	C	C	T	rs3183973	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	90	43	102	0	0.477778	0	C|0.675;T|0.325	0.325	strong	BBOX1,NS,carcinoma,0,1	BBOX1	46	1	NM_003986	exon5	c.C408T	p.H136H	TGAACACGCATAC	.	PASS	Atlas-SNP
CCDC18	343099	hgsc.bcm.edu	37	1	93672688	93672688	+	Silent	SNP	C	C	T	rs2783499	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93	40	88	0	0.430108	0	C|0.794;T|0.206	0.206	strong	.	CCDC18	93	.	NM_206886	exon9	c.C942T	p.N314N	TAACAACGGAAAA	.	PASS	Atlas-SNP
FAM53B	9679	hgsc.bcm.edu	37	10	126370517	126370517	+	Missense_Mutation	SNP	G	G	C	rs147832040	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	40	76	0	0.56338	0	G|0.998;C|0.002	0.002	strong	.	FAM53B	22	.	NM_014661	exon4	c.C565G	p.R189G	CAAATCGGTGGTG	.	PASS	Atlas-SNP
ZNF292	23036	hgsc.bcm.edu	37	6	87969480	87969480	+	Missense_Mutation	SNP	G	G	A	rs6910541	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	148	59	140	0	0.398649	0	G|0.875;A|0.125	0.125	strong	.	ZNF292	479	.	NM_015021	exon8	c.G6133A	p.V2045I	CAACTTGTAGAAA	.	PASS	Atlas-SNP
CCDC65	85478	hgsc.bcm.edu	37	12	49312593	49312593	+	Silent	SNP	A	A	G	rs10875893	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	125	67	118	0	0.536	0	A|0.678;G|0.322	0.322	strong	.	CCDC65	41	.	NM_033124	exon6	c.A933G	p.R311R	CCAAAGAACTCAG	.	PASS	Atlas-SNP
ZNF831	128611	hgsc.bcm.edu	37	20	57768399	57768399	+	Silent	SNP	T	T	C	rs442091	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49	31	66	1	0.632653	0.0151515	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	.	scavenged	Atlas-SNP
CCDC135	84229	hgsc.bcm.edu	37	16	57760115	57760115	+	Missense_Mutation	SNP	C	C	A	rs143054335	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	154	64	157	0	0.415584	0	C|1.000;A|0.000	0.000	strong	CCDC135,NS,carcinoma,0,1	CCDC135	97	1	NM_032269	exon13	c.C1894A	p.R632S	TCCAAGCGCGAGT	.	PASS	Atlas-SNP
ABHD12	26090	hgsc.bcm.edu	37	20	25282944	25282944	+	Silent	SNP	A	A	G	rs10966	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	29	44	0	0.54717	0	A|0.530;G|0.470	0.470	strong	.	ABHD12	46	.	NM_001042472	exon12	c.T1068C	p.D356D	TTTGAAATCTCGG	.	PASS	Atlas-SNP
PITPNM3	83394	hgsc.bcm.edu	37	17	6386947	6386947	+	Silent	SNP	G	G	A	rs34897053	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	157	82	127	0	0.522293	0	G|0.973;A|0.027	0.027	strong	.	PITPNM3	91	.	NM_031220	exon6	c.C477T	p.S159S	CAGCACGGAGCTG	.	PASS	Atlas-SNP
HMCN1	83872	hgsc.bcm.edu	37	1	186121996	186121996	+	Missense_Mutation	SNP	C	C	T	rs114629728	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	168	72	156	0	0.428571	0	C|0.996;T|0.004	0.004	strong	.	HMCN1	797	.	NM_031935	exon96	c.C15011T	p.T5004I	AAGTCACTGTAAA	.	PASS	Atlas-SNP
OR10H5	284433	hgsc.bcm.edu	37	19	15905431	15905431	+	Silent	SNP	T	T	C	rs4808381	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	216	103	215	0	0.476852	0	T|0.623;C|0.377	0.377	strong	.	OR10H5	49	.	NM_001004466	exon1	c.T573C	p.D191D	TGGAGATGATGTG	.	PASS	Atlas-SNP
MGAT5B	146664	hgsc.bcm.edu	37	17	74942478	74942478	+	Silent	SNP	C	C	T	rs8067984	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	30	60	0	0.46875	0	C|0.639;T|0.361	0.361	strong	.	MGAT5B	98	.	NM_198955	exon14	c.C1896T	p.Y632Y	ACCCTACGAGTAC	.	PASS	Atlas-SNP
ASB5	140458	hgsc.bcm.edu	37	4	177137988	177137988	+	Silent	SNP	C	C	T	rs6827525	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	159	80	202	0	0.503145	0	C|0.504;T|0.496	0.496	strong	.	ASB5	88	.	NM_080874	exon6	c.G843A	p.R281R	CAATATCCTTTCC	.	PASS	Atlas-SNP
RAB3B	5865	hgsc.bcm.edu	37	1	52399021	52399021	+	Silent	SNP	A	A	G	rs2230325	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	41	61	0	0.506173	0	A|0.931;G|0.069	0.069	strong	.	RAB3B	22	.	NM_002867	exon4	c.T441C	p.T147T	CTTCTCAGTGGGA	.	PASS	Atlas-SNP
EFCAB5	374786	hgsc.bcm.edu	37	17	28296327	28296327	+	Missense_Mutation	SNP	T	T	G	rs9897794	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	152	63	137	1	0.414474	0.00729927	T|0.452;G|0.548	0.548	strong	EFCAB5,NS,carcinoma,-2,1	EFCAB5	122	1	NM_198529	exon4	c.T709G	p.L237V	CAGAGGTTGATGA	.	scavenged	Atlas-SNP
DMXL2	23312	hgsc.bcm.edu	37	15	51829812	51829812	+	Missense_Mutation	SNP	G	G	A	rs17524906	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	141	71	142	0	0.503546	0	G|0.825;A|0.175	0.175	strong	DMXL2,colon,carcinoma,0,1	DMXL2	262	1	NM_001174117	exon11	c.C1490T	p.T497M	AGCAGCGTTTCAA	.	PASS	Atlas-SNP
ZNF710	374655	hgsc.bcm.edu	37	15	90610807	90610807	+	Silent	SNP	C	C	A	rs74038806	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	37	36	27	0	0.972973	0	C|0.923;A|0.077	0.077	strong	.	ZNF710	50	.	NM_198526	exon2	c.C438A	p.G146G	TGGCGGCTGCGAC	.	PASS	Atlas-SNP
CDH15	1013	hgsc.bcm.edu	37	16	89260195	89260195	+	Silent	SNP	G	G	A	rs62068507	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	13	7	20	0	0.538462	0	G|0.995;A|0.005	0.005	strong	.	CDH15	54	.	NM_004933	exon13	c.G2025A	p.P675P	TCACCCGACAGCG	.	PASS	Atlas-SNP
CRIP1	1396	hgsc.bcm.edu	37	14	105954687	105954687	+	Missense_Mutation	SNP	G	G	T	rs7824	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110	57	123	0	0.518182	0	C|0.064;G|0.923;T|0.013	0.013	strong	.	CRIP1	1	.	NM_001311	exon4	c.G155T	p.C52F	CCTACTGCAACCA	.	PASS	Atlas-SNP
STAB2	55576	hgsc.bcm.edu	37	12	104100617	104100617	+	Silent	SNP	C	C	T	rs697212	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	151	148	148	0	0.980132	0	T|0.403;G|0.003	0.403	strong	.	STAB2	370	.	NM_017564	exon38	c.C4044T	p.C1348C	GCCCTGCCCAGGG	.	PASS	Atlas-SNP
CCNT1	904	hgsc.bcm.edu	37	12	49087325	49087325	+	Missense_Mutation	SNP	T	T	C	rs61751603	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	32	55	0	0.477612	0	T|0.984;C|0.016	0.016	strong	.	CCNT1	55	.	NM_001240	exon9	c.A1672G	p.T558A	TATAGGTTTTATG	.	PASS	Atlas-SNP
CCDC105	126402	hgsc.bcm.edu	37	19	15133787	15133787	+	Silent	SNP	C	C	A	rs10424547	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	143	62	133	0	0.433566	0	C|0.749;A|0.251	0.251	strong	.	CCDC105	53	.	NM_173482	exon7	c.C1356A	p.I452I	GAACATCGGGCAT	.	PASS	Atlas-SNP
ESPNL	339768	hgsc.bcm.edu	37	2	239040218	239040218	+	Missense_Mutation	SNP	G	G	A	rs73102309	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	14	7	22	0	0.5	0	G|0.865;A|0.135	0.135	strong	.	ESPNL	63	.	NM_194312	exon9	c.G2863A	p.A955T	CACGCCGCCGTCC	.	PASS	Atlas-SNP
ZNF804B	219578	hgsc.bcm.edu	37	7	88964510	88964510	+	Silent	SNP	T	T	C	rs62469518	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	41	96	0	0.546667	0	T|0.939;C|0.061	0.061	strong	.	ZNF804B	322	.	NM_181646	exon4	c.T2214C	p.N738N	AGGTAATTTGCTC	.	PASS	Atlas-SNP
PRB4	5545	hgsc.bcm.edu	37	12	11461154	11461154	+	Splice_Site	SNP	C	C	G	rs7297795	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	104	48	121	0	0.461538	0	C|0.988;G|0.012	0.012	strong	.	PRB4	59	.	NM_002723	exon4	c.762+1G>C	.	ATCATACCTGTCA	.	PASS	Atlas-SNP
CLUL1	27098	hgsc.bcm.edu	37	18	618015	618015	+	Silent	SNP	C	C	G	rs116985056	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91	30	109	0	0.32967	0	C|0.999;G|0.001	0.001	strong	.	CLUL1	57	.	NM_199167	exon2	c.C15G	p.L5L	GCCACTCTTGGTG	.	PASS	Atlas-SNP
MRGPRE	116534	hgsc.bcm.edu	37	11	3249829	3249829	+	Silent	SNP	G	G	A	rs11026040	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60	28	51	0	0.466667	0	A|0.172;G|0.828	0.172	strong	.	MRGPRE	35	.	NM_001039165	exon2	c.C201T	p.C67C	ATCCGCGCAGGCC	.	PASS	Atlas-SNP
IL9	3578	hgsc.bcm.edu	37	5	135228165	135228165	+	Missense_Mutation	SNP	G	G	A	rs2069885	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	124	66	120	0	0.532258	0	G|0.890;A|0.110	0.110	strong	.	IL9	14	.	NM_000590	exon5	c.C350T	p.T117M	CCTGCCGTGGTTT	.	PASS	Atlas-SNP
NRAP	4892	hgsc.bcm.edu	37	10	115392919	115392919	+	Missense_Mutation	SNP	T	T	A	rs2270182	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	166	71	176	0	0.427711	0	T|0.718;A|0.282	0.282	strong	.	NRAP	208	.	NM_001261463	exon16	c.A1556T	p.N519I	AACTTATTTTTCT	.	PASS	Atlas-SNP
PIP4K2B	8396	hgsc.bcm.edu	37	17	36926731	36926731	+	Silent	SNP	T	T	G	rs228289	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	179	90	196	0	0.502793	0	T|0.663;G|0.337	0.337	strong	.	PIP4K2B	35	.	NM_003559	exon9	c.A1128C	p.T376T	CTTCTTTGTATCG	.	PASS	Atlas-SNP
ABHD11	83451	hgsc.bcm.edu	37	7	73151644	73151644	+	Silent	SNP	A	A	G	rs6460052	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	43	20	51	0	0.465116	0	A|0.410;G|0.590	0.590	strong	.	ABHD11	11	.	NM_148912	exon4	c.T540C	p.Y180Y	TGCCACATAGGTT	.	PASS	Atlas-SNP
F2	2147	hgsc.bcm.edu	37	11	46751059	46751059	+	Silent	SNP	G	G	A	rs5900	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48	27	37	0	0.5625	0	A|0.014;C|0.000;G|0.986	0.014	strong	.	F2	75	.	NM_000506	exon12	c.G1602A	p.P534P	GCGGCCGGTCTGC	.	PASS	Atlas-SNP
RBL2	5934	hgsc.bcm.edu	37	16	53481010	53481010	+	Missense_Mutation	SNP	A	A	G	rs17800727	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110	109	86	0	0.990909	0	A|0.828;G|0.172	0.172	strong	.	RBL2	115	.	NM_005611	exon4	c.A629G	p.Y210C	TTATATATGCAAA	.	PASS	Atlas-SNP
FYCO1	79443	hgsc.bcm.edu	37	3	46008011	46008011	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	135	71	147	0	0.525926	0	.	.	none	.	FYCO1	115	.	NM_024513	exon8	c.G2815C	p.A939P	AGGCTGCCTCTTT	.	PASS	Atlas-SNP
FAM71F1	84691	hgsc.bcm.edu	37	7	128359133	128359133	+	Missense_Mutation	SNP	C	C	T	rs6949056	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80	35	74	0	0.4375	0	C|0.765;N|0.000	.	strong	.	FAM71F1	42	.	NM_032599	exon3	c.C683T	p.S228L	GAGATTCGAAGGT	.	PASS	Atlas-SNP
BAZ2B	29994	hgsc.bcm.edu	37	2	160182374	160182374	+	Missense_Mutation	SNP	T	T	C	rs148382881	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	103	20	132	0	0.194175	0	T|0.987;C|0.013	0.013	strong	.	BAZ2B	196	.	NM_013450	exon35	c.A5999G	p.N2000S	GACTCATTAGTCT	.	PASS	Atlas-SNP
EPPK1	83481	hgsc.bcm.edu	37	8	144942794	144942794	+	Missense_Mutation	SNP	G	G	A	rs373737061		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82	44	66	0	0.536585	0	.	.	weak	EPPK1,NS,carcinoma,0,1	EPPK1	199	1	NM_031308	exon1	c.C4628T	p.T1543M	TCCAGCGTCTTCC	.	PASS	Atlas-SNP
ATP13A5	344905	hgsc.bcm.edu	37	3	193031875	193031875	+	Missense_Mutation	SNP	C	C	T	rs78188075	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	135	55	124	0	0.407407	0	C|0.971;T|0.029	0.029	strong	.	ATP13A5	171	.	NM_198505	exon19	c.G2266A	p.A756T	CAGAGGCAGGAAC	.	PASS	Atlas-SNP
EXTL1	2134	hgsc.bcm.edu	37	1	26357656	26357656	+	Missense_Mutation	SNP	C	C	A	rs2736831	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	120	120	129	0	1	0	C|0.442;A|0.558	0.558	strong	.	EXTL1	61	.	NM_004455	exon5	c.C1135A	p.H379N	TCAGCTCACCCCT	.	PASS	Atlas-SNP
RYR1	6261	hgsc.bcm.edu	37	19	38996990	38996990	+	Silent	SNP	T	T	C	rs2229146	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	122	60	107	0	0.491803	0	T|0.663;C|0.337	0.337	strong	RYR1,NS,carcinoma,0,1	RYR1	708	1	NM_001042723	exon55	c.T8589C	p.S2863S	CCTTAGTGCTGTT	.	PASS	Atlas-SNP
GALNT8	26290	hgsc.bcm.edu	37	12	4854722	4854722	+	Missense_Mutation	SNP	G	G	A	rs201387598	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94	43	111	0	0.457447	0	G|0.999;A|0.001	0.001	weak	.	GALNT8	89	.	NM_017417	exon5	c.G988A	p.E330K	AACTGGGAACTCT	.	PASS	Atlas-SNP
KIAA1551	55196	hgsc.bcm.edu	37	12	32138410	32138410	+	Silent	SNP	A	A	G	rs12827942	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	24	56	0	0.461538	0	A|0.921;G|0.079	0.079	strong	.	.	.	.	NM_018169	exon4	c.A4521G	p.E1507E	TAAAGAATCATTA	.	PASS	Atlas-SNP
SH3TC1	54436	hgsc.bcm.edu	37	4	8242499	8242499	+	Silent	SNP	G	G	A	rs1048506	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	37	78	0	0.711538	0	G|0.967;A|0.033	0.033	strong	.	SH3TC1	105	.	NM_018986	exon18	c.G3828A	p.Q1276Q	GGCACAGCTGAAG	.	PASS	Atlas-SNP
TEX264	51368	hgsc.bcm.edu	37	3	51737965	51737965	+	Missense_Mutation	SNP	G	G	A	rs11553574	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	38	19	34	0	0.5	0	G|0.875;A|0.125	0.125	strong	.	TEX264	18	.	NM_001243726	exon5	c.G875A	p.G292E	ACCCTGGGACTGA	.	PASS	Atlas-SNP
ADCK5	203054	hgsc.bcm.edu	37	8	145603114	145603114	+	Missense_Mutation	SNP	A	A	C	rs6599528	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	175	173	194	1	0.988571	0.00515464	A|0.433;C|0.567	0.567	strong	ADCK5,rectum,carcinoma,0,3	ADCK5	36	3	NM_174922	exon2	c.A51C	p.R17S	GCACAGAAGGCAG	.	PASS	Atlas-SNP
TMEM99	147184	hgsc.bcm.edu	37	17	38991052	38991052	+	Missense_Mutation	SNP	T	T	G	rs1044806	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	155	154	144	0	0.993548	0	T|0.907;G|0.093	0.093	strong	.	TMEM99	21	.	NM_001195386	exon3	c.T284G	p.L95R	AAGGACTTCTTCT	.	PASS	Atlas-SNP
UNC45A	55898	hgsc.bcm.edu	37	15	91489919	91489919	+	Silent	SNP	A	A	G	rs12911432	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	78	35	87	0	0.448718	0	A|0.952;G|0.048	0.048	strong	UNC45A,NS,carcinoma,0,1	UNC45A	57	1	NM_018671	exon10	c.A1275G	p.P425P	GGGCCCATGTGAC	.	PASS	Atlas-SNP
PDCD11	22984	hgsc.bcm.edu	37	10	105160184	105160184	+	Missense_Mutation	SNP	A	A	G	rs150893869	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	17	10	23	0	0.588235	0	A|0.995;G|0.005	0.005	strong	.	PDCD11	160	.	NM_014976	exon3	c.A133G	p.K45E	AAAAGAAAAAAGA	.	PASS	Atlas-SNP
TLN2	83660	hgsc.bcm.edu	37	15	63131091	63131091	+	Missense_Mutation	SNP	C	C	T	rs140301741	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	58	31	62	0	0.534483	0	C|0.998;T|0.002	0.002	strong	.	TLN2	253	.	NM_015059	exon55	c.C7411T	p.L2471F	GACAATCTTGTCC	.	PASS	Atlas-SNP
DUSP12	11266	hgsc.bcm.edu	37	1	161722204	161722204	+	Silent	SNP	C	C	T	rs1063179	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	223	102	211	0	0.457399	0	C|0.848;T|0.152	0.152	strong	.	DUSP12	20	.	NM_007240	exon4	c.C624T	p.T208T	AACTACCGTTTCA	.	PASS	Atlas-SNP
IZUMO2	126123	hgsc.bcm.edu	37	19	50666389	50666389	+	Silent	SNP	G	G	A	rs61742305	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60	27	57	0	0.45	0	G|0.859;A|0.141	0.141	strong	IZUMO2,NS,carcinoma,0,1	IZUMO2	26	1	NM_152358	exon1	c.C63T	p.C21C	CTGCAGGCAGCCC	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	14	7	29	0	0.5	0	C|0.806;T|0.194	0.194	strong	.	CARD10	55	.	NM_014550	exon4	c.G866A	p.R289Q	GTCAGCCGCTGGT	.	PASS	Atlas-SNP
MAPKAPK2	9261	hgsc.bcm.edu	37	1	206905043	206905043	+	Silent	SNP	C	C	T	rs4073250	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	166	93	135	0	0.560241	0	C|0.820;T|0.180	0.180	strong	.	MAPKAPK2	45	.	NM_004759	exon8	c.C951T	p.T317T	CATCACCGAGTTT	.	PASS	Atlas-SNP
NPLOC4	55666	hgsc.bcm.edu	37	17	79564304	79564304	+	Silent	SNP	G	G	T	rs62074671	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	56	17	60	0	0.303571	0	G|0.918;T|0.082	0.082	strong	.	NPLOC4	27	.	NM_017921	exon10	c.C960A	p.T320T	CTTTCGGGTATCT	.	PASS	Atlas-SNP
ANKS3	124401	hgsc.bcm.edu	37	16	4751045	4751045	+	Missense_Mutation	SNP	C	C	T	rs863980	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	146	143	176	0	0.979452	0	C|0.457;T|0.543	0.543	strong	ANKS3,caecum,carcinoma,0,2	ANKS3	44	2	NM_133450	exon11	c.G1210A	p.A404T	TTGCAGCGCGGGG	.	PASS	Atlas-SNP
OR1E1	8387	hgsc.bcm.edu	37	17	3301549	3301549	+	Silent	SNP	G	G	A	rs150988	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	240	103	233	0	0.429167	0	G|0.602;A|0.398	0.398	strong	.	OR1E1	37	.	NM_003553	exon1	c.C156T	p.D52D	ATGGGAGTCCAGT	.	PASS	Atlas-SNP
SNAPC4	6621	hgsc.bcm.edu	37	9	139275294	139275294	+	Missense_Mutation	SNP	G	G	C	rs3812571	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51	51	52	0	1	0	G|0.591;C|0.409	0.409	strong	SNAPC4,NS,carcinoma,0,2	SNAPC4	82	2	NM_003086	exon19	c.C2397G	p.H799Q	ATCGATGTGGAAC	.	PASS	Atlas-SNP
STX16	8675	hgsc.bcm.edu	37	20	57244396	57244396	+	Missense_Mutation	SNP	G	G	A	rs41276950	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	26	13	24	0	0.5	0	G|0.972;A|0.028	0.028	strong	.	STX16	36	.	NM_001001433	exon5	c.G443A	p.R148Q	GGGCCCGGGCCTG	.	PASS	Atlas-SNP
CLDN12	9069	hgsc.bcm.edu	37	7	90042176	90042176	+	Silent	SNP	C	C	T	rs17862175	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	124	53	124	0	0.427419	0	C|0.981;T|0.019	0.019	strong	.	CLDN12	32	.	NM_012129	exon3	c.C186T	p.D62D	GTATGACGGGAGC	.	PASS	Atlas-SNP
D2HGDH	728294	hgsc.bcm.edu	37	2	242674803	242674803	+	Missense_Mutation	SNP	G	G	A	rs77940364	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	27	16	49	0	0.592593	0	G|0.785;A|0.215	0.215	strong	.	D2HGDH	39	.	NM_152783	exon2	c.G164A	p.R55Q	CCGTGCGGCGCTT	.	PASS	Atlas-SNP
RHPN2	85415	hgsc.bcm.edu	37	19	33517507	33517507	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	23	2	15	0	0.0869565	0	.	.	none	RHPN2,face,carcinoma,0,2	RHPN2	107	2	NM_033103	exon3	c.G217A	p.V73M	GCCGCACTTGCTC	.	scavenged	Atlas-SNP
DLGAP5	9787	hgsc.bcm.edu	37	14	55619311	55619311	+	Silent	SNP	A	A	G	rs15870	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60	60	70	0	1	0	A|0.621;G|0.379	0.379	strong	.	DLGAP5	84	.	NM_014750	exon16	c.T2118C	p.N706N	TACATGATTTTCT	.	PASS	Atlas-SNP
VPS13C	54832	hgsc.bcm.edu	37	15	62214607	62214607	+	Missense_Mutation	SNP	C	C	T	rs12907567	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49	17	41	0	0.346939	0	C|0.946;T|0.054	0.054	strong	VPS13C,NS,carcinoma,0,1	VPS13C	506	1	NM_020821	exon54	c.G6964A	p.V2322M	GTGTCACGTCAGC	.	PASS	Atlas-SNP
POTEC	388468	hgsc.bcm.edu	37	18	14537949	14537949	+	Missense_Mutation	SNP	A	A	G	rs7505568	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	224	90	270	0	0.401786	0	A|0.792;G|0.208	0.208	strong	.	POTEC	129	.	NM_001137671	exon3	c.T661C	p.C221R	ACACACATTCATC	.	PASS	Atlas-SNP
PINK1	65018	hgsc.bcm.edu	37	1	20977000	20977000	+	Missense_Mutation	SNP	A	A	C	rs1043424	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	101	101	94	0	1	0	A|0.725;C|0.275	0.275	strong	.	PINK1	37	.	NM_032409	exon8	c.A1562C	p.N521T	TGAAGAATCTGAA	.	PASS	Atlas-SNP
GPSM1	26086	hgsc.bcm.edu	37	9	139235606	139235606	+	Missense_Mutation	SNP	G	G	C	rs78403475	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	39	115	0	0.481481	0	G|0.900;C|0.100	0.100	strong	GPSM1_ENST00000392945,caecum,carcinoma,-1,1	GPSM1	50	1	NM_015597	exon9	c.G1363C	p.A455P	GGGACAGCACAGG	.	PASS	Atlas-SNP
LEMD3	23592	hgsc.bcm.edu	37	12	65563416	65563416	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	9	66	0	0.142857	0	.	.	none	.	LEMD3	68	.	NM_001167614	exon1	c.G40A	p.D14N	CTCTCGGATGAGG	.	PASS	Atlas-SNP
MC1R	4157	hgsc.bcm.edu	37	16	89985844	89985844	+	Missense_Mutation	SNP	G	G	T	rs1805005	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	97	51	115	0	0.525773	0	G|0.944;T|0.056	0.056	strong	.	MC1R	20	.	NM_002386	exon1	c.G178T	p.V60L	CTGGTGGTGGCCA	.	PASS	Atlas-SNP
GAB4	128954	hgsc.bcm.edu	37	22	17446991	17446991	+	Silent	SNP	C	C	T	rs4819925	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94	36	90	0	0.382979	0	C|0.190;T|0.810	0.810	strong	GAB4,NS,carcinoma,0,1	GAB4	95	1	NM_001037814	exon6	c.G1287A	p.K429K	CTTACCCTTCTGG	.	PASS	Atlas-SNP
MMP17	4326	hgsc.bcm.edu	37	12	132326298	132326298	+	Missense_Mutation	SNP	G	G	A	rs35466884	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	39	83	0	0.52	0	G|0.780;A|0.220	0.220	strong	.	MMP17	77	.	NM_016155	exon5	c.G836A	p.R279H	CGCTGCGCTACGG	.	PASS	Atlas-SNP
SUN2	25777	hgsc.bcm.edu	37	22	39147235	39147235	+	Missense_Mutation	SNP	A	A	C	rs35496634	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	30	86	0	0.47619	0	A|0.927;C|0.073	0.073	strong	.	SUN2	59	.	NM_001199580	exon4	c.T266G	p.L89R	CCATGCAGTTCCT	.	PASS	Atlas-SNP
KIAA1804	0	hgsc.bcm.edu	37	1	233515102	233515102	+	Missense_Mutation	SNP	T	T	G	rs963981	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72	28	78	0	0.388889	0	T|0.771;G|0.223	0.223	strong	.	KIAA1804	129	.	NM_032435	exon9	c.T2350G	p.C784G	TCCACCTGTGGGG	.	PASS	Atlas-SNP
GCKR	2646	hgsc.bcm.edu	37	2	27730940	27730940	+	Missense_Mutation	SNP	T	T	C	rs1260326	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	153	79	133	0	0.51634	0	A|0.003;C|0.649	0.649	strong	.	GCKR	73	.	NM_001486	exon15	c.T1337C	p.L446P	CCTTGCTGGTGAG	.	PASS	Atlas-SNP
EXOSC8	11340	hgsc.bcm.edu	37	13	37580139	37580139	+	Silent	SNP	G	G	A	rs1127446	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	121	66	126	0	0.545455	0	G|0.659;A|0.341	0.341	strong	.	EXOSC8	16	.	NM_181503	exon6	c.G321A	p.Q107Q	TAGCCAGTTCATT	.	PASS	Atlas-SNP
CNTN5	53942	hgsc.bcm.edu	37	11	100226883	100226883	+	Missense_Mutation	SNP	T	T	A	rs1216183	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91	9	77	0	0.0989011	0	T|0.706;A|0.294	0.294	strong	CNTN5_ENST00000524871,colon,carcinoma,-2,2	CNTN5	324	2	NM_001243270	exon24	c.T3235A	p.S1079T	CTTCACTCTCTCT	.	PASS	Atlas-SNP
ERCC6	2074	hgsc.bcm.edu	37	10	50678369	50678369	+	Missense_Mutation	SNP	T	T	C	rs2228527	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	365	165	308	0	0.452055	0	T|0.820;C|0.180	0.180	strong	.	ERCC6	162	.	NM_000124	exon18	c.C3637G	p.L1213V	CGTCTCTGCAATG	.	PASS	Atlas-SNP
THUMPD3	25917	hgsc.bcm.edu	37	3	9406836	9406836	+	Silent	SNP	T	T	C	rs1054975	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	154	152	136	0	0.987013	0	T|0.410;C|0.590	0.590	strong	.	THUMPD3	46	.	NM_001114092	exon2	c.T84C	p.S28S	AGAAAGTGACCTC	.	PASS	Atlas-SNP
KRTAP10-4	386672	hgsc.bcm.edu	37	21	45994488	45994488	+	Missense_Mutation	SNP	G	G	T	rs396912	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	156	102	118	1	0.653846	0.00847458	G|0.785;T|0.215	0.215	strong	KRTAP10-4,colon,carcinoma,-1,1	KRTAP10-4	44	1	NM_198687	exon1	c.G853T	p.G285C	CCTGTCGGCTCTG	.	scavenged	Atlas-SNP
SEMA4A	64218	hgsc.bcm.edu	37	1	156146689	156146689	+	Silent	SNP	G	G	A	rs41265019	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72	33	79	0	0.458333	0	G|0.987;A|0.013	0.013	strong	.	SEMA4A	75	.	NM_001193300	exon15	c.G2187A	p.P729P	GGCCCCGTTAAGC	.	PASS	Atlas-SNP
KCNH3	23416	hgsc.bcm.edu	37	12	49951232	49951232	+	Silent	SNP	T	T	C	rs2241418	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	102	44	115	0	0.431373	0	T|0.792;C|0.208	0.208	strong	.	KCNH3	88	.	NM_012284	exon15	c.T2748C	p.G916G	GGAGGGTCCGTGC	.	PASS	Atlas-SNP
KRT6C	286887	hgsc.bcm.edu	37	12	52865918	52865918	+	Silent	SNP	G	G	C	rs425073	bycluster;by2hit2allele	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	153	49	199	0	0.320261	0	G|0.750;C|0.250	0.250	weak	.	KRT6C	55	.	NM_173086	exon2	c.C687G	p.V229V	TTCCCCGACGATG	.	PASS	Atlas-SNP
VAMP8	8673	hgsc.bcm.edu	37	2	85808737	85808737	+	Silent	SNP	A	A	G	rs1009	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	158	108	204	0	0.683544	0	A|0.547;G|0.453	0.453	strong	VAMP8,NS,carcinoma,0,1	VAMP8	10	1	NM_003761	exon3	c.A201G	p.R67R	GGCTCGAAAATTC	.	PASS	Atlas-SNP
KIAA0753	9851	hgsc.bcm.edu	37	17	6493198	6493198	+	Missense_Mutation	SNP	T	T	C	rs1443417	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	112	57	104	0	0.508929	0	T|0.340;C|0.660	0.660	strong	.	KIAA0753	63	.	NM_014804	exon18	c.A2687G	p.Q896R	CTGTGCTGCATAC	.	PASS	Atlas-SNP
USH1C	10083	hgsc.bcm.edu	37	11	17527386	17527386	+	Silent	SNP	A	A	G	rs369021714		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80	41	74	0	0.5125	0	.	.	weak	.	USH1C	157	.	NM_153676	exon19	c.T2124C	p.S708S	AACTTCAGATTTC	.	PASS	Atlas-SNP
ARPP21	10777	hgsc.bcm.edu	37	3	35725250	35725250	+	Silent	SNP	C	C	T	rs969818	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	111	109	115	0	0.981982	0	T|0.701;C|0.299;A|0.000	0.701	strong	.	ARPP21	153	.	NM_001267618	exon4	c.C204T	p.S68S	TCGCAGCCTTGCT	.	PASS	Atlas-SNP
ZNF138	7697	hgsc.bcm.edu	37	7	64291405	64291405	+	Missense_Mutation	SNP	G	G	A	rs118016824	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	97	47	103	0	0.484536	0	G|0.987;A|0.013	0.013	strong	.	ZNF138	43	.	NM_001160183	exon4	c.G296A	p.G99E	TCATGGGAAACAG	.	PASS	Atlas-SNP
TLK1	9874	hgsc.bcm.edu	37	2	171910313	171910313	+	Silent	SNP	C	C	T	rs11553951	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91	33	103	0	0.362637	0	C|0.814;T|0.186	0.186	strong	.	TLK1	134	.	NM_012290	exon8	c.G690A	p.Q230Q	CAGGTCCTGGATT	.	PASS	Atlas-SNP
QRICH2	84074	hgsc.bcm.edu	37	17	74289500	74289500	+	Silent	SNP	G	G	A	rs3803737	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	119	53	116	0	0.445378	0	G|0.557;A|0.443	0.443	strong	.	QRICH2	143	.	NM_032134	exon4	c.C810T	p.V270V	ATCCACGACAAAT	.	PASS	Atlas-SNP
DPCD	25911	hgsc.bcm.edu	37	10	103361088	103361088	+	Silent	SNP	C	C	T	rs7874	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	115	58	111	0	0.504348	0	C|0.854;T|0.146	0.146	strong	.	DPCD	15	.	NM_015448	exon4	c.C399T	p.N133N	AACCAACAAGAAG	.	PASS	Atlas-SNP
IL7R	3575	hgsc.bcm.edu	37	5	35874575	35874575	+	Missense_Mutation	SNP	C	C	T	rs6897932	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	297	137	295	0	0.461279	0	C|0.810;T|0.190	0.190	strong	IL7R,NS,carcinoma,-1,3	IL7R	200	3	NM_002185	exon6	c.C731T	p.T244I	TACTAACCATCAG	.	PASS	Atlas-SNP
NXPE1	120400	hgsc.bcm.edu	37	11	114393652	114393652	+	Missense_Mutation	SNP	C	C	T	rs10891692	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	165	165	154	0	1	0	C|0.645;T|0.355	0.355	strong	FAM55A,NS,adenoma,0,1	NXPE1	8	1	NM_152315	exon5	c.G631A	p.G211R	AGTCTCCCAGGAG	.	PASS	Atlas-SNP
HSD17B11	51170	hgsc.bcm.edu	37	4	88293887	88293887	+	Silent	SNP	G	G	A	rs6531985	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	36	91	0	0.507042	0	G|0.645;A|0.355	0.355	strong	.	HSD17B11	28	.	NM_016245	exon4	c.C531T	p.V177V	GACCGAGACATGT	.	PASS	Atlas-SNP
PRDM9	56979	hgsc.bcm.edu	37	5	23527324	23527324	+	Silent	SNP	T	T	A	rs200723191	byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73	14	63	0	0.191781	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
CNNM1	26507	hgsc.bcm.edu	37	10	101147720	101147720	+	Silent	SNP	C	C	T	rs17490682	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	99	44	105	0	0.444444	0	C|0.972;T|0.028	0.028	strong	.	CNNM1	101	.	NM_020348	exon8	c.C2484T	p.D828D	GGATGACCCCGCC	.	PASS	Atlas-SNP
NCOA3	8202	hgsc.bcm.edu	37	20	46279827	46279827	+	Silent	SNP	G	G	A	rs6018623	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	37	58	0	0.552239	0	G|0.861;A|0.139	0.139	strong	.	NCOA3	156	.	NM_181659	exon20	c.G3753A	p.Q1251Q	GCAGCAGCAGCAG	.	PASS	Atlas-SNP
PRTN3	5657	hgsc.bcm.edu	37	19	844020	844020	+	Missense_Mutation	SNP	G	G	A	rs351111	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	116	57	114	0	0.491379	0	G|0.546;A|0.454	0.454	strong	.	PRTN3	9	.	NM_002777	exon3	c.G355A	p.V119I	AACGACGTTCTCC	.	PASS	Atlas-SNP
FRMD1	79981	hgsc.bcm.edu	37	6	168458002	168458002	+	Silent	SNP	G	G	A	rs55991596	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72	37	77	0	0.513889	0	G|0.958;A|0.042	0.042	strong	.	FRMD1	52	.	NM_024919	exon11	c.C1425T	p.A475A	GACCCCGGCTGTC	.	PASS	Atlas-SNP
SPPL2C	162540	hgsc.bcm.edu	37	17	43923266	43923266	+	Missense_Mutation	SNP	G	G	A	rs62054815	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	59	58	44	0	0.983051	0	A|0.120;C|0.240	0.120	strong	.	.	.	.	NM_175882	exon1	c.G994A	p.A332T	CTGTGCGCAACCG	.	PASS	Atlas-SNP
SEC14L5	9717	hgsc.bcm.edu	37	16	5050897	5050897	+	Silent	SNP	G	G	C	rs2286966	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	50	29	66	0	0.58	0	G|0.589;C|0.411	0.411	strong	.	SEC14L5	79	.	NM_014692	exon10	c.G1101C	p.G367G	TGAGGGGAGCACA	.	PASS	Atlas-SNP
OLFM3	118427	hgsc.bcm.edu	37	1	102296279	102296279	+	Silent	SNP	T	T	C	rs10493973	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	128	70	157	0	0.546875	0	T|0.824;C|0.176	0.176	strong	.	OLFM3	178	.	NM_058170	exon3	c.A321G	p.K107K	CCGAAATTTTGCC	.	PASS	Atlas-SNP
CD109	135228	hgsc.bcm.edu	37	6	74481186	74481186	+	Missense_Mutation	SNP	C	C	T	rs41266745	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	43	23	57	0	0.534884	0	C|0.998;T|0.002	0.002	strong	.	CD109	170	.	NM_133493	exon15	c.C1709T	p.P570L	CTGAACCATCTGA	.	PASS	Atlas-SNP
UNC13C	440279	hgsc.bcm.edu	37	15	54847677	54847677	+	Silent	SNP	C	C	T	rs11639005	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	78	77	79	0	0.987179	0	C|0.625;T|0.375	0.375	strong	.	UNC13C	674	.	NM_001080534	exon27	c.C5925T	p.C1975C	ACAATGCGCTATA	.	PASS	Atlas-SNP
PTX3	5806	hgsc.bcm.edu	37	3	157155314	157155314	+	Missense_Mutation	SNP	C	C	A	rs3816527	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44	44	39	0	1	0	C|0.346;A|0.654	0.654	strong	.	PTX3	27	.	NM_002852	exon2	c.C143A	p.A48D	CGTGCGCCTGCGG	.	PASS	Atlas-SNP
ABP1	26	hgsc.bcm.edu	37	7	150557665	150557665	+	Missense_Mutation	SNP	C	C	G	rs1049793	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	20	57	0	0.327869	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
LARS	51520	hgsc.bcm.edu	37	5	145522992	145522992	+	Silent	SNP	C	C	T	rs146906828	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	88	45	79	0	0.511364	0	C|0.997;T|0.003	0.003	strong	.	LARS	100	.	NM_020117	exon19	c.G1860A	p.E620E	CGGAGACTCTGCC	.	PASS	Atlas-SNP
TPP1	1200	hgsc.bcm.edu	37	11	6636106	6636106	+	Silent	SNP	T	T	A	rs1128396	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	40	66	0	0.606061	0	T|0.785;A|0.215	0.215	strong	.	TPP1	71	.	NM_000391	exon12	c.A1542T	p.G514G	AAAGAGTCCTGCC	.	PASS	Atlas-SNP
IL17RA	23765	hgsc.bcm.edu	37	22	17590269	17590269	+	Silent	SNP	C	C	T	rs4819555	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55	55	51	0	1	0	C|0.753;T|0.247	0.247	strong	.	IL17RA	62	.	NM_014339	exon13	c.C2160T	p.P720P	CCTCCCCGTGGAC	.	PASS	Atlas-SNP
CARD14	79092	hgsc.bcm.edu	37	17	78157961	78157961	+	Missense_Mutation	SNP	G	G	A	rs114688446	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73	34	68	0	0.465753	0	A|0.001;G|0.994;T|0.005	0.001	strong	.	CARD14	98	.	NM_024110	exon4	c.G599A	p.S200N	TGCTCAGCCTCTC	.	PASS	Atlas-SNP
IGSF8	93185	hgsc.bcm.edu	37	1	160062727	160062727	+	Silent	SNP	A	A	G	rs2295621	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94	93	103	1	0.989362	0.00970874	A|0.840;G|0.160	0.160	strong	.	IGSF8	59	.	NM_052868	exon4	c.T1299C	p.H433H	CCGCACATGTACA	.	PASS	Atlas-SNP
ZBTB44	29068	hgsc.bcm.edu	37	11	130130758	130130758	+	Silent	SNP	G	G	A	rs202193079	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	35	28	28	0	0.8	0	G|0.999;A|0.001	0.001	strong	.	ZBTB44	41	.	NM_014155	exon2	c.C1011T	p.S337S	TATAGAGGAAGAC	.	PASS	Atlas-SNP
MED24	9862	hgsc.bcm.edu	37	17	38175866	38175866	+	Silent	SNP	G	G	A	rs11555254	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	122	60	95	0	0.491803	0	G|0.850;A|0.150	0.150	strong	.	MED24	89	.	NM_014815	exon26	c.C2886T	p.S962S	GGGGCTGGACATG	.	PASS	Atlas-SNP
SNX18	112574	hgsc.bcm.edu	37	5	53813830	53813830	+	Silent	SNP	A	A	C	rs76854460	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	7	6	19	0	0.857143	0	A|0.733;C|0.267	0.267	strong	SNX18_ENST00000381410,NS,carcinoma,0,2	SNX18	102	2	NM_052870	exon1	c.A48C	p.P16P	GAACCCAGGAGAG	.	PASS	Atlas-SNP
DSEL	92126	hgsc.bcm.edu	37	18	65179829	65179829	+	Missense_Mutation	SNP	G	G	A	rs2279269	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	156	152	161	0	0.974359	0	G|0.545;A|0.455	0.455	strong	.	DSEL	196	.	NM_032160	exon2	c.C2047T	p.P683S	TTGTGGGTTCCAT	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	378	371	292	0	0.981481	0	T|0.845;A|0.155	0.155	strong	.	CCL4	14	.	NM_002984	exon3	c.T238A	p.S80T	AGTGAATCCTGGG	.	PASS	Atlas-SNP
RABEP1	9135	hgsc.bcm.edu	37	17	5284770	5284770	+	Silent	SNP	G	G	A	rs1065483	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	39	73	0	0.481481	0	G|0.390;A|0.610	0.610	strong	.	RABEP1	59	.	NM_004703	exon17	c.G2457A	p.R819R	CCAGAGGGATTTT	.	PASS	Atlas-SNP
OR2L8	391190	hgsc.bcm.edu	37	1	248112754	248112754	+	Missense_Mutation	SNP	T	T	C	rs201126494	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	160	38	122	0	0.2375	0	T|0.945;C|0.055	0.055	strong	.	OR2L8	92	.	NM_001001963	exon1	c.T595C	p.F199L	ACAGTGTTTTTGA	.	PASS	Atlas-SNP
TROAP	10024	hgsc.bcm.edu	37	12	49723963	49723963	+	Silent	SNP	A	A	G	rs4243545	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	169	79	163	1	0.467456	0.00613497	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	.	scavenged	Atlas-SNP
DCAF10	79269	hgsc.bcm.edu	37	9	37860058	37860058	+	Silent	SNP	A	A	G	rs118047034	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	117	54	128	0	0.461538	0	A|0.984;G|0.016	0.016	strong	DCAF10,rectum,carcinoma,+1,1	DCAF10	31	1	NM_024345	exon6	c.A1179G	p.R393R	ACCACGAAATAGT	.	PASS	Atlas-SNP
CFI	3426	hgsc.bcm.edu	37	4	110681505	110681505	+	Silent	SNP	C	C	T	rs2298749	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	123	62	116	0	0.504065	0	C|0.702;T|0.298	0.298	strong	.	CFI	59	.	NM_000204	exon6	c.G804A	p.S268S	AACACCCGATTTG	.	PASS	Atlas-SNP
RGS1	5996	hgsc.bcm.edu	37	1	192545417	192545417	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	178	43	182	0	0.241573	0	.	.	none	.	RGS1	75	.	NM_002922	exon2	c.G140A	p.G47E	GTAGTGGAATGGA	.	PASS	Atlas-SNP
ZFPM1	161882	hgsc.bcm.edu	37	16	88599023	88599023	+	Silent	SNP	A	A	G	rs56041036	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	126	65	164	1	0.515873	0.00609756	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	.	scavenged	Atlas-SNP
POTEC	388468	hgsc.bcm.edu	37	18	14513764	14513764	+	Missense_Mutation	SNP	C	C	T	rs79575795		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	282	6	267	0	0.0212766	0	.	.	weak	POTEC,NS,carcinoma,0,17	POTEC	129	17	NM_001137671	exon10	c.G1430A	p.R477Q	TGTTTCCGGGTAT	.	scavenged	Atlas-SNP
FBXO10	26267	hgsc.bcm.edu	37	9	37537557	37537557	+	Silent	SNP	G	G	A	rs7044153	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	40	61	0	0.56338	0	G|0.429;A|0.571	0.571	strong	.	FBXO10	75	.	NM_012166	exon3	c.C969T	p.A323A	GCTAGAGGCTGGG	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	89	34	73	0	0.382022	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
NXPE4	54827	hgsc.bcm.edu	37	11	114442103	114442103	+	Missense_Mutation	SNP	A	A	G	rs550897	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	108	107	81	0	0.990741	0	T|0.007;G|0.608	0.608	strong	.	.	.	.	NM_001077639	exon6	c.T1192C	p.Y398H	AACAATATTTTTG	.	PASS	Atlas-SNP
VAMP5	10791	hgsc.bcm.edu	37	2	85818886	85818886	+	Silent	SNP	C	C	T	rs14976	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	116	115	137	0	0.991379	0	C|0.797;T|0.203	0.203	strong	.	VAMP5	13	.	NM_006634	exon2	c.C42T	p.N14N	GGCGAACGAGGTG	.	PASS	Atlas-SNP
GDPD4	220032	hgsc.bcm.edu	37	11	76954812	76954812	+	Missense_Mutation	SNP	T	T	C	rs11237145	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91	15	76	0	0.164835	0	C|0.254;N|0.000	0.254	strong	.	GDPD4	49	.	NM_182833	exon12	c.A1168G	p.I390V	TTTCAATGGATAC	.	PASS	Atlas-SNP
CDH23	64072	hgsc.bcm.edu	37	10	73537614	73537614	+	Missense_Mutation	SNP	G	G	A	rs17712523	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	108	45	119	0	0.416667	0	G|0.857;A|0.143	0.143	strong	CDH23,NS,carcinoma,0,1	CDH23	365	1	NM_022124	exon37	c.G5023A	p.V1675I	GCCATCGTCGCAG	.	PASS	Atlas-SNP
SMG8	55181	hgsc.bcm.edu	37	17	57290383	57290383	+	Silent	SNP	G	G	A	rs3744383	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	99	42	103	0	0.424242	0	G|0.551;A|0.449	0.449	strong	.	SMG8	79	.	NM_018149	exon3	c.G2199A	p.R733R	GAAGAGGCCAAAC	.	PASS	Atlas-SNP
RNF152	220441	hgsc.bcm.edu	37	18	59483310	59483310	+	Silent	SNP	G	G	A	rs4362478	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93	54	73	0	0.580645	0	G|0.959;A|0.041	0.041	strong	RNF152,NS,carcinoma,0,1	RNF152	37	1	NM_173557	exon2	c.C387T	p.S129S	GGTGACGGACTTC	.	PASS	Atlas-SNP
TULP4	56995	hgsc.bcm.edu	37	6	158923378	158923378	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82	4	87	0	0.0487805	0	.	.	none	.	TULP4	137	.	NM_020245	exon13	c.G2683A	p.G895S	AGCAGTGGCAACG	.	PASS	Atlas-SNP
CCDC80	151887	hgsc.bcm.edu	37	3	112356977	112356977	+	Silent	SNP	T	T	C	rs35149092	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	233	116	239	0	0.497854	0	T|0.996;C|0.004	0.004	strong	.	CCDC80	100	.	NM_199511	exon2	c.A1776G	p.E592E	ATCCTGTTCTGTT	.	PASS	Atlas-SNP
PLCXD1	55344	hgsc.bcm.edu	37	X	200860	200860	+	Silent	SNP	T	T	C	rs9785927	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	177	176	268	2	0.99435	0.00746269	T|0.204;C|0.796	0.796	strong	.	PLCXD1	18	.	NM_018390	exon2	c.T6C	p.G2G	GATGGGTGGGCAG	.	PASS	Atlas-SNP
DPCR1	135656	hgsc.bcm.edu	37	6	30919798	30919798	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	45	16	25	0	0.355556	0	.	.	none	.	DPCR1	99	.	NM_080870	exon2	c.A3557C	p.K1186T	CAGAAAAGCCTAC	.	PASS	Atlas-SNP
KTN1	3895	hgsc.bcm.edu	37	14	56119783	56119783	+	Missense_Mutation	SNP	G	G	A	rs139730003	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	163	75	154	0	0.460123	0	G|1.000;A|0.000	0.000	weak	.	KTN1	147	.	NM_004986	exon27	c.G2743A	p.A915T	GAAGTAGCACAAC	.	PASS	Atlas-SNP
IL31RA	133396	hgsc.bcm.edu	37	5	55210702	55210702	+	Silent	SNP	C	C	T	rs17701253	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	202	101	177	0	0.5	0	C|0.962;T|0.038	0.038	strong	.	IL31RA	84	.	NM_001242637	exon14	c.C1764T	p.T588T	GCCCACCGTTCCC	.	PASS	Atlas-SNP
MTHFD1	4522	hgsc.bcm.edu	37	14	64882380	64882380	+	Missense_Mutation	SNP	A	A	G	rs1950902	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	87	74	0	1	0	G|0.827;N|0.000	0.827	strong	MTHFD1,tonsil,carcinoma,0,1	MTHFD1	61	1	NM_005956	exon6	c.A401G	p.K134R	CTGGGAAACTTGC	.	PASS	Atlas-SNP
AGGF1	55109	hgsc.bcm.edu	37	5	76331449	76331449	+	Missense_Mutation	SNP	G	G	A	rs34203073	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	244	105	208	2	0.430328	0.00961538	G|0.986;A|0.014	0.014	strong	AGGF1,colon,carcinoma,0,1	AGGF1	71	1	NM_018046	exon3	c.G397A	p.E133K	GCTATCGAAACTT	.	scavenged	Atlas-SNP
BBS12	166379	hgsc.bcm.edu	37	4	123664446	123664446	+	Missense_Mutation	SNP	G	G	A	rs13135778	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	84	134	0	0.976744	0	G|0.857;A|0.143	0.143	strong	.	BBS12	63	.	NM_001178007	exon3	c.G1399A	p.D467N	GTGGGCGACGGGG	.	PASS	Atlas-SNP
CD44	960	hgsc.bcm.edu	37	11	35201842	35201842	+	Silent	SNP	C	C	T	rs1071695	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	153	57	154	0	0.372549	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
CDH11	1009	hgsc.bcm.edu	37	16	65022114	65022114	+	Silent	SNP	C	C	T	rs28216	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	232	117	256	1	0.50431	0.00390625	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
SORCS3	22986	hgsc.bcm.edu	37	10	106917003	106917003	+	Silent	SNP	G	G	A	rs150165918	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	26	45	0	0.419355	0	G|0.987;A|0.013	0.013	strong	.	SORCS3	282	.	NM_014978	exon10	c.G1590A	p.P530P	AGCTCCGGATGTG	.	PASS	Atlas-SNP
EPG5	57724	hgsc.bcm.edu	37	18	43514856	43514856	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	140	60	120	0	0.428571	0	.	.	none	.	EPG5	199	.	NM_020964	exon11	c.C2176T	p.L726F	GCATGAGGTAGAA	.	PASS	Atlas-SNP
BTN3A3	10384	hgsc.bcm.edu	37	6	26443853	26443853	+	Silent	SNP	C	C	A	rs56036950	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	268	53	268	0	0.197761	0	C|0.836;A|0.164	0.164	strong	.	BTN3A3	56	.	NM_006994	exon3	c.C51A	p.S17S	TGTCTCCCTCTTC	.	PASS	Atlas-SNP
FRMD6	122786	hgsc.bcm.edu	37	14	52186972	52186972	+	Silent	SNP	A	A	G	rs2277494	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	34	57	0	0.539683	0	A|0.700;G|0.300	0.300	strong	.	FRMD6	100	.	NM_001267046	exon11	c.A1224G	p.P408P	GGGGCCAGAAGAC	.	PASS	Atlas-SNP
SLC35G5	83650	hgsc.bcm.edu	37	8	11189184	11189184	+	Missense_Mutation	SNP	C	C	T	rs115295428	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	99	16	77	0	0.161616	0	C|0.978;T|0.022	0.022	strong	AMAC1L2,NS,carcinoma,0,1	.	.	1	NM_054028	exon1	c.C569T	p.T190I	ACACCACCCTGGG	.	scavenged	Atlas-SNP
TAP1	6890	hgsc.bcm.edu	37	6	32814942	32814942	+	Missense_Mutation	SNP	C	C	T	rs200925248		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	42	6	29	0	0.142857	0	.	.	weak	.	TAP1	39	.	NM_000593	exon10	c.G2123A	p.R708Q	GCCTGTCGCTGAC	.	PASS	Atlas-SNP
FAAH2	158584	hgsc.bcm.edu	37	X	57475132	57475132	+	Silent	SNP	T	T	C	rs1367830	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	118	118	84	0	1	0	T|0.496;0|0.015	.	strong	.	FAAH2	66	.	NM_174912	exon10	c.T1404C	p.P468P	ACGGCCTTTCAAC	.	PASS	Atlas-SNP
NEDD9	4739	hgsc.bcm.edu	37	6	11185533	11185533	+	Silent	SNP	G	G	A	rs1050775	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	157	154	160	2	0.980892	0.0125	G|0.457;A|0.543	0.543	strong	NEDD9_ENST00000379446,NS,carcinoma,0,1	NEDD9	191	1	NM_001142393	exon8	c.C2367T	p.T789T	GACTATGGTCTTG	.	scavenged	Atlas-SNP
DCAF13	25879	hgsc.bcm.edu	37	8	104427578	104427578	+	Silent	SNP	T	T	C	rs3134297	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48	26	65	0	0.541667	0	T|0.764;C|0.236	0.236	strong	DCAF13,NS,carcinoma,0,1	DCAF13	66	1	NM_015420	exon1	c.T360C	p.S120S	TGGAAGTAGTCTG	.	PASS	Atlas-SNP
PSMD9	5715	hgsc.bcm.edu	37	12	122353796	122353796	+	Missense_Mutation	SNP	A	A	G	rs14259	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80	41	69	0	0.5125	0	A|0.747;G|0.253	0.253	strong	.	PSMD9	8	.	NM_002813	exon5	c.A590G	p.E197G	GGGGGGAAAAACA	.	PASS	Atlas-SNP
OSBP2	23762	hgsc.bcm.edu	37	22	31266546	31266546	+	Silent	SNP	T	T	C	rs2301816	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98	45	84	0	0.459184	0	T|0.307;C|0.693	0.693	strong	.	OSBP2	52	.	NM_030758	exon3	c.T984C	p.A328A	CGGCGCTGCACTC	.	PASS	Atlas-SNP
MCCC1	56922	hgsc.bcm.edu	37	3	182804555	182804555	+	Missense_Mutation	SNP	C	C	T	rs375244642		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60	28	80	0	0.466667	0	.	.	weak	.	MCCC1	87	.	NM_020166	exon4	c.G295A	p.G99S	CGGGGCCGATGGA	.	PASS	Atlas-SNP
EXPH5	23086	hgsc.bcm.edu	37	11	108384207	108384207	+	Missense_Mutation	SNP	C	C	T	rs2846412	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	141	141	119	0	1	0	C|0.440;T|0.560	0.560	strong	.	EXPH5	193	.	NM_015065	exon6	c.G2027A	p.S676N	TTGCTGCTGGTCA	.	PASS	Atlas-SNP
LAMA1	284217	hgsc.bcm.edu	37	18	7012123	7012123	+	Silent	SNP	A	A	G	rs9946794	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	24	12	54	0	0.5	0	A|0.528;G|0.472	0.472	strong	LAMA1,NS,carcinoma,0,1	LAMA1	458	1	NM_005559	exon24	c.T3378C	p.G1126G	CTGAGGACCAAAG	.	PASS	Atlas-SNP
DPCR1	135656	hgsc.bcm.edu	37	6	30920124	30920124	+	Missense_Mutation	SNP	G	G	A	rs3132580	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	178	140	171	0	0.786517	0	G|0.913;A|0.087	0.087	strong	.	DPCR1	99	.	NM_080870	exon2	c.G3883A	p.E1295K	GGAAACGAGAGCC	.	PASS	Atlas-SNP
NAV2	89797	hgsc.bcm.edu	37	11	20117232	20117232	+	Silent	SNP	T	T	C	rs2289566	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	167	90	166	0	0.538922	0	T|0.656;C|0.344	0.344	strong	.	NAV2	255	.	NM_001244963	exon32	c.T6108C	p.H2036H	ACCACATCTCTTT	.	PASS	Atlas-SNP
MRPS24	64951	hgsc.bcm.edu	37	7	43906513	43906513	+	Missense_Mutation	SNP	A	A	G	rs670573	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44	35	41	0	0.795455	0	T|0.000;G|0.102;N|0.000;A|0.898	0.102	strong	.	MRPS24	9	.	NM_032014	exon4	c.T289C	p.W97R	TACCCCACATGAA	.	PASS	Atlas-SNP
IGSF22	283284	hgsc.bcm.edu	37	11	18727448	18727448	+	Missense_Mutation	SNP	T	T	C	rs1867877	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80	36	75	0	0.45	0	T|0.970;C|0.030	0.030	strong	.	IGSF22	211	.	NM_173588	exon22	c.A3826G	p.T1276A	TGAGCGTGCAGGT	.	PASS	Atlas-SNP
ACE	1636	hgsc.bcm.edu	37	17	61559923	61559923	+	Silent	SNP	C	C	T	rs4309	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	85	91	0	0.988372	0	C|0.639;T|0.361	0.361	strong	.	ACE	187	.	NM_000789	exon8	c.C1215T	p.P405P	TCTGCCCGTCTCC	.	PASS	Atlas-SNP
ZNF100	163227	hgsc.bcm.edu	37	19	21910451	21910451	+	Silent	SNP	A	A	C	rs75062026		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	19	51	0	0.404255	0	.	.	weak	.	ZNF100	62	.	NM_173531	exon5	c.T663G	p.T221T	ATGTTGAGTTAGG	.	PASS	Atlas-SNP
PCDH8	5100	hgsc.bcm.edu	37	13	53422553	53422553	+	Missense_Mutation	SNP	A	A	G	rs3742301	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	28	14	27	0	0.5	0	A|0.769;G|0.231	0.231	strong	.	PCDH8	95	.	NM_002590	exon1	c.T19C	p.W7R	TGCCCCAACGCCT	.	PASS	Atlas-SNP
CHAD	1101	hgsc.bcm.edu	37	17	48543154	48543154	+	Silent	SNP	G	G	A	rs2231507	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91	41	59	0	0.450549	0	G|0.964;A|0.036	0.036	strong	CHAD,upper_leg,malignant_melanoma,-2,1	CHAD	36	1	NM_001267	exon2	c.C852T	p.P284P	GTTGGAGGGTAGC	.	PASS	Atlas-SNP
TUBA3E	112714	hgsc.bcm.edu	37	2	130949491	130949491	+	Silent	SNP	G	G	A	rs60154251	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	127	32	164	0	0.251969	0	G|0.612;A|0.388	0.388	strong	TUBA3E,colon,carcinoma,-2,1	TUBA3E	73	1	NM_207312	exon5	c.C1266T	p.R422R	GTCCTCGCGGGCC	.	PASS	Atlas-SNP
INPP4B	8821	hgsc.bcm.edu	37	4	143324094	143324094	+	Silent	SNP	G	G	A	rs1982966	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	38	20	52	0	0.526316	0	G|0.743;A|0.257	0.257	strong	INPP4B,NS,carcinoma,0,1	INPP4B	132	1	NM_003866	exon8	c.C369T	p.D123D	TACGGTGTCATGA	.	PASS	Atlas-SNP
DPT	1805	hgsc.bcm.edu	37	1	168683476	168683476	+	Silent	SNP	C	C	T	rs35449613	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69	27	75	0	0.391304	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
ATP2A3	489	hgsc.bcm.edu	37	17	3845927	3845927	+	Silent	SNP	A	A	G	rs17846889	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	46	24	23	0	0.521739	0	G|0.461;C|0.000;A|0.539	0.461	strong	.	ATP2A3	148	.	NM_174956	exon12	c.T1518C	p.T506T	CTGGCCAGTAGGG	.	PASS	Atlas-SNP
LGR4	55366	hgsc.bcm.edu	37	11	27389739	27389739	+	Missense_Mutation	SNP	T	T	C	rs34804482	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	37	46	0	0.606557	0	T|0.983;C|0.017	0.017	strong	LGR4,right_upper_lobe,carcinoma,-1,1	LGR4	87	1	NM_018490	exon18	c.A2531G	p.D844G	CCACAGTCGTAGT	.	PASS	Atlas-SNP
APOBEC3H	164668	hgsc.bcm.edu	37	22	39497454	39497454	+	Missense_Mutation	SNP	G	G	C	rs139299	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60	60	66	0	1	0	G|0.453;C|0.547	0.547	strong	.	APOBEC3H	28	.	NM_001166003	exon3	c.G363C	p.K121N	GCAGAAGGGGCTG	.	PASS	Atlas-SNP
KIAA1211	57482	hgsc.bcm.edu	37	4	57180701	57180701	+	Missense_Mutation	SNP	A	A	G	rs181288707	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	12	9	16	2	0.75	0.125	A|0.989;G|0.011	0.011	strong	KIAA1211,NS,carcinoma,-2,1	KIAA1211	178	1	NM_020722	exon8	c.A1033G	p.R345G	GAGCGGAGGCGGC	.	scavenged	Atlas-SNP
CD276	80381	hgsc.bcm.edu	37	15	73996590	73996590	+	Silent	SNP	G	G	A	rs143255170	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	138	73	152	0	0.528986	0	G|0.974;A|0.026	0.026	strong	.	CD276	29	.	NM_001024736	exon6	c.G1146A	p.T382T	CATCACGTGCTCC	.	PASS	Atlas-SNP
MTMR2	8898	hgsc.bcm.edu	37	11	95580926	95580926	+	Silent	SNP	G	G	A	rs566204	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	234	37	177	0	0.15812	0	G|0.715;A|0.285	0.285	strong	.	MTMR2	79	.	NM_016156	exon10	c.C1131T	p.T377T	CCAGTGGGTTTCC	.	PASS	Atlas-SNP
LILRB5	10990	hgsc.bcm.edu	37	19	54759361	54759361	+	Missense_Mutation	SNP	T	T	C	rs12975366	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	156	75	170	2	0.480769	0.0117647	T|0.679;C|0.321	0.321	strong	LILRB5_ENST00000450632,colon,carcinoma,0,4	LILRB5	176	4	NM_001081442	exon5	c.A740G	p.D247G	CCGACATCAGAGC	.	scavenged	Atlas-SNP
DLG5	9231	hgsc.bcm.edu	37	10	79570873	79570873	+	Missense_Mutation	SNP	G	G	T	rs2289310	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	39	24	44	0	0.615385	0	G|0.944;T|0.056	0.056	strong	.	DLG5	154	.	NM_004747	exon23	c.C4442A	p.P1481Q	TTGGCTGGGGGGG	.	PASS	Atlas-SNP
MCM10	55388	hgsc.bcm.edu	37	10	13214753	13214753	+	Missense_Mutation	SNP	G	G	C	rs34630110	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	50	23	74	0	0.46	0	G|0.912;C|0.088	0.088	strong	.	MCM10	76	.	NM_182751	exon5	c.G583C	p.A195P	CCAAAGGCTTCAC	.	PASS	Atlas-SNP
FANCM	57697	hgsc.bcm.edu	37	14	45658449	45658449	+	Missense_Mutation	SNP	A	A	G	rs143662421	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	113	45	119	0	0.39823	0	A|0.992;G|0.008	0.008	strong	.	FANCM	225	.	NM_020937	exon20	c.A5224G	p.I1742V	GATACAATTTCCG	.	PASS	Atlas-SNP
CDH17	1015	hgsc.bcm.edu	37	8	95186382	95186382	+	Silent	SNP	G	G	A	rs3214050	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	99	43	91	0	0.434343	0	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	.	PASS	Atlas-SNP
PEPD	5184	hgsc.bcm.edu	37	19	33882222	33882222	+	Silent	SNP	G	G	A	rs17569	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91	43	88	0	0.472527	0	T|0.045;G|0.545;C|0.327;A|0.083	0.083	strong	.	PEPD	48	.	NM_000285	exon13	c.C1131T	p.H377H	CACGTCGTGCACG	.	PASS	Atlas-SNP
POM121	9883	hgsc.bcm.edu	37	7	72418992	72418992	+	Missense_Mutation	SNP	C	C	T	rs9955	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91	37	83	0	0.406593	0	C|0.882;T|0.118	0.118	strong	NSUN5P2,NS,carcinoma,0,1	POM121	131	1	NM_001257190	exon16	c.C2983T	p.P995S	TCCTTTCCCACCA	.	PASS	Atlas-SNP
CNPPD1	27013	hgsc.bcm.edu	37	2	220037666	220037666	+	Missense_Mutation	SNP	A	A	G	rs1127102	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	88	40	77	0	0.454545	0	A|0.553;G|0.447	0.447	strong	.	CNPPD1	22	.	NM_015680	exon8	c.T875C	p.L292P	TTAGCGAGAGACG	.	PASS	Atlas-SNP
SLC35G5	83650	hgsc.bcm.edu	37	8	11189215	11189215	+	Silent	SNP	C	C	A	rs151245433	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93	13	79	0	0.139785	0	C|0.988;A|0.011	0.011	strong	AMAC1L2,NS,carcinoma,0,1	.	.	1	NM_054028	exon1	c.C600A	p.G200G	GGGAGGCCTGGCG	.	scavenged	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9072221	9072221	+	Silent	SNP	G	G	A	rs66498329	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85	43	82	1	0.505882	0.0121951	G|0.787;A|0.213	0.213	strong	MUC16_ENST00000397910,NS,carcinoma,-1,3	MUC16	4315	3	NM_024690	exon3	c.C15225T	p.G5075G	CACTAGGCCAGAG	.	scavenged	Atlas-SNP
BAI2	576	hgsc.bcm.edu	37	1	32221913	32221913	+	Silent	SNP	G	G	A	rs4949223	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	109	108	98	0	0.990826	0	G|0.896;A|0.104	0.104	strong	.	BAI2	128	.	NM_001703	exon4	c.C525T	p.P175P	GGCAGCGGGCGCC	.	PASS	Atlas-SNP
TEX15	56154	hgsc.bcm.edu	37	8	30706224	30706224	+	Missense_Mutation	SNP	A	A	G	rs323347	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	104	49	88	0	0.471154	0	A|0.651;G|0.349	0.349	strong	.	TEX15	350	.	NM_031271	exon1	c.T310C	p.C104R	CAGCACAATCACC	.	PASS	Atlas-SNP
PCDHB11	56125	hgsc.bcm.edu	37	5	140580963	140580963	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	150	59	203	0	0.393333	0	.	.	none	.	PCDHB11	162	.	NM_018931	exon1	c.C1616T	p.P539L	GCTCCCCGGCTTT	.	PASS	Atlas-SNP
CAPG	822	hgsc.bcm.edu	37	2	85628983	85628983	+	Missense_Mutation	SNP	C	C	T	rs2229668	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	51	108	0	0.71831	0	C|0.890;T|0.110	0.110	strong	.	CAPG	32	.	NM_001256140	exon3	c.G121A	p.V41I	AGAAGACGCCCTG	.	PASS	Atlas-SNP
ZNF469	84627	hgsc.bcm.edu	37	16	88501971	88501971	+	Missense_Mutation	SNP	T	T	A	rs3812956	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	32	16	41	0	0.5	0	T|0.680;A|0.320	0.320	strong	.	ZNF469	121	.	NM_001127464	exon2	c.T8009A	p.L2670Q	CCACTCTGGGACC	.	PASS	Atlas-SNP
SV2C	22987	hgsc.bcm.edu	37	5	75594743	75594743	+	Missense_Mutation	SNP	G	G	A	rs31244	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	78	38	55	0	0.487179	0	G|0.892;A|0.108	0.108	strong	.	SV2C	97	.	NM_014979	exon10	c.G1627A	p.D543N	GTTTTTGACAACA	.	PASS	Atlas-SNP
ABCD2	225	hgsc.bcm.edu	37	12	40013392	40013392	+	Missense_Mutation	SNP	G	G	C	rs117275340	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	46	22	55	0	0.478261	0	G|0.986;C|0.014	0.014	strong	.	ABCD2	127	.	NM_005164	exon1	c.C26G	p.A9G	CGATCAGCTGCTG	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	191	96	143	0	0.502618	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
OR2T1	26696	hgsc.bcm.edu	37	1	248570057	248570057	+	Silent	SNP	T	T	C	rs138375160	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	157	73	181	0	0.464968	0	T|0.994;C|0.006	0.006	strong	.	OR2T1	89	.	NM_030904	exon1	c.T762C	p.V254V	CTGTGTTTTGATG	.	PASS	Atlas-SNP
ALB	213	hgsc.bcm.edu	37	4	74280774	74280774	+	Silent	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	125	30	98	0	0.24	0	.	.	none	.	ALB	132	.	NM_000477	exon9	c.A1081C	p.R361R	GCAAGAAGGCATC	.	PASS	Atlas-SNP
SF3B1	23451	hgsc.bcm.edu	37	2	198270136	198270136	+	Missense_Mutation	SNP	T	T	C	rs367701030	alternate_allele	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	156	44	177	0	0.282051	0	.	.	alt	.	SF3B1	1038	.	NM_012433	exon10	c.A1300G	p.T434A	TTGGAGTAGCTGT	.	PASS	Atlas-SNP
PRDM9	56979	hgsc.bcm.edu	37	5	23527471	23527471	+	Silent	SNP	C	C	A	rs183034145	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	43	9	80	1	0.209302	0.0125	C|0.981;A|0.019	0.019	strong	PRDM9,NS,carcinoma,+1,2	PRDM9	344	2	NM_020227	exon11	c.C2274A	p.R758R	CTTTCGCGATAAG	.	scavenged	Atlas-SNP
ADCY3	109	hgsc.bcm.edu	37	2	25064193	25064193	+	Silent	SNP	G	G	A	rs2241759	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	61	52	0	0.983871	0	G|0.520;A|0.480	0.480	strong	.	ADCY3	114	.	NM_004036	exon5	c.C1131T	p.P377P	GTAGTCGGGCAAG	.	PASS	Atlas-SNP
ANXA9	8416	hgsc.bcm.edu	37	1	150960593	150960593	+	Missense_Mutation	SNP	G	G	A	rs149528939	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	150	81	123	0	0.54	0	G|0.994;A|0.006	0.006	strong	.	ANXA9	28	.	NM_003568	exon11	c.G724A	p.G242R	AGCACTGGGCAAG	.	PASS	Atlas-SNP
QSER1	79832	hgsc.bcm.edu	37	11	32956492	32956492	+	Missense_Mutation	SNP	C	C	T	rs62618693	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	123	68	111	0	0.552846	0	C|0.977;T|0.023	0.023	strong	.	QSER1	153	.	NM_001076786	exon4	c.C3301T	p.R1101C	GGCAAACGCCAGA	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9056941	9056941	+	Missense_Mutation	SNP	A	A	G	rs10410136	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93	51	103	0	0.548387	0	A|0.797;G|0.203	0.203	strong	.	MUC16	4315	.	NM_024690	exon3	c.T30505C	p.F10169L	TCCTAAATCCAGA	.	PASS	Atlas-SNP
SLC22A18AS	5003	hgsc.bcm.edu	37	11	2909573	2909573	+	Missense_Mutation	SNP	G	G	A	rs139893801	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	33	60	0	0.515625	0	G|0.999;A|0.001	0.001	strong	.	SLC22A18AS	7	.	NM_007105	exon4	c.C599T	p.T200I	CGTCCTGTCATTC	.	PASS	Atlas-SNP
HSPG2	3339	hgsc.bcm.edu	37	1	22159774	22159774	+	Silent	SNP	G	G	A	rs2229486	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68	34	78	0	0.5	0	T|0.000;G|0.907;C|0.000;A|0.093	0.093	strong	.	HSPG2	311	.	NM_005529	exon80	c.C11082T	p.P3694P	TGAGTCGGGCCGG	.	PASS	Atlas-SNP
PTCRA	171558	hgsc.bcm.edu	37	6	42893121	42893121	+	Missense_Mutation	SNP	G	G	A	rs36111725	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	10	8	11	0	0.8	0	G|0.960;A|0.040	0.040	strong	.	PTCRA	24	.	NM_001243168	exon4	c.G592A	p.A198T	TCCCCCGCAACCA	.	PASS	Atlas-SNP
APLF	200558	hgsc.bcm.edu	37	2	68765205	68765205	+	Missense_Mutation	SNP	C	C	T	rs13404469	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	123	91	173	0	0.739837	0	C|0.910;T|0.090	0.090	strong	.	APLF	69	.	NM_173545	exon7	c.C1006T	p.L336F	GACTCACTTCAGG	.	PASS	Atlas-SNP
KIF16B	55614	hgsc.bcm.edu	37	20	16486698	16486698	+	Silent	SNP	G	G	A	rs2295115	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	32	65	0	0.5	0	G|0.760;A|0.240	0.240	strong	.	KIF16B	305	.	NM_001199865	exon8	c.C837T	p.L279L	AGTCACGAGGGAC	.	PASS	Atlas-SNP
PLCB1	23236	hgsc.bcm.edu	37	20	8737734	8737734	+	Silent	SNP	G	G	A	rs2076413	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57	20	80	0	0.350877	0	G|0.773;A|0.227	0.227	strong	.	PLCB1	394	.	NM_015192	exon24	c.T2565A	p.P855P	TGAAGCGAGAACG	.	PASS	Atlas-SNP
C3orf67	200844	hgsc.bcm.edu	37	3	58849343	58849343	+	Missense_Mutation	SNP	C	C	T	rs34631714	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	105	43	113	0	0.409524	0	C|0.998;T|0.002	0.002	strong	.	C3orf67	45	.	NM_198463	exon12	c.G1159A	p.V387M	TTGTCACACTGTT	.	PASS	Atlas-SNP
HS1BP3	64342	hgsc.bcm.edu	37	2	20824559	20824559	+	Silent	SNP	C	C	T	rs2305457	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	27	68	0	0.5	0	C|0.772;T|0.228	0.228	strong	.	HS1BP3	33	.	NM_022460	exon5	c.G717A	p.E239E	GAGCCCCTCATCA	.	PASS	Atlas-SNP
ACACB	32	hgsc.bcm.edu	37	12	109623516	109623516	+	Missense_Mutation	SNP	G	G	A	rs2300455	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	27	11	32	0	0.407407	0	G|0.846;A|0.154	0.154	strong	ACACB,colon,carcinoma,0,1	ACACB	330	1	NM_001093	exon11	c.G1951A	p.A651T	ATTGCCGCCAGAA	.	PASS	Atlas-SNP
CPSF1	29894	hgsc.bcm.edu	37	8	145623963	145623963	+	Silent	SNP	G	G	A	rs4317614	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	199	197	252	1	0.98995	0.00396825	G|0.629;A|0.371	0.371	strong	.	CPSF1	92	.	NM_013291	exon18	c.C1704T	p.D568D	GCGGCCGTCGTCG	.	PASS	Atlas-SNP
MAGEB3	4114	hgsc.bcm.edu	37	X	30254530	30254530	+	Silent	SNP	A	A	G	rs2071310	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	212	152	138	0	0.716981	0	A|0.567;0|0.003	.	strong	.	MAGEB3	54	.	NM_002365	exon5	c.A489G	p.V163V	GGTGGTATTTGGT	.	PASS	Atlas-SNP
KIAA1755	85449	hgsc.bcm.edu	37	20	36850940	36850940	+	Silent	SNP	G	G	C	rs41310010	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	40	17	32	0	0.425	0	G|0.891;C|0.109	0.109	strong	.	KIAA1755	145	.	NM_001029864	exon10	c.C2328G	p.P776P	TAGGCCGGGGTCC	.	PASS	Atlas-SNP
TNK2	10188	hgsc.bcm.edu	37	3	195615376	195615376	+	Silent	SNP	A	A	G	rs3747669	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	95	94	88	0	0.989474	0	A|0.584;G|0.416	0.416	strong	.	TNK2	246	.	NM_001010938	exon2	c.T273C	p.D91D	GAGGTCATCTCGG	.	PASS	Atlas-SNP
DNASE2B	58511	hgsc.bcm.edu	37	1	84878228	84878228	+	Silent	SNP	C	C	T	rs7511984	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48	29	34	0	0.604167	0	C|0.841;T|0.159	0.159	strong	.	DNASE2B	40	.	NM_021233	exon5	c.C744T	p.D248D	TCTTGACGGTATG	.	PASS	Atlas-SNP
RSPH10B	222967	hgsc.bcm.edu	37	7	5983063	5983063	+	Missense_Mutation	SNP	C	C	T	rs17853305		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	785	313	607	1	0.398726	0.00164745	.	.	weak	RSPH10B,NS,carcinoma,-1,2	RSPH10B	28	2	NM_173565	exon15	c.G1650A	p.M550I	GTAACTCATAGAG	.	PASS	Atlas-SNP
STK17A	9263	hgsc.bcm.edu	37	7	43664280	43664280	+	Missense_Mutation	SNP	A	A	G	rs1044141	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	35	35	59	0	1	0	A|0.185;G|0.815	0.815	strong	.	STK17A	31	.	NM_004760	exon7	c.A1084G	p.K362E	GAAACCAAGGAAT	.	PASS	Atlas-SNP
MINK1	50488	hgsc.bcm.edu	37	17	4796274	4796274	+	Missense_Mutation	SNP	T	T	C	rs11556634	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	106	55	115	0	0.518868	0	A|0.000;C|0.651;G|0.000;T|0.348	0.651	strong	.	MINK1	110	.	NM_153827	exon20	c.T2312C	p.V771A	GTCCAGTCTCCTC	.	PASS	Atlas-SNP
CTAGE5	4253	hgsc.bcm.edu	37	14	39818028	39818028	+	Missense_Mutation	SNP	A	A	G	rs1140952	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	121	63	100	0	0.520661	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
NPFFR1	64106	hgsc.bcm.edu	37	10	72015409	72015409	+	Silent	SNP	C	C	A	rs10999212	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	126	65	117	0	0.515873	0	C|0.843;A|0.157	0.157	strong	.	NPFFR1	21	.	NM_022146	exon4	c.G597T	p.P199P	GTAGAGCGGGTAG	.	PASS	Atlas-SNP
TLR3	7098	hgsc.bcm.edu	37	4	187004217	187004217	+	Silent	SNP	C	C	T	rs3775290	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	139	64	135	0	0.460432	0	C|0.727;T|0.273	0.273	strong	TLR3,caecum,carcinoma,0,1	TLR3	83	1	NM_003265	exon4	c.C1377T	p.F459F	TATTTTCGAAATC	.	PASS	Atlas-SNP
GIP	2695	hgsc.bcm.edu	37	17	47041771	47041771	+	Missense_Mutation	SNP	G	G	A	rs367741847		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	109	67	110	0	0.614679	0	.	.	weak	.	GIP	15	.	NM_004123	exon3	c.C158T	p.A53V	CCTTCCGCGTACC	.	PASS	Atlas-SNP
ICOSLG	23308	hgsc.bcm.edu	37	21	45656774	45656774	+	Missense_Mutation	SNP	C	C	T	rs11558819	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	60	50	0	0.983607	0	C|0.738;T|0.262	0.262	strong	ICOSLG,NS,carcinoma,0,1	ICOSLG	20	1	NM_015259	exon3	c.G382A	p.V128I	CCTCAACGCTCAA	.	PASS	Atlas-SNP
RYR1	6261	hgsc.bcm.edu	37	19	38995438	38995438	+	Silent	SNP	T	T	C	rs2960340	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	46	25	51	0	0.543478	0	T|0.657;C|0.343	0.343	strong	RYR1,NS,carcinoma,0,1	RYR1	708	1	NM_001042723	exon51	c.T8118C	p.I2706I	CGCCATTGCCGGG	.	PASS	Atlas-SNP
ZNF700	90592	hgsc.bcm.edu	37	19	12059645	12059645	+	Missense_Mutation	SNP	A	A	G	rs12327617	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	35	18	38	0	0.514286	0	A|0.938;G|0.062	0.062	strong	.	ZNF700	81	.	NM_001271848	exon4	c.A815G	p.E272G	TACATGAAAGAAC	.	PASS	Atlas-SNP
SPTBN1	6711	hgsc.bcm.edu	37	2	54858511	54858511	+	Silent	SNP	C	C	T	rs1052788	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	114	58	102	0	0.508772	0	C|0.759;T|0.241	0.241	strong	SPTBN1,NS,carcinoma,0,1	SPTBN1	378	1	NM_003128	exon16	c.C3327T	p.N1109N	CAAGAACGAGATC	.	PASS	Atlas-SNP
SERPINB7	8710	hgsc.bcm.edu	37	18	61471523	61471523	+	Missense_Mutation	SNP	G	G	A	rs17782413	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	20	11	29	0	0.55	0	G|0.824;A|0.176	0.176	strong	.	SERPINB7	66	.	NM_001261830	exon8	c.G797A	p.R266Q	CAAGGCGAATGAC	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	103	50	106	0	0.485437	0	G|0.754;T|0.246	0.246	strong	.	CNPY3	25	.	NM_006586	exon6	c.G692T	p.S231I	AGAGCAGCAGGGC	.	PASS	Atlas-SNP
OR12D3	81797	hgsc.bcm.edu	37	6	29342271	29342271	+	Missense_Mutation	SNP	G	G	A	rs369042428		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	106	29	124	0	0.273585	0	.	.	weak	.	OR12D3	55	.	NM_030959	exon1	c.C794T	p.T265I	ATGGAGGTGGCTG	.	PASS	Atlas-SNP
CTNNA1	1495	hgsc.bcm.edu	37	5	138266552	138266552	+	Silent	SNP	C	C	G	rs11552052	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	150	74	169	0	0.493333	0	C|0.983;G|0.017	0.017	strong	.	CTNNA1	114	.	NM_001903	exon16	c.C2226G	p.V742V	GGATGTCATCAGT	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29910725	29910725	+	Missense_Mutation	SNP	C	C	G	rs199474430	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	156	14	190	0	0.0897436	0	C|0.921;G|0.080	0.080	strong	.	HLA-A	89	.	NM_001242758	exon2	c.C265G	p.R89G	GAGACACGGAATG	.	PASS	Atlas-SNP
EEF1D	1936	hgsc.bcm.edu	37	8	144671955	144671955	+	Silent	SNP	C	C	T	rs61757370	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55	29	53	0	0.527273	0	C|0.987;T|0.013	0.013	strong	.	EEF1D	48	.	NM_001130053	exon3	c.G297A	p.A99A	CAGGTCCGCGGGG	.	PASS	Atlas-SNP
ATP2A1	487	hgsc.bcm.edu	37	16	28898778	28898778	+	Silent	SNP	C	C	G	rs113803159	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69	39	65	0	0.565217	0	C|0.995;G|0.005	0.005	strong	.	ATP2A1	116	.	NM_004320	exon8	c.C663G	p.G221G	CTTGGGCATCGTG	.	PASS	Atlas-SNP
DACT2	168002	hgsc.bcm.edu	37	6	168708678	168708678	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	41	8	59	0	0.195122	0	.	.	none	.	DACT2	46	.	NM_214462	exon4	c.G1759C	p.A587P	CTTGGGCTGAGGT	.	PASS	Atlas-SNP
ESPL1	9700	hgsc.bcm.edu	37	12	53670545	53670545	+	Missense_Mutation	SNP	C	C	A	rs1318648	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49	43	57	0	0.877551	0	C|0.400;N|0.000	.	strong	.	ESPL1	158	.	NM_012291	exon8	c.C1842A	p.S614R	GCTGAGCCCCGAG	.	PASS	Atlas-SNP
SPNS1	83985	hgsc.bcm.edu	37	16	28995211	28995211	+	Silent	SNP	C	C	T	rs113165798	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44	24	44	0	0.545455	0	C|0.995;T|0.005	0.005	strong	.	SPNS1	47	.	NM_001142448	exon12	c.C1425T	p.G475G	GGGCGGCGCAGCC	.	PASS	Atlas-SNP
BZRAP1	9256	hgsc.bcm.edu	37	17	56393840	56393840	+	Missense_Mutation	SNP	G	G	C	rs61739511	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	50	31	47	0	0.62	0	G|0.952;C|0.048	0.048	strong	.	BZRAP1	287	.	NM_004758	exon15	c.C1934G	p.A645G	TCTGGCGCAGCTG	.	PASS	Atlas-SNP
COL7A1	1294	hgsc.bcm.edu	37	3	48628014	48628014	+	Missense_Mutation	SNP	G	G	A	rs2228561	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	128	75	112	0	0.585938	0	G|0.914;A|0.086	0.086	strong	.	COL7A1	320	.	NM_000094	exon14	c.C1784T	p.P595L	GTTTCCGGCTCTA	.	PASS	Atlas-SNP
ASAH1	427	hgsc.bcm.edu	37	8	17927327	17927327	+	Missense_Mutation	SNP	T	T	C	rs1049874	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	31	31	69	0	1	0	T|0.579;C|0.421	0.421	strong	.	ASAH1	71	.	NM_004315	exon4	c.A325G	p.I109V	GCATAATTTTTCC	.	PASS	Atlas-SNP
UBASH3A	53347	hgsc.bcm.edu	37	21	43824123	43824123	+	Silent	SNP	G	G	C	rs2277799	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	150	150	110	1	1	0.00909091	G|0.601;C|0.399	0.399	strong	.	UBASH3A	72	.	NM_018961	exon1	c.G69C	p.S23S	CCCCTCGCTCCTG	.	PASS	Atlas-SNP
SLC39A4	55630	hgsc.bcm.edu	37	8	145639681	145639681	+	Missense_Mutation	SNP	G	G	C	rs1871534	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	212	102	210	0	0.481132	0	G|0.744;C|0.256	0.256	strong	.	SLC39A4	54	.	NM_130849	exon6	c.C1114G	p.L372V	CAGTGAGTGCACC	.	PASS	Atlas-SNP
C14orf37	145407	hgsc.bcm.edu	37	14	58604850	58604850	+	Silent	SNP	A	A	C	rs11626667	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	42	79	0	0.5	0	A|0.965;C|0.035	0.035	strong	.	C14orf37	87	.	NM_001001872	exon2	c.T1227G	p.V409V	AATGGAAACTTTC	.	PASS	Atlas-SNP
ZSWIM8	23053	hgsc.bcm.edu	37	10	75559077	75559077	+	Silent	SNP	G	G	A	rs11000780	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	45	22	47	0	0.488889	0	G|0.880;A|0.120	0.120	strong	.	.	.	.	NM_015037	exon21	c.G4494A	p.P1498P	ATACCCGGGTCCA	.	PASS	Atlas-SNP
C21orf2	755	hgsc.bcm.edu	37	21	45750346	45750346	+	Silent	SNP	C	C	A	rs2070573	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	33	13	43	0	0.393939	0	C|0.728;A|0.272	0.272	strong	.	C21orf2	10	.	NM_001271441	exon6	c.G999T	p.P333P	ACTGACCGGCACA	.	PASS	Atlas-SNP
WDFY4	57705	hgsc.bcm.edu	37	10	50038800	50038800	+	Silent	SNP	A	A	G	rs3747874	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	222	108	205	0	0.486486	0	A|0.353;G|0.647	0.647	strong	.	WDFY4	205	.	NM_020945	exon38	c.A6396G	p.Q2132Q	GGCACAAAGGCAG	.	PASS	Atlas-SNP
TREX2	11219	hgsc.bcm.edu	37	X	152710522	152710522	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	20	7	21	0	0.35	0	.	.	none	.	TREX2	36	.	NM_080701	exon2	c.G367T	p.D123Y	GGAAATCATAATC	.	PASS	Atlas-SNP
VWA3A	146177	hgsc.bcm.edu	37	16	22143031	22143031	+	Missense_Mutation	SNP	G	G	A	rs199942653		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	220	92	262	1	0.418182	0.00381679	G|0.999;A|0.001	0.001	weak	.	VWA3A	115	.	NM_173615	exon19	c.G1853A	p.G618D	CTGGGGGCATCCC	.	PASS	Atlas-SNP
GPSM2	29899	hgsc.bcm.edu	37	1	109440215	109440215	+	Missense_Mutation	SNP	G	G	A	rs41279678	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	36	17	43	0	0.472222	0	G|0.908;A|0.092	0.092	strong	.	GPSM2	56	.	NM_013296	exon4	c.G380A	p.R127Q	GTCAGCGACACCT	.	PASS	Atlas-SNP
PPYR1	5540	hgsc.bcm.edu	37	10	47087078	47087078	+	Missense_Mutation	SNP	G	G	T	rs2229967	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	112	32	107	0	0.285714	0	G|0.725;T|0.275	0.275	strong	PPYR1,colon,carcinoma,0,1	PPYR1	54	1	NM_005972	exon3	c.G295T	p.A99S	CTGACCGCCGTCT	.	PASS	Atlas-SNP
PTPRD	5789	hgsc.bcm.edu	37	9	8389364	8389364	+	Silent	SNP	C	C	G	rs2279776	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	105	52	128	0	0.495238	0	C|0.506;G|0.494	0.494	strong	.	PTPRD	1348	.	NM_002839	exon37	c.G4254C	p.G1418G	CCTATACCCATCT	.	PASS	Atlas-SNP
ZC3H12D	340152	hgsc.bcm.edu	37	6	149795522	149795522	+	Missense_Mutation	SNP	G	G	A	rs7747948	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	32	20	19	0	0.625	0	G|0.788;A|0.212	0.212	strong	.	ZC3H12D	21	.	NM_207360	exon2	c.C158T	p.P53L	GCAGCCGGGTGCT	.	PASS	Atlas-SNP
USP11	8237	hgsc.bcm.edu	37	X	47092423	47092423	+	Missense_Mutation	SNP	G	G	A	rs149757747	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	21	70	0	0.259259	0	G|1.000;A|0.000	0.000	strong	.	USP11	93	.	NM_004651	exon1	c.G110A	p.C37Y	TTGGCTGTAGAAG	.	PASS	Atlas-SNP
HLA-DPB1	3115	hgsc.bcm.edu	37	6	33048686	33048686	+	Missense_Mutation	SNP	G	G	A	rs1042169	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	20	4	25	0	0.2	0	A|0.392;G|0.603;T|0.005	0.392	strong	.	HLA-DPB1	28	.	NM_002121	exon2	c.G338A	p.G113D	AGCTGGGCGGGCC	.	PASS	Atlas-SNP
TLE6	79816	hgsc.bcm.edu	37	19	2994903	2994903	+	Silent	SNP	T	T	C	rs34831575	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	45	21	48	0	0.466667	0	T|0.715;C|0.285	0.285	strong	.	TLE6	68	.	NM_001143986	exon17	c.T1620C	p.P540P	GGTGCCTGAGATG	.	PASS	Atlas-SNP
CTC1	80169	hgsc.bcm.edu	37	17	8139463	8139463	+	Silent	SNP	G	G	A	rs74506939	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	120	55	98	0	0.458333	0	G|0.849;A|0.151	0.151	strong	.	CTC1	75	.	NM_025099	exon6	c.C990T	p.D330D	CTTGGGGTCAGCC	.	PASS	Atlas-SNP
ALPP	250	hgsc.bcm.edu	37	2	233245026	233245026	+	Missense_Mutation	SNP	G	G	A	rs71421640		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	287	9	302	1	0.0313589	0.00331126	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
TNIP2	79155	hgsc.bcm.edu	37	4	2744087	2744087	+	Missense_Mutation	SNP	G	G	A	rs2269495	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82	26	132	0	0.317073	0	G|0.671;N|0.001	.	strong	TNIP2,NS,carcinoma,0,1	TNIP2	28	1	NM_024309	exon6	c.C1187T	p.A396V	CTCTGGGCCGCGC	.	PASS	Atlas-SNP
C9orf156	51531	hgsc.bcm.edu	37	9	100684719	100684719	+	Silent	SNP	A	A	C	rs3183928	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	33	18	46	0	0.545455	0	T|0.181;G|0.063	.	strong	C9orf156,NS,carcinoma,0,1	C9orf156	35	1	NM_016481	exon1	c.T57G	p.V19V	CGGCTTAACGCAG	.	PASS	Atlas-SNP
KIAA1731	85459	hgsc.bcm.edu	37	11	93400796	93400796	+	Silent	SNP	C	C	T	rs67112133	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110	78	110	0	0.709091	0	C|0.864;T|0.136	0.136	strong	KIAA1731_ENST00000325212,NS,carcinoma,0,1	KIAA1731	173	1	NM_033395	exon3	c.C132T	p.I44I	AGATATCGCCTTA	.	PASS	Atlas-SNP
CCT6A	908	hgsc.bcm.edu	37	7	56129511	56129511	+	Silent	SNP	A	A	G	rs4927	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	224	109	201	0	0.486607	0	A|0.904;G|0.096	0.096	strong	.	CCT6A	44	.	NM_001762	exon12	c.A1419G	p.S473S	AGAATCAGGTCAG	.	PASS	Atlas-SNP
PTPLA	9200	hgsc.bcm.edu	37	10	17636309	17636309	+	Missense_Mutation	SNP	G	G	A	rs1053926	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	172	87	159	0	0.505814	0	G|0.764;A|0.236	0.236	strong	.	PTPLA	34	.	NM_014241	exon6	c.C679T	p.H227Y	TCACATGCGGCAA	.	PASS	Atlas-SNP
FUT6	2528	hgsc.bcm.edu	37	19	5831672	5831672	+	Missense_Mutation	SNP	G	G	C	rs61745631	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	518	155	566	0	0.299228	0	G|0.090;C|0.910	0.910	strong	.	FUT6	30	.	NM_000150	exon3	c.C907G	p.R303G	GGTACCGGGCCAG	.	PASS	Atlas-SNP
TAS2R60	338398	hgsc.bcm.edu	37	7	143141475	143141475	+	Silent	SNP	T	T	C	rs4595035	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	40	20	44	0	0.5	0	T|0.360;C|0.640	0.640	strong	TAS2R60,colon,carcinoma,+1,1	TAS2R60	55	1	NM_177437	exon1	c.T930C	p.R310R	GAGTCGTCGTTCC	.	PASS	Atlas-SNP
HLA-G	3135	hgsc.bcm.edu	37	6	29796376	29796376	+	Missense_Mutation	SNP	C	C	A	rs12722477	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	126	15	122	0	0.119048	0	C|0.838;A|0.162	0.162	strong	.	HLA-G	90	.	NM_002127	exon4	c.C400A	p.L134I	CGCCTCCTCCGCG	.	PASS	Atlas-SNP
FAM26F	441168	hgsc.bcm.edu	37	6	116783330	116783330	+	Missense_Mutation	SNP	G	G	A	rs3087828		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	14	14	17	0	1	0	.	.	weak	.	FAM26F	12	.	NM_001010919	exon2	c.G238A	p.E80K	CTCACCGGATGCT	.	PASS	Atlas-SNP
RAD23B	5887	hgsc.bcm.edu	37	9	110084328	110084328	+	Missense_Mutation	SNP	C	C	T	rs1805329	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	133	62	120	0	0.466165	0	C|0.850;T|0.150	0.150	strong	.	RAD23B	31	.	NM_002874	exon7	c.C746T	p.A249V	CTGGGGCTCCTCA	.	PASS	Atlas-SNP
F5	2153	hgsc.bcm.edu	37	1	169510233	169510233	+	Silent	SNP	G	G	A	rs9332607	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	228	218	264	0	0.95614	0	G|0.698;A|0.302	0.302	strong	.	F5	301	.	NM_000130	exon13	c.C4095T	p.T1365T	AGAAAGGGTTGTA	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9048170	9048170	+	Missense_Mutation	SNP	G	G	A	rs10417600	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	104	57	103	0	0.548077	0	G|0.796;A|0.204	0.204	strong	.	MUC16	4315	.	NM_024690	exon5	c.C33461T	p.S11154F	ACCAGAGAGGTCA	.	PASS	Atlas-SNP
BANF2	140836	hgsc.bcm.edu	37	20	17716416	17716416	+	Missense_Mutation	SNP	C	C	G	rs1053993	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	70	70	79	0	1	0	C|0.647;G|0.353	0.353	strong	.	BANF2	12	.	NM_001159495	exon3	c.C254G	p.T85S	AGCAGACTTCTCA	.	PASS	Atlas-SNP
ZNF134	7693	hgsc.bcm.edu	37	19	58132106	58132106	+	Missense_Mutation	SNP	A	A	C	rs34034473	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	45	23	45	0	0.511111	0	A|0.917;C|0.083	0.083	strong	ZNF134,caecum,carcinoma,0,1	ZNF134	34	1	NM_003435	exon3	c.A619C	p.S207R	GAGTGCAGCGAAT	.	PASS	Atlas-SNP
MAGEB4	4115	hgsc.bcm.edu	37	X	30261002	30261002	+	Silent	SNP	A	A	G	rs2071311	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	133	133	83	0	1	0	A|0.120;G|0.880	0.880	strong	.	MAGEB4	75	.	NM_002367	exon1	c.A750G	p.V250V	TCTGGTACAGGAA	.	PASS	Atlas-SNP
ZFYVE28	57732	hgsc.bcm.edu	37	4	2275835	2275835	+	Silent	SNP	G	G	A	rs2051561	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	65	98	0	0.984848	0	G|0.575;A|0.425	0.425	strong	.	ZFYVE28	79	.	NM_020972	exon9	c.C2160T	p.F720F	GCCGTGGAACCTG	.	PASS	Atlas-SNP
PIGQ	9091	hgsc.bcm.edu	37	16	632283	632283	+	Missense_Mutation	SNP	G	G	A	rs7187227	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	143	62	139	0	0.433566	0	G|0.853;A|0.147	0.147	strong	.	PIGQ	43	.	NM_004204	exon10	c.G1567A	p.G523S	GAGGCCGGCAGGC	.	PASS	Atlas-SNP
CDH23	64072	hgsc.bcm.edu	37	10	73550969	73550969	+	Missense_Mutation	SNP	G	G	A	rs10466026	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	40	62	0	0.47619	0	G|0.661;A|0.339	0.339	strong	CDH23,colon,carcinoma,0,2	CDH23	365	2	NM_022124	exon45	c.G6130A	p.E2044K	CTGGCTGAGGACA	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	235	136	165	0	0.578723	0	A|0.706;G|0.294	0.294	strong	.	ANKRD13A	39	.	NM_033121	exon5	c.A426G	p.P142P	ATGCCCAAATGAT	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9072875	9072875	+	Silent	SNP	G	G	A	rs73009098	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	439	193	414	0	0.439636	0	G|0.809;A|0.191	0.191	strong	.	MUC16	4315	.	NM_024690	exon3	c.C14571T	p.V4857V	AGATGTGACTTTA	.	PASS	Atlas-SNP
HYDIN	54768	hgsc.bcm.edu	37	16	71015329	71015329	+	Missense_Mutation	SNP	G	G	T	rs78763837	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	127	47	122	0	0.370079	0	.	.	weak	LOC652153,NS,haematopoietic_neoplasm,0,2	HYDIN	788	2	NM_001270974	exon29	c.C4475A	p.P1492H	ATTTGGGGAAAGA	.	PASS	Atlas-SNP
LCMT2	9836	hgsc.bcm.edu	37	15	43621483	43621483	+	Missense_Mutation	SNP	C	C	T	rs144228208	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	45	93	0	0.714286	0	C|1.000;T|0.000	0.000	weak	LCMT2,NS,carcinoma,-1,1	LCMT2	48	1	NM_014793	exon1	c.G1205A	p.G402D	TGGCTGCCTTTCC	.	PASS	Atlas-SNP
SLC39A14	23516	hgsc.bcm.edu	37	8	22262321	22262321	+	Missense_Mutation	SNP	T	T	C	rs896378	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	103	102	85	0	0.990291	0	C|0.584;N|0.000	0.584	strong	.	SLC39A14	59	.	NM_001135153	exon2	c.T98C	p.L33P	CATCCCTGGGTGC	.	PASS	Atlas-SNP
TRIM31	11074	hgsc.bcm.edu	37	6	30080274	30080274	+	Silent	SNP	G	G	A	rs2517598	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	121	96	117	0	0.793388	0	G|0.878;A|0.122	0.122	strong	.	TRIM31	40	.	NM_007028	exon2	c.C309T	p.H103H	GAAATAGTGGAAC	.	PASS	Atlas-SNP
ADAMTS14	140766	hgsc.bcm.edu	37	10	72517830	72517830	+	Missense_Mutation	SNP	G	G	A	rs10999516	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48	18	48	0	0.375	0	G|0.824;A|0.176	0.176	strong	.	ADAMTS14	148	.	NM_139155	exon20	c.G3059A	p.S1020N	TCTGCAGCCTGCC	.	PASS	Atlas-SNP
CXCL16	58191	hgsc.bcm.edu	37	17	4638737	4638737	+	Missense_Mutation	SNP	A	A	G	rs1050998	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	46	71	0	0.534884	0	G|0.428;N|0.001	0.428	strong	CXCL16_ENST00000293778,NS,carcinoma,0,1	CXCL16	30	1	NM_022059	exon4	c.T425C	p.I142T	TGAGAAATTGGGG	.	PASS	Atlas-SNP
LTF	4057	hgsc.bcm.edu	37	3	46501213	46501213	+	Missense_Mutation	SNP	T	T	C	rs1126478	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	170	79	194	0	0.464706	0	T|0.446;C|0.554	0.554	strong	.	LTF	98	.	NM_002343	exon2	c.A140G	p.K47R	CGCACTTTTCTCA	.	PASS	Atlas-SNP
ETNK1	55500	hgsc.bcm.edu	37	12	22814036	22814036	+	Silent	SNP	A	A	G	rs4963793	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	36	105	0	0.48	0	A|0.810;G|0.190	0.190	strong	.	ETNK1	61	.	NM_018638	exon4	c.A864G	p.E288E	CCAGGAAGAGATG	.	PASS	Atlas-SNP
TMEM200A	114801	hgsc.bcm.edu	37	6	130761867	130761867	+	Silent	SNP	T	T	C	rs12207253	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55	25	56	0	0.454545	0	T|0.971;C|0.029	0.029	strong	.	TMEM200A	108	.	NM_001258277	exon3	c.T300C	p.N100N	AACAAATGAAACT	.	PASS	Atlas-SNP
FECH	2235	hgsc.bcm.edu	37	18	55226383	55226383	+	Silent	SNP	G	G	C	rs536765	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	35	35	35	0	1	0	G|0.249;C|0.751	0.751	strong	.	FECH	42	.	NM_001012515	exon7	c.C816G	p.P272P	AGACATGGGCAGT	.	PASS	Atlas-SNP
QRICH2	84074	hgsc.bcm.edu	37	17	74289875	74289875	+	Silent	SNP	C	C	T	rs6501882	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	104	43	118	0	0.413462	0	C|0.558;T|0.442	0.442	strong	.	QRICH2	143	.	NM_032134	exon4	c.G435A	p.G145G	CTGTCTCCCAGTA	.	PASS	Atlas-SNP
LSM5	23658	hgsc.bcm.edu	37	7	32529936	32529936	+	Silent	SNP	G	G	C	rs1584614	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	56	56	93	0	1	0	G|0.237;C|0.763	0.763	strong	LSM5,NS,carcinoma,0,1	LSM5	9	1	NM_012322	exon1	c.C42G	p.P14P	ACCTAAGGGCAGC	.	PASS	Atlas-SNP
DDX23	9416	hgsc.bcm.edu	37	12	49229991	49229991	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	135	34	158	0	0.251852	0	.	.	none	.	DDX23	82	.	NM_004818	exon11	c.T1295C	p.I432T	ACACCAATGATGT	.	PASS	Atlas-SNP
GCDH	2639	hgsc.bcm.edu	37	19	13008607	13008607	+	Silent	SNP	G	G	T	rs1060218	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	56	53	59	0	0.946429	0	G|0.732;T|0.268	0.268	strong	GCDH_ENST00000457854,NS,carcinoma,+2,2	GCDH	76	2	NM_013976	exon11	c.C1173T	p.S391S	GGGGGGGAATGGG	.	PASS	Atlas-SNP
ATP13A4	84239	hgsc.bcm.edu	37	3	193180592	193180592	+	Silent	SNP	G	G	A	rs59451116	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	104	48	96	0	0.461538	0	G|0.762;A|0.238	0.238	strong	.	ATP13A4	154	.	NM_032279	exon13	c.C1482T	p.D494D	CAAGCCGTCCCTT	.	PASS	Atlas-SNP
CPN1	1369	hgsc.bcm.edu	37	10	101802262	101802262	+	Silent	SNP	G	G	A	rs61733667	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	77	31	74	0	0.402597	0	G|0.971;A|0.029	0.029	strong	.	CPN1	62	.	NM_001308	exon9	c.C1299T	p.H433H	GACTCCGTGCCTT	.	PASS	Atlas-SNP
SPAG17	200162	hgsc.bcm.edu	37	1	118644430	118644430	+	Silent	SNP	A	A	G	rs10754367	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	145	60	178	0	0.413793	0	A|0.430;G|0.570	0.570	strong	.	SPAG17	263	.	NM_206996	exon5	c.T567C	p.N189N	TGGTGCATTTGCC	.	PASS	Atlas-SNP
CFHR3	10878	hgsc.bcm.edu	37	1	196757392	196757392	+	Silent	SNP	C	C	T	rs61735322	byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	104	44	52	0	0.423077	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
DMKN	93099	hgsc.bcm.edu	37	19	35998362	35998362	+	Silent	SNP	T	T	G	rs4254439	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82	45	70	0	0.548781	0	G|0.367;N|0.002	0.367	strong	.	DMKN	116	.	NM_001190348	exon9	c.A1126C	p.R376R	TCACCCTATAATT	.	PASS	Atlas-SNP
SYT17	51760	hgsc.bcm.edu	37	16	19195130	19195130	+	Silent	SNP	C	C	T	rs11541511	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55	26	62	2	0.472727	0.0322581	C|0.887;T|0.113	0.113	strong	SYT17,colon,carcinoma,+1,1	SYT17	51	1	NM_016524	exon5	c.C612T	p.R204R	CGTGCGCGTGATC	.	scavenged	Atlas-SNP
TEX15	56154	hgsc.bcm.edu	37	8	30703431	30703431	+	Missense_Mutation	SNP	T	T	C	rs323346	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	136	70	132	0	0.514706	0	A|0.004;C|0.320	0.320	strong	.	TEX15	350	.	NM_031271	exon1	c.A3103G	p.I1035V	ATATTATTGCATA	.	PASS	Atlas-SNP
NBPF10	100132406	hgsc.bcm.edu	37	1	145296478	145296478	+	Missense_Mutation	SNP	G	G	T	rs6663523	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51	29	32	0	0.568627	0	G|0.500;T|0.500	0.500	strong	.	NBPF10	221	.	NM_001039703	exon3	c.G400T	p.D134Y	ACTCCGGATGAGC	.	PASS	Atlas-SNP
ASGR2	433	hgsc.bcm.edu	37	17	7012079	7012079	+	Missense_Mutation	SNP	C	C	T	rs2304978	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	135	62	178	0	0.459259	0	C|0.777;T|0.223	0.223	strong	ASGR2,NS,carcinoma,0,2	ASGR2	38	2	NM_080912	exon3	c.G253A	p.G85R	GGCCCCCGTGACC	.	PASS	Atlas-SNP
ENPP3	5169	hgsc.bcm.edu	37	6	132061420	132061420	+	Missense_Mutation	SNP	G	G	A	rs17601580	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	37	72	0	0.5	0	G|0.897;A|0.103	0.103	strong	.	ENPP3	117	.	NM_005021	exon24	c.G2357A	p.S786N	TGACCAGTTGTAA	.	PASS	Atlas-SNP
SHROOM3	57619	hgsc.bcm.edu	37	4	77631425	77631425	+	Missense_Mutation	SNP	T	T	A	rs3821979	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	90	40	90	0	0.444444	0	T|0.843;A|0.157	0.157	strong	.	SHROOM3	134	.	NM_020859	exon3	c.T440A	p.L147H	TTAAACTTCGGCT	.	PASS	Atlas-SNP
ARHGAP32	9743	hgsc.bcm.edu	37	11	128842603	128842603	+	Silent	SNP	G	G	A	rs376118787		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	137	40	128	0	0.291971	0	.	.	weak	.	ARHGAP32	307	.	NM_001142685	exon21	c.C3756T	p.P1252P	CTCTTCGGGGGAC	.	PASS	Atlas-SNP
ABLIM3	22885	hgsc.bcm.edu	37	5	148618836	148618836	+	Missense_Mutation	SNP	C	C	T	rs201076202	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	179	85	189	0	0.47486	0	.	.	weak	.	ABLIM3	91	.	NM_014945	exon12	c.C1070T	p.S357F	CCTACTCCCAGGT	.	PASS	Atlas-SNP
ZNF74	7625	hgsc.bcm.edu	37	22	20761063	20761063	+	Silent	SNP	G	G	A	rs2228236	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	65	28	56	0	0.430769	0	G|0.859;A|0.141	0.141	strong	.	ZNF74	54	.	NM_003426	exon5	c.G1740A	p.E580E	CAGCGAGGGGAAG	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	22	48	0	0.468085	0	A|0.674;G|0.326	0.326	strong	.	TSNARE1	59	.	NM_145003	exon2	c.T52C	p.F18L	CCCCGAAAGGGCC	.	PASS	Atlas-SNP
SAGE1	55511	hgsc.bcm.edu	37	X	134986700	134986700	+	Silent	SNP	T	T	C	rs12014884	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	257	54	178	0	0.210117	0	T|0.806;C|0.194	0.194	strong	.	SAGE1	160	.	NM_018666	exon4	c.T285C	p.N95N	TGATAATGTCTTG	.	PASS	Atlas-SNP
METTL22	79091	hgsc.bcm.edu	37	16	8722629	8722629	+	Missense_Mutation	SNP	G	G	C	rs2270286	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	89	47	131	0	0.52809	0	G|0.810;C|0.190	0.190	strong	.	METTL22	23	.	NM_024109	exon3	c.G176C	p.W59S	ACTCTTGGACAGA	.	PASS	Atlas-SNP
MOV10	4343	hgsc.bcm.edu	37	1	113237171	113237171	+	Silent	SNP	A	A	G	rs883593	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	88	54	71	0	0.613636	0	A|0.765;G|0.235	0.235	strong	MOV10,NS,carcinoma,0,1	MOV10	74	1	NM_020963	exon9	c.A1392G	p.T464T	GCTGACAGGGCGC	.	PASS	Atlas-SNP
ZNF577	84765	hgsc.bcm.edu	37	19	52376952	52376952	+	Silent	SNP	T	T	A	rs8107969	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	31	49	0	0.574074	0	T|0.527;A|0.473	0.473	strong	.	ZNF577	63	.	NM_032679	exon7	c.A291T	p.V97V	CTGGATTACAAAA	.	PASS	Atlas-SNP
KIF27	55582	hgsc.bcm.edu	37	9	86465131	86465131	+	Missense_Mutation	SNP	T	T	C	rs74425200		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	441	194	429	0	0.439909	0	.	.	weak	.	KIF27	103	.	NM_017576	exon16	c.A3439G	p.M1147V	GAACCATATTATC	.	PASS	Atlas-SNP
DAGLA	747	hgsc.bcm.edu	37	11	61505168	61505168	+	Silent	SNP	G	G	A	rs198444	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85	49	94	0	0.576471	0	G|0.536;A|0.464	0.464	strong	DAGLA,NS,carcinoma,+1,1	DAGLA	109	1	NM_006133	exon15	c.G1524A	p.A508A	GGATGCGATGGAG	.	PASS	Atlas-SNP
TAS2R30	259293	hgsc.bcm.edu	37	12	11286214	11286214	+	Missense_Mutation	SNP	C	C	G	rs200082783	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	140	11	189	1	0.0785714	0.00529101	C|0.944;G|0.055	0.055	strong	TAS2R30,NS,carcinoma,0,1	TAS2R30	28	1	NM_001097643	exon1	c.G630C	p.Q210H	ATGGAGCTGCATC	.	scavenged	Atlas-SNP
BEST2	54831	hgsc.bcm.edu	37	19	12866544	12866544	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	147	21	123	0	0.142857	0	.	.	none	.	BEST2	35	.	NM_017682	exon6	c.C830T	p.T277I	TCTTCACCCTCTT	.	PASS	Atlas-SNP
OR10H5	284433	hgsc.bcm.edu	37	19	15905002	15905002	+	Silent	SNP	T	T	C	rs56548474		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	156	70	163	0	0.448718	0	.	.	weak	.	OR10H5	49	.	NM_001004466	exon1	c.T144C	p.T48T	GGCCACTGTCTGG	.	PASS	Atlas-SNP
ARHGAP32	9743	hgsc.bcm.edu	37	11	128842873	128842873	+	Silent	SNP	T	T	C	rs581258	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	133	114	116	0	0.857143	0	T|0.809;G|0.002	.	strong	.	ARHGAP32	307	.	NM_001142685	exon21	c.A3486G	p.E1162E	GGCCTTTTCTGGG	.	PASS	Atlas-SNP
CNPPD1	27013	hgsc.bcm.edu	37	2	220037756	220037756	+	Missense_Mutation	SNP	A	A	G	rs1043160	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	31	11	38	0	0.354839	0	A|0.545;G|0.455	0.455	strong	.	CNPPD1	22	.	NM_015680	exon8	c.T785C	p.I262T	GTAGGGATGCAGG	.	PASS	Atlas-SNP
ZNF256	10172	hgsc.bcm.edu	37	19	58453342	58453342	+	Silent	SNP	T	T	C	rs959231	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85	37	85	0	0.435294	0	T|0.741;C|0.259	0.259	strong	.	ZNF256	117	.	NM_005773	exon3	c.A834G	p.Q278Q	AGAGCTTTGCCTA	.	PASS	Atlas-SNP
LOXHD1	125336	hgsc.bcm.edu	37	18	44159672	44159672	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	154	74	136	0	0.480519	0	.	.	none	.	LOXHD1	367	.	NM_144612	exon13	c.T1730G	p.L577R	CCAAAAAGGCAGA	.	PASS	Atlas-SNP
CSMD2	114784	hgsc.bcm.edu	37	1	34038214	34038214	+	Missense_Mutation	SNP	T	T	C	rs2641962	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	37	68	0	0.552239	0	C|0.495;N|0.000	0.495	strong	.	CSMD2	946	.	NM_052896	exon51	c.A7660G	p.M2554V	TGTACATGGCCTT	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	156	46	154	2	0.294872	0.012987	A|0.625;G|0.375	0.375	strong	KCNJ12,NS,neuroblastoma,0,1	.	.	1	NM_001194958	exon3	c.A745G	p.I249V	GACCAGATCGACA	.	scavenged	Atlas-SNP
DSG2	1829	hgsc.bcm.edu	37	18	29126108	29126108	+	Missense_Mutation	SNP	T	T	G	rs142841727	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	107	53	116	0	0.495327	0	T|0.995;G|0.005	0.005	strong	DSG2,NS,lymphoid_neoplasm,0,1	DSG2	115	1	NM_001943	exon15	c.T2759G	p.V920G	AAAAGGTAGCTAC	.	PASS	Atlas-SNP
COLGALT2	23127	hgsc.bcm.edu	37	1	183909717	183909717	+	Silent	SNP	G	G	A	rs2296713	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	135	68	135	0	0.503704	0	G|0.828;A|0.172	0.172	strong	.	.	.	.	NM_015101	exon11	c.C1602T	p.P534P	TCACACGGGATGC	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228434467	228434467	+	Silent	SNP	T	T	C	rs7517108	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	114	42	119	0	0.368421	0	T|0.327;C|0.673	0.673	strong	.	OBSCN	2142	.	NM_001271223	exon14	c.T4272C	p.A1424A	TGAGGCTGGGGGC	.	PASS	Atlas-SNP
TAS2R20	259295	hgsc.bcm.edu	37	12	11149769	11149769	+	Missense_Mutation	SNP	T	T	C	rs10845281	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	129	58	133	0	0.449612	0	T|0.675;C|0.325	0.325	strong	.	TAS2R20	17	.	NM_176889	exon1	c.A706G	p.I236V	GTAATATGAGGAA	.	PASS	Atlas-SNP
CAP1	10487	hgsc.bcm.edu	37	1	40535913	40535913	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	127	2	119	0	0.015748	0	.	.	none	CAP1,NS,carcinoma,-1,1	CAP1	38	1	NM_006367	exon10	c.C1076T	p.T359M	TCAACACGACATT	.	scavenged	Atlas-SNP
WNK2	65268	hgsc.bcm.edu	37	9	95993326	95993326	+	Silent	SNP	T	T	C	rs11787888	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	162	70	190	0	0.432099	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
TPO	7173	hgsc.bcm.edu	37	2	1460004	1460004	+	Missense_Mutation	SNP	G	G	T	rs4927611	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	95	49	88	0	0.515789	0	G|0.632;T|0.368	0.368	strong	.	TPO	224	.	NM_175719	exon7	c.G769T	p.A257S	GGAGGGGCTGACT	.	PASS	Atlas-SNP
WDR18	57418	hgsc.bcm.edu	37	19	991968	991968	+	Silent	SNP	T	T	C	rs1127043	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	8	8	26	0	1	0	T|0.651;C|0.349	0.349	strong	.	WDR18	20	.	NM_024100	exon8	c.T945C	p.N315N	CACCAATGCCGCC	.	PASS	Atlas-SNP
MRC2	9902	hgsc.bcm.edu	37	17	60766283	60766283	+	Missense_Mutation	SNP	C	C	T	rs201851897	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	118	35	135	0	0.29661	0	C|1.000;T|0.000	0.000	strong	MRC2,NS,carcinoma,0,1	MRC2	126	1	NM_006039	exon23	c.C3296T	p.T1099M	GCTGCACGGAGGA	.	PASS	Atlas-SNP
DSPP	1834	hgsc.bcm.edu	37	4	88536551	88536551	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69	8	119	0	0.115942	0	.	.	none	DSPP,NS,carcinoma,-2,3	DSPP	174	3	NM_014208	exon5	c.G2737A	p.D913N	AGCAGTGACAGCA	.	PASS	Atlas-SNP
SYNE1	23345	hgsc.bcm.edu	37	6	152443744	152443744	+	Missense_Mutation	SNP	G	G	T	rs2295190	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44	23	62	0	0.522727	0	G|0.898;T|0.102	0.102	strong	.	SYNE1	3227	.	NM_182961	exon146	c.C26221A	p.L8741M	TGAACAGGAAGCC	.	PASS	Atlas-SNP
TENM4	26011	hgsc.bcm.edu	37	11	78380199	78380199	+	Silent	SNP	C	C	T	rs61745709	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	183	20	127	0	0.10929	0	C|0.950;T|0.050	0.050	strong	.	.	.	.	NM_001098816	exon32	c.G7191A	p.Q2397Q	GATGATCTGAAAG	.	PASS	Atlas-SNP
CA5A	763	hgsc.bcm.edu	37	16	87921846	87921846	+	Silent	SNP	T	T	A	rs72816311	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	163	85	123	0	0.521472	0	T|0.825;A|0.175	0.175	strong	.	CA5A	32	.	NM_001739	exon7	c.A807T	p.A269A	ACCAAGTGCAGAA	.	PASS	Atlas-SNP
HDC	3067	hgsc.bcm.edu	37	15	50544871	50544871	+	Silent	SNP	G	G	A	rs34406040	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98	47	81	0	0.479592	0	G|0.983;A|0.017	0.017	strong	.	HDC	86	.	NM_002112	exon8	c.C888T	p.A296A	GGAGTCGGCATAC	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	148	87	200	0	0.587838	0	G|0.694;N|0.000	.	strong	.	IL31RA	84	.	NM_001242637	exon12	c.G1586A	p.S529N	TGGCCAGCACCAG	.	PASS	Atlas-SNP
XPO5	57510	hgsc.bcm.edu	37	6	43492578	43492578	+	Silent	SNP	G	G	A	rs2257082	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	21	68	0	0.28	0	G|0.652;N|0.002	.	strong	.	XPO5	79	.	NM_020750	exon30	c.C3303T	p.Y1101Y	TGCCTCGTATATC	.	PASS	Atlas-SNP
KLHDC7A	127707	hgsc.bcm.edu	37	1	18807953	18807953	+	Missense_Mutation	SNP	C	C	A	rs11261022	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48	17	47	0	0.354167	0	C|0.671;A|0.329	0.329	strong	.	KLHDC7A	60	.	NM_152375	exon1	c.C478A	p.R160S	TTCCCCCGCTTGG	.	PASS	Atlas-SNP
TFDP2	7029	hgsc.bcm.edu	37	3	141724328	141724328	+	Silent	SNP	T	T	C	rs7627056	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	99	57	123	1	0.575758	0.00813008	T|0.967;C|0.033	0.033	strong	TFDP2_ENST00000489671,NS,carcinoma,0,1	TFDP2	44	1	NM_001178139	exon4	c.A141G	p.L47L	TTTTGGTAAAATC	.	scavenged	Atlas-SNP
FOXO1	2308	hgsc.bcm.edu	37	13	41239736	41239736	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	207	46	106	0	0.222222	0	.	.	none	.	FOXO1	110	.	NM_002015	exon1	c.G614A	p.S205N	GCCGAGCTGTTGC	.	PASS	Atlas-SNP
PYGL	5836	hgsc.bcm.edu	37	14	51378517	51378517	+	Missense_Mutation	SNP	C	C	G	rs35026927	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	164	81	160	0	0.493902	0	C|0.996;G|0.004	0.004	strong	PYGL,colon,carcinoma,+2,1	PYGL	77	1	NM_002863	exon16	c.G1900C	p.D634H	TAGGGTCATTGTT	.	PASS	Atlas-SNP
LRP1B	53353	hgsc.bcm.edu	37	2	141260668	141260668	+	Silent	SNP	A	A	G	rs4444457	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	70	70	135	0	1	0	A|0.460;G|0.540	0.540	strong	.	LRP1B	1315	.	NM_018557	exon54	c.T8526C	p.Y2842Y	CTGTCGATATCCT	.	PASS	Atlas-SNP
LILRB1	10859	hgsc.bcm.edu	37	19	55145454	55145454	+	Missense_Mutation	SNP	G	G	A	rs1138736	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	183	88	186	0	0.480874	0	G|0.895;A|0.105	0.105	strong	.	LILRB1	140	.	NM_001081637	exon9	c.G1345A	p.G449R	CCCACCGGGTCGG	.	PASS	Atlas-SNP
CAGE1	285782	hgsc.bcm.edu	37	6	7387236	7387236	+	Silent	SNP	G	G	A	rs9406026	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83	62	80	0	0.746988	0	G|0.618;A|0.382	0.382	strong	.	CAGE1	165	.	NM_001170693	exon2	c.C171T	p.T57T	GGTGCCGGTGGTT	.	PASS	Atlas-SNP
EXPH5	23086	hgsc.bcm.edu	37	11	108385251	108385251	+	Missense_Mutation	SNP	C	C	T	rs11212684	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	185	148	140	1	0.8	0.00714286	C|0.973;T|0.027	0.027	strong	.	EXPH5	193	.	NM_015065	exon6	c.G983A	p.R328Q	GCCGACCGTTGCC	.	PASS	Atlas-SNP
SFI1	9814	hgsc.bcm.edu	37	22	31971351	31971351	+	Missense_Mutation	SNP	C	C	T	rs78295829	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	90	48	82	0	0.533333	0	C|0.983;T|0.017	0.017	strong	.	SFI1	78	.	NM_001007467	exon10	c.C1057T	p.R353W	GCCCTGCGGCGCG	.	PASS	Atlas-SNP
TRIM26	7726	hgsc.bcm.edu	37	6	30154199	30154199	+	Silent	SNP	T	T	C	rs2074473	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	65	51	46	0	0.784615	0	T|0.583;C|0.417	0.417	strong	.	TRIM26	74	.	NM_001242783	exon9	c.A1074G	p.L358L	GCTGCCTAGCACC	.	PASS	Atlas-SNP
OR2L2	26246	hgsc.bcm.edu	37	1	248202474	248202474	+	Missense_Mutation	SNP	A	A	G	rs144950416	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	168	38	88	0	0.22619	0	A|0.990;G|0.010	0.010	strong	.	OR2L2	115	.	NM_001004686	exon1	c.A905G	p.Q302R	TGACACAAGTGAT	.	PASS	Atlas-SNP
ASXL3	80816	hgsc.bcm.edu	37	18	31320229	31320229	+	Missense_Mutation	SNP	A	A	G	rs2282632	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80	80	67	0	1	0	G|0.767;N|0.000	0.767	strong	.	ASXL3	405	.	NM_030632	exon11	c.A2861G	p.N954S	TAAGAAATGAAAG	.	PASS	Atlas-SNP
ARHGEF4	50649	hgsc.bcm.edu	37	2	131688587	131688587	+	Silent	SNP	G	G	A	rs6718816	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	42	7	81	1	0.166667	0.0123457	G|0.748;A|0.252	0.252	strong	ARHGEF4,NS,carcinoma,+2,1	ARHGEF4	89	1	NM_032995	exon3	c.G57A	p.A19A	GAAGGCGTTCCAC	.	scavenged	Atlas-SNP
SALL3	27164	hgsc.bcm.edu	37	18	76754549	76754549	+	Missense_Mutation	SNP	T	T	C	rs35578880	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	45	22	55	1	0.488889	0.0181818	T|0.963;C|0.037	0.037	strong	SALL3,NS,carcinoma,-1,1	SALL3	162	1	NM_171999	exon2	c.T2558C	p.V853A	ACTCGGTCATGAG	.	scavenged	Atlas-SNP
KDM4C	23081	hgsc.bcm.edu	37	9	6984236	6984236	+	Missense_Mutation	SNP	G	G	A	rs2296067	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	116	48	90	0	0.413793	0	G|0.743;A|0.257	0.257	strong	KDM4C_ENST00000381306,NS,carcinoma,0,4	KDM4C	186	4	NM_001146696	exon10	c.G1252A	p.D418N	GAAGTCGATGGGG	.	PASS	Atlas-SNP
HCFC1	3054	hgsc.bcm.edu	37	X	153215839	153215839	+	Silent	SNP	G	G	A	rs3027875	bycluster;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	67	56	0	0.943662	0	G|0.712;A|0.288	0.288	strong	.	HCFC1	284	.	NM_005334	exon24	c.C5859T	p.C1953C	GGGCCCGCAGTAC	.	PASS	Atlas-SNP
SLC45A4	57210	hgsc.bcm.edu	37	8	142228909	142228909	+	Missense_Mutation	SNP	G	G	A	rs753778	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	55	86	0	0.632184	0	G|0.657;A|0.343	0.343	strong	.	SLC45A4	71	.	NM_001080431	exon4	c.C677T	p.P226L	CCGTGCGGCTCGC	.	PASS	Atlas-SNP
SLC22A5	6584	hgsc.bcm.edu	37	5	131721174	131721174	+	Silent	SNP	A	A	G	rs274558	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	113	67	108	0	0.59292	0	A|0.579;G|0.421	0.421	strong	.	SLC22A5	34	.	NM_003060	exon4	c.A807G	p.L269L	GGTGCTATGCGTG	.	PASS	Atlas-SNP
APOA4	337	hgsc.bcm.edu	37	11	116692324	116692324	+	Silent	SNP	G	G	A	rs2234668	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	36	7	37	0	0.194444	0	G|0.971;A|0.029	0.029	strong	.	APOA4	51	.	NM_000482	exon3	c.C450T	p.A150A	CTGCTCGGCCTGC	.	PASS	Atlas-SNP
RTFDC1	51507	hgsc.bcm.edu	37	20	55088404	55088404	+	Missense_Mutation	SNP	A	A	G	rs1059768	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85	85	90	0	1	0	A|0.172;G|0.828	0.828	strong	.	.	.	.	NM_016407	exon6	c.A511G	p.M171V	GTCATCATGCTCA	.	PASS	Atlas-SNP
TJP2	9414	hgsc.bcm.edu	37	9	71862975	71862975	+	Silent	SNP	C	C	T	rs2282336	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	51	41	0	0.980769	0	C|0.770;T|0.230	0.230	strong	.	TJP2	120	.	NM_001170416	exon19	c.C2808T	p.T936T	CTTAACCGCCATG	.	PASS	Atlas-SNP
SYCE1	93426	hgsc.bcm.edu	37	10	135369532	135369532	+	Missense_Mutation	SNP	T	T	C	rs3747881	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	35	20	50	0	0.571429	0	T|0.851;C|0.149	0.149	strong	.	SYCE1	81	.	NM_001143763	exon9	c.A548G	p.K183R	ATCTCCTTTGCCA	.	PASS	Atlas-SNP
EXT1	2131	hgsc.bcm.edu	37	8	118832020	118832020	+	Silent	SNP	G	G	A	rs17439693	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	123	122	108	0	0.99187	0	G|0.849;A|0.151	0.151	strong	.	EXT1	98	.	NM_000127	exon6	c.C1431T	p.P477P	TTTGGAGGGGGGC	.	PASS	Atlas-SNP
PAAF1	80227	hgsc.bcm.edu	37	11	73620537	73620537	+	Missense_Mutation	SNP	C	C	G	rs3741138	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	195	159	162	0	0.815385	0	C|0.891;G|0.109	0.109	strong	.	PAAF1	39	.	NM_025155	exon7	c.C626G	p.A209G	GCTCAGCCTGCTT	.	PASS	Atlas-SNP
ZNF438	220929	hgsc.bcm.edu	37	10	31138817	31138817	+	Missense_Mutation	SNP	G	G	A	rs10160116	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	142	142	140	0	1	0	G|0.641;A|0.359	0.359	strong	.	ZNF438	90	.	NM_182755	exon7	c.C517T	p.P173S	GACTGGGTTTGTA	.	PASS	Atlas-SNP
SCARF1	8578	hgsc.bcm.edu	37	17	1542190	1542190	+	Missense_Mutation	SNP	G	G	A	rs2272011	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100	47	104	0	0.47	0	G|0.385;A|0.615	0.615	strong	SCARF1,caecum,carcinoma,0,2	SCARF1	46	2	NM_145350	exon8	c.C1274T	p.A425V	CTGCCCGCGATGA	.	PASS	Atlas-SNP
RRAGC	64121	hgsc.bcm.edu	37	1	39311617	39311617	+	Silent	SNP	T	T	G	rs11549874	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	209	104	235	0	0.497608	0	T|0.948;G|0.052	0.052	strong	.	RRAGC	28	.	NM_022157	exon6	c.A1042C	p.R348R	CTTTTCTTTCAAA	.	PASS	Atlas-SNP
DENND2D	79961	hgsc.bcm.edu	37	1	111730901	111730901	+	Silent	SNP	C	C	T	rs608881	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	99	36	142	0	0.363636	0	T|0.178;G|0.008	0.178	strong	.	DENND2D	50	.	NM_024901	exon11	c.G1191A	p.E397E	ATTTGCCTCCCGC	.	PASS	Atlas-SNP
ACACB	32	hgsc.bcm.edu	37	12	109647006	109647006	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	115	51	109	0	0.443478	0	.	.	none	ACACB,caecum,adenoma,-1,1	ACACB	330	1	NM_001093	exon20	c.C3097T	p.R1033W	ACCCTCCGGCACC	.	PASS	Atlas-SNP
ANKRD18A	253650	hgsc.bcm.edu	37	9	38595886	38595886	+	Missense_Mutation	SNP	T	T	C	rs2996347	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	95	43	107	0	0.452632	0	T|0.680;C|0.320	0.320	strong	ANKRD18A,NS,carcinoma,0,1	ANKRD18A	49	1	NM_147195	exon9	c.A1451G	p.N484S	AAGGTATTGAACT	.	PASS	Atlas-SNP
KLK1	3816	hgsc.bcm.edu	37	19	51323232	51323232	+	Missense_Mutation	SNP	T	T	C	rs5517	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	178	87	163	0	0.488764	0	T|0.707;C|0.293	0.293	strong	.	KLK1	27	.	NM_002257	exon4	c.A556G	p.K186E	CTTTTTTGCACTC	.	PASS	Atlas-SNP
PLEKHA6	22874	hgsc.bcm.edu	37	1	204226896	204226896	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	95	2	94	0	0.0210526	0	.	.	none	PLEKHA6,colon,carcinoma,0,1	PLEKHA6	115	1	NM_014935	exon9	c.G1109A	p.R370Q	TCCGGCCGCACTC	.	scavenged	Atlas-SNP
OR13C5	138799	hgsc.bcm.edu	37	9	107360851	107360851	+	Missense_Mutation	SNP	T	T	C	rs1523678	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	126	59	140	0	0.468254	0	T|0.634;C|0.366	0.366	strong	.	OR13C5	60	.	NM_001004482	exon1	c.A844G	p.I282V	AGAATATGAATAT	.	PASS	Atlas-SNP
GAK	2580	hgsc.bcm.edu	37	4	844781	844781	+	Silent	SNP	G	G	A	rs75072999	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	137	137	204	0	1	0	G|0.939;A|0.061	0.061	strong	GAK,rectum,carcinoma,0,1	GAK	104	1	NM_005255	exon26	c.C3600T	p.T1200T	TGCAATGGTCTTT	.	PASS	Atlas-SNP
ABCA13	154664	hgsc.bcm.edu	37	7	48336844	48336844	+	Silent	SNP	C	C	T	rs6583546	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68	68	113	0	1	0	C|0.254;T|0.746	0.746	strong	.	ABCA13	1192	.	NM_152701	exon22	c.C9135T	p.L3045L	AAGCCTCGAGGAA	.	PASS	Atlas-SNP
FCGBP	8857	hgsc.bcm.edu	37	19	40399385	40399385	+	Missense_Mutation	SNP	C	C	T	rs78608182	byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	183	44	185	1	0.240437	0.00540541	C|0.500;T|0.500	0.500	strong	FCGBP,NS,carcinoma,0,2	FCGBP	416	2	NM_003890	exon13	c.G6310A	p.G2104R	GTGGTCCGTGGCA	.	scavenged	Atlas-SNP
C7orf57	136288	hgsc.bcm.edu	37	7	48081095	48081095	+	Missense_Mutation	SNP	G	G	T	rs10951942	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	17	4	23	0	0.235294	0	G|0.632;T|0.368	0.368	strong	C7orf57_ENST00000348904,colon,carcinoma,-1,2	C7orf57	59	2	NM_001100159	exon3	c.G220T	p.A74S	AAGCTCGCGAAAC	.	PASS	Atlas-SNP
SEC63	11231	hgsc.bcm.edu	37	6	108214694	108214694	+	Missense_Mutation	SNP	C	C	T	rs17854547	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	89	38	76	0	0.426966	0	C|0.969;T|0.031	0.031	strong	.	SEC63	79	.	NM_007214	exon16	c.G1666A	p.V556I	TCCCAACGACTCC	.	PASS	Atlas-SNP
DOCK10	55619	hgsc.bcm.edu	37	2	225670901	225670901	+	Missense_Mutation	SNP	G	G	C	rs4674941	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93	45	107	0	0.483871	0	G|0.790;C|0.209	0.209	strong	.	DOCK10	308	.	NM_014689	exon34	c.C3756G	p.I1252M	ATGTTTGATAGCT	.	PASS	Atlas-SNP
OR2L8	391190	hgsc.bcm.edu	37	1	248112546	248112546	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	172	21	161	0	0.122093	0	.	.	none	OR2L8,NS,carcinoma,0,1	OR2L8	92	1	NM_001001963	exon1	c.C387T	p.L129L	TCCTCTCCACTAT	.	scavenged	Atlas-SNP
AKAP1	8165	hgsc.bcm.edu	37	17	55183813	55183813	+	Missense_Mutation	SNP	A	A	G	rs34535433	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	42	62	0	0.666667	0	A|0.944;G|0.056	0.056	strong	.	AKAP1	73	.	NM_001242902	exon3	c.A988G	p.S330G	GAGGAGAGCTTGG	.	PASS	Atlas-SNP
KRTAP10-2	386679	hgsc.bcm.edu	37	21	45971109	45971109	+	Missense_Mutation	SNP	G	G	A	rs77233671		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	7	89	0	0.0921053	0	.	.	weak	KRTAP10-2,caecum,carcinoma,0,1	KRTAP10-2	21	1	NM_198693	exon1	c.C233T	p.S78L	CAGCACGAGGGCG	.	scavenged	Atlas-SNP
EGFLAM	133584	hgsc.bcm.edu	37	5	38438505	38438505	+	Missense_Mutation	SNP	G	G	C	rs35767836	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	123	54	107	0	0.439024	0	G|0.987;C|0.013	0.013	strong	.	EGFLAM	302	.	NM_001205301	exon17	c.G2412C	p.E804D	GAAGGAGGGCTAT	.	PASS	Atlas-SNP
IGSF10	285313	hgsc.bcm.edu	37	3	151155620	151155620	+	Silent	SNP	G	G	A	rs6781302	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49	23	46	0	0.469388	0	G|0.352;A|0.648	0.648	strong	.	IGSF10	279	.	NM_178822	exon6	c.C6729T	p.N2243N	AGTTCTGTTTGTA	.	PASS	Atlas-SNP
FAM170B	170370	hgsc.bcm.edu	37	10	50340304	50340304	+	Missense_Mutation	SNP	C	C	A	rs17773851	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55	29	60	0	0.527273	0	C|0.765;A|0.235	0.235	strong	.	FAM170B	20	.	NM_001164484	exon2	c.G206T	p.R69L	CAGTCCCGCATCC	.	PASS	Atlas-SNP
PLEC	5339	hgsc.bcm.edu	37	8	144997671	144997671	+	Silent	SNP	G	G	A	rs200062782	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	12	9	22	0	0.75	0	G|0.998;A|0.002	0.002	weak	.	PLEC	1144	.	NM_201380	exon31	c.C6837T	p.A2279A	TTGCTCGGCCTCC	.	PASS	Atlas-SNP
EYS	346007	hgsc.bcm.edu	37	6	65300640	65300640	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	176	2	146	0	0.0113636	0	.	.	none	EYS_ENST00000370621,NS,carcinoma,+1,1	EYS	527	1	NM_001142800	exon26	c.A5120G	p.Y1707C	ATGCCATATTGTC	.	scavenged	Atlas-SNP
SIGLEC15	284266	hgsc.bcm.edu	37	18	43420177	43420177	+	Silent	SNP	G	G	A	rs61104666	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	30	70	0	0.483871	0	G|0.844;A|0.156	0.156	strong	.	SIGLEC15	10	.	NM_213602	exon5	c.G876A	p.E292E	CACAGAGCATCTG	.	PASS	Atlas-SNP
USP6	9098	hgsc.bcm.edu	37	17	5042894	5042894	+	Missense_Mutation	SNP	T	T	C	rs8073787	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	35	19	35	0	0.542857	0	T|0.322;C|0.678	0.678	strong	USP6_ENST00000250066,NS,carcinoma,-1,2	USP6	213	2	NM_004505	exon14	c.T1423C	p.W475R	TTTGAATGGAGCT	.	PASS	Atlas-SNP
LRRC18	474354	hgsc.bcm.edu	37	10	50121454	50121454	+	Silent	SNP	G	G	A	rs41302987	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	187	94	179	0	0.502674	0	G|0.956;A|0.044	0.044	strong	.	LRRC18	52	.	NM_001006939	exon1	c.C747T	p.D249D	CCAGGAGTCCTTG	.	PASS	Atlas-SNP
MGAT5B	146664	hgsc.bcm.edu	37	17	74922706	74922706	+	Silent	SNP	C	C	T	rs33966966	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	34	18	51	0	0.529412	0	C|0.816;T|0.184	0.184	strong	.	MGAT5B	98	.	NM_198955	exon9	c.C1218T	p.F406F	CACCTTCGGGACG	.	PASS	Atlas-SNP
MDN1	23195	hgsc.bcm.edu	37	6	90402482	90402482	+	Missense_Mutation	SNP	G	G	A	rs9294445	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	26	80	0	0.366197	0	G|0.429;A|0.571	0.571	strong	.	MDN1	478	.	NM_014611	exon63	c.C10267T	p.H3423Y	TGCTGTGGAGTGA	.	PASS	Atlas-SNP
ECHDC3	79746	hgsc.bcm.edu	37	10	11805339	11805339	+	Silent	SNP	C	C	T	rs17850531	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	15	9	19	0	0.6	0	C|0.831;T|0.169	0.169	strong	.	ECHDC3	12	.	NM_024693	exon5	c.C708T	p.I236I	GCGGATCGCTAGG	.	PASS	Atlas-SNP
CIITA	4261	hgsc.bcm.edu	37	16	11016045	11016045	+	Silent	SNP	C	C	T	rs2229322	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	78	42	96	0	0.538462	0	C|0.893;T|0.107	0.107	strong	CIITA,NS,carcinoma,0,1	CIITA	92	1	NM_000246	exon17	c.C3171T	p.C1057C	CATCTGCGACGTG	.	PASS	Atlas-SNP
STK17B	9262	hgsc.bcm.edu	37	2	197004439	197004439	+	Silent	SNP	A	A	G	rs1054537	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	123	70	147	0	0.569106	0	A|0.349;G|0.651	0.651	strong	.	STK17B	28	.	NM_004226	exon7	c.T741C	p.I247I	TTGAGAAATATTG	.	PASS	Atlas-SNP
PSG1	5669	hgsc.bcm.edu	37	19	43372386	43372386	+	Silent	SNP	T	T	C	rs1064491	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	114	49	117	0	0.429825	0	T|0.797;C|0.203	0.203	strong	.	PSG1	196	.	NM_001184826	exon5	c.A1110G	p.E370E	AAACTTTTCATTA	.	PASS	Atlas-SNP
TYRO3	7301	hgsc.bcm.edu	37	15	41860490	41860490	+	Missense_Mutation	SNP	T	T	A	rs12148316	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	106	17	138	0	0.160377	0	T|0.803;A|0.197	0.197	strong	TYRO3_ENST00000263798,colon,carcinoma,0,2	TYRO3	169	2	NM_006293	exon8	c.T1037A	p.I346N	AAGTGATCCCCGA	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	36	39	0	0.679245	0	0|0.025;A|0.455	0.455	strong	.	GPR112	459	.	NM_153834	exon6	c.C1103A	p.P368H	AACCACCTACACC	.	PASS	Atlas-SNP
EVPL	2125	hgsc.bcm.edu	37	17	74017579	74017579	+	Silent	SNP	G	G	C	rs138421545	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	118	42	110	0	0.355932	0	G|0.995;C|0.005	0.005	strong	EVPL,NS,carcinoma,0,1	EVPL	155	1	NM_001988	exon9	c.C981G	p.T327T	CAGCTGGGTCTCC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195505774	195505774	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69	7	87	2	0.101449	0.0229885	.	.	none	MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	NM_018406	exon2	c.C12677A	p.P4226H	GTGACAGGAAGAG	.	scavenged	Atlas-SNP
SLC44A5	204962	hgsc.bcm.edu	37	1	75699771	75699771	+	Silent	SNP	A	A	G	rs10493565	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	102	44	107	0	0.431373	0	A|0.766;G|0.234	0.234	strong	SLC44A5,NS,carcinoma,0,1	SLC44A5	231	1	NM_152697	exon12	c.T753C	p.I251I	CATGGCAATCGTC	.	PASS	Atlas-SNP
NLRP8	126205	hgsc.bcm.edu	37	19	56473502	56473502	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	150	8	159	0	0.0533333	0	.	.	none	.	NLRP8	225	.	NM_176811	exon4	c.G2112C	p.K704N	TGATAAGCTGGAA	.	PASS	Atlas-SNP
TMEM2	23670	hgsc.bcm.edu	37	9	74344821	74344821	+	Silent	SNP	T	T	C	rs25693	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	113	65	158	0	0.575221	0	T|0.937;C|0.063	0.063	strong	.	TMEM2	112	.	NM_013390	exon10	c.A1989G	p.S663S	GAAAGTTGAAACA	.	PASS	Atlas-SNP
CARD9	64170	hgsc.bcm.edu	37	9	139265870	139265870	+	Silent	SNP	G	G	A	rs11145769	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	102	52	121	0	0.509804	0	G|0.955;A|0.045	0.045	strong	CARD9,NS,carcinoma,0,1	CARD9	47	1	NM_052813	exon3	c.C228T	p.Y76Y	GGCCACGTAGCCC	.	PASS	Atlas-SNP
PPP2R3A	5523	hgsc.bcm.edu	37	3	135722264	135722264	+	Missense_Mutation	SNP	A	A	G	rs17197552	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	160	78	180	0	0.4875	0	A|0.779;G|0.221	0.221	strong	.	PPP2R3A	114	.	NM_002718	exon2	c.A1924G	p.S642G	TGTAGAAGTCCTG	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179579093	179579093	+	Missense_Mutation	SNP	T	T	C	rs12693164	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	187	71	175	0	0.379679	0	T|0.765;C|0.235	0.235	strong	TTN_ENST00000342992,colon,carcinoma,0,1	TTN	18412	1	NM_001267550	exon91	c.A26408G	p.N8803S	CCAGCATTGGCTG	.	PASS	Atlas-SNP
CRABP2	1382	hgsc.bcm.edu	37	1	156670344	156670344	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	175	3	163	0	0.0171429	0	.	.	none	CRABP2,NS,carcinoma,-1,1	CRABP2	13	1	NM_001199723	exon4	c.A356G	p.E119G	ATCAGTTCCCCAT	.	scavenged	Atlas-SNP
ACACB	32	hgsc.bcm.edu	37	12	109693982	109693982	+	Silent	SNP	C	C	T	rs3742023	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	125	71	101	0	0.568	0	C|0.719;T|0.281	0.281	strong	.	ACACB	330	.	NM_001093	exon44	c.C6204T	p.H2068H	TGACCACGGCAGT	.	PASS	Atlas-SNP
CNTN6	27255	hgsc.bcm.edu	37	3	1424850	1424850	+	Silent	SNP	T	T	G	rs2291100	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	157	157	128	0	1	0	T|0.724;G|0.276	0.276	strong	.	CNTN6	245	.	NM_014461	exon18	c.T2391G	p.S797S	CTACTCTGGGGAA	.	PASS	Atlas-SNP
PROKR1	10887	hgsc.bcm.edu	37	2	68882468	68882468	+	Silent	SNP	T	T	C	rs6722313	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	95	66	120	0	0.694737	0	T|0.606;C|0.394	0.394	strong	.	PROKR1	69	.	NM_138964	exon2	c.T942C	p.F314F	CGTGTTTGTGAAG	.	PASS	Atlas-SNP
NBPF10	100132406	hgsc.bcm.edu	37	1	145302775	145302775	+	Missense_Mutation	SNP	T	T	G	rs71241610		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	12	48	7	0.190476	0.145833	T|0.500;G|0.500	0.500	weak	NBPF10_ENST00000369338,NS,carcinoma,0,2	NBPF10	221	2	NM_001039703	exon8	c.T1213G	p.Y405D	ACTCCGTATGAGC	.	scavenged	Atlas-SNP
MRC2	9902	hgsc.bcm.edu	37	17	60741917	60741917	+	Missense_Mutation	SNP	G	G	A	rs2014055	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	28	88	0	0.41791	0	G|0.890;A|0.110	0.110	strong	.	MRC2	126	.	NM_006039	exon2	c.G127A	p.V43I	CCCAACGTCTTCC	.	PASS	Atlas-SNP
XPC	7508	hgsc.bcm.edu	37	3	14199887	14199887	+	Missense_Mutation	SNP	G	G	A	rs2228000	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	36	53	0	0.545455	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
SMC1B	27127	hgsc.bcm.edu	37	22	45767421	45767421	+	Missense_Mutation	SNP	C	C	T	rs56174639	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	145	55	130	0	0.37931	0	C|0.874;T|0.126	0.126	strong	.	SMC1B	215	.	NM_148674	exon14	c.G2243A	p.C748Y	ATAATACATTGAG	.	PASS	Atlas-SNP
PPFIA4	8497	hgsc.bcm.edu	37	1	203024767	203024767	+	Silent	SNP	C	C	T	rs3736314	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	189	188	146	0	0.994709	0	C|0.848;T|0.152	0.152	strong	.	PPFIA4	139	.	NM_015053	exon3	c.C519T	p.A173A	TGCTGCCCAGGAC	.	PASS	Atlas-SNP
C11orf84	144097	hgsc.bcm.edu	37	11	63585804	63585804	+	Silent	SNP	C	C	A	rs643634	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	43	25	32	0	0.581395	0	C|0.623;A|0.377	0.377	strong	.	C11orf84	33	.	NM_138471	exon3	c.C574A	p.R192R	AGGAGCCGGCCCA	.	PASS	Atlas-SNP
KIAA1244	57221	hgsc.bcm.edu	37	6	138584685	138584685	+	Missense_Mutation	SNP	T	T	G	rs7764091	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	23	10	23	0	0.434783	0	T|0.728;G|0.272	0.272	strong	.	KIAA1244	236	.	NM_020340	exon12	c.T2065G	p.S689A	CTCCTGTCTCTCT	.	PASS	Atlas-SNP
LHX2	9355	hgsc.bcm.edu	37	9	126776410	126776410	+	Silent	SNP	C	C	T	rs144291200	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	183	83	217	0	0.453552	0	C|0.996;T|0.004	0.004	strong	.	LHX2	30	.	NM_004789	exon2	c.C291T	p.D97D	CAAGGACGGTAGC	.	PASS	Atlas-SNP
PLIN4	729359	hgsc.bcm.edu	37	19	4511680	4511680	+	Silent	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	17	68	9	0.223684	0.132353	.	.	none	PLIN4_ENST00000301286,right_lower_lobe,carcinoma,0,2	PLIN4	191	2	NM_001080400	exon3	c.T2250C	p.D750D	CACAGCATCTTTA	.	scavenged	Atlas-SNP
CCDC94	55702	hgsc.bcm.edu	37	19	4254375	4254375	+	Silent	SNP	C	C	T	rs11085068	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	107	62	90	0	0.579439	0	C|0.632;T|0.368	0.368	strong	CCDC94,NS,carcinoma,0,1	CCDC94	28	1	NM_018074	exon4	c.C294T	p.Y98Y	AGACTACACCATG	.	PASS	Atlas-SNP
JARID2	3720	hgsc.bcm.edu	37	6	15513482	15513482	+	Silent	SNP	G	G	A	rs2235258	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51	51	56	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
TNS3	64759	hgsc.bcm.edu	37	7	47436497	47436497	+	Silent	SNP	G	G	A	rs17544028	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	21	5	69	0	0.238095	0	G|0.892;A|0.108	0.108	strong	.	TNS3	140	.	NM_022748	exon16	c.C924T	p.S308S	GTGTTCGGACCCT	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228402508	228402508	+	Silent	SNP	C	C	T	rs2776853	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49	26	56	0	0.530612	0	C|0.687;T|0.313	0.313	strong	.	OBSCN	2142	.	NM_001271223	exon5	c.C1537T	p.L513L	CCTCCCCTGCAAC	.	PASS	Atlas-SNP
TIGD1	200765	hgsc.bcm.edu	37	2	233413648	233413648	+	Silent	SNP	G	G	A	rs72991949	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	4	4	4	0	1	0	G|0.858;A|0.142	0.142	strong	.	TIGD1	17	.	NM_145702	exon1	c.C945T	p.Y315Y	CTCCTCGTATATC	.	PASS	Atlas-SNP
C1orf101	257044	hgsc.bcm.edu	37	1	244724092	244724092	+	Silent	SNP	G	G	A	rs7544794	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	139	65	115	0	0.467626	0	G|0.779;A|0.221	0.221	strong	.	C1orf101	158	.	NM_173807	exon10	c.G1152A	p.S384S	TCTATCGGTGACT	.	PASS	Atlas-SNP
SLITRK2	84631	hgsc.bcm.edu	37	X	144906370	144906370	+	Silent	SNP	A	A	G	rs45540333	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	174	122	130	0	0.701149	0	A|0.986;G|0.014	0.014	strong	.	SLITRK2	221	.	NM_001144005	exon5	c.A2427G	p.K809K	CAGGAAATGCTTT	.	PASS	Atlas-SNP
ADRB2	154	hgsc.bcm.edu	37	5	148206917	148206917	+	Silent	SNP	C	C	A	rs1042718	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	107	59	115	0	0.551402	0	C|0.747;A|0.253	0.253	strong	.	ADRB2	42	.	NM_000024	exon1	c.C523A	p.R175R	TGGTACCGGGCCA	.	PASS	Atlas-SNP
NXPE4	54827	hgsc.bcm.edu	37	11	114441943	114441943	+	Missense_Mutation	SNP	G	G	A	rs10891705	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	198	196	172	0	0.989899	0	G|0.639;A|0.361	0.361	strong	.	.	.	.	NM_001077639	exon6	c.C1352T	p.A451V	TTGAGGGCCCTTC	.	PASS	Atlas-SNP
PIDD	55367	hgsc.bcm.edu	37	11	804212	804212	+	Silent	SNP	C	C	A	rs7104785	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	132	131	127	0	0.992424	0	C|0.567;A|0.433	0.433	strong	.	PIDD	76	.	NM_145887	exon2	c.G177T	p.L59L	CAGCTGCAGAGGC	.	PASS	Atlas-SNP
HECTD1	25831	hgsc.bcm.edu	37	14	31619392	31619392	+	Silent	SNP	T	T	C	rs11620816	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	163	70	207	0	0.429448	0	C|0.246;T|0.754	0.246	strong	.	HECTD1	159	.	NM_015382	exon13	c.A1968G	p.Q656Q	ACCTTGTTGCAAT	.	PASS	Atlas-SNP
ZHX2	22882	hgsc.bcm.edu	37	8	123964953	123964953	+	Silent	SNP	C	C	T	rs3808600	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	39	76	0	0.481481	0	C|0.762;T|0.238	0.238	strong	.	ZHX2	106	.	NM_014943	exon3	c.C1203T	p.T401T	AGTCACCAACCAT	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	155	66	187	0	0.425806	0	C|0.466;N|0.000	0.466	strong	.	MYH4	349	.	NM_017533	exon26	c.A3318G	p.I1106M	TAGCTGTATTGCA	.	PASS	Atlas-SNP
CDH22	64405	hgsc.bcm.edu	37	20	44806643	44806643	+	Silent	SNP	G	G	A	rs34603854	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110	57	129	0	0.518182	0	G|0.916;A|0.084	0.084	strong	.	CDH22	112	.	NM_021248	exon11	c.C1857T	p.A619A	GGAGGCGGCCATG	.	PASS	Atlas-SNP
MTX1	4580	hgsc.bcm.edu	37	1	155178782	155178782	+	Missense_Mutation	SNP	A	A	T	rs760077	bycluster;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	22	22	20	0	1	0	A|0.304;T|0.696	0.696	strong	.	MTX1	17	.	NM_198883	exon1	c.A187T	p.T63S	CGTGACACTCCGA	.	PASS	Atlas-SNP
TBCD	6904	hgsc.bcm.edu	37	17	80899281	80899281	+	Silent	SNP	G	G	A	rs9390	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	25	25	19	0	1	0	A|0.453;C|0.000;G|0.546;T|0.000	0.453	strong	.	TBCD	94	.	NM_005993	exon38	c.G3486A	p.A1162A	GGACGCGGAGCTT	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	150	72	133	0	0.48	0	C|0.676;A|0.324	0.324	strong	.	.	.	.	NM_183061	exon18	c.G2303T	p.S768I	TTAGAACTTGTAA	.	PASS	Atlas-SNP
EHF	26298	hgsc.bcm.edu	37	11	34668143	34668143	+	Silent	SNP	C	C	T	rs2281910	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	32	80	0	0.516129	0	C|0.792;T|0.208	0.208	strong	.	EHF	38	.	NM_001206616	exon3	c.C321T	p.L107L	GCACCTCTGCAGC	.	PASS	Atlas-SNP
SETX	23064	hgsc.bcm.edu	37	9	135203530	135203530	+	Missense_Mutation	SNP	A	A	C	rs3739922	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	151	78	129	0	0.516556	0	A|0.931;C|0.069	0.069	strong	.	SETX	234	.	NM_015046	exon10	c.T3455G	p.F1152C	TCACAAAATTCTT	.	PASS	Atlas-SNP
CPA4	51200	hgsc.bcm.edu	37	7	129962414	129962414	+	Silent	SNP	C	C	T	rs2306848	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	121	61	103	0	0.504132	0	C|0.941;T|0.059	0.059	strong	.	CPA4	47	.	NM_016352	exon11	c.C1164T	p.T388T	CGGGACCTATGGC	.	PASS	Atlas-SNP
POTEC	388468	hgsc.bcm.edu	37	18	14543057	14543057	+	Missense_Mutation	SNP	T	T	G	rs9807633	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	201	80	162	0	0.39801	0	T|0.701;G|0.299	0.299	strong	.	POTEC	129	.	NM_001137671	exon1	c.A89C	p.H30P	AAGCGGTGGTGAA	.	PASS	Atlas-SNP
KIAA1211	57482	hgsc.bcm.edu	37	4	57182647	57182647	+	Silent	SNP	G	G	A	rs3822003	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	34	21	42	0	0.617647	0	G|0.773;A|0.227	0.227	strong	.	KIAA1211	178	.	NM_020722	exon8	c.G2979A	p.A993A	CCGAGCGGGGAGG	.	PASS	Atlas-SNP
USP51	158880	hgsc.bcm.edu	37	X	55514818	55514818	+	Silent	SNP	C	C	T	rs3126255	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	83	83	0	0.988095	0	C|0.528;T|0.472	0.472	strong	.	USP51	71	.	NM_201286	exon2	c.G555A	p.E185E	CTCGACCTCCAGC	.	PASS	Atlas-SNP
IDO2	169355	hgsc.bcm.edu	37	8	39872935	39872935	+	Nonsense_Mutation	SNP	T	T	A	rs4503083	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	135	135	144	1	1	0.00694444	T|0.758;A|0.242	0.242	strong	.	IDO2	78	.	NM_194294	exon11	c.T1077A	p.Y359X	GAGCTATCACATC	.	PASS	Atlas-SNP
LRRC2	79442	hgsc.bcm.edu	37	3	46592987	46592987	+	Missense_Mutation	SNP	A	A	G	rs28687398	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	20	79	0	0.384615	0	A|0.904;G|0.096	0.096	strong	.	LRRC2	37	.	NM_024512	exon2	c.T95C	p.V32A	CTTTCCACCTCCT	.	PASS	Atlas-SNP
MYBL1	4603	hgsc.bcm.edu	37	8	67478431	67478431	+	Missense_Mutation	SNP	T	T	G	rs61729530	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	123	70	102	0	0.569106	0	T|0.991;G|0.009	0.009	strong	.	MYBL1	73	.	NM_001080416	exon15	c.A1998C	p.E666D	ATGTATTTCCAAT	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29912386	29912386	+	Missense_Mutation	SNP	G	G	C	rs1137160	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	196	48	124	0	0.244898	0	G|0.868;C|0.132	0.132	strong	HLA-A,colon,carcinoma,0,1	HLA-A	89	1	NM_001242758	exon5	c.G1005C	p.K335N	GAGGAAGAGCTCA	.	PASS	Atlas-SNP
FGD5	152273	hgsc.bcm.edu	37	3	14862049	14862049	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	32	84	0	0.380952	0	.	.	none	FGD5_ENST00000285046,NS,carcinoma,0,2	FGD5	248	2	NM_152536	exon1	c.G1471A	p.G491S	GTGGCCGGCTATG	.	PASS	Atlas-SNP
CDH11	1009	hgsc.bcm.edu	37	16	65038674	65038674	+	Silent	SNP	G	G	A	rs35182	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100	56	77	0	0.56	0	G|0.923;A|0.077	0.077	strong	.	CDH11	260	.	NM_001797	exon3	c.C99T	p.P33P	GAAGGAGGGCCGC	.	PASS	Atlas-SNP
GALNT18	374378	hgsc.bcm.edu	37	11	11354346	11354346	+	Silent	SNP	T	T	C	rs901553	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49	22	45	0	0.44898	0	C|0.397;N|0.000	0.397	strong	GALNTL4,NS,carcinoma,0,1	.	.	1	NM_198516	exon8	c.A1311G	p.A437A	CTTCCTTGCAGTG	.	PASS	Atlas-SNP
DOCK6	57572	hgsc.bcm.edu	37	19	11326504	11326504	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	129	4	98	0	0.0310078	0	.	.	none	DOCK6,NS,carcinoma,0,1	DOCK6	104	1	NM_020812	exon31	c.C3994T	p.R1332X	CTTGTCGAGCTCC	.	scavenged	Atlas-SNP
SMTNL2	342527	hgsc.bcm.edu	37	17	4495740	4495740	+	Missense_Mutation	SNP	G	G	A	rs12449695	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	35	35	28	0	1	0	G|0.713;A|0.287	0.287	strong	.	SMTNL2	57	.	NM_001114974	exon2	c.G484A	p.A162T	CCGGGGGCAGGTA	.	PASS	Atlas-SNP
PARVB	29780	hgsc.bcm.edu	37	22	44395451	44395451	+	Missense_Mutation	SNP	T	T	C	rs1007863	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	114	54	107	0	0.473684	0	T|0.506;C|0.494	0.494	strong	PARVB,NS,carcinoma,0,1	PARVB	44	1	NM_001003828	exon2	c.T109C	p.W37R	TGCAGCTGGGGCC	.	PASS	Atlas-SNP
MAPKBP1	23005	hgsc.bcm.edu	37	15	42105918	42105918	+	Missense_Mutation	SNP	C	C	G	rs1201689	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	118	35	142	0	0.29661	0	C|0.662;G|0.338	0.338	strong	.	MAPKBP1	120	.	NM_001128608	exon10	c.C937G	p.L313V	CACTTCCTTAGCA	.	PASS	Atlas-SNP
LYST	1130	hgsc.bcm.edu	37	1	235887393	235887393	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	128	14	150	0	0.109375	0	.	.	none	.	LYST	370	.	NM_000081	exon39	c.G9250A	p.D3084N	CATTATCTCTCAA	.	PASS	Atlas-SNP
PIP4K2C	79837	hgsc.bcm.edu	37	12	57985204	57985204	+	Silent	SNP	C	C	T	rs11537654	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	172	170	177	1	0.988372	0.00564972	C|0.763;T|0.237	0.237	strong	.	PIP4K2C	50	.	NM_001146258	exon1	c.C132T	p.A44A	GGCGGCCGACCCG	.	PASS	Atlas-SNP
SAG	6295	hgsc.bcm.edu	37	2	234255547	234255547	+	Missense_Mutation	SNP	G	G	A	rs1046974	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69	35	58	0	0.507246	0	G|0.696;A|0.304	0.304	strong	.	SAG	77	.	NM_000541	exon16	c.G1207A	p.V403I	AATGACGTTGATG	.	PASS	Atlas-SNP
ATP7B	540	hgsc.bcm.edu	37	13	52544805	52544805	+	Missense_Mutation	SNP	C	C	G	rs1801244	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	183	183	151	0	1	0	C|0.579;G|0.421	0.421	strong	.	ATP7B	123	.	NM_000053	exon3	c.G1366C	p.V456L	CCTGCACAGATGT	.	PASS	Atlas-SNP
ANGPTL4	51129	hgsc.bcm.edu	37	19	8438716	8438716	+	Silent	SNP	G	G	A	rs11672433	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	37	74	0	0.440476	0	G|0.911;A|0.089	0.089	strong	ANGPTL4,NS,carcinoma,0,1	ANGPTL4	21	1	NM_139314	exon7	c.G1167A	p.P389P	CTACCCGCTGCAG	.	PASS	Atlas-SNP
TSEN54	283989	hgsc.bcm.edu	37	17	73513289	73513289	+	Silent	SNP	C	C	G	rs6501818	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	39	74	0	0.448276	0	C|0.822;G|0.178	0.178	strong	.	TSEN54	27	.	NM_207346	exon4	c.C333G	p.R111R	GCAGCGCCTTCAC	.	PASS	Atlas-SNP
MST1	4485	hgsc.bcm.edu	37	3	49723784	49723784	+	Silent	SNP	C	C	A	rs9713651	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	165	68	122	0	0.412121	0	C|0.562;A|0.438	0.438	strong	.	MST1	84	.	NM_020998	exon8	c.G978T	p.P326P	CTGATGCGGGATT	.	PASS	Atlas-SNP
BPIFB2	80341	hgsc.bcm.edu	37	20	31609581	31609581	+	Silent	SNP	C	C	T	rs17124003	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	114	54	75	1	0.473684	0.0133333	C|0.672;N|0.000	.	strong	BPIL1,NS,carcinoma,0,1	.	.	1	NM_025227	exon15	c.C1311T	p.V437V	CTATGTCGCCCCT	.	scavenged	Atlas-SNP
PCDHA9	9752	hgsc.bcm.edu	37	5	140228413	140228413	+	Missense_Mutation	SNP	C	C	A	rs17844323	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	148	38	221	2	0.256757	0.00904977	C|0.819;A|0.181	0.181	strong	PCDHA9_ENST00000532602,bladder,carcinoma,+2,2	PCDHA9	373	2	NM_031857	exon1	c.C333A	p.D111E	CGTAGACAGGCCG	.	scavenged	Atlas-SNP
MKI67	4288	hgsc.bcm.edu	37	10	129904917	129904917	+	Silent	SNP	G	G	A	rs1894410	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	106	47	87	0	0.443396	0	G|0.863;N|0.000	.	strong	.	MKI67	363	.	NM_002417	exon13	c.C5187T	p.N1729N	TTTTTCGTTAGTC	.	PASS	Atlas-SNP
SYT6	148281	hgsc.bcm.edu	37	1	114680540	114680540	+	Silent	SNP	C	C	T	rs201787036	alternate_allele	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	234	122	215	0	0.521368	0	.	.	alt	SYT6,NS,carcinoma,0,1	SYT6	66	1	NM_205848	exon3	c.G393A	p.S131S	ATCCACCGACTTC	.	PASS	Atlas-SNP
C22orf26	55267	hgsc.bcm.edu	37	22	46447714	46447714	+	Missense_Mutation	SNP	T	T	C	rs59929908	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44	21	29	0	0.477273	0	T|0.897;C|0.103	0.103	strong	.	C22orf26	1	.	NM_018280	exon2	c.A410G	p.Q137R	CATACCTGTAATT	.	PASS	Atlas-SNP
HCAR1	27198	hgsc.bcm.edu	37	12	123214166	123214166	+	Missense_Mutation	SNP	G	G	A	rs140482291	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	70	36	48	0	0.514286	0	G|0.998;A|0.002	0.002	strong	.	HCAR1	21	.	NM_032554	exon1	c.C721T	p.L241F	AATAGAGTCTAGC	.	PASS	Atlas-SNP
PAQR9	344838	hgsc.bcm.edu	37	3	142681249	142681249	+	Silent	SNP	G	G	A	rs62276870	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73	30	72	0	0.410959	0	G|0.946;A|0.054	0.054	strong	.	PAQR9	57	.	NM_198504	exon1	c.C930T	p.S310S	CTGGTGGCTGTGG	.	PASS	Atlas-SNP
OR5K3	403277	hgsc.bcm.edu	37	3	98110414	98110414	+	Missense_Mutation	SNP	T	T	A	rs199575537	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	27	2	23	0	0.0740741	0	.	.	weak	OR5K3,NS,carcinoma,0,2	OR5K3	60	2	NM_001005516	exon1	c.T905A	p.I302N	AAAAAATTATGAA	.	scavenged	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29911951	29911951	+	Silent	SNP	C	C	T	rs74658171	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	290	30	185	0	0.103448	0	.	.	weak	.	HLA-A	89	.	NM_001242758	exon4	c.C672T	p.T224T	GGCCACCCTGAGG	.	PASS	Atlas-SNP
TTLL6	284076	hgsc.bcm.edu	37	17	46877063	46877063	+	Missense_Mutation	SNP	G	G	A	rs61739953	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	96	50	71	0	0.520833	0	G|0.953;A|0.047	0.047	strong	.	TTLL6	113	.	NM_001130918	exon6	c.C671T	p.P224L	GAATCCGGCTTAC	.	PASS	Atlas-SNP
SSH3	54961	hgsc.bcm.edu	37	11	67072382	67072382	+	Silent	SNP	C	C	T	rs61731786	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	172	29	145	0	0.168605	0	C|0.964;T|0.036	0.036	strong	.	SSH3	54	.	NM_017857	exon3	c.C243T	p.F81F	AGACTTCGGGCAA	.	PASS	Atlas-SNP
FLJ44635	0	hgsc.bcm.edu	37	X	71379881	71379881	+	Missense_Mutation	SNP	G	G	A	rs6624600	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	149	45	99	0	0.302013	0	G|0.566;A|0.434	0.434	strong	.	FLJ44635	13	.	NM_207422	exon2	c.G202A	p.E68K	GGTACCGAAAGCA	.	PASS	Atlas-SNP
NCF2	4688	hgsc.bcm.edu	37	1	183542387	183542387	+	Missense_Mutation	SNP	T	T	C	rs2274064	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	58	58	97	0	1	0	T|0.538;C|0.462	0.462	strong	.	NCF2	69	.	NM_001127651	exon6	c.A542G	p.K181R	AACAGCTTGCCCA	.	PASS	Atlas-SNP
CST1	1469	hgsc.bcm.edu	37	20	23731426	23731426	+	Silent	SNP	C	C	T	rs13045477	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	108	108	129	1	1	0.00775194	C|0.665;T|0.335	0.335	strong	CST1,NS,carcinoma,0,1	CST1	37	1	NM_001898	exon1	c.G78A	p.E26E	CCTATCCTCCTCC	.	PASS	Atlas-SNP
MTR	4548	hgsc.bcm.edu	37	1	237048500	237048500	+	Missense_Mutation	SNP	A	A	G	rs1805087	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	47	52	2	1	0.0384615	A|0.786;G|0.214	0.214	strong	MTR,rectum,carcinoma,+1,1	MTR	127	1	NM_000254	exon26	c.A2756G	p.D919G	GACAGGACCATTA	.	scavenged	Atlas-SNP
TNK2	10188	hgsc.bcm.edu	37	3	195595054	195595054	+	Silent	SNP	C	C	T	rs7516	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	27	86	0	0.421875	0	C|0.921;T|0.079	0.079	strong	TNK2_ENST00000381916,NS,carcinoma,0,3	TNK2	246	3	NM_001010938	exon13	c.G2304A	p.P768P	CTGGGGCGGGAGG	.	PASS	Atlas-SNP
OR2Z1	284383	hgsc.bcm.edu	37	19	8841588	8841588	+	Silent	SNP	C	C	G	rs147384704	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	136	72	164	0	0.529412	0	C|0.981;G|0.019	0.019	strong	OR2Z1,NS,carcinoma,0,1	OR2Z1	53	1	NM_001004699	exon1	c.C198G	p.L66L	CCAGCTCTCCCTG	.	PASS	Atlas-SNP
MCM3	4172	hgsc.bcm.edu	37	6	52144221	52144221	+	Silent	SNP	C	C	T	rs2307331	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	28	16	38	0	0.571429	0	C|0.954;T|0.046	0.046	strong	.	MCM3	63	.	NM_002388	exon5	c.G843A	p.Q281Q	CACCACCTGAACC	.	PASS	Atlas-SNP
DNAH7	56171	hgsc.bcm.edu	37	2	196791276	196791276	+	Silent	SNP	T	T	G	rs1489802	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	26	65	0	0.42623	0	T|0.505;G|0.495	0.495	strong	.	DNAH7	512	.	NM_018897	exon22	c.A3486C	p.A1162A	AAAAGTTGCATCT	.	PASS	Atlas-SNP
SIRPG	55423	hgsc.bcm.edu	37	20	1617069	1617069	+	Silent	SNP	A	A	G	rs2277761	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	277	147	274	0	0.530686	0	A|0.776;G|0.224	0.224	strong	SIRPG,NS,carcinoma,-1,1	SIRPG	61	1	NM_001039508	exon3	c.T513C	p.H171H	GAAGCCATGGGAC	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228465346	228465346	+	Missense_Mutation	SNP	A	A	G	rs493945	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68	30	62	0	0.441176	0	A|0.659;G|0.341	0.341	strong	.	OBSCN	2142	.	NM_001271223	exon29	c.A8020G	p.N2674D	ACTGACAACGTGC	.	PASS	Atlas-SNP
SEC16B	89866	hgsc.bcm.edu	37	1	177908852	177908852	+	Missense_Mutation	SNP	C	C	T	rs943762	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	118	59	113	0	0.5	0	C|0.838;T|0.162	0.162	strong	.	SEC16B	92	.	NM_033127	exon18	c.G2188A	p.G730R	TTCCTCCGGCTCC	.	PASS	Atlas-SNP
GLTPD2	388323	hgsc.bcm.edu	37	17	4693054	4693054	+	Silent	SNP	G	G	A	rs12951761	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	53	71	0	0.981481	0	G|0.443;A|0.557	0.557	strong	.	GLTPD2	15	.	NM_001014985	exon4	c.G339A	p.E113E	CCGCAGGTTCCTG	.	PASS	Atlas-SNP
DZIP3	9666	hgsc.bcm.edu	37	3	108381023	108381023	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	170	6	154	0	0.0352941	0	.	.	none	DZIP3,NS,neuroblastoma,-1,1	DZIP3	111	1	NM_014648	exon21	c.A2342C	p.N781T	AAGAAAACCAAAT	.	scavenged	Atlas-SNP
LRP2BP	55805	hgsc.bcm.edu	37	4	186299260	186299260	+	Silent	SNP	A	A	G	rs2030802	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	115	63	127	0	0.547826	0	A|0.641;G|0.359	0.359	strong	LRP2BP,NS,carcinoma,0,1	LRP2BP	34	1	NM_018409	exon1	c.T81C	p.F27F	CTGGAAAAATTTT	.	PASS	Atlas-SNP
FAM120A	23196	hgsc.bcm.edu	37	9	96238578	96238578	+	Silent	SNP	C	C	T	rs10821135	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	142	142	137	1	1	0.00729927	C|0.447;T|0.553	0.553	strong	FAM120A,NS,carcinoma,+2,2	FAM120A	105	2	NM_014612	exon3	c.C762T	p.H254H	CTTTCACTGGAGT	.	PASS	Atlas-SNP
WDR11	55717	hgsc.bcm.edu	37	10	122663585	122663585	+	Silent	SNP	G	G	A	rs1652727	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	42	24	52	0	0.571429	0	G|0.301;A|0.699	0.699	strong	.	WDR11	95	.	NM_018117	exon24	c.G2958A	p.L986L	TAATCTGCAGGAA	.	PASS	Atlas-SNP
RMND5A	64795	hgsc.bcm.edu	37	2	86979093	86979093	+	Silent	SNP	G	G	A	rs10186663	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	125	15	195	0	0.12	0	G|0.330;A|0.670	0.670	strong	.	RMND5A	33	.	NM_022780	exon3	c.G360A	p.E120E	CAATGAGGTGATG	.	PASS	Atlas-SNP
VWA3B	200403	hgsc.bcm.edu	37	2	98844674	98844674	+	Missense_Mutation	SNP	C	C	G	rs7601049	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	31	14	22	0	0.451613	0	C|0.354;G|0.646	0.646	strong	.	VWA3B	138	.	NM_144992	exon15	c.C2029G	p.L677V	GAAGATCTGACTC	.	PASS	Atlas-SNP
EGFR	1956	hgsc.bcm.edu	37	7	55229255	55229255	+	Missense_Mutation	SNP	G	G	A	rs2227983	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44	25	52	0	0.568182	0	A|0.243;C|0.000;G|0.757;T|0.000	0.243	strong	.	EGFR	20426	.	NM_005228	exon13	c.G1562A	p.R521K	AGCCCAGGGACTG	.	PASS	Atlas-SNP
SGCG	6445	hgsc.bcm.edu	37	13	23824783	23824783	+	Silent	SNP	T	T	G	rs1800351	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49	49	65	0	1	0	T|0.510;G|0.490	0.490	strong	.	SGCG	64	.	NM_000231	exon4	c.T312G	p.L104L	TCTGCTTCTACAA	.	PASS	Atlas-SNP
ERAP2	64167	hgsc.bcm.edu	37	5	96215680	96215680	+	Silent	SNP	C	C	T	rs41506651	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	112	59	154	0	0.526786	0	C|0.928;T|0.072	0.072	strong	.	ERAP2	77	.	NM_001130140	exon2	c.C291T	p.I97I	GAAGATCGAAGTC	.	PASS	Atlas-SNP
PCDH10	57575	hgsc.bcm.edu	37	4	134072208	134072208	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	43	10	58	0	0.232558	0	.	.	none	PCDH10,NS,carcinoma,-2,2	PCDH10	290	2	NM_032961	exon1	c.C913G	p.P305A	CTCTCGCCGCGCA	.	PASS	Atlas-SNP
FAM160B1	57700	hgsc.bcm.edu	37	10	116615045	116615045	+	Silent	SNP	T	T	C	rs3180654	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100	47	110	0	0.47	0	C|0.312;T|0.688	0.312	strong	.	FAM160B1	107	.	NM_020940	exon14	c.T1893C	p.F631F	TTTCTTTGAAGGT	.	PASS	Atlas-SNP
NAGPA	51172	hgsc.bcm.edu	37	16	5075542	5075542	+	Silent	SNP	G	G	A	rs887854	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	138	70	161	0	0.507246	0	G|0.253;N|0.000	.	strong	.	NAGPA	30	.	NM_016256	exon10	c.C1485T	p.N495N	CTCCCCGTTCATC	.	PASS	Atlas-SNP
PMP2	5375	hgsc.bcm.edu	37	8	82357112	82357112	+	Silent	SNP	T	T	C	rs2229015	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	114	52	112	0	0.45614	0	T|0.706;C|0.294	0.294	strong	.	PMP2	21	.	NM_002677	exon2	c.A186G	p.E62E	GGAGATTTCTGTA	.	PASS	Atlas-SNP
ATP9B	374868	hgsc.bcm.edu	37	18	76870397	76870397	+	Silent	SNP	G	G	A	rs492657	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	25	61	0	0.531915	0	G|0.862;A|0.138	0.138	strong	.	ATP9B	96	.	NM_198531	exon3	c.G336A	p.E112E	GAAAGAGCTGAAA	.	PASS	Atlas-SNP
ADAM30	11085	hgsc.bcm.edu	37	1	120437884	120437884	+	Missense_Mutation	SNP	A	A	G	rs2641348	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	147	67	156	0	0.455782	0	A|0.830;G|0.170	0.170	strong	.	ADAM30	88	.	NM_021794	exon1	c.T1076C	p.L359P	CAATTAAGCCTAC	.	PASS	Atlas-SNP
PTX4	390667	hgsc.bcm.edu	37	16	1536372	1536372	+	Silent	SNP	G	G	A	rs28444604	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82	40	77	0	0.487805	0	G|0.895;A|0.105	0.105	strong	.	PTX4	46	.	NM_001013658	exon3	c.C990T	p.P330P	GGATCCGGGCAGC	.	PASS	Atlas-SNP
SMC1B	27127	hgsc.bcm.edu	37	22	45782903	45782903	+	Silent	SNP	T	T	C	rs6007010	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	90	42	98	1	0.466667	0.0102041	T|0.518;C|0.482	0.482	strong	SMC1B_ENST00000357450,NS,carcinoma,-1,4	SMC1B	215	4	NM_148674	exon11	c.A1755G	p.L585L	CTCCCTTAGTCTT	.	scavenged	Atlas-SNP
HTR5A	3361	hgsc.bcm.edu	37	7	154862621	154862621	+	Silent	SNP	T	T	A	rs6320	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	29	17	26	0	0.586207	0	T|0.726;A|0.274	0.274	strong	HTR5A,NS,carcinoma,+1,2	HTR5A	114	2	NM_024012	exon1	c.T12A	p.P4P	TTTACCTGTGAAC	.	PASS	Atlas-SNP
GPRIN1	114787	hgsc.bcm.edu	37	5	176026146	176026146	+	Silent	SNP	C	C	T	rs79403503	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	96	32	130	0	0.333333	0	C|0.779;T|0.221	0.221	strong	.	GPRIN1	77	.	NM_052899	exon2	c.G690A	p.P230P	CTTCCTCGGTGAC	.	PASS	Atlas-SNP
PIGM	93183	hgsc.bcm.edu	37	1	160000435	160000435	+	Missense_Mutation	SNP	A	A	T	rs12409352	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	107	58	133	0	0.542056	0	A|0.892;T|0.108	0.108	strong	.	PIGM	27	.	NM_145167	exon1	c.T1095A	p.F365L	CCCTATAAACCAT	.	PASS	Atlas-SNP
RAB11FIP3	9727	hgsc.bcm.edu	37	16	570737	570737	+	Silent	SNP	G	G	A	rs142673366	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93	37	91	0	0.397849	0	G|0.999;A|0.001	0.001	strong	.	RAB11FIP3	31	.	NM_014700	exon14	c.G2169A	p.A723A	GGAGGCGATTCAG	.	PASS	Atlas-SNP
RNF207	388591	hgsc.bcm.edu	37	1	6278414	6278414	+	Missense_Mutation	SNP	A	A	G	rs709209	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93	53	78	0	0.569892	0	A|0.586;G|0.414	0.414	strong	.	RNF207	45	.	NM_207396	exon17	c.A1718G	p.N573S	GGAACAACGCGGC	.	PASS	Atlas-SNP
MBOAT1	154141	hgsc.bcm.edu	37	6	20124710	20124710	+	Missense_Mutation	SNP	G	G	A	rs146228602	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85	14	92	0	0.164706	0	G|0.999;A|0.001	0.001	strong	MBOAT1,NS,carcinoma,+1,1	MBOAT1	48	1	NM_001080480	exon8	c.C836T	p.P279L	CGAGCCGGAAAGC	.	PASS	Atlas-SNP
CHEK2	11200	hgsc.bcm.edu	37	22	29091841	29091841	+	Silent	SNP	G	G	A	rs79357544		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	101	7	84	1	0.0693069	0.0119048	.	.	weak	CHEK2,bladder,carcinoma,0,38	CHEK2	438	38	NM_001005735	exon12	c.C1245T	p.S415S	AATCTTGGAGTGC	.	scavenged	Atlas-SNP
VPS13D	55187	hgsc.bcm.edu	37	1	12342990	12342990	+	Missense_Mutation	SNP	G	G	A	rs41279452	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	135	50	109	0	0.37037	0	G|0.993;A|0.007	0.007	strong	.	VPS13D	316	.	NM_015378	exon21	c.G4831A	p.E1611K	GTGAAGGAAGTCA	.	PASS	Atlas-SNP
MARC2	54996	hgsc.bcm.edu	37	1	220928376	220928376	+	Silent	SNP	T	T	C	rs371348	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	132	62	136	0	0.469697	0	T|0.947;C|0.053	0.053	strong	.	.	.	.	NM_017898	exon2	c.T360C	p.N120N	TGAGAATAACTGC	.	PASS	Atlas-SNP
BANK1	55024	hgsc.bcm.edu	37	4	102839287	102839287	+	Missense_Mutation	SNP	G	G	A	rs3733197	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	125	55	127	0	0.44	0	G|0.725;A|0.275	0.275	strong	.	BANK1	95	.	NM_017935	exon7	c.G1147A	p.A383T	GACCCCGCACATA	.	PASS	Atlas-SNP
ZFP36L2	678	hgsc.bcm.edu	37	2	43452618	43452618	+	Missense_Mutation	SNP	C	C	T	rs11675632	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	26	13	40	0	0.5	0	C|0.947;T|0.053	0.053	strong	.	ZFP36L2	56	.	NM_006887	exon2	c.G325A	p.G109S	CTGTGCCGCCGCC	.	PASS	Atlas-SNP
LTBP2	4053	hgsc.bcm.edu	37	14	75052587	75052587	+	Missense_Mutation	SNP	G	G	A	rs149952751	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	95	50	145	0	0.526316	0	G|0.998;A|0.002	0.002	strong	LTBP2,NS,carcinoma,0,1	LTBP2	158	1	NM_000428	exon3	c.C800T	p.S267L	GGCGGCGACTGTG	.	PASS	Atlas-SNP
GRM6	2916	hgsc.bcm.edu	37	5	178415937	178415937	+	Silent	SNP	A	A	G	rs2067011	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	109	109	175	0	1	0	A|0.500;G|0.500	0.500	strong	.	GRM6	149	.	NM_000843	exon6	c.T1353C	p.N451N	CTCACCATTGAAG	.	PASS	Atlas-SNP
ELTD1	64123	hgsc.bcm.edu	37	1	79411968	79411968	+	Missense_Mutation	SNP	C	C	A	rs41313381	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	125	62	110	0	0.496	0	C|0.981;A|0.019	0.019	strong	.	ELTD1	143	.	NM_022159	exon3	c.G316T	p.V106F	TACAGACGGTTCC	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	144	119	150	0	0.826389	0	G|0.703;A|0.297	0.297	strong	.	ANKK1	83	.	NM_178510	exon8	c.G2137A	p.E713K	CTGGTCGAGGCAG	.	PASS	Atlas-SNP
ZNF774	342132	hgsc.bcm.edu	37	15	90903311	90903311	+	Missense_Mutation	SNP	A	A	G	rs2589957	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	74	135	0	0.986667	0	A|0.386;G|0.614	0.614	strong	.	ZNF774	35	.	NM_001004309	exon4	c.A248G	p.N83S	AGGACAATTCTGA	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179430997	179430997	+	Missense_Mutation	SNP	G	G	A	rs3731746	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	130	63	121	0	0.484615	0	T|0.000;G|0.681;N|0.000;A|0.318	0.318	strong	.	TTN	18412	.	NM_001267550	exon326	c.C79862T	p.T26621M	TCAGGCGTTGGAC	.	PASS	Atlas-SNP
NALCN	259232	hgsc.bcm.edu	37	13	101736075	101736075	+	Silent	SNP	A	A	G	rs686141	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	43	42	53	0	0.976744	0	A|0.256;G|0.744	0.744	strong	.	NALCN	431	.	NM_052867	exon31	c.T3570C	p.L1190L	AGGCGGAAGATGA	.	PASS	Atlas-SNP
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32610529	32610529	+	Silent	SNP	A	A	G	rs13379	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	157	64	77	0	0.407643	0	A|0.973;G|0.027	0.027	strong	.	HLA-DQA1	52	.	NM_002122	exon4	c.A756G	p.Q252Q	ACACCAAGGGCCA	.	PASS	Atlas-SNP
VSIG10L	147645	hgsc.bcm.edu	37	19	51844978	51844978	+	Silent	SNP	G	G	T	rs8105710	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	34	49	0	0.557377	0	G|0.400;T|0.600	0.600	strong	.	VSIG10L	40	.	NM_001163922	exon2	c.C324A	p.S108S	GAAGGGGGAAACC	.	PASS	Atlas-SNP
H2BFWT	158983	hgsc.bcm.edu	37	X	103267865	103267865	+	Missense_Mutation	SNP	C	C	T	rs553509	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	97	93	69	0	0.958763	0	C|0.378;0|0.003	.	strong	.	H2BFWT	33	.	NM_001002916	exon1	c.G368A	p.R123H	GCCAGGCGACCAG	.	PASS	Atlas-SNP
PTX4	390667	hgsc.bcm.edu	37	16	1537839	1537839	+	Missense_Mutation	SNP	G	G	A	rs2745101	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	39	75	0	0.590909	0	G|0.753;A|0.247	0.247	strong	.	PTX4	46	.	NM_001013658	exon2	c.C259T	p.R87W	GTGACCGGTTGAC	.	PASS	Atlas-SNP
PRKG2	5593	hgsc.bcm.edu	37	4	82126121	82126121	+	Silent	SNP	C	C	G	rs17484474	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	130	70	139	0	0.538462	0	C|0.973;G|0.027	0.027	strong	PRKG2_ENST00000395578,bladder,carcinoma,-2,6	PRKG2	195	6	NM_006259	exon1	c.G81C	p.R27R	CTTGTTCCGCAGA	.	PASS	Atlas-SNP
HLTF	6596	hgsc.bcm.edu	37	3	148756993	148756993	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73	22	69	0	0.30137	0	.	.	none	.	HLTF	87	.	NM_139048	exon23	c.G2639A	p.R880H	TCCAAACGAGTAA	.	PASS	Atlas-SNP
TRPA1	8989	hgsc.bcm.edu	37	8	72984041	72984041	+	Missense_Mutation	SNP	C	C	G	rs16937976	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	133	63	124	0	0.473684	0	C|0.874;G|0.126	0.126	strong	TRPA1,right_upper_lobe,carcinoma,+1,2	TRPA1	256	2	NM_007332	exon2	c.G173C	p.R58T	TCACATCTTTTTA	.	PASS	Atlas-SNP
CELF4	56853	hgsc.bcm.edu	37	18	34846518	34846518	+	Silent	SNP	G	G	A	rs145042940	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	58	22	79	0	0.37931	0	G|0.999;A|0.001	0.001	strong	.	CELF4	90	.	NM_020180	exon9	c.C1143T	p.A381A	CACTCCGGCGTAG	.	PASS	Atlas-SNP
TRIM52	84851	hgsc.bcm.edu	37	5	180687212	180687212	+	Silent	SNP	C	C	T	rs918388	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	144	143	172	0	0.993056	0	C|0.784;T|0.216	0.216	strong	.	TRIM52	20	.	NM_032765	exon1	c.G603A	p.L201L	GTTGGCCAGCTGC	.	PASS	Atlas-SNP
TSNARE1	203062	hgsc.bcm.edu	37	8	143425720	143425720	+	Missense_Mutation	SNP	T	T	C	rs10100935	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	125	123	150	0	0.984	0	T|0.418;C|0.582	0.582	strong	.	TSNARE1	59	.	NM_145003	exon4	c.A352G	p.T118A	GGGTAGTGCTGGG	.	PASS	Atlas-SNP
CDH5	1003	hgsc.bcm.edu	37	16	66420885	66420885	+	Silent	SNP	C	C	T	rs1130844	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	33	68	0	0.515625	0	C|0.420;N|0.001	.	strong	.	CDH5	111	.	NM_001795	exon3	c.C384T	p.G128G	CACTGGCGAAAAC	.	PASS	Atlas-SNP
BEST1	7439	hgsc.bcm.edu	37	11	61730234	61730234	+	Silent	SNP	T	T	C	rs1800009	bycluster;byfrequency;bysubmitter;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	40	94	0	0.493827	0	C|0.406;N|0.000	0.406	strong	.	BEST1	85	.	NM_004183	exon10	c.T1608C	p.T536T	GAAAACTGTGGAG	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9084216	9084216	+	Silent	SNP	T	T	C	rs1609459	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	149	75	164	0	0.503356	0	T|0.767;C|0.233	0.233	strong	.	MUC16	4315	.	NM_024690	exon1	c.A7599G	p.A2533A	AGTTGATGCTAGA	.	PASS	Atlas-SNP
DEK	7913	hgsc.bcm.edu	37	6	18237661	18237661	+	Silent	SNP	C	C	T	rs1013062	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	204	48	186	0	0.235294	0	C|0.837;T|0.163	0.163	strong	.	DEK	31	.	NM_003472	exon8	c.G849A	p.K283K	TGCTTTCTTAACA	.	PASS	Atlas-SNP
SPATA21	374955	hgsc.bcm.edu	37	1	16736132	16736132	+	Missense_Mutation	SNP	T	T	C	rs4661746	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	32	32	39	0	1	0	T|0.794;C|0.206	0.206	strong	.	SPATA21	47	.	NM_198546	exon6	c.A551G	p.Q184R	CTGCTCTGGTGCA	.	PASS	Atlas-SNP
PDCD6IP	10015	hgsc.bcm.edu	37	3	33893987	33893987	+	Missense_Mutation	SNP	A	A	G	rs9813017	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	156	61	155	0	0.391026	0	A|0.901;G|0.099	0.099	strong	.	PDCD6IP	62	.	NM_001162429	exon13	c.A1664G	p.N555S	TTGTAAATGTCTT	.	PASS	Atlas-SNP
CCDC86	79080	hgsc.bcm.edu	37	11	60610065	60610065	+	Silent	SNP	G	G	A	rs2074420	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	24	64	1	0.45283	0.015625	G|0.725;A|0.275	0.275	strong	CCDC86,NS,carcinoma,0,1	CCDC86	24	1	NM_024098	exon1	c.G468A	p.P156P	ACCGCCGGTCCCA	.	scavenged	Atlas-SNP
VPS13C	54832	hgsc.bcm.edu	37	15	62165577	62165577	+	Silent	SNP	G	G	A	rs17303894	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	165	59	175	0	0.357576	0	G|0.932;A|0.068	0.068	strong	VPS13C,NS,carcinoma,0,1	VPS13C	506	1	NM_020821	exon78	c.C10446T	p.T3482T	AGAACCGGTGATT	.	PASS	Atlas-SNP
OFD1	8481	hgsc.bcm.edu	37	X	13786875	13786875	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	211	48	157	0	0.227488	0	.	.	none	.	OFD1	109	.	NM_003611	exon22	c.C2967T	p.D989D	AGTGGACACGCTG	.	PASS	Atlas-SNP
TMEM2	23670	hgsc.bcm.edu	37	9	74345158	74345158	+	Silent	SNP	G	G	A	rs25694	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44	21	50	0	0.477273	0	G|0.935;A|0.065	0.065	strong	.	TMEM2	112	.	NM_013390	exon9	c.C1785T	p.T595T	CCCAATGGTGTCT	.	PASS	Atlas-SNP
DNAAF1	123872	hgsc.bcm.edu	37	16	84209609	84209609	+	Missense_Mutation	SNP	C	C	T	rs34777958	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	90	46	95	0	0.511111	0	C|0.988;T|0.012	0.012	strong	DNAAF1,NS,carcinoma,-1,1	DNAAF1	81	1	NM_178452	exon11	c.C1769T	p.T590M	ACTACACGTCACT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195507998	195507998	+	Missense_Mutation	SNP	G	G	C	rs199622660		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	21	93	0	0.244186	0	.	.	weak	.	MUC4	1505	.	NM_018406	exon2	c.C10453G	p.H3485D	TGGTGTGACCTGT	.	PASS	Atlas-SNP
INO80D	54891	hgsc.bcm.edu	37	2	206872126	206872126	+	Silent	SNP	C	C	T	rs116331438	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	241	118	202	0	0.489627	0	C|0.999;T|0.001	0.001	strong	INO80D_ENST00000403263,NS,carcinoma,0,2	INO80D	134	2	NM_017759	exon10	c.G1800A	p.P600P	GTCATCCGGCAAC	.	PASS	Atlas-SNP
IKZF1	10320	hgsc.bcm.edu	37	7	50467767	50467767	+	Silent	SNP	C	C	A	rs61731355	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	23	17	32	0	0.73913	0	C|0.852;A|0.148	0.148	strong	IKZF1_ENST00000331340,NS,carcinoma,0,1	IKZF1	613	1	NM_006060	exon8	c.C1002A	p.P334P	GACGCCCCCGGGC	.	PASS	Atlas-SNP
PLCB3	5331	hgsc.bcm.edu	37	11	64026639	64026639	+	Missense_Mutation	SNP	G	G	A	rs12146487	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	19	9	27	0	0.473684	0	G|0.903;A|0.097	0.097	strong	.	PLCB3	103	.	NM_000932	exon13	c.G1448A	p.R483H	CCGGGCGCAAGCG	.	PASS	Atlas-SNP
SPRR3	6707	hgsc.bcm.edu	37	1	152975941	152975941	+	Missense_Mutation	SNP	C	C	G	rs1055935	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	152	65	161	0	0.427632	0	C|0.409;G|0.590	0.590	strong	.	SPRR3	45	.	NM_001097589	exon2	c.C445G	p.L149V	ACAAAGCTACCAG	.	PASS	Atlas-SNP
DDX60L	91351	hgsc.bcm.edu	37	4	169362557	169362557	+	Missense_Mutation	SNP	C	C	G	rs13151700	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	142	142	155	1	1	0.00645161	C|0.615;G|0.385	0.385	strong	.	DDX60L	116	.	NM_001012967	exon10	c.G1225C	p.V409L	TTCCAACGTTAAA	.	PASS	Atlas-SNP
POLRMT	5442	hgsc.bcm.edu	37	19	629846	629846	+	Silent	SNP	G	G	A	rs55649970	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	56	30	84	0	0.535714	0	G|0.500;A|0.500	0.500	weak	POLRMT,NS,NS,0,1	POLRMT	91	1	NM_005035	exon3	c.C516T	p.A172A	GCACCCGGCCATC	.	PASS	Atlas-SNP
FERMT3	83706	hgsc.bcm.edu	37	11	63988045	63988045	+	Silent	SNP	G	G	A	rs3802932	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	34	65	0	0.539683	0	G|0.808;A|0.192	0.192	strong	URP2,NS,carcinoma,0,2	FERMT3	51	2	NM_178443	exon12	c.G1461A	p.P487P	GGGCCCGGGCAAC	.	PASS	Atlas-SNP
CCDC15	80071	hgsc.bcm.edu	37	11	124857708	124857708	+	Missense_Mutation	SNP	G	G	A	rs4936966	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	103	82	83	1	0.796117	0.0120482	G|0.721;A|0.279	0.279	strong	CCDC15_ENST00000344762,colon,carcinoma,0,7	CCDC15	134	7	NM_025004	exon8	c.G1586A	p.G529D	ATCAAGGCCAGGA	.	scavenged	Atlas-SNP
PDXDC1	23042	hgsc.bcm.edu	37	16	15129940	15129940	+	Silent	SNP	C	C	T	rs3198697	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	43	14	56	0	0.325581	0	C|0.746;T|0.254	0.254	strong	.	PDXDC1	59	.	NM_015027	exon23	c.C2175T	p.H725H	CAGTCACATTGAA	.	PASS	Atlas-SNP
AFAP1L2	84632	hgsc.bcm.edu	37	10	116073801	116073801	+	Silent	SNP	T	T	C	rs621375	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	101	42	107	0	0.415842	0	C|0.337;N|0.000	0.337	strong	.	AFAP1L2	90	.	NM_032550	exon7	c.A621G	p.K207K	GGAGGATTTGTAG	.	PASS	Atlas-SNP
VWA5B2	90113	hgsc.bcm.edu	37	3	183955109	183955109	+	Silent	SNP	C	C	T	rs843334	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	99	33	84	0	0.333333	0	C|0.817;T|0.183	0.183	strong	.	VWA5B2	47	.	NM_138345	exon11	c.C1629T	p.P543P	GACCCCCCGGGAG	.	PASS	Atlas-SNP
HEY2	23493	hgsc.bcm.edu	37	6	126080522	126080522	+	Silent	SNP	G	G	C	rs61737181	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	30	61	0	0.566038	0	G|0.925;C|0.075	0.075	strong	.	HEY2	44	.	NM_012259	exon5	c.G588C	p.L196L	AGCCCTGCTCCAG	.	PASS	Atlas-SNP
ATP13A2	23400	hgsc.bcm.edu	37	1	17313654	17313654	+	Silent	SNP	C	C	T	rs761421	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	39	28	38	0	0.717949	0	C|0.600;T|0.400	0.400	strong	.	ATP13A2	85	.	NM_022089	exon26	c.G2970A	p.V990V	TGGCCGCACCCGT	.	PASS	Atlas-SNP
PLEKHH1	57475	hgsc.bcm.edu	37	14	68029313	68029313	+	Missense_Mutation	SNP	G	G	A	rs2236235	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48	21	41	0	0.4375	0	G|0.809;N|0.000	.	strong	.	PLEKHH1	118	.	NM_020715	exon7	c.G965A	p.R322Q	CCCCGCGGGACAG	.	PASS	Atlas-SNP
SLC4A7	9497	hgsc.bcm.edu	37	3	27490194	27490194	+	Silent	SNP	T	T	C	rs13096477	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	173	75	160	0	0.433526	0	T|0.851;C|0.149	0.149	strong	.	SLC4A7	119	.	NM_001258379	exon3	c.A225G	p.R75R	TTTTCTTCTCCGG	.	PASS	Atlas-SNP
DNAH3	55567	hgsc.bcm.edu	37	16	20959918	20959918	+	Missense_Mutation	SNP	G	G	A	rs2301620	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	33	82	0	0.52381	0	G|0.929;A|0.071	0.071	strong	.	DNAH3	1142	.	NM_017539	exon57	c.C11230T	p.R3744W	GACGCCGGTCTTT	.	PASS	Atlas-SNP
ACAN	176	hgsc.bcm.edu	37	15	89415247	89415247	+	Missense_Mutation	SNP	C	C	G	rs3817428	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	96	47	94	0	0.489583	0	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	.	PASS	Atlas-SNP
PCDHGA5	56110	hgsc.bcm.edu	37	5	140745959	140745959	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	101	48	128	0	0.475248	0	.	.	none	.	PCDHGA5	215	.	NM_032054	exon1	c.G2062A	p.D688N	GATCTGGACCTCA	.	PASS	Atlas-SNP
ADPGK	83440	hgsc.bcm.edu	37	15	73052845	73052845	+	Silent	SNP	A	A	G	rs8023358	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57	26	60	0	0.45614	0	A|0.822;G|0.178	0.178	strong	.	ADPGK	19	.	NM_031284	exon4	c.T546C	p.G182G	CTTTGGACCAACT	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	63	69	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
ELTD1	64123	hgsc.bcm.edu	37	1	79358827	79358827	+	Missense_Mutation	SNP	G	G	T	rs1968956	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	32	8	56	0	0.25	0	G|0.980;T|0.020	0.020	strong	.	ELTD1	143	.	NM_022159	exon13	c.C1797A	p.H599Q	TGCAGTGTGACGA	.	PASS	Atlas-SNP
PRG4	10216	hgsc.bcm.edu	37	1	186273994	186273994	+	Missense_Mutation	SNP	C	C	T	rs2273779	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	168	168	160	0	1	0	C|0.726;T|0.274	0.274	strong	.	PRG4	259	.	NM_005807	exon6	c.C538T	p.R180W	ACAATTCGGAAAA	.	PASS	Atlas-SNP
OR2T34	127068	hgsc.bcm.edu	37	1	248737348	248737348	+	Silent	SNP	G	G	A	rs61833442	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	365	95	263	0	0.260274	0	G|0.787;A|0.213	0.213	strong	OR2T34,NS,carcinoma,-2,1	OR2T34	72	1	NM_001001821	exon1	c.C711T	p.A237A	GCGGCCGGCGGCA	.	PASS	Atlas-SNP
ADCK3	56997	hgsc.bcm.edu	37	1	227149203	227149203	+	Silent	SNP	G	G	A	rs11549708	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	189	90	189	0	0.47619	0	G|0.849;A|0.151	0.151	strong	.	ADCK3	77	.	NM_020247	exon2	c.G117A	p.A39A	CATGGCGGCCAGG	.	PASS	Atlas-SNP
NALCN	259232	hgsc.bcm.edu	37	13	101720300	101720300	+	Silent	SNP	T	T	G	rs1289556	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	70	70	84	0	1	0	T|0.558;G|0.442	0.442	strong	.	NALCN	431	.	NM_052867	exon39	c.A4416C	p.I1472I	CCATATTATTTGA	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	52	56	0	0.619048	0	C|0.863;T|0.137	0.137	strong	.	COL6A2	351	.	NM_001849	exon28	c.C2979T	p.R993R	TGACCGCGCCGCC	.	PASS	Atlas-SNP
SENP6	26054	hgsc.bcm.edu	37	6	76376552	76376552	+	Silent	SNP	G	G	A	rs17414687	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	86	71	0	1	0	G|0.773;A|0.227	0.227	strong	SENP6_ENST00000447266,NS,carcinoma,0,2	SENP6	189	2	NM_015571	exon10	c.G1119A	p.A373A	AGCAGCGCTAAAT	.	PASS	Atlas-SNP
OR3A1	4994	hgsc.bcm.edu	37	17	3195503	3195503	+	Missense_Mutation	SNP	C	C	T	rs703903	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	162	70	142	0	0.432099	0	A|0.000;C|0.493;T|0.507	0.507	strong	.	OR3A1	46	.	NM_002550	exon1	c.G374A	p.R125Q	AGGAATCGGTCAT	.	PASS	Atlas-SNP
TBC1D17	79735	hgsc.bcm.edu	37	19	50387729	50387729	+	Silent	SNP	C	C	T	rs35681527	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	154	74	161	0	0.480519	0	C|0.873;G|0.000;T|0.127	0.127	strong	.	TBC1D17	39	.	NM_024682	exon12	c.C1257T	p.G419G	CCAGGGCATGAGT	.	PASS	Atlas-SNP
SEPT12	124404	hgsc.bcm.edu	37	16	4837545	4837545	+	Silent	SNP	A	A	G	rs9673735	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	38	90	0	0.5	0	A|0.743;G|0.257	0.257	strong	SEPT12,colon,carcinoma,0,2	SEPT12	40	2	NM_144605	exon2	c.T102C	p.A34A	CAGCACAGCCTCA	.	PASS	Atlas-SNP
DSPP	1834	hgsc.bcm.edu	37	4	88536457	88536457	+	Silent	SNP	T	T	C	rs142031576	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	11	71	0	0.144737	0	.	.	weak	.	DSPP	174	.	NM_014208	exon5	c.T2643C	p.D881D	CAGTGATAGCAGT	.	PASS	Atlas-SNP
GRIA3	2892	hgsc.bcm.edu	37	X	122537277	122537277	+	Silent	SNP	T	T	C	rs502434	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79	79	57	0	1	0	T|0.440;0|0.004	.	strong	.	GRIA3	386	.	NM_000828	exon9	c.T1200C	p.N400N	CTGGAATGAGTAT	.	PASS	Atlas-SNP
HBP1	26959	hgsc.bcm.edu	37	7	106826381	106826381	+	Silent	SNP	C	C	T	rs7794598	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	31	65	0	0.413333	0	C|0.818;T|0.182	0.182	strong	.	HBP1	31	.	NM_001244262	exon4	c.C564T	p.H188H	AAGACACGAAAGG	.	PASS	Atlas-SNP
HSPG2	3339	hgsc.bcm.edu	37	1	22179244	22179244	+	Missense_Mutation	SNP	C	C	T	rs35669711	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98	48	107	0	0.489796	0	C|0.965;T|0.035	0.035	strong	.	HSPG2	311	.	NM_005529	exon52	c.G6673A	p.G2225S	GGGGGCCGGAGGT	.	PASS	Atlas-SNP
KRTAP10-4	386672	hgsc.bcm.edu	37	21	45993727	45993727	+	Missense_Mutation	SNP	A	A	C	rs76503724		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79	38	86	0	0.481013	0	.	.	weak	KRTAP10-4,NS,carcinoma,0,1	KRTAP10-4	44	1	NM_198687	exon1	c.A92C	p.D31A	TGGACGACTGCCC	.	PASS	Atlas-SNP
LYST	1130	hgsc.bcm.edu	37	1	235918870	235918870	+	Silent	SNP	T	T	G	rs61738992	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	88	41	96	0	0.465909	0	T|0.976;G|0.024	0.024	strong	.	LYST	370	.	NM_000081	exon25	c.A7137C	p.L2379L	GTTGGCTAGCAAG	.	PASS	Atlas-SNP
GRIN2B	2904	hgsc.bcm.edu	37	12	14018777	14018777	+	Silent	SNP	G	G	C	rs7301328	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	114	66	88	0	0.578947	0	G|0.580;C|0.420	0.420	strong	.	GRIN2B	303	.	NM_000834	exon2	c.C366G	p.P122P	CAGGATGGGGGTG	.	PASS	Atlas-SNP
FECH	2235	hgsc.bcm.edu	37	18	55221648	55221648	+	Silent	SNP	T	T	C	rs536560	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	87	91	0	1	0	T|0.244;C|0.756	0.756	strong	FECH,NS,carcinoma,0,1	FECH	42	1	NM_001012515	exon9	c.A939G	p.P313P	GGGCATTGGACCA	.	PASS	Atlas-SNP
CELF5	60680	hgsc.bcm.edu	37	19	3224896	3224896	+	Silent	SNP	G	G	C	rs17852497	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	115	58	104	0	0.504348	0	G|0.815;C|0.185	0.185	strong	CELF5,NS,carcinoma,0,1	CELF5	32	1	NM_021938	exon1	c.G159C	p.P53P	GATCCCGCGGCAC	.	PASS	Atlas-SNP
SLC28A3	64078	hgsc.bcm.edu	37	9	86917301	86917301	+	Missense_Mutation	SNP	T	T	C	rs10868138	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	42	21	40	0	0.5	0	T|0.894;C|0.106	0.106	strong	.	SLC28A3	72	.	NM_001199633	exon5	c.A338G	p.Y113C	ACCAGATAACCTG	.	PASS	Atlas-SNP
RPAIN	84268	hgsc.bcm.edu	37	17	5326145	5326145	+	Missense_Mutation	SNP	C	C	G	rs12761	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	126	59	140	0	0.468254	0	C|0.669;G|0.330	0.330	strong	.	RPAIN	24	.	NM_001160246	exon3	c.C309G	p.N103K	GATCAACCAAGGT	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	121	50	124	0	0.413223	0	C|0.352;T|0.648	0.648	strong	.	KRTAP10-9	24	.	NM_198690	exon1	c.C769T	p.R257C	TCCTCCCGCCAGC	.	PASS	Atlas-SNP
TRABD2A	129293	hgsc.bcm.edu	37	2	85051122	85051122	+	Missense_Mutation	SNP	G	G	A	rs1649292	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	70	54	97	0	0.771429	0	G|0.843;A|0.157	0.157	strong	.	.	.	.	NM_001080824	exon5	c.G1142T	p.R381L	AGTCGCGGCCTCC	.	PASS	Atlas-SNP
NKX1-2	390010	hgsc.bcm.edu	37	10	126136112	126136112	+	Silent	SNP	A	A	G	rs7075981	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	40	22	47	0	0.55	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
SP140L	93349	hgsc.bcm.edu	37	2	231222675	231222675	+	Missense_Mutation	SNP	T	T	C	rs4973318	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	65	37	74	0	0.569231	0	T|0.905;C|0.095	0.095	strong	.	SP140L	68	.	NM_138402	exon3	c.T263C	p.M88T	ATAAAATGTTTGA	.	PASS	Atlas-SNP
AQP5	362	hgsc.bcm.edu	37	12	50358888	50358888	+	Silent	SNP	G	G	A	rs41308104	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	77	41	60	0	0.532468	0	G|0.988;A|0.012	0.012	strong	.	AQP5	19	.	NM_001651	exon4	c.G726A	p.T242T	AGGCACGTATGAG	.	PASS	Atlas-SNP
PLCB1	23236	hgsc.bcm.edu	37	20	8717713	8717713	+	Silent	SNP	G	G	A	rs3761170	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	127	57	150	0	0.448819	0	G|0.932;A|0.068	0.068	strong	.	PLCB1	394	.	NM_015192	exon20	c.G2082A	p.Q694Q	AGTTGGGACTTAC	.	PASS	Atlas-SNP
SOCS7	30837	hgsc.bcm.edu	37	17	36552190	36552190	+	Missense_Mutation	SNP	A	A	G	rs55687042	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	42	22	42	0	0.52381	0	A|0.971;G|0.029	0.029	strong	.	SOCS7	22	.	NM_014598	exon9	c.A1715G	p.K572R	TTTCCAAACAGAA	.	PASS	Atlas-SNP
TCOF1	6949	hgsc.bcm.edu	37	5	149755340	149755340	+	Silent	SNP	G	G	T	rs7701163	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	113	61	93	0	0.539823	0	G|0.910;T|0.090	0.090	strong	.	TCOF1	154	.	NM_001135243	exon12	c.G1761T	p.G587G	CAAGGGGCCCCCT	.	PASS	Atlas-SNP
SMC6	79677	hgsc.bcm.edu	37	2	17884495	17884495	+	Missense_Mutation	SNP	C	C	T	rs1065381	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80	44	77	0	0.55	0	C|0.738;T|0.262	0.262	strong	.	SMC6	102	.	NM_001142286	exon19	c.G2071A	p.A691T	CAAGGGCAGATAA	.	PASS	Atlas-SNP
ARHGAP12	94134	hgsc.bcm.edu	37	10	32097650	32097650	+	Missense_Mutation	SNP	C	C	T	rs34750454	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	102	31	102	0	0.303922	0	C|0.987;T|0.013	0.013	weak	.	ARHGAP12	79	.	NM_018287	exon19	c.G2293A	p.V765I	CCTTAACAGCAGC	.	PASS	Atlas-SNP
ZNF750	79755	hgsc.bcm.edu	37	17	80788492	80788492	+	Silent	SNP	A	A	G	rs12948179	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	109	56	106	0	0.513761	0	A|0.595;G|0.405	0.405	strong	.	ZNF750	60	.	NM_024702	exon3	c.T1698C	p.P566P	GAAGGCAGGCCTC	.	PASS	Atlas-SNP
SEC61A1	29927	hgsc.bcm.edu	37	3	127774411	127774411	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	158	64	155	0	0.405063	0	.	.	none	.	SEC61A1	39	.	NM_013336	exon3	c.T128C	p.L43S	TCTTCTTAGTGTG	.	PASS	Atlas-SNP
ITPR3	3710	hgsc.bcm.edu	37	6	33648144	33648144	+	Silent	SNP	C	C	T	rs11967839	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	16	58	0	0.253968	0	C|0.890;T|0.110	0.110	strong	.	ITPR3	409	.	NM_002224	exon32	c.C4263T	p.Y1421Y	CTGCTACGTGGAC	.	PASS	Atlas-SNP
HOXB13	10481	hgsc.bcm.edu	37	17	46805590	46805590	+	Silent	SNP	G	G	A	rs8556	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	40	66	0	0.533333	0	G|0.835;A|0.165	0.165	strong	.	HOXB13	28	.	NM_006361	exon1	c.C366T	p.S122S	GGGGCGGCTGGGG	.	PASS	Atlas-SNP
DDX18	8886	hgsc.bcm.edu	37	2	118575215	118575215	+	Missense_Mutation	SNP	C	C	G	rs1052637	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	85	139	0	0.988372	0	C|0.601;G|0.399	0.399	strong	.	DDX18	79	.	NM_006773	exon2	c.C281G	p.T94S	TATTAACCAATGG	.	PASS	Atlas-SNP
AFAP1L1	134265	hgsc.bcm.edu	37	5	148695859	148695859	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	124	13	91	0	0.104839	0	.	.	none	.	AFAP1L1	86	.	NM_001146337	exon11	c.C1260T	p.P420P	GGTTCCCTGCTGT	.	PASS	Atlas-SNP
CTXN3	613212	hgsc.bcm.edu	37	5	126993263	126993263	+	Missense_Mutation	SNP	A	A	T	rs248709	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	77	37	62	0	0.480519	0	A|0.308;T|0.692	0.692	strong	.	CTXN3	19	.	NM_001048252	exon3	c.A50T	p.E17V	GGAACGAATCAGC	.	PASS	Atlas-SNP
PDIA2	64714	hgsc.bcm.edu	37	16	334580	334580	+	Silent	SNP	G	G	C	rs432925	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	41	64	0	0.539474	0	G|0.756;C|0.244	0.244	strong	.	PDIA2	51	.	NM_006849	exon2	c.G393C	p.P131P	GCACCCGGAGGAG	.	PASS	Atlas-SNP
ESPNL	339768	hgsc.bcm.edu	37	2	239040343	239040343	+	Silent	SNP	G	G	A	rs73102311	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	40	73	0	0.526316	0	G|0.914;A|0.086	0.086	strong	.	ESPNL	63	.	NM_194312	exon9	c.G2988A	p.K996K	GGAGAAGGAAGCT	.	PASS	Atlas-SNP
HPS3	84343	hgsc.bcm.edu	37	3	148881673	148881673	+	Silent	SNP	C	C	T	rs3732557	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73	34	53	0	0.465753	0	C|0.849;T|0.151	0.151	strong	.	HPS3	104	.	NM_032383	exon14	c.C2526T	p.H842H	GGTTCACGTCGTA	.	PASS	Atlas-SNP
CRTAC1	55118	hgsc.bcm.edu	37	10	99625319	99625319	+	Missense_Mutation	SNP	C	C	T	rs56007204	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	78	34	75	1	0.435897	0.0133333	C|0.846;T|0.154	0.154	strong	CRTAC1,NS,adenoma,0,2	CRTAC1	86	2	NM_018058	exon15	c.G1972A	p.E658K	TGGGCTCGCAGCT	.	scavenged	Atlas-SNP
CXorf30	645090	hgsc.bcm.edu	37	X	36317108	36317108	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	150	59	120	0	0.393333	0	.	.	none	.	CXorf30	76	.	NM_001098843	exon7	c.A41C	p.E14A	GCATTGAAATACC	.	PASS	Atlas-SNP
THSD7A	221981	hgsc.bcm.edu	37	7	11581121	11581121	+	Missense_Mutation	SNP	T	T	C	rs47	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	184	184	211	0	1	0	T|0.170;C|0.827	0.827	strong	.	THSD7A	219	.	NM_015204	exon6	c.A1747G	p.N583D	CGCAGTTTCCCAG	.	PASS	Atlas-SNP
MBD3L3	653657	hgsc.bcm.edu	37	19	7056553	7056553	+	Missense_Mutation	SNP	C	C	T	rs3745554	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	157	65	213	0	0.414013	0	C|0.881;T|0.119	0.119	strong	MBD3L3,NS,haematopoietic_neoplasm,0,1	MBD3L3	12	1	NM_001164425	exon2	c.G407A	p.R136H	GGGCTGCGCACAC	.	scavenged	Atlas-SNP
DFNB31	25861	hgsc.bcm.edu	37	9	117166311	117166311	+	Silent	SNP	G	G	A	rs34963246	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55	24	45	0	0.436364	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
PRKCDBP	112464	hgsc.bcm.edu	37	11	6340525	6340525	+	Silent	SNP	A	A	T	rs12570	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	12	12	28	0	1	0	A|0.354;T|0.646	0.646	strong	PRKCDBP,NS,carcinoma,0,1	PRKCDBP	19	1	NM_145040	exon2	c.T654A	p.A218A	GGCTTCAGCGCTC	.	PASS	Atlas-SNP
PRDM16	63976	hgsc.bcm.edu	37	1	3301721	3301721	+	Silent	SNP	C	C	T	rs2282198	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	145	70	128	0	0.482759	0	C|0.713;T|0.287	0.287	strong	.	PRDM16	147	.	NM_022114	exon4	c.C444T	p.S148S	GATCTCCGAAGAC	.	PASS	Atlas-SNP
KCNH3	23416	hgsc.bcm.edu	37	12	49951377	49951377	+	Missense_Mutation	SNP	C	C	T	rs59261129	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55	26	53	0	0.472727	0	C|0.914;T|0.086	0.086	strong	.	KCNH3	88	.	NM_012284	exon15	c.C2893T	p.R965C	CACCCTCGTCCGG	.	PASS	Atlas-SNP
CASC5	57082	hgsc.bcm.edu	37	15	40916801	40916801	+	Missense_Mutation	SNP	A	A	G	rs16970911	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	34	10	87	0	0.294118	0	A|0.945;G|0.055	0.055	strong	.	CASC5	269	.	NM_170589	exon11	c.A4417G	p.T1473A	TTCTCAACCGACC	.	PASS	Atlas-SNP
EPS8L2	64787	hgsc.bcm.edu	37	11	721570	721570	+	Silent	SNP	C	C	T	rs7635	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49	49	78	1	1	0.0128205	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	.	scavenged	Atlas-SNP
MYO15A	51168	hgsc.bcm.edu	37	17	18041507	18041507	+	Silent	SNP	C	C	T	rs2280777	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	56	24	45	0	0.428571	0	C|0.501;N|0.000	.	strong	.	MYO15A	268	.	NM_016239	exon16	c.C4954T	p.L1652L	ATCTCACTGAAGC	.	PASS	Atlas-SNP
UTP14A	10813	hgsc.bcm.edu	37	X	129045815	129045815	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	17	66	0	0.257576	0	.	.	none	.	UTP14A	74	.	NM_006649	exon6	c.G455A	p.R152Q	AGAACCGGCAGGC	.	PASS	Atlas-SNP
CDC25C	995	hgsc.bcm.edu	37	5	137627769	137627769	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91	32	97	0	0.351648	0	.	.	none	.	CDC25C	37	.	NM_001790	exon8	c.C652G	p.P218A	TCTCTGGCATCGA	.	PASS	Atlas-SNP
SDK2	54549	hgsc.bcm.edu	37	17	71426670	71426670	+	Silent	SNP	G	G	A	rs1105354	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44	23	35	0	0.522727	0	G|0.818;A|0.182	0.182	strong	.	SDK2	219	.	NM_001144952	exon12	c.C1563T	p.H521H	GGGGTCGTGGGTC	.	PASS	Atlas-SNP
GZMM	3004	hgsc.bcm.edu	37	19	549080	549080	+	Silent	SNP	A	A	G	rs59771750	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	36	79	0	0.545455	0	A|0.953;G|0.047	0.047	strong	.	GZMM	11	.	NM_005317	exon4	c.A507G	p.Q169Q	CCTCCAAGTGCTG	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	35	17	45	0	0.485714	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
MAN1C1	57134	hgsc.bcm.edu	37	1	26110236	26110236	+	Missense_Mutation	SNP	G	G	A	rs79507311	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	40	27	31	0	0.675	0	G|0.990;A|0.010	0.010	strong	.	MAN1C1	48	.	NM_020379	exon12	c.G1849A	p.V617M	CTCCCGGTGAACC	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1263234	1263234	+	Silent	SNP	A	A	G	rs56117556	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	106	48	115	0	0.45283	0	A|0.960;G|0.040	0.040	strong	.	MUC5B	473	.	NM_002458	exon31	c.A5124G	p.T1708T	GGGCACATGGCGC	.	PASS	Atlas-SNP
RYR1	6261	hgsc.bcm.edu	37	19	39010023	39010023	+	Silent	SNP	C	C	T	rs2229145	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82	45	81	0	0.548781	0	C|0.961;T|0.039	0.039	strong	.	RYR1	708	.	NM_001042723	exon67	c.C10188T	p.D3396D	GCGGGACGAGTTC	.	PASS	Atlas-SNP
SLC6A13	6540	hgsc.bcm.edu	37	12	333237	333237	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	5	96	0	0.0581395	0	.	.	none	.	SLC6A13	62	.	NM_016615	exon11	c.G1232A	p.R411H	TTCTTGCGGAACA	.	PASS	Atlas-SNP
ARRB2	409	hgsc.bcm.edu	37	17	4622638	4622638	+	Silent	SNP	C	C	T	rs1045280	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98	36	135	0	0.367347	0	C|0.376;T|0.624	0.624	strong	.	ARRB2	30	.	NM_001257328	exon11	c.C903T	p.S301S	GCTCAGCGACAAC	.	PASS	Atlas-SNP
TPR	7175	hgsc.bcm.edu	37	1	186321242	186321242	+	Missense_Mutation	SNP	C	C	T	rs61744267	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	31	9	45	0	0.290323	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
RBMXL3	139804	hgsc.bcm.edu	37	X	114424148	114424148	+	Silent	SNP	G	G	A	rs62601525	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	120	23	68	0	0.191667	0	G|0.929;A|0.071	0.071	strong	.	RBMXL3	83	.	NM_001145346	exon1	c.G144A	p.S48S	CAAGTCGAGGGGC	.	PASS	Atlas-SNP
GFM1	85476	hgsc.bcm.edu	37	3	158366900	158366900	+	Missense_Mutation	SNP	G	G	A	rs2303909	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	43	24	65	0	0.55814	0	G|0.424;N|0.000	.	strong	.	GFM1	83	.	NM_024996	exon5	c.G643A	p.V215I	GGTATTGTAGATC	.	PASS	Atlas-SNP
MLLT10	8028	hgsc.bcm.edu	37	10	21827796	21827796	+	Silent	SNP	G	G	A	rs1802669	bycluster;byfrequency;bysubmitter;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	56	24	69	0	0.428571	0	A|0.343;G|0.657;T|0.000	0.343	strong	.	MLLT10	183	.	NM_001195626	exon2	c.G195A	p.P65P	TGGACCGTGGTTT	.	PASS	Atlas-SNP
EPHB4	2050	hgsc.bcm.edu	37	7	100417879	100417879	+	Missense_Mutation	SNP	C	C	T	rs201531252		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	46	24	49	0	0.521739	0	C|0.999;T|0.001	0.001	weak	.	EPHB4	106	.	NM_004444	exon5	c.G848A	p.G283E	CAGGACCCTTCTC	.	PASS	Atlas-SNP
CAND2	23066	hgsc.bcm.edu	37	3	12848822	12848822	+	Missense_Mutation	SNP	T	T	C	rs11718898	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	109	106	144	0	0.972477	0	C|0.622;N|0.000	0.622	strong	.	CAND2	138	.	NM_001162499	exon3	c.T230C	p.V77A	TGGTGGTCAAAGT	.	PASS	Atlas-SNP
GCDH	2639	hgsc.bcm.edu	37	19	13010520	13010520	+	Missense_Mutation	SNP	A	A	G	rs8012	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110	110	136	0	1	0	A|0.293;G|0.706	0.706	strong	GCDH_ENST00000457854,NS,carcinoma,+1,1	GCDH	76	1	NM_013976	exon12	c.T1250G	p.L417R	TCGTTCAGATGTG	.	PASS	Atlas-SNP
MMRN1	22915	hgsc.bcm.edu	37	4	90857479	90857479	+	Missense_Mutation	SNP	G	G	A	rs12646270	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	97	55	110	0	0.56701	0	G|0.939;A|0.061	0.061	strong	MMRN1,NS,carcinoma,0,2	MMRN1	174	2	NM_007351	exon6	c.G2648A	p.G883D	AAAAAGGCAGTGT	.	PASS	Atlas-SNP
TLR5	7100	hgsc.bcm.edu	37	1	223285200	223285200	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69	30	74	1	0.434783	0.0135135	.	.	none	TLR5,NS,carcinoma,+1,1	TLR5	86	1	NM_003268	exon6	c.C1174T	p.R392X	TGTCTCGGAGATC	.	scavenged	Atlas-SNP
GTPBP8	29083	hgsc.bcm.edu	37	3	112718352	112718352	+	Missense_Mutation	SNP	G	G	T	rs1054263	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	180	73	247	0	0.405556	0	G|0.948;T|0.052	0.052	strong	GTPBP8,lymph_node,lymphoid_neoplasm,0,1	GTPBP8	22	1	NM_014170	exon5	c.G726T	p.Q242H	GCTTCAGATCCAG	.	PASS	Atlas-SNP
TMEM2	23670	hgsc.bcm.edu	37	9	74360096	74360096	+	Missense_Mutation	SNP	C	C	T	rs25689	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	115	53	100	0	0.46087	0	T|0.248;C|0.752	0.248	strong	.	TMEM2	112	.	NM_001135820	exon4	c.G872A	p.R291H	TCATTGCGGTATT	.	PASS	Atlas-SNP
BMP10	27302	hgsc.bcm.edu	37	2	69093413	69093413	+	Missense_Mutation	SNP	G	G	A	rs34008398	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	209	151	285	0	0.722488	0	G|0.991;A|0.009	0.009	strong	.	BMP10	70	.	NM_014482	exon2	c.C625T	p.R209C	GCCAACGTCTGAT	.	PASS	Atlas-SNP
IMPDH1	3614	hgsc.bcm.edu	37	7	128038555	128038555	+	Silent	SNP	C	C	G	rs2288550	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	97	97	92	0	1	0	C|0.868;G|0.132	0.132	strong	.	IMPDH1	38	.	NM_000883	exon10	c.G987C	p.L329L	ACAGAGCAGCTGC	.	PASS	Atlas-SNP
CHUK	1147	hgsc.bcm.edu	37	10	101977883	101977883	+	Missense_Mutation	SNP	C	C	T	rs2230804	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	42	74	0	0.482759	0	C|0.431;T|0.569	0.569	strong	.	CHUK	71	.	NM_001278	exon9	c.G802A	p.V268I	CTACTACTAAACT	.	PASS	Atlas-SNP
USP40	55230	hgsc.bcm.edu	37	2	234394569	234394569	+	Silent	SNP	A	A	G	rs2603547	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60	60	72	0	1	0	A|0.749;G|0.251	0.251	strong	.	USP40	174	.	NM_018218	exon28	c.T3285C	p.Y1095Y	AGGGGCATAGGTC	.	PASS	Atlas-SNP
ATP6V1C2	245973	hgsc.bcm.edu	37	2	10908893	10908893	+	Missense_Mutation	SNP	A	A	G	rs1198849	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60	30	67	0	0.5	0	A|0.600;G|0.400	0.400	strong	.	ATP6V1C2	73	.	NM_001039362	exon6	c.A427G	p.N143D	GCCTACAACACTC	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	133	59	134	0	0.443609	0	A|0.343;G|0.657	0.657	strong	.	KRTAP10-9	24	.	NM_198690	exon1	c.A545G	p.Y182C	AGTCCTACTGTGT	.	PASS	Atlas-SNP
CACNA1A	773	hgsc.bcm.edu	37	19	13409390	13409390	+	Silent	SNP	C	C	T	rs16025	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	143	84	95	1	0.587413	0.0105263	C|0.871;T|0.129	0.129	strong	CACNA1A_ENST00000360228,NS,carcinoma,0,4	CACNA1A	715	4	NM_001127221	exon19	c.G3060A	p.R1020R	GTCCTCCCTCCGC	.	scavenged	Atlas-SNP
PRKD1	5587	hgsc.bcm.edu	37	14	30066797	30066797	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	143	29	126	0	0.202797	0	.	.	none	.	PRKD1	316	.	NM_002742	exon16	c.C2334T	p.S778S	TGTGCCGCTTAGG	.	PASS	Atlas-SNP
CCDC88B	283234	hgsc.bcm.edu	37	11	64109118	64109118	+	Missense_Mutation	SNP	T	T	G	rs647152	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	109	60	157	2	0.550459	0.0127389	T|0.649;G|0.351	0.351	strong	CCDC88B,NS,carcinoma,0,1	CCDC88B	89	1	NM_032251	exon7	c.T579G	p.D193E	GCCAGATCCTGGG	.	scavenged	Atlas-SNP
PSRC1	84722	hgsc.bcm.edu	37	1	109824250	109824250	+	Silent	SNP	G	G	A	rs35358959	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	138	66	121	0	0.478261	0	G|0.944;A|0.056	0.056	strong	.	PSRC1	12	.	NM_001032291	exon4	c.C510T	p.N170N	CTTCATGTTGGAG	.	PASS	Atlas-SNP
SMCR9	140776	hgsc.bcm.edu	37	17	17326605	17326605	+	Silent	SNP	A	A	G	rs7225831	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	16	11	14	0	0.6875	0	A|0.600;G|0.400	0.400	strong	.	.	.	.	NM_001243312	exon3	c.A420G	p.A140A	TGGGGCAAATGCC	.	PASS	Atlas-SNP
ATP2C2	9914	hgsc.bcm.edu	37	16	84449161	84449161	+	Silent	SNP	C	C	T	rs3743651	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	28	68	0	0.518519	0	C|0.917;T|0.083	0.083	strong	.	ATP2C2	75	.	NM_014861	exon7	c.C588T	p.I196I	CTCGATCGGAGAC	.	PASS	Atlas-SNP
FASTKD2	22868	hgsc.bcm.edu	37	2	207632128	207632128	+	Silent	SNP	C	C	T	rs150195745		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49	25	55	0	0.510204	0	C|1.000;T|0.000	0.000	weak	.	FASTKD2	49	.	NM_001136193	exon2	c.C711T	p.H237H	TCTTCACGCCATA	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9084299	9084299	+	Missense_Mutation	SNP	T	T	C	rs1609458	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	97	96	119	0	0.989691	0	T|0.562;C|0.438	0.438	strong	MUC16_ENST00000397910,colon,carcinoma,0,2	MUC16	4315	2	NM_024690	exon1	c.A7516G	p.T2506A	CACTGGTCCATGT	.	PASS	Atlas-SNP
TSPYL4	23270	hgsc.bcm.edu	37	6	116575083	116575083	+	Missense_Mutation	SNP	C	C	A	rs2232470	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	70	82	0	0.985915	0	C|0.176;A|0.824	0.824	strong	.	TSPYL4	18	.	NM_021648	exon1	c.G89T	p.R30L	TGGTCTCGGTCCG	.	PASS	Atlas-SNP
POLQ	10721	hgsc.bcm.edu	37	3	121208294	121208294	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	150	38	178	0	0.253333	0	.	.	none	.	POLQ	273	.	NM_199420	exon16	c.G3484A	p.A1162T	CAACAGCTACTCC	.	PASS	Atlas-SNP
SBNO2	22904	hgsc.bcm.edu	37	19	1127720	1127720	+	Silent	SNP	G	G	A	rs2074916	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	38	62	0	0.513514	0	G|0.833;A|0.167	0.167	strong	SBNO2_ENST00000250872,NS,carcinoma,0,2	SBNO2	112	2	NM_014963	exon5	c.C324T	p.S108S	GGACGAGGAGAAG	.	PASS	Atlas-SNP
BCAM	4059	hgsc.bcm.edu	37	19	45322744	45322744	+	Missense_Mutation	SNP	A	A	G	rs1135062	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	107	57	105	0	0.53271	0	A|0.703;G|0.297	0.297	strong	BCAM,NS,adenoma,0,1	BCAM	53	1	NM_001013257	exon12	c.A1615G	p.T539A	TTCGGCACCGGTG	.	PASS	Atlas-SNP
HIP1R	9026	hgsc.bcm.edu	37	12	123345296	123345296	+	Missense_Mutation	SNP	G	G	A	rs141813189	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	177	82	145	0	0.463277	0	G|0.999;A|0.001	0.001	strong	.	HIP1R	68	.	NM_003959	exon28	c.G2731A	p.A911T	GAGATCGCAGCCA	.	PASS	Atlas-SNP
SACS	26278	hgsc.bcm.edu	37	13	23929095	23929095	+	Silent	SNP	T	T	C	rs1536365	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82	30	85	0	0.365854	0	T|0.909;C|0.091	0.091	strong	.	SACS	871	.	NM_014363	exon8	c.A1656G	p.L552L	GCTGAATAGAGGC	.	PASS	Atlas-SNP
KIAA1377	57562	hgsc.bcm.edu	37	11	101829006	101829006	+	Missense_Mutation	SNP	G	G	A	rs61743062	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	99	84	59	0	0.848485	0	G|0.981;A|0.019	0.019	strong	.	KIAA1377	111	.	NM_020802	exon5	c.G614A	p.R205K	ACATGAGGGCAAC	.	PASS	Atlas-SNP
NT5DC3	51559	hgsc.bcm.edu	37	12	104208868	104208868	+	Silent	SNP	C	C	T	rs10861107	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	37	94	0	0.45679	0	C|0.828;T|0.172	0.172	strong	.	NT5DC3	113	.	NM_001031701	exon2	c.G240A	p.L80L	TGGATTCAACAAG	.	PASS	Atlas-SNP
RYR1	6261	hgsc.bcm.edu	37	19	38995975	38995975	+	Silent	SNP	G	G	A	rs2915952	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	101	41	152	0	0.405941	0	G|0.684;A|0.316	0.316	strong	RYR1,NS,carcinoma,0,1	RYR1	708	1	NM_001042723	exon53	c.G8337A	p.E2779E	TGGAGAGAACATA	.	PASS	Atlas-SNP
TDP2	51567	hgsc.bcm.edu	37	6	24653283	24653283	+	Silent	SNP	T	T	C	rs11559067	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	74	74	0	0.860465	0	T|0.977;C|0.023	0.023	strong	.	TDP2	29	.	NM_016614	exon6	c.A735G	p.L245L	TTTCTTTAAAACC	.	PASS	Atlas-SNP
CTAGE5	4253	hgsc.bcm.edu	37	14	39818076	39818076	+	Missense_Mutation	SNP	A	A	G	rs61742363	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	129	61	88	0	0.472868	0	A|0.988;G|0.012	0.012	strong	.	CTAGE5	75	.	NM_001247989	exon23	c.A2158G	p.R720G	TTGAGAAGAGGAC	.	PASS	Atlas-SNP
ADAM9	8754	hgsc.bcm.edu	37	8	38854660	38854660	+	Silent	SNP	C	C	A	rs148707472	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	43	22	46	0	0.511628	0	C|0.964;A|0.036	0.036	strong	.	ADAM9	66	.	NM_003816	exon1	c.C78A	p.V26V	CCCAGTCCTCGGT	.	PASS	Atlas-SNP
RAP1GAP2	23108	hgsc.bcm.edu	37	17	2930339	2930339	+	Silent	SNP	G	G	A	rs4790115	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	217	100	212	0	0.460829	0	G|0.567;A|0.433	0.433	strong	RAP1GAP2_ENST00000254695,colon,carcinoma,0,2	RAP1GAP2	90	2	NM_015085	exon22	c.G2082A	p.P694P	CACCCCGATCATC	.	PASS	Atlas-SNP
SYT9	143425	hgsc.bcm.edu	37	11	7324584	7324584	+	Missense_Mutation	SNP	G	G	A	rs78477754	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	39	22	43	0	0.564103	0	G|0.974;A|0.026	0.026	strong	.	SYT9	91	.	NM_175733	exon2	c.G460A	p.V154M	GTCCGCGTGCAGC	.	PASS	Atlas-SNP
KCNJ11	3767	hgsc.bcm.edu	37	11	17408496	17408496	+	Silent	SNP	C	C	T	rs8175351	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73	30	88	0	0.410959	0	C|0.986;T|0.014	0.014	strong	.	KCNJ11	39	.	NM_000525	exon1	c.G1143A	p.K381K	GCTGAACTTGGGC	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9090531	9090531	+	Silent	SNP	T	T	C	rs12976721	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	245	108	238	1	0.440816	0.00420168	T|0.772;C|0.228	0.228	strong	MUC16_ENST00000397910,NS,carcinoma,0,2	MUC16	4315	2	NM_024690	exon1	c.A1284G	p.E428E	TTCTGTTTCCTTT	.	PASS	Atlas-SNP
S100A7A	338324	hgsc.bcm.edu	37	1	153390649	153390649	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	184	47	155	0	0.255435	0	.	.	none	.	S100A7A	24	.	NM_176823	exon2	c.A91G	p.S31G	AAGCCAAGCCTGC	.	PASS	Atlas-SNP
DND1	373863	hgsc.bcm.edu	37	5	140050940	140050940	+	Missense_Mutation	SNP	C	C	T	rs77880328	bycluster;byfrequency;alternate_allele	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	761	127	322	0	0.166886	0	A|0.029;G|0.971	.	alt	DND1,NS,carcinoma,0,1	DND1	15	1	NM_194249	exon4	c.G1000A	p.E334K	CAGACTCACTGAG	.	scavenged	Atlas-SNP
NRF1	4899	hgsc.bcm.edu	37	7	129297332	129297332	+	Silent	SNP	T	T	G	rs1882094	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82	82	76	0	1	0	T|0.531;G|0.469	0.469	strong	NRF1,NS,adenoma,0,1	NRF1	40	1	NM_005011	exon2	c.T141G	p.S47S	TTCTTCTCCCGAG	.	PASS	Atlas-SNP
HLX	3142	hgsc.bcm.edu	37	1	221057573	221057573	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	136	40	114	1	0.294118	0.00877193	.	.	none	HLX,NS,carcinoma,0,1	HLX	67	1	NM_021958	exon4	c.C994T	p.R332W	AAGTGGCGGCACT	.	scavenged	Atlas-SNP
NANOG	79923	hgsc.bcm.edu	37	12	7945757	7945757	+	Silent	SNP	C	C	T	rs78166980		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	113	106	97	0	0.938053	0	.	.	weak	.	NANOG	30	.	NM_024865	exon2	c.C363T	p.S121S	CCTCAGCCTCCAG	.	PASS	Atlas-SNP
KIF4A	24137	hgsc.bcm.edu	37	X	69561780	69561780	+	Missense_Mutation	SNP	T	T	G	rs1199457	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	175	125	133	0	0.714286	0	T|0.841;0|0.015	.	strong	.	KIF4A	118	.	NM_012310	exon11	c.T1265G	p.L422W	TCATTTTGGTAAG	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9086123	9086123	+	Missense_Mutation	SNP	A	A	C	rs10402812	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	109	50	91	0	0.458716	0	A|0.765;C|0.235	0.235	strong	.	MUC16	4315	.	NM_024690	exon1	c.T5692G	p.Y1898D	CTGTGTAAGTCAT	.	PASS	Atlas-SNP
MAGEB18	286514	hgsc.bcm.edu	37	X	26157792	26157792	+	Silent	SNP	C	C	T	rs5944318	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	102	38	94	0	0.372549	0	C|0.368;T|0.632	0.632	strong	.	MAGEB18	67	.	NM_173699	exon2	c.C690T	p.A230A	ATATGCCGATAGG	.	PASS	Atlas-SNP
SSTR4	6754	hgsc.bcm.edu	37	20	23017017	23017017	+	Silent	SNP	T	T	C	rs2567609	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110	53	117	0	0.481818	0	T|0.514;C|0.486	0.486	strong	SSTR4,colon,carcinoma,0,2	SSTR4	83	2	NM_001052	exon1	c.T897C	p.L299L	TATCCTTAGCTAT	.	PASS	Atlas-SNP
MICALL2	79778	hgsc.bcm.edu	37	7	1482101	1482101	+	Missense_Mutation	SNP	C	C	G	rs12540098	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	107	38	101	0	0.35514	0	C|0.807;G|0.193	0.193	strong	.	MICALL2	63	.	NM_182924	exon7	c.G1438C	p.A480P	GAACAGCGGCAGT	.	PASS	Atlas-SNP
NOX3	50508	hgsc.bcm.edu	37	6	155774608	155774608	+	Silent	SNP	C	C	T	rs34960420	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	172	64	114	0	0.372093	0	C|0.888;T|0.112	0.112	strong	.	NOX3	93	.	NM_015718	exon4	c.G270A	p.P90P	CCTCCACGGTCCT	.	PASS	Atlas-SNP
WNK1	65125	hgsc.bcm.edu	37	12	922913	922913	+	Missense_Mutation	SNP	T	T	C	rs200234585		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	31	77	0	0.462687	0	.	.	weak	.	WNK1	403	.	NM_001184985	exon2	c.T865C	p.S289P	TGGGAATCCACAG	.	PASS	Atlas-SNP
SAMD9	54809	hgsc.bcm.edu	37	7	92734451	92734451	+	Silent	SNP	A	A	G	rs6965201	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	113	113	94	0	1	0	A|0.525;G|0.475	0.475	strong	.	SAMD9	239	.	NM_001193307	exon2	c.T960C	p.Y320Y	CTGGAAATAATCA	.	PASS	Atlas-SNP
KIR2DL4	3805	hgsc.bcm.edu	37	19	55324635	55324635	+	Silent	SNP	T	T	C	rs649216	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68	11	181	0	0.161765	0	T|0.315;C|0.685	0.685	strong	KIR2DL4,NS,carcinoma,0,2	KIR2DL4	62	2	NM_001080772	exon6	c.C762C	p.F254F	CCTCTTTACCATC	.	PASS	Atlas-SNP
POLL	27343	hgsc.bcm.edu	37	10	103340144	103340144	+	Silent	SNP	A	A	G	rs3730476	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	132	60	115	0	0.454545	0	A|0.771;G|0.229	0.229	strong	.	POLL	43	.	NM_013274	exon8	c.T1224C	p.S408S	CAGCCCAGAGTTA	.	PASS	Atlas-SNP
SLC9A3	6550	hgsc.bcm.edu	37	5	476353	476353	+	Silent	SNP	C	C	T	rs2230437	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	28	57	0	0.444444	0	C|0.706;T|0.294	0.294	strong	SLC9A3,NS,carcinoma,0,1	SLC9A3	89	1	NM_004174	exon13	c.G2031A	p.A677A	CTTGGCCGCCTTC	.	PASS	Atlas-SNP
HABP2	3026	hgsc.bcm.edu	37	10	115334124	115334124	+	Silent	SNP	C	C	T	rs3740530	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	29	102	0	0.391892	0	C|0.467;T|0.533	0.533	strong	.	HABP2	52	.	NM_004132	exon3	c.C183T	p.H61H	TACCCACGCTGAG	.	PASS	Atlas-SNP
RC3H2	54542	hgsc.bcm.edu	37	9	125652757	125652757	+	Silent	SNP	G	G	A	rs10818759	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	124	62	136	0	0.5	0	G|0.685;A|0.315	0.315	strong	.	RC3H2	150	.	NM_018835	exon4	c.C417T	p.N139N	TTGACAGTTTACA	.	PASS	Atlas-SNP
INPP5B	3633	hgsc.bcm.edu	37	1	38348506	38348506	+	Silent	SNP	G	G	A	rs41307896	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	284	124	255	0	0.43662	0	G|0.897;A|0.103	0.103	strong	.	INPP5B	76	.	NM_005540	exon14	c.C1404T	p.D468D	TTGAAAGTCCTTC	.	PASS	Atlas-SNP
MFSD10	10227	hgsc.bcm.edu	37	4	2935528	2935528	+	Silent	SNP	C	C	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	149	115	181	0	0.771812	0	.	.	none	.	MFSD10	22	.	NM_001120	exon1	c.G123T	p.L41L	CAGCAGCAGCGTG	.	PASS	Atlas-SNP
PSG5	5673	hgsc.bcm.edu	37	19	43680051	43680051	+	Missense_Mutation	SNP	C	C	T	rs1058285	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	13	12	51	0	0.923077	0	C|0.311;T|0.689	0.689	strong	PSG5,NS,carcinoma,+1,1	PSG5	58	1	NM_002781	exon3	c.G680A	p.R227H	TCACTGCGCATGC	.	PASS	Atlas-SNP
ZC3H12C	85463	hgsc.bcm.edu	37	11	110035301	110035301	+	Silent	SNP	A	A	G	rs1026607	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	13	68	0	0.160494	0	A|0.729;G|0.271	0.271	strong	.	ZC3H12C	83	.	NM_033390	exon6	c.A1491G	p.T497T	AAGGACACAAGTC	.	PASS	Atlas-SNP
PLEC	5339	hgsc.bcm.edu	37	8	144992103	144992103	+	Silent	SNP	T	T	C	rs6558406	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	106	50	105	0	0.471698	0	T|0.520;C|0.480	0.480	strong	PLEC_ENST00000436759,NS,carcinoma,0,3	PLEC	1144	3	NM_201380	exon32	c.A12297G	p.T4099T	AAAGGCTGTGCCG	.	PASS	Atlas-SNP
OR13D1	286365	hgsc.bcm.edu	37	9	107457725	107457725	+	Silent	SNP	G	G	A	rs12338899	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	38	74	0	0.535211	0	G|0.786;A|0.214	0.214	strong	.	OR13D1	42	.	NM_001004484	exon1	c.G1023A	p.L341L	ACATCTGCATTTA	.	PASS	Atlas-SNP
ZNF236	7776	hgsc.bcm.edu	37	18	74637167	74637167	+	Silent	SNP	C	C	T	rs61739891	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60	60	67	0	1	0	C|0.973;T|0.027	0.027	strong	.	ZNF236	325	.	NM_007345	exon22	c.C3678T	p.H1226H	CTGTCACGTCTGC	.	PASS	Atlas-SNP
RELL2	285613	hgsc.bcm.edu	37	5	141019110	141019110	+	Missense_Mutation	SNP	C	C	A	rs14251	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69	39	64	0	0.565217	0	C|0.567;A|0.433	0.433	strong	.	RELL2	24	.	NM_173828	exon4	c.C397A	p.L133I	CCTTGCCTCCATT	.	PASS	Atlas-SNP
CD19	930	hgsc.bcm.edu	37	16	28944396	28944396	+	Missense_Mutation	SNP	C	C	G	rs2904880	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	14	8	24	0	0.571429	0	C|0.215;G|0.785	0.785	strong	.	CD19	65	.	NM_001178098	exon3	c.C520G	p.L174V	CCGTGTCTCCCAC	.	PASS	Atlas-SNP
PDCD11	22984	hgsc.bcm.edu	37	10	105174869	105174869	+	Silent	SNP	G	G	A	rs2271750	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	133	62	129	0	0.466165	0	G|0.863;A|0.137	0.137	strong	.	PDCD11	160	.	NM_014976	exon12	c.G1479A	p.P493P	GAATCCGGAGAAG	.	PASS	Atlas-SNP
RAD21L1	642636	hgsc.bcm.edu	37	20	1210647	1210647	+	Missense_Mutation	SNP	T	T	C	rs450739	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	38	19	39	0	0.5	0	T|0.506;C|0.494	0.494	strong	.	RAD21L1	51	.	NM_001136566	exon3	c.T268C	p.C90R	ACATTTTGCCCAG	.	PASS	Atlas-SNP
GOLGA3	2802	hgsc.bcm.edu	37	12	133389998	133389998	+	Silent	SNP	T	T	C	rs7134809	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	78	37	63	0	0.474359	0	T|0.897;C|0.103	0.103	strong	.	GOLGA3	234	.	NM_001172557	exon4	c.A414G	p.T138T	AGAATCTGTAGAG	.	PASS	Atlas-SNP
KRTAP9-4	85280	hgsc.bcm.edu	37	17	39406002	39406002	+	Silent	SNP	G	G	A	rs12952568	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	43	20	56	0	0.465116	0	G|0.941;A|0.059	0.059	strong	.	KRTAP9-4	30	.	NM_033191	exon1	c.G30A	p.Q10Q	CTGTCAGCCTACA	.	PASS	Atlas-SNP
PRDM9	56979	hgsc.bcm.edu	37	5	23510038	23510038	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	172	50	215	0	0.290698	0	.	.	none	.	PRDM9	344	.	NM_020227	exon4	c.C203A	p.A68D	TCAGAGCCACTCG	.	PASS	Atlas-SNP
DSC3	1825	hgsc.bcm.edu	37	18	28610988	28610988	+	Missense_Mutation	SNP	C	C	T	rs276938	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	90	49	107	0	0.544444	0	T|0.384;G|0.001	0.384	strong	.	DSC3	225	.	NM_024423	exon3	c.G305A	p.R102K	TGTTTCCTTTTGT	.	PASS	Atlas-SNP
OR6C76	390326	hgsc.bcm.edu	37	12	55820685	55820685	+	Silent	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	154	50	116	0	0.324675	0	.	.	none	.	OR6C76	98	.	NM_001005183	exon1	c.T648G	p.T216T	CTATACTTACATC	.	PASS	Atlas-SNP
MCF2L2	23101	hgsc.bcm.edu	37	3	182941927	182941927	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	77	4	96	0	0.0519481	0	.	.	none	.	MCF2L2	164	.	NM_015078	exon19	c.A2167G	p.R723G	TTGCCCTAGCTCG	.	PASS	Atlas-SNP
NTF3	4908	hgsc.bcm.edu	37	12	5604064	5604064	+	Silent	SNP	T	T	C	rs200399901	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	37	19	28	0	0.513514	0	T|0.999;C|0.001	0.001	strong	.	NTF3	50	.	NM_001102654	exon2	c.T723C	p.T241T	ACTGACTTCAGAG	.	PASS	Atlas-SNP
UHRF2	115426	hgsc.bcm.edu	37	9	6413640	6413640	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	16	7	24	0	0.4375	0	.	.	none	.	UHRF2	50	.	NM_152896	exon1	c.G150A	p.K50K	GGGCAAGCAGGTG	.	PASS	Atlas-SNP
RSPH10B	222967	hgsc.bcm.edu	37	7	6798735	6798735	+	Missense_Mutation	SNP	G	G	A	rs199536223	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	1243	540	1021	1	0.434433	0.000979432	G|0.994;A|0.006	0.006	weak	RSPH10B2,NS,carcinoma,0,2	RSPH10B	28	2	NM_173565	exon4	c.G275A	p.R92H	AGGTTCGTGGGCT	.	scavenged	Atlas-SNP
SETD4	54093	hgsc.bcm.edu	37	21	37420606	37420606	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	15	63	0	0.211268	0	.	.	none	.	SETD4	37	.	NM_001007259	exon5	c.A296C	p.K99T	ACTTACTTAGTAA	.	PASS	Atlas-SNP
NUP214	8021	hgsc.bcm.edu	37	9	134020092	134020092	+	Missense_Mutation	SNP	C	C	T	rs103612	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69	37	83	0	0.536232	0	C|0.333;N|0.001	.	strong	.	NUP214	166	.	NM_005085	exon12	c.C1720T	p.P574S	ATGAAGCCCTCCT	.	PASS	Atlas-SNP
FAM83E	54854	hgsc.bcm.edu	37	19	49116438	49116438	+	Silent	SNP	A	A	G	rs376524	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	97	45	118	2	0.463918	0.0169492	A|0.708;G|0.292	0.292	strong	FAM83E,colon,carcinoma,0,1	FAM83E	34	1	NM_017708	exon1	c.T192C	p.V64V	GCCCTGAACCTCA	.	scavenged	Atlas-SNP
BCAN	63827	hgsc.bcm.edu	37	1	156622252	156622252	+	Missense_Mutation	SNP	G	G	A	rs1056695	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	21	51	0	0.446809	0	G|0.678;A|0.322	0.322	strong	.	BCAN	174	.	NM_198427	exon8	c.G1510A	p.E504K	CAGGAGGAGTCAC	.	PASS	Atlas-SNP
DGKG	1608	hgsc.bcm.edu	37	3	186006566	186006566	+	Silent	SNP	T	T	C	rs710443	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	112	50	113	0	0.446429	0	T|0.313;C|0.687	0.687	strong	.	DGKG	98	.	NM_001346	exon6	c.A477G	p.V159V	CAGGTATACCACT	.	PASS	Atlas-SNP
HLA-DMA	3108	hgsc.bcm.edu	37	6	32917544	32917544	+	Missense_Mutation	SNP	C	C	T	rs201644248		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	11	82	0	0.130952	0	.	.	weak	.	HLA-DMA	20	.	NM_006120	exon3	c.G496A	p.V166I	CAGGGACGGAATG	.	PASS	Atlas-SNP
CLDN24	100132463	hgsc.bcm.edu	37	4	184243174	184243174	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	147	8	150	0	0.0544218	0	.	.	none	.	CLDN24	5	.	NM_001185149	exon1	c.C406A	p.P136T	AGACGGGAACCAG	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179605180	179605180	+	Silent	SNP	C	C	T	rs746578	bycluster;byfrequency;bysubmitter;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	152	76	148	0	0.5	0	T|0.233;C|0.757;A|0.010	0.233	strong	TTN_ENST00000359218,colon,carcinoma,-1,1	TTN	18412	1	NM_001267550	exon48	c.G12780A	p.A4260A	GATGAGCGCACTT	.	PASS	Atlas-SNP
KCNQ1	3784	hgsc.bcm.edu	37	11	2797237	2797237	+	Silent	SNP	G	G	A	rs1057128	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49	30	57	0	0.612245	0	G|0.838;A|0.162	0.162	strong	KCNQ1,NS,carcinoma,0,1	KCNQ1	60	1	NM_000218	exon13	c.G1638A	p.S546S	GTACTCGCAGGGC	.	PASS	Atlas-SNP
ASB10	136371	hgsc.bcm.edu	37	7	150878332	150878332	+	Silent	SNP	G	G	A	rs61743170	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	151	76	175	0	0.503311	0	G|0.914;A|0.086	0.086	strong	.	ASB10	99	.	NM_001142459	exon3	c.C798T	p.A266A	GGCCTCGGCATCG	.	PASS	Atlas-SNP
C2CD4A	145741	hgsc.bcm.edu	37	15	62359914	62359914	+	Silent	SNP	C	C	T	rs12911068	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	33	17	43	0	0.515152	0	C|0.949;T|0.051	0.051	strong	.	C2CD4A	3	.	NM_207322	exon2	c.C102T	p.T34T	CACCACCGCCGCG	.	PASS	Atlas-SNP
ZDHHC11	79844	hgsc.bcm.edu	37	5	825297	825297	+	Silent	SNP	A	A	G	rs1808545	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	138	15	95	0	0.108696	0	A|0.977;G|0.023	0.023	strong	.	ZDHHC11	97	.	NM_024786	exon8	c.T1005C	p.D335D	ATCCCCATCCTGG	.	PASS	Atlas-SNP
ZBTB46	140685	hgsc.bcm.edu	37	20	62378349	62378349	+	Silent	SNP	C	C	T	rs5019252	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	28	15	44	0	0.535714	0	C|0.724;T|0.276	0.276	strong	ZBTB46,rectum,carcinoma,0,1	ZBTB46	72	1	NM_025224	exon5	c.G1704A	p.E568E	GTCTTCCTCATCC	.	PASS	Atlas-SNP
ALPK3	57538	hgsc.bcm.edu	37	15	85383145	85383145	+	Missense_Mutation	SNP	C	C	G	rs3803403	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	32	73	0	0.5	0	C|0.808;G|0.192	0.192	strong	.	ALPK3	289	.	NM_020778	exon5	c.C1241G	p.T414S	TCGACACTCTGCG	.	PASS	Atlas-SNP
ACSS1	84532	hgsc.bcm.edu	37	20	24994289	24994289	+	Missense_Mutation	SNP	C	C	T	rs6050249	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	29	44	0	0.47541	0	C|0.785;T|0.215	0.215	strong	ACSS1,colon,carcinoma,0,2	ACSS1	46	2	NM_001252677	exon10	c.G1462A	p.V488M	CCTCCACGACGCT	.	PASS	Atlas-SNP
PRAMEF10	343071	hgsc.bcm.edu	37	1	12954921	12954921	+	Missense_Mutation	SNP	A	A	G	rs199792484	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	127	17	34	0	0.133858	0	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
SLC15A4	121260	hgsc.bcm.edu	37	12	129278864	129278864	+	Silent	SNP	A	A	G	rs1059312	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	89	85	78	0	0.955056	0	A|0.574;G|0.426	0.426	strong	.	SLC15A4	41	.	NM_145648	exon8	c.T1611C	p.F537F	CAGAAGAAAAAAG	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	193	193	195	0	1	0	C|0.417;T|0.583	0.583	strong	.	PON3	59	.	NM_000940	exon4	c.G297A	p.A99A	TTCTAGCGCTTGT	.	PASS	Atlas-SNP
LDHAL6B	92483	hgsc.bcm.edu	37	15	59499274	59499274	+	Silent	SNP	C	C	A	rs3809528	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85	40	70	0	0.470588	0	C|0.586;A|0.414	0.414	strong	.	LDHAL6B	30	.	NM_033195	exon1	c.C135A	p.T45T	CTTCACCCCCGTG	.	PASS	Atlas-SNP
OCA2	4948	hgsc.bcm.edu	37	15	28090173	28090173	+	Silent	SNP	C	C	T	rs12592307	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	144	82	159	0	0.569444	0	C|0.769;T|0.231	0.231	strong	OCA2,NS,carcinoma,0,1	OCA2	173	1	NM_000275	exon23	c.G2364A	p.S788S	GTTTGCCGACGCG	.	PASS	Atlas-SNP
KRTAP4-11	653240	hgsc.bcm.edu	37	17	39274415	39274415	+	Silent	SNP	C	C	T	rs425487		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72	3	58	1	0.0416667	0.0172414	.	.	weak	KRTAP4-11,NS,carcinoma,-1,11	KRTAP4-11	94	11	NM_033059	exon1	c.G153A	p.R51R	CTGGGGCCTGCAG	.	scavenged	Atlas-SNP
METTL11B	149281	hgsc.bcm.edu	37	1	170135765	170135765	+	Silent	SNP	T	T	C	rs6669514	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	112	67	114	0	0.598214	0	T|0.746;C|0.254	0.254	strong	.	METTL11B	18	.	NM_001136107	exon3	c.T453C	p.F151F	ATCCTTTCTCCTT	.	PASS	Atlas-SNP
WBSCR17	64409	hgsc.bcm.edu	37	7	71142240	71142240	+	Silent	SNP	G	G	A	rs77485397	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49	25	45	0	0.510204	0	G|0.995;A|0.005	0.005	strong	WBSCR17,NS,carcinoma,+1,2	WBSCR17	208	2	NM_022479	exon9	c.G1449A	p.P483P	GGGGCCGCTGGAG	.	PASS	Atlas-SNP
SYNE3	161176	hgsc.bcm.edu	37	14	95910933	95910933	+	Silent	SNP	T	T	C	rs9919918	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	26	53	0	0.412698	0	C|0.242;N|0.000	0.242	strong	C14orf49,NS,carcinoma,0,1	SYNE3	130	1	NM_152592	exon9	c.A1665G	p.A555A	AAAAGCTGCTCCA	.	PASS	Atlas-SNP
ATP2A3	489	hgsc.bcm.edu	37	17	3848013	3848013	+	Silent	SNP	A	A	C	rs1800911	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	128	54	127	0	0.421875	0	A|0.610;C|0.390	0.390	strong	.	ATP2A3	148	.	NM_174956	exon10	c.T1272G	p.A424A	GTCCAGAGCCGAG	.	PASS	Atlas-SNP
PCDHB15	56121	hgsc.bcm.edu	37	5	140627020	140627020	+	Missense_Mutation	SNP	G	G	T	rs77506821	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	9	6	17	0	0.666667	0	G|0.941;T|0.059	0.059	strong	.	PCDHB15	138	.	NM_018935	exon1	c.G1874T	p.R625L	AGGTGCGCACCGC	.	PASS	Atlas-SNP
TLR4	7099	hgsc.bcm.edu	37	9	120476365	120476365	+	Silent	SNP	G	G	A	rs5030721	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	24	57	0	0.393443	0	G|0.993;A|0.007	0.007	strong	.	TLR4	220	.	NM_138554	exon3	c.G1959A	p.K653K	CTATAAGTTCTAT	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179398823	179398823	+	Silent	SNP	G	G	A	rs2857265	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	126	60	125	0	0.47619	0	G|0.802;A|0.198	0.198	strong	.	TTN	18412	.	NM_001267550	exon358	c.C102519T	p.G34173G	TCGGACGCCAAAG	.	PASS	Atlas-SNP
OR5P2	120065	hgsc.bcm.edu	37	11	7817959	7817959	+	Silent	SNP	G	G	A	rs73406603	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	61	67	0	1	0	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	.	PASS	Atlas-SNP
KCNH2	3757	hgsc.bcm.edu	37	7	150648789	150648789	+	Silent	SNP	T	T	C	rs1805121	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	141	79	156	1	0.560284	0.00641026	T|0.477;C|0.523	0.523	strong	KCNH2_ENST00000430723,NS,carcinoma,0,2	KCNH2	157	2	NM_000238	exon7	c.A1692G	p.L564L	GCAGGCTAGCCAG	.	scavenged	Atlas-SNP
DDX47	51202	hgsc.bcm.edu	37	12	12967127	12967127	+	Silent	SNP	C	C	T	rs1051374	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	148	69	211	0	0.466216	0	C|0.686;T|0.314	0.314	strong	.	DDX47	37	.	NM_201224	exon2	c.C150T	p.I50I	CAAGATCCAGATT	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9088330	9088330	+	Missense_Mutation	SNP	G	G	A	rs17000947	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	133	66	137	0	0.496241	0	G|0.811;A|0.189	0.189	strong	.	MUC16	4315	.	NM_024690	exon1	c.C3485T	p.T1162I	TTGGGAGTAGGAG	.	PASS	Atlas-SNP
UTP20	27340	hgsc.bcm.edu	37	12	101755803	101755803	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	18	79	0	0.236842	0	.	.	none	.	UTP20	222	.	NM_014503	exon44	c.G5755A	p.G1919R	CAGGTCGGAGATT	.	PASS	Atlas-SNP
BBS2	583	hgsc.bcm.edu	37	16	56545175	56545175	+	Missense_Mutation	SNP	T	T	C	rs11373	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	28	46	0	0.538462	0	T|0.778;C|0.222	0.222	strong	.	BBS2	67	.	NM_031885	exon3	c.A367G	p.I123V	GCACAATTGCATT	.	PASS	Atlas-SNP
SLC2A6	11182	hgsc.bcm.edu	37	9	136337168	136337168	+	Missense_Mutation	SNP	G	G	A	rs3094378	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60	33	58	0	0.55	0	G|0.943;A|0.057	0.057	strong	.	SLC2A6	31	.	NM_017585	exon10	c.C1499T	p.T500M	CTCCCCGTGCGGA	.	PASS	Atlas-SNP
SLC7A3	84889	hgsc.bcm.edu	37	X	70146398	70146398	+	Silent	SNP	A	A	G	rs4360450	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	146	146	115	0	1	0	A|0.284;G|0.716	0.716	strong	.	SLC7A3	76	.	NM_032803	exon10	c.T1599C	p.S533S	AGTGGAACTCTGT	.	PASS	Atlas-SNP
RIN3	79890	hgsc.bcm.edu	37	14	93118692	93118692	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98	2	101	0	0.0204082	0	.	.	none	RIN3,NS,carcinoma,+1,1	RIN3	81	1	NM_024832	exon6	c.G1298A	p.G433D	AGCAAGGCCAGGA	.	scavenged	Atlas-SNP
DNAJB8	165721	hgsc.bcm.edu	37	3	128181777	128181777	+	Silent	SNP	A	A	G	rs2659690	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82	82	56	0	1	0	G|0.508;N|0.000	0.508	strong	.	DNAJB8	34	.	NM_153330	exon3	c.T312C	p.F104F	GCCACCAAAAAAC	.	PASS	Atlas-SNP
WDR44	54521	hgsc.bcm.edu	37	X	117528056	117528056	+	Missense_Mutation	SNP	G	G	A	rs17271416	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	196	138	143	0	0.704082	0	0|0.015;A|0.144	0.144	strong	.	WDR44	188	.	NM_001184965	exon5	c.G865A	p.A289T	CTAACCGCAAGCA	.	PASS	Atlas-SNP
SERTAD1	29950	hgsc.bcm.edu	37	19	40928944	40928944	+	Silent	SNP	A	A	G	rs4150992	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	99	43	99	0	0.434343	0	A|0.715;G|0.285	0.285	strong	.	SERTAD1	18	.	NM_013376	exon2	c.T510C	p.L170L	GCCCTCAAGCCCA	.	PASS	Atlas-SNP
ERAL1	26284	hgsc.bcm.edu	37	17	27185814	27185814	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	2	93	1	0.0229885	0.0107527	.	.	none	ERAL1,colon,carcinoma,+1,1	ERAL1	28	1	NM_005702	exon7	c.T932C	p.L311P	CAGCCCTAAGCCA	.	scavenged	Atlas-SNP
OR5A2	219981	hgsc.bcm.edu	37	11	59189912	59189912	+	Missense_Mutation	SNP	G	G	A	rs1453547	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69	28	78	0	0.405797	0	G|0.820;A|0.180	0.180	strong	.	OR5A2	35	.	NM_001001954	exon1	c.C515T	p.P172L	ATATAGGGCCCAC	.	PASS	Atlas-SNP
DNAH9	1770	hgsc.bcm.edu	37	17	11650958	11650958	+	Missense_Mutation	SNP	G	G	A	rs61743635	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	95	94	95	0	0.989474	0	G|0.922;A|0.078	0.078	strong	.	DNAH9	695	.	NM_001372	exon32	c.G6485A	p.R2162K	TGCTGAGGTCCTT	.	PASS	Atlas-SNP
DDR2	4921	hgsc.bcm.edu	37	1	162729613	162729613	+	Silent	SNP	C	C	T	rs56351141	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82	29	107	0	0.353659	0	C|0.991;T|0.009	0.009	strong	DDR2_ENST00000367922,right_upper_lobe,carcinoma,0,2	DDR2	228	2	NM_001014796	exon9	c.C699T	p.T233T	ATTGACCGATGGT	.	PASS	Atlas-SNP
MON1B	22879	hgsc.bcm.edu	37	16	77228866	77228866	+	Silent	SNP	T	T	C	rs2232504	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	92	42	99	0	0.456522	0	T|0.276;C|0.724	0.724	strong	MON1B,NS,carcinoma,+2,1	MON1B	55	1	NM_014940	exon4	c.T1110C	p.V370V	CCTGGTTGAAGAT	.	PASS	Atlas-SNP
CCDC146	57639	hgsc.bcm.edu	37	7	76866265	76866265	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69	30	81	0	0.434783	0	.	.	none	.	CCDC146	87	.	NM_020879	exon3	c.T158C	p.L53S	GCTAGTTACATGC	.	PASS	Atlas-SNP
PRAMEF11	440560	hgsc.bcm.edu	37	1	12884981	12884981	+	Missense_Mutation	SNP	T	T	C	rs71225486		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	349	173	369	0	0.495702	0	T|0.500;C|0.500	0.500	weak	.	PRAMEF11	72	.	NM_001146344	exon4	c.A1130G	p.Q377R	CTTTCCTGCGGGG	.	PASS	Atlas-SNP
DUSP13	51207	hgsc.bcm.edu	37	10	76855412	76855412	+	Silent	SNP	G	G	A	rs3740317	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	102	57	92	0	0.558824	0	G|0.642;A|0.358	0.358	strong	DUSP13_ENST00000356369,NS,carcinoma,0,1	DUSP13	82	1	NM_001007273	exon5	c.C594T	p.D198D	GTTGTCGTCCGCC	.	PASS	Atlas-SNP
SIGLEC10	89790	hgsc.bcm.edu	37	19	51919267	51919267	+	Silent	SNP	A	A	G	rs7258638	bycluster;byfrequency;by2hit2allele	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	125	21	109	0	0.168	0	A|0.996;G|0.004	0.004	strong	.	SIGLEC10	112	.	NM_001171157	exon5	c.T909C	p.P303P	GGGTCTAGGGCCC	.	PASS	Atlas-SNP
PACSIN2	11252	hgsc.bcm.edu	37	22	43289473	43289473	+	Silent	SNP	G	G	A	rs5759013	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	34	34	37	0	1	0	G|0.724;A|0.276	0.276	strong	PACSIN2,NS,carcinoma,-2,1	PACSIN2	48	1	NM_007229	exon3	c.C207T	p.L69L	CTCCACGAGCTGC	.	PASS	Atlas-SNP
RIN2	54453	hgsc.bcm.edu	37	20	19951534	19951534	+	Missense_Mutation	SNP	T	T	A	rs3803981	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	117	116	99	0	0.991453	0	T|0.818;A|0.182	0.182	strong	RIN2_ENST00000255006,NS,carcinoma,0,3	RIN2	126	3	NM_001242581	exon7	c.T736A	p.S246T	GCCAAGTCGGAGG	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	29	83	0	0.432836	0	A|0.506;G|0.494	0.494	strong	.	NINL	148	.	NM_025176	exon17	c.T3039C	p.S1013S	CTCCACACTGTGC	.	PASS	Atlas-SNP
PCIF1	63935	hgsc.bcm.edu	37	20	44574722	44574722	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83	22	61	0	0.26506	0	.	.	none	.	PCIF1	51	.	NM_022104	exon13	c.C1396T	p.P466S	TTCCTGCCCCGGG	.	PASS	Atlas-SNP
THSD7A	221981	hgsc.bcm.edu	37	7	11676377	11676377	+	Silent	SNP	G	G	A	rs2074598	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	138	68	171	0	0.492754	0	G|0.745;N|0.000	.	strong	.	THSD7A	219	.	NM_015204	exon2	c.C402T	p.P134P	AATCACGGGCTGA	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29912281	29912281	+	Silent	SNP	G	G	A	rs1136917	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	140	32	138	0	0.228571	0	G|0.872;A|0.128	0.128	strong	.	HLA-A	89	.	NM_001242758	exon5	c.G900A	p.L300L	AGAGCTGTCTTCC	.	PASS	Atlas-SNP
NMUR2	56923	hgsc.bcm.edu	37	5	151777633	151777633	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83	5	64	0	0.060241	0	.	.	none	NMUR2,NS,carcinoma,0,1	NMUR2	111	1	NM_020167	exon2	c.A799C	p.N267H	TCTTGTTGACTGA	.	PASS	Atlas-SNP
MON2	23041	hgsc.bcm.edu	37	12	62926398	62926398	+	Silent	SNP	G	G	A	rs7957417	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	107	54	110	0	0.504673	0	G|0.636;A|0.364	0.364	strong	.	MON2	160	.	NM_015026	exon12	c.G1581A	p.S527S	ACAGTCGACAGAA	.	PASS	Atlas-SNP
TNC	3371	hgsc.bcm.edu	37	9	117797597	117797597	+	Silent	SNP	T	T	C	rs12347433	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	28	10	40	0	0.357143	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
MUC2	4583	hgsc.bcm.edu	37	11	1093364	1093364	+	Missense_Mutation	SNP	C	C	G	rs113138128	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49	10	40	1	0.204082	0.025	C|0.500;G|0.500	0.500	weak	MUC2_ENST00000441003,NS,carcinoma,0,6	MUC2	614	6	NM_002457	exon30	c.C5183G	p.T1728S	CCACCACTACGGT	.	scavenged	Atlas-SNP
FMN2	56776	hgsc.bcm.edu	37	1	240370934	240370934	+	Missense_Mutation	SNP	G	G	C	rs4997328	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	13	121	1	0.19697	0.00826446	G|0.781;C|0.219	0.219	strong	FMN2,NS,carcinoma,0,3	FMN2	451	3	NM_020066	exon5	c.G2822C	p.G941A	GAGCGGGAATACC	.	scavenged	Atlas-SNP
PRAMEF2	65122	hgsc.bcm.edu	37	1	12919934	12919934	+	Missense_Mutation	SNP	A	A	G	rs3204805	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	154	55	120	0	0.357143	0	A|0.846;G|0.154	0.154	strong	.	PRAMEF2	85	.	NM_023014	exon3	c.A674G	p.Y225C	AGCTTTATTGTTA	.	PASS	Atlas-SNP
ATP6V0A4	50617	hgsc.bcm.edu	37	7	138418910	138418910	+	Silent	SNP	G	G	A	rs1026435	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	65	65	72	0	1	0	G|0.304;A|0.696	0.696	strong	.	ATP6V0A4	93	.	NM_130841	exon15	c.C1662T	p.F554F	GACACCGAAAACC	.	PASS	Atlas-SNP
HCN2	610	hgsc.bcm.edu	37	19	605093	605093	+	Silent	SNP	G	G	A	rs55839339	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72	34	82	0	0.472222	0	G|0.984;A|0.016	0.016	strong	.	HCN2	36	.	NM_001194	exon3	c.G1089A	p.A363A	CAGCGCGGTGATG	.	PASS	Atlas-SNP
HELLS	3070	hgsc.bcm.edu	37	10	96313960	96313960	+	Silent	SNP	A	A	C	rs11188019	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	175	86	157	0	0.491429	0	A|0.531;C|0.469	0.469	strong	.	HELLS	63	.	NM_018063	exon3	c.A231C	p.I77I	CAATATATACTCC	.	PASS	Atlas-SNP
MRGPRE	116534	hgsc.bcm.edu	37	11	3249972	3249972	+	Missense_Mutation	SNP	C	C	A	rs200284450	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	43	21	45	0	0.488372	0	.	.	weak	.	MRGPRE	35	.	NM_001039165	exon2	c.G58T	p.D20Y	CCACATCCTCCTG	.	PASS	Atlas-SNP
KANSL1	284058	hgsc.bcm.edu	37	17	44248769	44248769	+	Silent	SNP	T	T	C	rs1881193	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	384	382	209	0	0.994792	0	T|0.841;C|0.159	0.159	strong	.	.	.	.	NM_001193466	exon2	c.A741G	p.R247R	TGATAATCTACTG	.	PASS	Atlas-SNP
FYCO1	79443	hgsc.bcm.edu	37	3	46010007	46010007	+	Silent	SNP	T	T	C	rs13071283	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	37	22	23	0	0.594595	0	T|0.917;C|0.083	0.083	strong	.	FYCO1	115	.	NM_024513	exon8	c.A819G	p.Q273Q	CTGCAGTTGCTCC	.	PASS	Atlas-SNP
KLHL12	59349	hgsc.bcm.edu	37	1	202888947	202888947	+	Silent	SNP	T	T	C	rs3182429	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	126	61	156	0	0.484127	0	T|0.778;C|0.222	0.222	strong	.	KLHL12	50	.	NM_021633	exon3	c.A285G	p.T95T	ATGTACTGTTTCT	.	PASS	Atlas-SNP
SEC23B	10483	hgsc.bcm.edu	37	20	18505200	18505200	+	Missense_Mutation	SNP	G	G	T	rs36023150	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	113	50	124	0	0.442478	0	G|0.992;T|0.008	0.008	strong	SEC23B,NS,carcinoma,0,1	SEC23B	70	1	NM_032985	exon5	c.G490T	p.V164L	GCTCTGGTGGGTC	.	PASS	Atlas-SNP
B4GALNT1	2583	hgsc.bcm.edu	37	12	58022555	58022555	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69	26	91	0	0.376812	0	.	.	none	.	B4GALNT1	53	.	NM_001478	exon8	c.A943A	p.T315T	GCTTGTCGCTGTC	.	PASS	Atlas-SNP
TEX26	122046	hgsc.bcm.edu	37	13	31543095	31543095	+	Silent	SNP	C	C	T	rs2274869	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	99	37	117	0	0.373737	0	C|0.784;T|0.216	0.216	strong	.	.	.	.	NM_152325	exon6	c.C720T	p.Y240Y	TGACTACGACAAA	.	PASS	Atlas-SNP
LYPD5	284348	hgsc.bcm.edu	37	19	44303066	44303066	+	Missense_Mutation	SNP	C	C	G	rs11547806	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	125	125	169	0	1	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
CLCNKB	1188	hgsc.bcm.edu	37	1	16378739	16378739	+	Silent	SNP	G	G	A	rs34652156	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	318	314	395	0	0.987421	0	G|0.967;A|0.033	0.033	strong	.	CLCNKB	50	.	NM_000085	exon15	c.G1455A	p.A485A	CACGGCGCTGCTG	.	PASS	Atlas-SNP
PCSK1	5122	hgsc.bcm.edu	37	5	95733112	95733112	+	Silent	SNP	A	A	G	rs6233	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	87	118	0	1	0	A|0.628;G|0.372	0.372	strong	.	PCSK1	93	.	NM_000439	exon12	c.T1650C	p.N550N	GTCCCAATTCTTA	.	PASS	Atlas-SNP
ENDOG	2021	hgsc.bcm.edu	37	9	131584631	131584631	+	Silent	SNP	C	C	T	rs2280844	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	90	48	101	0	0.533333	0	C|0.923;T|0.077	0.077	strong	.	ENDOG	8	.	NM_004435	exon3	c.C636T	p.Y212Y	ATCCTACGTAAAG	.	PASS	Atlas-SNP
EVA1A	84141	hgsc.bcm.edu	37	2	75720664	75720664	+	Silent	SNP	G	G	A	rs6741778	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	32	10	56	0	0.3125	0	G|0.745;A|0.255	0.255	strong	.	.	.	.	NM_032181	exon4	c.C157T	p.L53L	TCACCAGAGCAGC	.	PASS	Atlas-SNP
SAMM50	25813	hgsc.bcm.edu	37	22	44368204	44368204	+	Silent	SNP	A	A	G	rs3177036	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	106	49	96	0	0.462264	0	A|0.383;G|0.617	0.617	strong	.	SAMM50	30	.	NM_015380	exon5	c.A411G	p.G137G	GGTTGGAAACAAT	.	PASS	Atlas-SNP
TATDN3	128387	hgsc.bcm.edu	37	1	212965284	212965284	+	Silent	SNP	C	C	G	rs61736926	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	147	74	140	7	0.503401	0.05	C|0.772;G|0.228	0.228	strong	TATDN3,NS,carcinoma,0,1	TATDN3	23	1	NM_001146170	exon1	c.C21G	p.G7G	CGTAGGCTTGGTG	.	scavenged	Atlas-SNP
CDON	50937	hgsc.bcm.edu	37	11	125830970	125830970	+	Missense_Mutation	SNP	A	A	T	rs684535	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	162	162	149	1	1	0.00671141	A|0.238;T|0.762	0.762	strong	.	CDON	137	.	NM_001243597	exon20	c.T3731A	p.I1244N	ATGTTGATCTCTG	.	PASS	Atlas-SNP
ZNF99	7652	hgsc.bcm.edu	37	19	22942325	22942325	+	Missense_Mutation	SNP	G	G	C	rs7255780	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	77	37	81	0	0.480519	0	G|0.635;C|0.364	0.364	strong	.	ZNF99	273	.	NM_001080409	exon4	c.C386G	p.A129G	TTATAAGCTTCTT	.	PASS	Atlas-SNP
ANKMY2	57037	hgsc.bcm.edu	37	7	16655387	16655387	+	Silent	SNP	C	C	T	rs11540037	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	77	14	89	0	0.181818	0	T|0.144;G|0.146;C|0.687;A|0.024	0.144	strong	.	ANKMY2	46	.	NM_020319	exon5	c.G513A	p.T171T	AAGATTCGTTGTG	.	PASS	Atlas-SNP
VPS13C	54832	hgsc.bcm.edu	37	15	62174894	62174894	+	Silent	SNP	A	A	G	rs17303915	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82	40	89	0	0.487805	0	A|0.943;G|0.057	0.057	strong	.	VPS13C	506	.	NM_020821	exon69	c.T9525C	p.I3175I	GCTACGAATAGGG	.	PASS	Atlas-SNP
ACIN1	22985	hgsc.bcm.edu	37	14	23549380	23549380	+	Silent	SNP	G	G	A	rs1885098	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	149	70	143	0	0.469799	0	G|0.871;A|0.129	0.129	strong	.	ACIN1	147	.	NM_001164814	exon6	c.C1338T	p.P446P	GACAGCGGGGGCT	.	PASS	Atlas-SNP
PDE6A	5145	hgsc.bcm.edu	37	5	149323772	149323772	+	Silent	SNP	G	G	A	rs2277926	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60	34	79	0	0.566667	0	G|0.807;A|0.193	0.193	strong	PDE6A,NS,carcinoma,0,1	PDE6A	98	1	NM_000440	exon1	c.C465T	p.N155N	CTCTGTGTTGGGG	.	PASS	Atlas-SNP
AKR7A3	22977	hgsc.bcm.edu	37	1	19611227	19611227	+	Silent	SNP	G	G	A	rs1065658	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	132	131	143	0	0.992424	0	G|0.842;A|0.158	0.158	strong	.	AKR7A3	30	.	NM_012067	exon5	c.C657T	p.P219P	GCCCACGGGCTGT	.	PASS	Atlas-SNP
ARHGEF11	9826	hgsc.bcm.edu	37	1	156928576	156928576	+	Missense_Mutation	SNP	C	C	T	rs142957547	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	134	58	131	0	0.432836	0	C|0.996;T|0.004	0.004	strong	.	ARHGEF11	168	.	NM_198236	exon17	c.G1460A	p.R487H	ACTTGGCGCTCTC	.	PASS	Atlas-SNP
NEK11	79858	hgsc.bcm.edu	37	3	130992385	130992385	+	Missense_Mutation	SNP	T	T	C	rs16836266	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	101	53	104	0	0.524752	0	C|0.166;N|0.000	0.166	strong	.	NEK11	76	.	NM_024800	exon17	c.T1685C	p.V562A	ACAGTGTGATGGC	.	PASS	Atlas-SNP
EML5	161436	hgsc.bcm.edu	37	14	89206861	89206861	+	Missense_Mutation	SNP	G	G	A	rs139652502	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	153	66	185	0	0.431373	0	G|0.994;A|0.006	0.006	strong	EML5,colon,NS,+1,1	EML5	141	1	NM_183387	exon5	c.C581T	p.T194M	TCACCCGTCTTAC	.	PASS	Atlas-SNP
MAGIX	79917	hgsc.bcm.edu	37	X	49021052	49021052	+	Silent	SNP	C	C	T	rs12843494	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	117	83	78	0	0.709402	0	C|0.926;0|0.013	.	strong	.	MAGIX	25	.	NM_001099681	exon3	c.C204T	p.S68S	TGTTAGCGTGCTG	.	PASS	Atlas-SNP
AKR1B15	441282	hgsc.bcm.edu	37	7	134264286	134264286	+	Silent	SNP	C	C	T	rs6467538	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	42	106	0	0.518519	0	C|0.651;T|0.349	0.349	strong	.	AKR1B15	105	.	NM_001080538	exon12	c.C1020T	p.F340F	TCCCTTCGATGCA	.	PASS	Atlas-SNP
ATAD2B	54454	hgsc.bcm.edu	37	2	24046426	24046426	+	Silent	SNP	G	G	A	rs75866363	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57	25	43	0	0.438596	0	G|0.968;A|0.032	0.032	strong	ATAD2B_ENST00000238789,colon,carcinoma,0,1	ATAD2B	110	1	NM_001242338	exon16	c.C1833T	p.A611A	GATATCGGCTCCA	.	PASS	Atlas-SNP
LAMC3	10319	hgsc.bcm.edu	37	9	133911706	133911706	+	Silent	SNP	C	C	T	rs2275131	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	90	89	89	0	0.988889	0	C|0.579;T|0.421	0.421	strong	LAMC3,NS,carcinoma,0,1	LAMC3	167	1	NM_006059	exon4	c.C963T	p.A321A	GGCTGCCCACGAG	.	PASS	Atlas-SNP
C4orf47	441054	hgsc.bcm.edu	37	4	186366181	186366181	+	Missense_Mutation	SNP	G	G	A	rs74560263	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	237	96	248	1	0.405063	0.00403226	G|0.938;A|0.062	0.062	strong	.	C4orf47	13	.	NM_001114357	exon6	c.G778A	p.A260T	TATGTGGCTAAAT	.	PASS	Atlas-SNP
NUP107	57122	hgsc.bcm.edu	37	12	69115698	69115698	+	Silent	SNP	G	G	A	rs17851475	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82	31	108	0	0.378049	0	G|0.782;A|0.218	0.218	strong	.	NUP107	88	.	NM_020401	exon16	c.G1389A	p.Q463Q	AGAACAGGAGATC	.	PASS	Atlas-SNP
PIK3AP1	118788	hgsc.bcm.edu	37	10	98469507	98469507	+	Missense_Mutation	SNP	C	C	A	rs3748229	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	27	73	1	0.519231	0.0136986	C|0.621;A|0.379	0.379	strong	PIK3AP1,caecum,carcinoma,+2,1	PIK3AP1	111	1	NM_152309	exon2	c.G247T	p.A83S	GCAAGGCGGGCTT	.	scavenged	Atlas-SNP
CDHR1	92211	hgsc.bcm.edu	37	10	85972043	85972043	+	Silent	SNP	A	A	G	rs10749482	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	114	56	111	0	0.491228	0	A|0.585;G|0.415	0.415	strong	.	CDHR1	122	.	NM_001171971	exon15	c.A1662G	p.E554E	CATGGAAGGCAAG	.	PASS	Atlas-SNP
ADRB2	154	hgsc.bcm.edu	37	5	148206646	148206646	+	Silent	SNP	G	G	A	rs113509650	byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	147	65	155	0	0.442177	0	G|0.772;A|0.228	0.228	strong	.	ADRB2	42	.	NM_000024	exon1	c.G252A	p.L84L	GGGCCTGGCAGTG	.	PASS	Atlas-SNP
PSG2	5670	hgsc.bcm.edu	37	19	43585334	43585334	+	Silent	SNP	T	T	G	rs79582550	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	152	13	160	0	0.0855263	0	T|0.944;G|0.056	0.056	strong	PSG2,NS,carcinoma,-1,2	PSG2	84	2	NM_031246	exon2	c.A129C	p.P43P	AACTTTTGGTGGC	.	scavenged	Atlas-SNP
DPYSL5	56896	hgsc.bcm.edu	37	2	27121394	27121394	+	Silent	SNP	G	G	A	rs79644076	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	223	110	213	1	0.493274	0.00469484	G|0.995;A|0.005	0.005	strong	.	DPYSL5	69	.	NM_001253724	exon2	c.G27A	p.R9R	CGTGAGGATCCTC	.	PASS	Atlas-SNP
GRK7	131890	hgsc.bcm.edu	37	3	141497150	141497150	+	Silent	SNP	C	C	T	rs1533501	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	70	26	73	0	0.371429	0	C|0.953;T|0.047	0.047	strong	.	GRK7	65	.	NM_139209	exon1	c.C24T	p.D8D	CCTGGACAACCTG	.	PASS	Atlas-SNP
TTC9C	283237	hgsc.bcm.edu	37	11	62505764	62505764	+	Silent	SNP	C	C	T	rs6675	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	14	7	13	0	0.5	0	T|0.143;G|0.159;C|0.672;A|0.026	0.143	strong	.	TTC9C	12	.	NM_173810	exon3	c.C426T	p.A142A	AGATGCCAACGTC	.	PASS	Atlas-SNP
ESX1	80712	hgsc.bcm.edu	37	X	103495552	103495552	+	Missense_Mutation	SNP	T	T	C	rs41305431	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	36	25	42	0	0.694444	0	T|0.951;C|0.049	0.049	strong	.	ESX1	57	.	NM_153448	exon4	c.A578G	p.K193R	TTCCACTTGGCTC	.	PASS	Atlas-SNP
VMAC	400673	hgsc.bcm.edu	37	19	5908969	5908969	+	Missense_Mutation	SNP	G	G	A	rs10404195	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	30	55	1	0.46875	0.0181818	G|0.872;A|0.128	0.128	strong	VMAC,NS,carcinoma,0,1	VMAC	5	1	NM_001017921	exon2	c.G326A	p.R109H	TCTGCCGCCGCCG	.	scavenged	Atlas-SNP
PPP1CC	5501	hgsc.bcm.edu	37	12	111160003	111160003	+	Silent	SNP	G	G	A	rs1973505	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	103	42	115	0	0.407767	0	G|0.770;A|0.230	0.230	strong	.	PPP1CC	22	.	NM_002710	exon6	c.C819T	p.C273C	CTCTCCGCAATAA	.	PASS	Atlas-SNP
SGK223	0	hgsc.bcm.edu	37	8	8234714	8234714	+	Missense_Mutation	SNP	C	C	T	rs3896980	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	23	51	0	0.442308	0	C|0.612;T|0.388	0.388	strong	.	.	.	.	NM_001080826	exon2	c.G1205A	p.R402Q	GCCTCCCGGGGGT	.	PASS	Atlas-SNP
ZNF692	55657	hgsc.bcm.edu	37	1	249150116	249150116	+	Missense_Mutation	SNP	G	G	C	rs13313088	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	39	64	0	0.549296	0	G|0.850;C|0.150	0.150	strong	.	ZNF692	41	.	NM_001136036	exon7	c.C704G	p.P235R	GGGGAAGGCAGTA	.	PASS	Atlas-SNP
SLITRK2	84631	hgsc.bcm.edu	37	X	144904252	144904252	+	Silent	SNP	G	G	A	rs3810704	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	125	82	68	0	0.656	0	G|0.836;A|0.164	0.164	strong	.	SLITRK2	221	.	NM_001144005	exon5	c.G309A	p.T103T	CCGAACGGGGGCA	.	PASS	Atlas-SNP
GPD1	2819	hgsc.bcm.edu	37	12	50503269	50503269	+	Silent	SNP	C	C	T	rs836180	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	89	33	84	0	0.370787	0	C|0.726;T|0.274	0.274	strong	.	GPD1	23	.	NM_005276	exon8	c.C1017T	p.I339I	ATTCATCCACTGC	.	PASS	Atlas-SNP
CA5A	763	hgsc.bcm.edu	37	16	87938398	87938398	+	Silent	SNP	G	G	A	rs7186698	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	230	109	225	0	0.473913	0	G|0.840;A|0.160	0.160	strong	.	CA5A	32	.	NM_001739	exon3	c.C453T	p.P151P	CTCTGCGGGGTAC	.	PASS	Atlas-SNP
ZSCAN4	201516	hgsc.bcm.edu	37	19	58189287	58189287	+	Silent	SNP	C	C	T	rs9676604	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85	41	93	0	0.482353	0	C|0.827;T|0.173	0.173	strong	ZSCAN4,NS,carcinoma,0,1	ZSCAN4	72	1	NM_152677	exon4	c.C402T	p.H134H	GGTCCACGTCCAC	.	PASS	Atlas-SNP
PRG4	10216	hgsc.bcm.edu	37	1	186277989	186277989	+	Silent	SNP	A	A	G	rs3737940	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	109	108	73	0	0.990826	0	A|0.735;G|0.265	0.265	strong	.	PRG4	259	.	NM_005807	exon7	c.A3138G	p.P1046P	AAAACCAAAGACG	.	PASS	Atlas-SNP
PLCG1	5335	hgsc.bcm.edu	37	20	39797465	39797465	+	Missense_Mutation	SNP	T	T	C	rs753381	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	149	59	137	1	0.395973	0.00729927	T|0.302;C|0.698	0.698	strong	PLCG1,NS,malignant_melanoma,-1,1	PLCG1	111	1	NM_182811	exon21	c.T2438C	p.I813T	CCTTCATCAAGAG	.	scavenged	Atlas-SNP
CD276	80381	hgsc.bcm.edu	37	15	74002006	74002006	+	Missense_Mutation	SNP	G	G	A	rs3825859	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85	42	95	0	0.494118	0	G|0.949;A|0.051	0.051	strong	.	CD276	29	.	NM_001024736	exon8	c.G1522A	p.G508R	CAGGATGGGGAGG	.	PASS	Atlas-SNP
IL10RA	3587	hgsc.bcm.edu	37	11	117864047	117864047	+	Silent	SNP	A	A	G	rs2256111	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98	81	106	0	0.826531	0	A|0.496;G|0.504	0.504	strong	.	IL10RA	46	.	NM_001558	exon4	c.A459G	p.A153A	CCCCGCAAATGAC	.	PASS	Atlas-SNP
UBQLNL	143630	hgsc.bcm.edu	37	11	5536852	5536852	+	Missense_Mutation	SNP	A	A	G	rs2017434	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	131	72	142	0	0.549618	0	A|0.689;G|0.311	0.311	strong	UBQLNL,colon,carcinoma,0,1	UBQLNL	74	1	NM_145053	exon1	c.T820C	p.Y274H	CAGCATAGTTCTG	.	PASS	Atlas-SNP
PCDHB11	56125	hgsc.bcm.edu	37	5	140579834	140579834	+	Missense_Mutation	SNP	G	G	A	rs61743184	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82	41	103	0	0.5	0	G|0.988;A|0.012	0.012	strong	.	PCDHB11	162	.	NM_018931	exon1	c.G487A	p.G163R	GATGTAGGAATCA	.	PASS	Atlas-SNP
AK8	158067	hgsc.bcm.edu	37	9	135703450	135703450	+	Missense_Mutation	SNP	G	G	T	rs114347984	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49	18	55	0	0.367347	0	G|0.997;T|0.003	0.003	strong	.	AK8	45	.	NM_152572	exon7	c.C506A	p.T169K	AGGACCGTGTCTG	.	PASS	Atlas-SNP
GORAB	92344	hgsc.bcm.edu	37	1	170521376	170521376	+	Missense_Mutation	SNP	G	G	A	rs913257	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98	46	120	0	0.469388	0	G|0.448;A|0.552	0.552	strong	.	GORAB	41	.	NM_152281	exon5	c.G958A	p.E320K	CTACACGAACAAG	.	PASS	Atlas-SNP
PRKAR2B	5577	hgsc.bcm.edu	37	7	106685448	106685448	+	Silent	SNP	G	G	T	rs75385144	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55	29	47	0	0.527273	0	G|0.707;T|0.293	0.293	strong	.	PRKAR2B	34	.	NM_002736	exon1	c.G96T	p.A32A	GTTCGCGCTGCAG	.	PASS	Atlas-SNP
CPNE7	27132	hgsc.bcm.edu	37	16	89644001	89644001	+	Missense_Mutation	SNP	T	T	C	rs455527	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	130	64	91	0	0.492308	0	T|0.915;C|0.085	0.085	strong	.	CPNE7	56	.	NM_153636	exon2	c.T229C	p.F77L	AAGGTCTTCACGG	.	PASS	Atlas-SNP
HELB	92797	hgsc.bcm.edu	37	12	66698895	66698895	+	Missense_Mutation	SNP	T	T	C	rs4430553	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	50	50	53	0	1	0	T|0.468;C|0.532	0.532	strong	.	HELB	90	.	NM_033647	exon2	c.T572C	p.L191P	TGTTCCTAGACAA	.	PASS	Atlas-SNP
ACTG1	71	hgsc.bcm.edu	37	17	79479101	79479101	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	37	10	73	0	0.27027	0	.	.	none	ACTG1,spleen,lymphoid_neoplasm,0,1	ACTG1	55	1	NM_001614	exon3	c.T191A	p.I64N	GTCAGGATGCCAC	.	PASS	Atlas-SNP
C4orf17	84103	hgsc.bcm.edu	37	4	100443784	100443784	+	Silent	SNP	C	C	G	rs61732380	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100	47	85	0	0.47	0	C|0.769;G|0.231	0.231	strong	.	C4orf17	42	.	NM_032149	exon3	c.C255G	p.S85S	CCCCTCCAGCACT	.	PASS	Atlas-SNP
ELAC2	60528	hgsc.bcm.edu	37	17	12899963	12899963	+	Silent	SNP	T	T	C	rs11545302	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	27	13	21	0	0.481481	0	T|0.745;C|0.255;A|0.000	0.255	strong	.	ELAC2	48	.	NM_018127	exon17	c.A1560G	p.T520T	CCCAAATGTGCCC	.	PASS	Atlas-SNP
OR2A2	442361	hgsc.bcm.edu	37	7	143807304	143807304	+	Missense_Mutation	SNP	T	T	C	rs10252253	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57	30	71	0	0.526316	0	T|0.806;C|0.194	0.194	strong	OR2A2,colon,carcinoma,0,1	OR2A2	48	1	NM_001005480	exon1	c.T629C	p.L210P	GGCCTCTTTCCTT	.	PASS	Atlas-SNP
CEP192	55125	hgsc.bcm.edu	37	18	13068132	13068132	+	Missense_Mutation	SNP	T	T	C	rs578208	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	45	20	70	0	0.444444	0	A|0.001;C|0.718	0.718	strong	.	CEP192	340	.	NM_032142	exon23	c.T4654C	p.S1552P	AAGGAATCCGTCC	.	PASS	Atlas-SNP
THRAP3	9967	hgsc.bcm.edu	37	1	36752152	36752152	+	Silent	SNP	C	C	T	rs2242428	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	124	62	131	0	0.5	0	C|0.710;T|0.290	0.290	strong	THRAP3,NS,carcinoma,+1,2	THRAP3	93	2	NM_005119	exon4	c.C321T	p.Y107Y	AAACTACCGCTCA	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	26	8	55	0	0.307692	0	T|0.938;C|0.062	0.062	strong	.	PITRM1	109	.	NM_014889	exon1	c.A23G	p.Q8R	AGGCCCTGCCGCC	.	PASS	Atlas-SNP
XYLT1	64131	hgsc.bcm.edu	37	16	17202801	17202801	+	Silent	SNP	G	G	A	rs34511974	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	114	58	107	0	0.508772	0	G|0.888;A|0.112	0.112	strong	XYLT1,colon,carcinoma,0,1	XYLT1	147	1	NM_022166	exon12	c.C2631T	p.P877P	GAGGACGGGGTTT	.	PASS	Atlas-SNP
FYCO1	79443	hgsc.bcm.edu	37	3	46007823	46007823	+	Missense_Mutation	SNP	G	G	T	rs71622515	alternate_allele	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	158	64	149	0	0.405063	0	GTT|0.500;TTC|0.500	.	alt	.	FYCO1	115	.	NM_024513	exon8	c.C3003A	p.N1001K	GAGGGTGTTGAGC	.	PASS	Atlas-SNP
EXO1	9156	hgsc.bcm.edu	37	1	242030151	242030151	+	Missense_Mutation	SNP	A	A	G	rs735943	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60	31	47	0	0.516667	0	T|0.001;G|0.609	0.609	strong	.	EXO1	103	.	NM_006027	exon9	c.A1061G	p.H354R	GAAGTCATAGTTG	.	PASS	Atlas-SNP
EPB41L4A	64097	hgsc.bcm.edu	37	5	111531387	111531387	+	Silent	SNP	A	A	T	rs149373122	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	77	37	86	0	0.480519	0	A|0.993;T|0.007	0.007	strong	.	EPB41L4A	130	.	NM_022140	exon16	c.T1395A	p.G465G	ATCTTCACCACTG	.	PASS	Atlas-SNP
WDFY4	57705	hgsc.bcm.edu	37	10	49998824	49998824	+	Silent	SNP	C	C	T	rs10857644	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	142	79	111	0	0.556338	0	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	.	PASS	Atlas-SNP
CCT6B	10693	hgsc.bcm.edu	37	17	33269648	33269648	+	Missense_Mutation	SNP	C	C	G	rs2230553	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	40	17	44	0	0.425	0	C|0.717;G|0.283	0.283	strong	.	CCT6B	63	.	NM_006584	exon7	c.G740C	p.G247A	AAGAAACCAGAGT	.	PASS	Atlas-SNP
TMIGD2	126259	hgsc.bcm.edu	37	19	4294807	4294807	+	Missense_Mutation	SNP	G	G	A	rs78320454	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79	42	79	0	0.531646	0	G|0.889;A|0.111	0.111	strong	.	TMIGD2	38	.	NM_144615	exon3	c.C413T	p.P138L	TGTGTGGGGTCAT	.	PASS	Atlas-SNP
SPHK1	8877	hgsc.bcm.edu	37	17	74383475	74383475	+	Silent	SNP	T	T	C	rs3744037	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100	45	65	0	0.45	0	T|0.796;C|0.204	0.204	strong	.	SPHK1	24	.	NM_182965	exon6	c.T1221C	p.Y407Y	GGTATATGTGCCC	.	PASS	Atlas-SNP
FXYD4	53828	hgsc.bcm.edu	37	10	43869097	43869097	+	Splice_Site	SNP	C	C	A	rs10899795	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	25	14	17	0	0.56	0	C|0.603;A|0.397	0.397	strong	.	FXYD4	9	.	.	.	.	.	TCCTCTCGCTGAC	.	PASS	Atlas-SNP
KEAP1	9817	hgsc.bcm.edu	37	19	10600442	10600442	+	Silent	SNP	G	G	C	rs1048290	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100	50	88	0	0.5	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
KANSL1	284058	hgsc.bcm.edu	37	17	44248837	44248837	+	Missense_Mutation	SNP	T	T	C	rs35643216	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	315	164	190	0	0.520635	0	T|0.857;C|0.143	0.143	strong	.	.	.	.	NM_001193466	exon2	c.A673G	p.N225D	TATTATTGCTATA	.	PASS	Atlas-SNP
MRO	83876	hgsc.bcm.edu	37	18	48333203	48333203	+	Missense_Mutation	SNP	C	C	G	rs4940019	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	53	45	0	1	0	C|0.579;G|0.421	0.421	strong	.	MRO	36	.	NM_001127175	exon3	c.G159C	p.R53S	CTGGAACCTCAGT	.	PASS	Atlas-SNP
KLRG1	10219	hgsc.bcm.edu	37	12	9142297	9142297	+	Silent	SNP	T	T	C	rs1805723	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51	24	38	0	0.470588	0	T|0.639;C|0.361	0.361	strong	.	KLRG1	16	.	NM_005810	exon1	c.T66C	p.Y22Y	TGACTATGGACCA	.	PASS	Atlas-SNP
SMCR8	140775	hgsc.bcm.edu	37	17	18220674	18220674	+	Missense_Mutation	SNP	C	C	T	rs8080966	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	88	37	84	0	0.420455	0	C|0.770;T|0.230	0.230	strong	.	SMCR8	62	.	NM_144775	exon1	c.C1571T	p.P524L	CCTGCCCCTCTGA	.	PASS	Atlas-SNP
FAM83E	54854	hgsc.bcm.edu	37	19	49116359	49116359	+	Missense_Mutation	SNP	T	T	C	rs447802	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	105	42	156	0	0.4	0	T|0.521;C|0.479	0.479	strong	FAM83E,NS,carcinoma,0,2	FAM83E	34	2	NM_017708	exon1	c.A271G	p.T91A	CATCGGTGGTGGT	.	PASS	Atlas-SNP
GRM6	2916	hgsc.bcm.edu	37	5	178416063	178416063	+	Silent	SNP	G	G	A	rs2645339	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	97	96	116	0	0.989691	0	G|0.502;A|0.498	0.498	strong	GRM6,NS,adenoma,0,1	GRM6	149	1	NM_000843	exon6	c.C1227T	p.Y409Y	AATGGCGTACACC	.	PASS	Atlas-SNP
ABCC1	4363	hgsc.bcm.edu	37	16	16139714	16139714	+	Silent	SNP	T	T	C	rs35587	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69	32	68	0	0.463768	0	T|0.576;C|0.424	0.424	strong	.	ABCC1	156	.	NM_004996	exon9	c.T1062C	p.N354N	CGTGAATGACACG	.	PASS	Atlas-SNP
ANKRD6	22881	hgsc.bcm.edu	37	6	90338863	90338863	+	Silent	SNP	C	C	T	rs9353687	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	50	18	56	0	0.36	0	C|0.815;T|0.185	0.185	strong	.	ANKRD6	51	.	NM_001242809	exon15	c.C1518T	p.C506C	CTGGTGCATGTTA	.	PASS	Atlas-SNP
OGDHL	55753	hgsc.bcm.edu	37	10	50944528	50944528	+	Missense_Mutation	SNP	C	C	A	rs140281439	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	28	58	0	0.444444	0	C|0.998;A|0.002	0.002	strong	OGDHL,NS,carcinoma,0,1	OGDHL	149	1	NM_018245	exon21	c.G2629T	p.A877S	GTGCTGCGGCCCC	.	PASS	Atlas-SNP
BTG1	694	hgsc.bcm.edu	37	12	92539189	92539189	+	Silent	SNP	G	G	A	rs201780644	by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	106	30	109	0	0.283019	0	G|1.000;A|0.000	0.000	strong	.	BTG1	30	.	NM_001731	exon1	c.C123T	p.S41S	GCTCTGGCTGAAG	.	PASS	Atlas-SNP
COG6	57511	hgsc.bcm.edu	37	13	40293428	40293428	+	Missense_Mutation	SNP	T	T	C	rs41286961	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	162	106	87	0	0.654321	0	T|0.946;C|0.054	0.054	strong	.	COG6	49	.	NM_001145079	exon14	c.T1340C	p.M447T	CACTCATGTTGCT	.	PASS	Atlas-SNP
MED14	9282	hgsc.bcm.edu	37	X	40573157	40573157	+	Silent	SNP	G	G	A	rs6520683	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	97	57	94	0	0.587629	0	G|0.693;A|0.307	0.307	strong	.	MED14	108	.	NM_004229	exon5	c.C525T	p.D175D	AATTTTGTCCTGC	.	PASS	Atlas-SNP
TSPEAR	54084	hgsc.bcm.edu	37	21	45949769	45949769	+	Silent	SNP	G	G	A	rs117791519	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57	40	36	0	0.701754	0	G|0.996;A|0.004	0.004	strong	.	TSPEAR	110	.	NM_144991	exon5	c.C702T	p.N234N	CGGGGCGTTCCTG	.	PASS	Atlas-SNP
DNAH5	1767	hgsc.bcm.edu	37	5	13762972	13762972	+	Silent	SNP	T	T	C	rs6554812	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73	29	72	0	0.39726	0	T|0.714;C|0.286	0.286	strong	DNAH5,NS,carcinoma,-2,1	DNAH5	868	1	NM_001369	exon60	c.A10140G	p.E3380E	CAAAAATTCTATC	.	PASS	Atlas-SNP
DUSP4	1846	hgsc.bcm.edu	37	8	29197672	29197672	+	Silent	SNP	A	A	G	rs583034	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	35	20	25	0	0.571429	0	A|0.447;G|0.553	0.553	strong	.	DUSP4	58	.	NM_001394	exon2	c.T522C	p.S174S	TGTGGCACTGGGG	.	PASS	Atlas-SNP
RTN4IP1	84816	hgsc.bcm.edu	37	6	107076783	107076783	+	Silent	SNP	A	A	T	rs1987623	bycluster;byfrequency;bysubmitter;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	118	118	130	1	1	0.00769231	A|0.608;T|0.392	0.392	strong	.	RTN4IP1	31	.	NM_032730	exon1	c.T114A	p.P38P	GCTCCTAGGAGAG	.	PASS	Atlas-SNP
SOGA3	387104	hgsc.bcm.edu	37	6	127797179	127797179	+	Silent	SNP	G	G	A	rs3734448	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	38	16	56	0	0.421053	0	G|0.657;A|0.343	0.343	strong	.	.	.	.	NM_001012279	exon6	c.C1992T	p.A664A	CAGGTCGGCCACG	.	PASS	Atlas-SNP
XRRA1	143570	hgsc.bcm.edu	37	11	74563077	74563077	+	Silent	SNP	G	G	A	rs2304683	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	105	103	88	0	0.980952	0	G|0.689;A|0.311	0.311	strong	.	XRRA1	46	.	NM_182969	exon13	c.C1197T	p.C399C	GAACTCGCAGAGA	.	PASS	Atlas-SNP
TRIM67	440730	hgsc.bcm.edu	37	1	231335983	231335983	+	Silent	SNP	C	C	T	rs139376072	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57	22	67	0	0.385965	0	C|0.992;T|0.008	0.008	strong	.	TRIM67	160	.	NM_001004342	exon4	c.C1353T	p.N451N	GGAGAACGACCCC	.	PASS	Atlas-SNP
KRAS	3845	hgsc.bcm.edu	37	12	25362777	25362777	+	Silent	SNP	A	A	G	rs1137282	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	122	63	102	0	0.516393	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
C1orf177	163747	hgsc.bcm.edu	37	1	55273580	55273580	+	Missense_Mutation	SNP	G	G	T	rs9782980	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98	98	78	0	1	0	G|0.474;T|0.526	0.526	strong	.	C1orf177	36	.	NM_001110533	exon4	c.G376T	p.G126C	GGCCCCGGCTCCT	.	PASS	Atlas-SNP
SEC16B	89866	hgsc.bcm.edu	37	1	177902388	177902388	+	Silent	SNP	G	G	A	rs3813647	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	32	62	0	0.477612	0	G|0.878;A|0.122	0.122	strong	.	SEC16B	92	.	NM_033127	exon22	c.C2784T	p.P928P	TCCAGCGGGGGAT	.	PASS	Atlas-SNP
MLL3	58508	hgsc.bcm.edu	37	7	151962183	151962183	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	288	20	245	0	0.0694444	0	.	.	none	MLL3_ENST00000355193,right_upper_lobe,carcinoma,0,2	MLL3	1564	2	NM_170606	exon8	c.T1124G	p.V375G	GGAGTAACCGCTA	.	scavenged	Atlas-SNP
VCPIP1	80124	hgsc.bcm.edu	37	8	67577670	67577670	+	Silent	SNP	G	G	A	rs3808602	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	238	110	214	0	0.462185	0	G|0.858;A|0.142	0.142	strong	.	VCPIP1	110	.	NM_025054	exon1	c.C1524T	p.Y508Y	AAAGCTGTAATTT	.	PASS	Atlas-SNP
POLL	27343	hgsc.bcm.edu	37	10	103340056	103340056	+	Missense_Mutation	SNP	G	G	A	rs3730477	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	111	55	116	0	0.495495	0	G|0.858;A|0.142	0.142	strong	.	POLL	43	.	NM_013274	exon8	c.C1312T	p.R438W	GGGACCGGCCATC	.	PASS	Atlas-SNP
FAM86B1	85002	hgsc.bcm.edu	37	8	12044042	12044042	+	Silent	SNP	G	G	A	rs76431111	byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	160	25	154	0	0.15625	0	G|0.500;A|0.500	0.500	strong	FAM86B1,NS,carcinoma,0,1	FAM86B1	7	1	NM_001083537	exon5	c.C459T	p.S153S	AGGGTCGCTGAAG	.	scavenged	Atlas-SNP
ZC3H4	23211	hgsc.bcm.edu	37	19	47585517	47585517	+	Silent	SNP	G	G	C	rs7250850	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	186	185	152	0	0.994624	0	G|0.552;C|0.448	0.448	strong	.	ZC3H4	96	.	NM_015168	exon10	c.C1254G	p.L418L	CTTTGGGAGTTCG	.	PASS	Atlas-SNP
YAE1D1	57002	hgsc.bcm.edu	37	7	39606107	39606107	+	Silent	SNP	G	G	A	rs1051162	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	18	18	40	0	1	0	G|0.842;A|0.158	0.158	strong	C7orf36,NS,carcinoma,0,1	YAE1D1	2	1	NM_020192	exon1	c.G90A	p.A30A	CCTGGCGCAGCGG	.	PASS	Atlas-SNP
CCDC39	339829	hgsc.bcm.edu	37	3	180377529	180377529	+	Missense_Mutation	SNP	G	G	C	rs112738198	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	89	42	85	0	0.47191	0	G|0.983;C|0.017	0.017	strong	.	CCDC39	242	.	NM_181426	exon5	c.C545G	p.T182S	TCCAAAGTTAGTC	.	PASS	Atlas-SNP
C3orf30	152405	hgsc.bcm.edu	37	3	118865647	118865647	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	22	68	0	0.468085	0	.	.	none	C3orf30,NS,carcinoma,0,1	C3orf30	64	1	NM_152539	exon1	c.G611A	p.R204Q	CTGAGCGAAGAAC	.	PASS	Atlas-SNP
GORASP1	64689	hgsc.bcm.edu	37	3	39140352	39140352	+	Missense_Mutation	SNP	C	C	A	rs138864486	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	131	58	107	0	0.442748	0	C|0.993;A|0.007	0.007	strong	.	GORASP1	42	.	NM_031899	exon8	c.G949T	p.D317Y	TGTTGTCCAAGAG	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1270965	1270965	+	Silent	SNP	G	G	A	rs114687104	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	167	63	165	0	0.377246	0	G|0.958;A|0.042	0.042	strong	MUC5B,NS,haematopoietic_neoplasm,0,2	MUC5B	473	2	NM_002458	exon31	c.G12855A	p.P4285P	CAGCCCGGCCACC	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1265831	1265831	+	Missense_Mutation	SNP	T	T	C	rs200031789	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	306	39	256	5	0.127451	0.0195312	T|0.998;C|0.002	0.002	weak	MUC5AC,NS,carcinoma,0,1	MUC5B	473	1	NM_002458	exon31	c.T7721C	p.V2574A	AGACTGTCCACAC	.	scavenged	Atlas-SNP
APOB	338	hgsc.bcm.edu	37	2	21238367	21238367	+	Missense_Mutation	SNP	C	C	T	rs12713843	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	39	22	59	0	0.564103	0	C|0.997;T|0.003	0.003	strong	APOB,NS,carcinoma,0,1	APOB	761	1	NM_000384	exon22	c.G3383A	p.R1128H	TGCAAACGGGGTA	.	PASS	Atlas-SNP
KCNMA1	3778	hgsc.bcm.edu	37	10	78944590	78944590	+	Silent	SNP	G	G	A	rs1131824	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	20	64	0	0.384615	0	G|0.579;A|0.421	0.421	strong	.	KCNMA1	370	.	NM_001161352	exon4	c.C687T	p.F229F	CAAGCCGAAGTAG	.	PASS	Atlas-SNP
CXorf21	80231	hgsc.bcm.edu	37	X	30577846	30577846	+	Silent	SNP	A	A	C	rs887369	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	130	34	100	0	0.261538	0	A|0.160;0|0.002	.	strong	.	CXorf21	42	.	NM_025159	exon3	c.T627G	p.V209V	ATTCAGAACTGCA	.	PASS	Atlas-SNP
COX11	1353	hgsc.bcm.edu	37	17	53038654	53038654	+	Missense_Mutation	SNP	A	A	C	rs1802212	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	35	63	0	0.530303	0	A|0.835;C|0.165	0.165	strong	.	COX11	16	.	NM_001162861	exon4	c.T682G	p.S228A	ACGTAGACTCTGT	.	PASS	Atlas-SNP
HNF1A	6927	hgsc.bcm.edu	37	12	121435427	121435427	+	Missense_Mutation	SNP	G	G	A	rs2464196	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	127	124	114	0	0.976378	0	G|0.725;A|0.275	0.275	strong	.	HNF1A	302	.	NM_000545	exon7	c.G1460A	p.S487N	CCCAGAGCCCCTT	.	PASS	Atlas-SNP
TNXB	7148	hgsc.bcm.edu	37	6	32064726	32064726	+	Missense_Mutation	SNP	T	T	C	rs1150752	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	233	178	264	0	0.763949	0	T|0.967;C|0.033	0.033	strong	.	TNXB	553	.	NM_019105	exon3	c.A904G	p.T302A	CGCCAGTGTAGCC	.	PASS	Atlas-SNP
LAMA1	284217	hgsc.bcm.edu	37	18	7011413	7011413	+	Silent	SNP	G	G	A	rs619106	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82	44	103	0	0.536585	0	G|0.609;A|0.391	0.391	strong	LAMA1,NS,carcinoma,0,1	LAMA1	458	1	NM_005559	exon25	c.C3573T	p.T1191T	CCCCTCGGTCGTG	.	PASS	Atlas-SNP
VWA5B2	90113	hgsc.bcm.edu	37	3	183951431	183951431	+	Missense_Mutation	SNP	C	C	T	rs902417	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	125	58	110	0	0.464	0	C|0.788;T|0.212	0.212	strong	VWA5B2,NS,carcinoma,0,1	VWA5B2	47	1	NM_138345	exon4	c.C598T	p.P200S	GCTGCCCCTCGGG	.	PASS	Atlas-SNP
NLRC5	84166	hgsc.bcm.edu	37	16	57101340	57101340	+	Missense_Mutation	SNP	T	T	C	rs7190199	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	193	107	187	1	0.554404	0.00534759	T|0.912;C|0.088	0.088	strong	.	NLRC5	186	.	NM_032206	exon34	c.T4364C	p.V1455A	TTCTTGTCGGGCA	.	PASS	Atlas-SNP
SLC7A1	6541	hgsc.bcm.edu	37	13	30110256	30110256	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	31	78	0	0.43662	0	.	.	none	.	SLC7A1	64	.	NM_003045	exon3	c.G70C	p.E24Q	TCTCCTCCCGGCT	.	PASS	Atlas-SNP
PARVA	55742	hgsc.bcm.edu	37	11	12525965	12525965	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	131	63	160	0	0.480916	0	.	.	none	.	PARVA	27	.	NM_018222	exon6	c.G766C	p.V256L	CAAGTGGTTGTGG	.	PASS	Atlas-SNP
NPAP1	23742	hgsc.bcm.edu	37	15	24922230	24922230	+	Missense_Mutation	SNP	C	C	G	rs3742950	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49	17	62	0	0.346939	0	C|0.509;G|0.491	0.491	strong	.	.	.	.	NM_018958	exon1	c.C1216G	p.Q406E	CCTGTGCAGACCA	.	PASS	Atlas-SNP
SETD9	133383	hgsc.bcm.edu	37	5	56209735	56209735	+	Missense_Mutation	SNP	A	A	G	rs40497	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55	28	57	0	0.509091	0	A|0.788;G|0.212	0.212	strong	.	.	.	.	NM_153706	exon4	c.A625G	p.K209E	CCTTTAAAAATGA	.	PASS	Atlas-SNP
ADCK1	57143	hgsc.bcm.edu	37	14	78392115	78392115	+	Silent	SNP	G	G	A	rs55721310	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	33	73	0	0.5	0	G|0.991;A|0.009	0.009	strong	.	ADCK1	81	.	NM_020421	exon9	c.G1017A	p.T339T	GCTCACGGAAGAA	.	PASS	Atlas-SNP
PKD1	5310	hgsc.bcm.edu	37	16	2164244	2164244	+	Missense_Mutation	SNP	G	G	A	rs139963923		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	24	78	0	0.380952	0	G|1.000;A|0.000	0.000	weak	.	PKD1	184	.	NM_000296	exon11	c.C2780T	p.T927M	TCCGCCGTCACCC	.	PASS	Atlas-SNP
PTGFRN	5738	hgsc.bcm.edu	37	1	117529458	117529458	+	Missense_Mutation	SNP	G	G	A	rs10801922	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	26	58	0	0.553191	0	G|0.560;A|0.440	0.440	strong	PTGFRN,NS,carcinoma,-2,1	PTGFRN	91	1	NM_020440	exon9	c.G2509A	p.V837I	ATCGGCGTCGGTC	.	PASS	Atlas-SNP
OVOL2	58495	hgsc.bcm.edu	37	20	18022362	18022362	+	Silent	SNP	G	G	T	rs6111803	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	66	55	0	1	0	G|0.945;T|0.055	0.055	strong	.	OVOL2	18	.	NM_021220	exon3	c.C327A	p.T109T	GCCTGTGGTGAAC	.	PASS	Atlas-SNP
PACSIN2	11252	hgsc.bcm.edu	37	22	43278220	43278220	+	Silent	SNP	C	C	T	rs2899365	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	71	53	0	0.959459	0	C|0.642;T|0.358	0.358	strong	.	PACSIN2	48	.	NM_007229	exon7	c.G876A	p.P292P	CATGCCCGGCCCG	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1093272	1093272	+	Silent	SNP	A	A	C	rs56230143		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	37	6	36	0	0.162162	0	.	.	weak	MUC2_ENST00000441003,NS,carcinoma,0,8	MUC2	614	8	NM_002457	exon30	c.A5091C	p.T1697T	CCCAACATCGACA	.	scavenged	Atlas-SNP
FSHR	2492	hgsc.bcm.edu	37	2	49191041	49191041	+	Missense_Mutation	SNP	C	C	T	rs6165	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93	90	103	0	0.967742	0	C|0.525;T|0.475	0.475	strong	.	FSHR	164	.	NM_000145	exon10	c.G919A	p.A307T	CCCTAGCCTGAGT	.	PASS	Atlas-SNP
VANGL1	81839	hgsc.bcm.edu	37	1	116206871	116206871	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	46	25	60	0	0.543478	0	.	.	none	.	VANGL1	65	.	NM_138959	exon4	c.A794G	p.Y265C	GCTTCTACAGCCT	.	PASS	Atlas-SNP
RNF215	200312	hgsc.bcm.edu	37	22	30782089	30782089	+	Silent	SNP	A	A	G	rs5997629	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48	20	40	0	0.416667	0	A|0.674;G|0.326	0.326	strong	.	RNF215	19	.	NM_001017981	exon3	c.T471C	p.L157L	GATGAGAAGAAGC	.	PASS	Atlas-SNP
DAGLA	747	hgsc.bcm.edu	37	11	61487690	61487690	+	Silent	SNP	G	G	A	rs198430	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69	35	70	0	0.507246	0	G|0.742;A|0.258	0.258	strong	DAGLA,NS,carcinoma,0,1	DAGLA	109	1	NM_006133	exon2	c.G63A	p.P21P	CCTACCGGCCATC	.	PASS	Atlas-SNP
PIGT	51604	hgsc.bcm.edu	37	20	44048224	44048224	+	Silent	SNP	T	T	C	rs147475258	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	88	35	57	0	0.397727	0	T|0.999;C|0.001	0.001	strong	.	PIGT	85	.	NM_001184729	exon5	c.T675C	p.V225V	CCCTGTTTGCAGA	.	PASS	Atlas-SNP
CYP2A7	1549	hgsc.bcm.edu	37	19	41382544	41382544	+	Silent	SNP	G	G	A	rs116333747	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	254	119	202	0	0.468504	0	G|0.992;A|0.008	0.008	strong	.	CYP2A7	71	.	NM_000764	exon8	c.C1191T	p.S397S	CAGCACGGAGCCC	.	PASS	Atlas-SNP
TMCC2	9911	hgsc.bcm.edu	37	1	205238275	205238275	+	Silent	SNP	A	A	G	rs1768586	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	197	99	180	0	0.502538	0	A|0.748;G|0.252	0.252	strong	.	TMCC2	89	.	NM_014858	exon3	c.A945G	p.A315A	TGTGGCAGAGTAT	.	PASS	Atlas-SNP
PCDHB16	57717	hgsc.bcm.edu	37	5	140564454	140564454	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	152	50	133	0	0.328947	0	.	.	none	.	PCDHB16	159	.	NM_020957	exon1	c.T2320G	p.F774V	CCCAACTTCTCTC	.	PASS	Atlas-SNP
ETV3L	440695	hgsc.bcm.edu	37	1	157069154	157069154	+	Silent	SNP	A	A	G	rs16838075	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	78	42	100	0	0.538462	0	A|0.729;G|0.271	0.271	strong	.	ETV3L	73	.	NM_001004341	exon2	c.T75C	p.D25D	GGCCCAATCAGGG	.	PASS	Atlas-SNP
MAGI2	9863	hgsc.bcm.edu	37	7	78636484	78636484	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	25	100	0	0.337838	0	.	.	none	MAGI2,caecum,carcinoma,0,1	MAGI2	246	1	NM_012301	exon2	c.T340G	p.L114V	ATCGTAAGTTGAG	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1081112	1081112	+	Missense_Mutation	SNP	G	G	C	rs41345745	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	86	108	1	1	0.00925926	G|0.716;C|0.284	0.284	strong	.	MUC2	614	.	NM_002457	exon11	c.G1408C	p.E470Q	CTCAACGAGCTGC	.	PASS	Atlas-SNP
OR2T3	343173	hgsc.bcm.edu	37	1	248637391	248637391	+	Missense_Mutation	SNP	C	C	T	rs150934113	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	413	44	478	1	0.106538	0.00209205	C|0.956;T|0.044	0.044	strong	OR2T3,colon,carcinoma,0,1	OR2T3	79	1	NM_001005495	exon1	c.C740T	p.S247F	CCTGCTCCTCCCA	.	scavenged	Atlas-SNP
SLC52A3	113278	hgsc.bcm.edu	37	20	746098	746098	+	Silent	SNP	G	G	A	rs3746808	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	35	82	0	0.564516	0	G|0.754;A|0.246	0.246	strong	.	.	.	.	NM_033409	exon2	c.C321T	p.A107A	CAAGAAGGCGATG	.	PASS	Atlas-SNP
HDAC10	83933	hgsc.bcm.edu	37	22	50686830	50686830	+	Silent	SNP	G	G	A	rs35820251	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	36	18	40	0	0.5	0	A|0.024;C|0.000;G|0.976	0.024	strong	.	HDAC10	29	.	NM_032019	exon11	c.C978T	p.A326A	GGGTGGGGCCGGG	.	PASS	Atlas-SNP
PM20D1	148811	hgsc.bcm.edu	37	1	205819104	205819104	+	Missense_Mutation	SNP	G	G	A	rs11540014	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	139	77	122	0	0.553957	0	G|0.889;A|0.111	0.111	strong	.	PM20D1	56	.	NM_152491	exon1	c.C97T	p.H33Y	TTTGATGCTCCCC	.	PASS	Atlas-SNP
TUFT1	7286	hgsc.bcm.edu	37	1	151512895	151512895	+	Missense_Mutation	SNP	A	A	G	rs3828054	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60	27	64	0	0.45	0	A|0.885;G|0.115	0.115	strong	TUFT1,NS,carcinoma,0,1	TUFT1	32	1	NM_020127	exon1	c.A53G	p.Q18R	AGGACCAGGCGGC	.	PASS	Atlas-SNP
CARD14	79092	hgsc.bcm.edu	37	17	78166385	78166385	+	Silent	SNP	C	C	T	rs11658460	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	166	65	170	0	0.391566	0	C|0.895;T|0.105	0.105	strong	CARD14_ENST00000309710,NS,carcinoma,0,2	CARD14	98	2	NM_024110	exon9	c.C1323T	p.D441D	CAGAGACGACAGC	.	PASS	Atlas-SNP
ARHGEF4	50649	hgsc.bcm.edu	37	2	131688783	131688783	+	Missense_Mutation	SNP	G	G	A	rs61750360	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	11	73	0	0.203704	0	G|0.866;A|0.134	0.134	strong	.	ARHGEF4	89	.	NM_032995	exon3	c.G253A	p.V85I	GCCCACGTCGAAA	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	48	97	0	0.551724	0	A|0.732;G|0.268	0.268	strong	.	MLX	17	.	NM_170607	exon7	c.A668G	p.Q223R	CACACCAGGACAA	.	PASS	Atlas-SNP
TUBA3C	7278	hgsc.bcm.edu	37	13	19751544	19751544	+	Silent	SNP	C	C	T	rs61735701	byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	275	129	257	1	0.469091	0.00389105	C|0.737;T|0.263	0.263	strong	.	TUBA3C	166	.	NM_006001	exon4	c.G579A	p.T193T	CAGGGTCGTGTGG	.	PASS	Atlas-SNP
MBTPS1	8720	hgsc.bcm.edu	37	16	84125394	84125394	+	Silent	SNP	G	G	A	rs113848224	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	90	36	120	0	0.4	0	G|0.998;A|0.002	0.002	strong	.	MBTPS1	85	.	NM_003791	exon7	c.C906T	p.D302D	TAACACGTCGATC	.	PASS	Atlas-SNP
SOGA1	140710	hgsc.bcm.edu	37	20	35414905	35414905	+	Missense_Mutation	SNP	G	G	T	rs73109216	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	16	10	20	0	0.625	0	G|0.950;T|0.050	0.050	strong	.	SOGA1	136	.	NM_080627	exon15	c.C4969A	p.L1657I	GGGGGAGTGCCCT	.	PASS	Atlas-SNP
GGT1	2678	hgsc.bcm.edu	37	22	25023419	25023419	+	Silent	SNP	C	C	T	rs202087650	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	292	34	228	4	0.116438	0.0175439	C|0.989;T|0.011	0.011	strong	GGT1,NS,carcinoma,0,2	GGT1	68	2	NM_013430	exon12	c.C1041T	p.S347S	GACCTCCGAGTTC	.	scavenged	Atlas-SNP
ADAMTS14	140766	hgsc.bcm.edu	37	10	72503344	72503344	+	Silent	SNP	G	G	A	rs10999502	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	127	69	99	0	0.543307	0	G|0.768;A|0.232	0.232	strong	ADAMTS14,NS,adenoma,0,1	ADAMTS14	148	1	NM_139155	exon13	c.G1974A	p.T658T	GGACACGGGGGAC	.	PASS	Atlas-SNP
TERT	7015	hgsc.bcm.edu	37	5	1294086	1294086	+	Silent	SNP	C	C	T	rs2736098	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	16	16	13	0	1	0	C|0.792;T|0.208	0.208	strong	.	TERT	2594	.	NM_001193376	exon2	c.G915A	p.A305A	GGGGCCCGCGTGG	.	PASS	Atlas-SNP
LRP1B	53353	hgsc.bcm.edu	37	2	141773397	141773397	+	Silent	SNP	C	C	A	rs78806080	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	104	20	129	0	0.192308	0	C|0.957;A|0.043	0.043	strong	.	LRP1B	1315	.	NM_018557	exon13	c.G2058T	p.R686R	AATCTGCCGATTG	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29910761	29910761	+	Missense_Mutation	SNP	G	G	A	rs1136688	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	118	118	186	0	1	0	A|0.386;G|0.614	0.386	strong	.	HLA-A	89	.	NM_001242758	exon2	c.G301A	p.D101N	CGAGTGGACCTGG	.	PASS	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149503834	149503834	+	Nonsense_Mutation	SNP	G	G	T	rs141503732	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	161	87	159	0	0.540373	0	G|0.996;T|0.004	0.004	strong	.	.	.	.	NM_198455	exon59	c.G8662T	p.E2888X	TGCCCAGAGAACA	.	PASS	Atlas-SNP
PSPC1	55269	hgsc.bcm.edu	37	13	20279879	20279879	+	Missense_Mutation	SNP	T	T	C	rs200516102	byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	452	140	566	4	0.309735	0.00706714	T|0.998;C|0.002	0.002	strong	PSPC1,NS,haematopoietic_neoplasm,0,1	PSPC1	61	1	NM_001042414	exon9	c.A1309G	p.M437V	GACCCATTGGTGG	.	scavenged	Atlas-SNP
PLEKHH3	79990	hgsc.bcm.edu	37	17	40822678	40822678	+	Silent	SNP	C	C	T	rs2277618	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	26	77	0	0.412698	0	C|0.843;T|0.157	0.157	strong	.	PLEKHH3	49	.	NM_024927	exon10	c.G1467A	p.G489G	TCTCCACCCGGAG	.	PASS	Atlas-SNP
PXK	54899	hgsc.bcm.edu	37	3	58410554	58410554	+	Missense_Mutation	SNP	C	C	T	rs34579268	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	150	79	144	0	0.526667	0	C|0.691;T|0.309	0.309	strong	PXK_ENST00000356151,brain,glioma,0,1	PXK	89	1	NM_017771	exon18	c.C1604T	p.A535V	CCGAGGCACCTGC	.	PASS	Atlas-SNP
LRRC47	57470	hgsc.bcm.edu	37	1	3712513	3712513	+	Silent	SNP	G	G	C	rs148481344	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	59	34	80	2	0.576271	0.025	G|0.985;C|0.015	0.015	strong	LRRC47,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	LRRC47	42	1	NM_020710	exon1	c.C528G	p.G176G	CAGCGCGCCGGGG	.	scavenged	Atlas-SNP
BAIAP2L1	55971	hgsc.bcm.edu	37	7	97922875	97922875	+	Silent	SNP	G	G	A	rs13008	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	95	93	83	0	0.978947	0	G|0.717;A|0.283	0.283	strong	.	BAIAP2L1	61	.	NM_018842	exon14	c.C1494T	p.R498R	AGTCGGGCGGAGT	.	PASS	Atlas-SNP
TM9SF1	10548	hgsc.bcm.edu	37	14	24662177	24662177	+	Missense_Mutation	SNP	C	C	T	rs10583	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	105	54	77	0	0.514286	0	C|0.908;T|0.092	0.092	strong	.	TM9SF1	58	.	NM_001014842	exon3	c.G644A	p.R215H	CTCCGACGCTCCA	.	PASS	Atlas-SNP
PPP1R15A	23645	hgsc.bcm.edu	37	19	49377873	49377873	+	Silent	SNP	G	G	A	rs35023389	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	28	80	0	0.4375	0	G|0.860;A|0.140	0.140	strong	.	PPP1R15A	48	.	NM_014330	exon2	c.G1383A	p.L461L	AGCCTTGGGAGAA	.	PASS	Atlas-SNP
IL2RB	3560	hgsc.bcm.edu	37	22	37524619	37524619	+	Missense_Mutation	SNP	G	G	T	rs228942	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44	23	54	0	0.522727	0	G|0.839;T|0.161	0.161	strong	.	IL2RB	44	.	NM_000878	exon10	c.C1173A	p.D391E	ATCAGGGTCTTCC	.	PASS	Atlas-SNP
FAM220A	84792	hgsc.bcm.edu	37	7	6370305	6370305	+	Missense_Mutation	SNP	C	C	G	rs3750039	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	107	57	83	0	0.53271	0	C|0.397;G|0.603	0.603	strong	.	.	.	.	NM_001037163	exon2	c.G481C	p.V161L	CCGGCACTTTTTG	.	PASS	Atlas-SNP
FAM83G	644815	hgsc.bcm.edu	37	17	18881605	18881605	+	Missense_Mutation	SNP	C	C	A	rs201344489	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	119	72	119	0	0.605042	0	C|0.998;A|0.002	0.002	strong	.	FAM83G	51	.	NM_001039999	exon5	c.G1374T	p.Q458H	CTGGTGCTGGGCG	.	PASS	Atlas-SNP
TGFBR3	7049	hgsc.bcm.edu	37	1	92262874	92262874	+	Silent	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	163	162	127	0	0.993865	0	.	.	none	.	TGFBR3	103	.	NM_001195684	exon4	c.A216G	p.A72A	CTGGCCTGCAGTG	.	PASS	Atlas-SNP
RNF213	57674	hgsc.bcm.edu	37	17	78363847	78363847	+	Silent	SNP	G	G	A	rs3185057	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	106	49	102	0	0.462264	0	G|0.916;A|0.084	0.084	strong	RNF213_ENST00000411702,caecum,carcinoma,0,2	RNF213	766	2	NM_001256071	exon67	c.G15321A	p.A5107A	CAAAGCGGATCTG	.	PASS	Atlas-SNP
CACNA2D4	93589	hgsc.bcm.edu	37	12	1910786	1910786	+	Missense_Mutation	SNP	C	C	T	rs62621429	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	32	49	0	0.52459	0	C|0.979;T|0.021	0.021	strong	.	CACNA2D4	220	.	NM_172364	exon30	c.G2746A	p.D916N	CACCATCCACCTC	.	PASS	Atlas-SNP
C12orf77	196415	hgsc.bcm.edu	37	12	25148927	25148927	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	179	42	120	0	0.234637	0	.	.	none	.	C12orf77	18	.	NM_001101339	exon3	c.G221A	p.S74N	CGTATGCTGTCCA	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	45	45	51	0	1	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
DOCK1	1793	hgsc.bcm.edu	37	10	129245684	129245684	+	Missense_Mutation	SNP	G	G	A	rs869801	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	37	80	0	0.493333	0	G|0.786;A|0.214	0.214	strong	DOCK1,NS,carcinoma,0,1	DOCK1	188	1	NM_001380	exon51	c.G5377A	p.A1793T	ACGGGGGCGGACG	.	PASS	Atlas-SNP
SLC2A2	6514	hgsc.bcm.edu	37	3	170732300	170732300	+	Missense_Mutation	SNP	G	G	A	rs5400	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110	44	128	0	0.4	0	G|0.776;A|0.224	0.224	strong	.	SLC2A2	71	.	NM_000340	exon3	c.C329T	p.T110I	GATGCAGTCATTC	.	PASS	Atlas-SNP
C1orf173	127254	hgsc.bcm.edu	37	1	75097426	75097426	+	Missense_Mutation	SNP	G	G	C	rs11210490	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	246	245	237	0	0.995935	0	G|0.588;C|0.412	0.412	strong	.	C1orf173	380	.	NM_001002912	exon7	c.C790G	p.P264A	CATTTGGAGCAGT	.	PASS	Atlas-SNP
DAGLB	221955	hgsc.bcm.edu	37	7	6449496	6449496	+	Missense_Mutation	SNP	T	T	C	rs2303361	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	122	70	94	0	0.57377	0	T|0.832;C|0.168	0.168	strong	.	DAGLB	74	.	NM_139179	exon15	c.A1991G	p.Q664R	ACCCCTTGTGCTG	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	56	54	0	0.666667	0	0|0.015;C|0.478	0.478	strong	.	GPR112	459	.	NM_153834	exon6	c.T4618C	p.S1540P	AAATCTTCTAAAA	.	PASS	Atlas-SNP
PGPEP1L	145814	hgsc.bcm.edu	37	15	99511793	99511793	+	Missense_Mutation	SNP	C	C	G	rs1521484	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	133	69	125	0	0.518797	0	C|0.537;G|0.463	0.463	strong	.	PGPEP1L	26	.	NM_001102612	exon5	c.G505C	p.E169Q	GCATTTCCTGGAT	.	PASS	Atlas-SNP
RPA1	6117	hgsc.bcm.edu	37	17	1795180	1795180	+	Silent	SNP	T	T	C	rs2230931	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48	23	57	0	0.479167	0	T|0.751;C|0.249	0.249	strong	.	RPA1	48	.	NM_002945	exon15	c.T1605C	p.S535S	GGAGTCTGCTGAA	.	PASS	Atlas-SNP
FHIT	2272	hgsc.bcm.edu	37	3	59997112	59997112	+	Silent	SNP	G	G	A	rs1130972	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	126	58	98	0	0.460317	0	G|0.893;A|0.107	0.107	strong	.	FHIT	44	.	NM_002012	exon7	c.C264T	p.A88A	CTGTCCGGCTTCG	.	PASS	Atlas-SNP
FAM135B	51059	hgsc.bcm.edu	37	8	139165068	139165068	+	Silent	SNP	C	C	T	rs3763590	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	78	39	75	0	0.5	0	C|0.632;T|0.368	0.368	strong	.	FAM135B	423	.	NM_015912	exon13	c.G1650A	p.V550V	GGTCAGCACTGGG	.	PASS	Atlas-SNP
ACAT1	38	hgsc.bcm.edu	37	11	107992346	107992346	+	Missense_Mutation	SNP	G	G	C	rs3741056	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	58	51	68	0	0.87931	0	G|0.710;C|0.290	0.290	strong	.	ACAT1	35	.	NM_000019	exon1	c.G13C	p.A5P	GTGCTGGCGGCAC	.	PASS	Atlas-SNP
LMTK2	22853	hgsc.bcm.edu	37	7	97822210	97822210	+	Silent	SNP	G	G	A	rs3801294	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	24	36	0	0.510638	0	G|0.650;A|0.350	0.350	strong	.	LMTK2	228	.	NM_014916	exon11	c.G2433A	p.P811P	TTCCCCGGAAGTG	.	PASS	Atlas-SNP
ACAN	176	hgsc.bcm.edu	37	15	89402447	89402447	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100	47	115	0	0.47	0	.	.	none	.	ACAN	220	.	NM_001135	exon12	c.G6631A	p.V2211I	CTGGGCGTTGTCA	.	PASS	Atlas-SNP
UNC13C	440279	hgsc.bcm.edu	37	15	54841874	54841874	+	Silent	SNP	A	A	G	rs9302181	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	33	32	45	0	0.969697	0	A|0.596;G|0.404	0.404	strong	.	UNC13C	674	.	NM_001080534	exon26	c.A5862G	p.Q1954Q	TGGACAATTATCC	.	PASS	Atlas-SNP
ZNF853	54753	hgsc.bcm.edu	37	7	6660790	6660790	+	Silent	SNP	G	G	A	rs940873	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	58	32	80	0	0.551724	0	G|0.644;A|0.356	0.356	strong	.	ZNF853	32	.	NM_017560	exon3	c.G168A	p.E56E	GGAAGAGCCTCAG	.	PASS	Atlas-SNP
ARHGAP33	115703	hgsc.bcm.edu	37	19	36278470	36278470	+	Silent	SNP	C	C	G	rs231235	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48	21	58	0	0.4375	0	C|0.531;G|0.469	0.469	strong	.	ARHGAP33	102	.	NM_052948	exon21	c.C2520G	p.A840A	CAGTGCCCAGCTC	.	PASS	Atlas-SNP
DDX60L	91351	hgsc.bcm.edu	37	4	169325233	169325233	+	Missense_Mutation	SNP	T	T	A	rs17540213	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	130	59	143	0	0.453846	0	T|0.950;A|0.050	0.050	strong	.	DDX60L	116	.	NM_001012967	exon25	c.A3238T	p.S1080C	CCGGACTAAGGTT	.	PASS	Atlas-SNP
SHC3	53358	hgsc.bcm.edu	37	9	91652977	91652977	+	Silent	SNP	G	G	A	rs56005403	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	40	20	29	0	0.5	0	G|0.990;A|0.010	0.010	strong	.	SHC3	66	.	NM_016848	exon11	c.C1587T	p.G529G	AAAGGAGCCCGGG	.	PASS	Atlas-SNP
FABP7	2173	hgsc.bcm.edu	37	6	123104889	123104889	+	Missense_Mutation	SNP	G	G	A	rs77153426	alternate_allele	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	137	65	120	0	0.474453	0	.	.	alt	.	FABP7	10	.	NM_001446	exon4	c.G376A	p.V126I	GTTGCTGTTCGCC	.	PASS	Atlas-SNP
PABPN1L	390748	hgsc.bcm.edu	37	16	88931274	88931274	+	Missense_Mutation	SNP	C	C	T	rs76267236	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	165	81	134	0	0.490909	0	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	.	PASS	Atlas-SNP
SUGP1	57794	hgsc.bcm.edu	37	19	19390185	19390185	+	Silent	SNP	G	G	A	rs11555053	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	46	28	35	0	0.608696	0	G|0.805;A|0.195	0.195	strong	SUGP1,NS,carcinoma,0,1	SUGP1	63	1	NM_172231	exon10	c.C1365T	p.Y455Y	CATGTCGTACATC	.	PASS	Atlas-SNP
BSPRY	54836	hgsc.bcm.edu	37	9	116132334	116132334	+	Missense_Mutation	SNP	C	C	T	rs3088235	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	23	44	0	0.489362	0	C|0.852;T|0.148	0.148	strong	.	BSPRY	21	.	NM_017688	exon6	c.C1121T	p.T374I	CCGGCACAGTGCT	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	179	179	199	0	1	0	G|0.597;N|0.001	0.597	strong	.	CAND2	138	.	NM_001162499	exon8	c.A1223G	p.Q408R	AAACACAGCCCCC	.	PASS	Atlas-SNP
ACAA1	30	hgsc.bcm.edu	37	3	38167095	38167095	+	Missense_Mutation	SNP	A	A	G	rs2229528	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100	46	105	0	0.46	0	T|0.067;G|0.026	0.026	strong	.	ACAA1	32	.	NM_001607	exon11	c.T1160C	p.V387A	GTGATGACCTGTC	.	PASS	Atlas-SNP
ANKRD26	22852	hgsc.bcm.edu	37	10	27317840	27317840	+	Missense_Mutation	SNP	C	C	T	rs10829163	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	156	156	190	0	1	0	C|0.724;T|0.276	0.276	strong	.	ANKRD26	179	.	NM_014915	exon27	c.G3913A	p.V1305I	TTTTGACTGTAAC	.	PASS	Atlas-SNP
NSDHL	50814	hgsc.bcm.edu	37	X	152018832	152018832	+	Silent	SNP	T	T	G	rs5969919	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	127	90	90	0	0.708661	0	0|0.015;G|0.819	0.819	strong	.	NSDHL	33	.	NM_015922	exon3	c.T132G	p.G44G	GATCGGTGGCTCT	.	PASS	Atlas-SNP
WDR11	55717	hgsc.bcm.edu	37	10	122665459	122665459	+	Silent	SNP	C	C	G	rs3740307	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72	37	79	0	0.513889	0	C|0.885;G|0.115	0.115	strong	WDR11,NS,carcinoma,0,1	WDR11	95	1	NM_018117	exon27	c.C3363G	p.V1121V	ACAAGTCAATCAG	.	PASS	Atlas-SNP
CYP4A22	284541	hgsc.bcm.edu	37	1	47607851	47607851	+	Missense_Mutation	SNP	A	A	T	rs55910803		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	133	73	145	0	0.548872	0	.	.	weak	.	CYP4A22	60	.	NM_001010969	exon4	c.A454T	p.N152Y	TTCCACAATGACA	.	PASS	Atlas-SNP
PHLDB1	23187	hgsc.bcm.edu	37	11	118509668	118509668	+	Silent	SNP	A	A	G	rs483598	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	126	126	107	0	1	0	A|0.454;G|0.546	0.546	strong	.	PHLDB1	103	.	NM_001144758	exon11	c.A2595G	p.E865E	GCAGGAATCAGAA	.	PASS	Atlas-SNP
NOC3L	64318	hgsc.bcm.edu	37	10	96100094	96100094	+	Silent	SNP	C	C	A	rs140939496	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	213	89	223	0	0.41784	0	C|0.979;A|0.021	0.021	strong	.	NOC3L	67	.	NM_022451	exon16	c.G1719T	p.L573L	AATATTCAGAACA	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29911222	29911222	+	Missense_Mutation	SNP	C	C	T	rs1059535	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110	70	123	0	0.636364	0	C|0.912;T|0.088	0.088	strong	.	HLA-A	89	.	NM_001242758	exon3	c.C521T	p.A174V	AGGCGGCCCATGA	.	PASS	Atlas-SNP
KIAA1586	57691	hgsc.bcm.edu	37	6	56918304	56918304	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83	31	74	0	0.373494	0	.	.	none	.	KIAA1586	59	.	NM_020931	exon4	c.G1007A	p.C336Y	TCCAGTGCACAAT	.	PASS	Atlas-SNP
ENGASE	64772	hgsc.bcm.edu	37	17	77075667	77075667	+	Silent	SNP	T	T	C	rs3744183	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48	16	70	1	0.333333	0.0142857	T|0.737;C|0.263	0.263	strong	ENGASE,caecum,adenoma,0,1	ENGASE	55	1	NM_001042573	exon4	c.T513C	p.I171I	CACCATTCCCCCA	.	scavenged	Atlas-SNP
HNRNPUL1	11100	hgsc.bcm.edu	37	19	41809995	41809995	+	Silent	SNP	A	A	G	rs1056854	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	25	61	0	0.409836	0	A|0.867;G|0.133	0.133	strong	.	HNRNPUL1	73	.	NM_007040	exon13	c.A2091G	p.P697P	GCCGCCACCACAG	.	PASS	Atlas-SNP
WDR44	54521	hgsc.bcm.edu	37	X	117528142	117528142	+	Silent	SNP	C	C	T	rs6603401	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	126	84	105	0	0.666667	0	C|0.475;T|0.525	0.525	strong	.	WDR44	188	.	NM_001184965	exon5	c.C951T	p.T317T	AGTTACCGCCCAG	.	PASS	Atlas-SNP
NOTCH2NL	388677	hgsc.bcm.edu	37	1	145273431	145273431	+	Silent	SNP	A	A	G	rs17421312	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	1054	127	1048	0	0.120493	0	A|0.962;G|0.038	0.038	strong	.	NOTCH2NL	100	.	NM_203458	exon3	c.A285G	p.Q95Q	CTGTCAAGTCGGG	.	PASS	Atlas-SNP
VSIG10L	147645	hgsc.bcm.edu	37	19	51841417	51841417	+	Missense_Mutation	SNP	C	C	T	rs34380065	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	20	10	16	0	0.5	0	C|0.464;T|0.536	0.536	strong	.	VSIG10L	40	.	NM_001163922	exon6	c.G1775A	p.R592Q	CCCAACCGTGTCT	.	PASS	Atlas-SNP
SGK1	6446	hgsc.bcm.edu	37	6	134494661	134494661	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	23	82	0	0.283951	0	.	.	none	SGK1_ENST00000367858,lymph_node,lymphoid_neoplasm,0,3	SGK1	387	3	NM_001143676	exon6	c.C557T	p.P186L	GCATGAGGATTGG	.	PASS	Atlas-SNP
CCDC15	80071	hgsc.bcm.edu	37	11	124863136	124863136	+	Silent	SNP	C	C	A	rs7951202	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	43	35	46	0	0.813953	0	C|0.719;A|0.281	0.281	strong	.	CCDC15	134	.	NM_025004	exon11	c.C2211A	p.P737P	AGTGCCCTTGGTA	.	PASS	Atlas-SNP
KIAA1614	57710	hgsc.bcm.edu	37	1	180897569	180897569	+	Silent	SNP	C	C	T	rs3747958	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	129	68	135	0	0.527132	0	C|0.600;T|0.400	0.400	strong	.	KIAA1614	75	.	NM_020950	exon4	c.C1065T	p.T355T	CAGGACCGTTGGT	.	PASS	Atlas-SNP
WDFY4	57705	hgsc.bcm.edu	37	10	50038878	50038878	+	Missense_Mutation	SNP	G	G	C	rs41283281	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	194	103	175	0	0.530928	0	G|0.954;C|0.046	0.046	strong	.	WDFY4	205	.	NM_020945	exon38	c.G6474C	p.E2158D	TGAAGAGGTCACA	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	179	179	177	0	1	0	A|0.627;G|0.373	0.373	strong	.	DNAL4	5	.	NM_005740	exon2	c.T36C	p.D12D	CTTATAATCAGCC	.	PASS	Atlas-SNP
KIR3DL1	3811	hgsc.bcm.edu	37	19	55340835	55340835	+	Silent	SNP	C	C	T	rs45459293	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	10	10	35	0	1	0	C|0.913;T|0.087	0.087	strong	.	KIR3DL1	174	.	NM_013289	exon7	c.C1020T	p.H340H	CCTGCACATTCTG	.	PASS	Atlas-SNP
CEP19	84984	hgsc.bcm.edu	37	3	196435534	196435534	+	Missense_Mutation	SNP	T	T	C	rs6776064	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	42	20	54	0	0.47619	0	T|0.571;C|0.429	0.429	strong	.	CEP19	22	.	NM_032898	exon2	c.A7G	p.M3V	TTCCCATGTACAT	.	PASS	Atlas-SNP
FCGBP	8857	hgsc.bcm.edu	37	19	40392496	40392496	+	Missense_Mutation	SNP	C	C	T	rs143680639	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	176	47	182	0	0.267045	0	C|0.970;T|0.030	0.030	strong	FCGBP,rectum,carcinoma,0,1	FCGBP	416	1	NM_003890	exon16	c.G8008A	p.G2670R	GTGGCCCTGTGGG	.	PASS	Atlas-SNP
TMEM200C	645369	hgsc.bcm.edu	37	18	5891637	5891637	+	Silent	SNP	C	C	A	rs28656885	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	42	26	58	0	0.619048	0	C|0.642;A|0.358	0.358	strong	.	TMEM200C	30	.	NM_001080209	exon1	c.G426T	p.P142P	GGAGGACGGGGAG	.	PASS	Atlas-SNP
SMYD4	114826	hgsc.bcm.edu	37	17	1703156	1703156	+	Missense_Mutation	SNP	T	T	C	rs61753098	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	33	11	37	0	0.333333	0	T|0.985;C|0.015	0.015	strong	.	SMYD4	50	.	NM_052928	exon5	c.A1532G	p.H511R	CCTGTGTGTTGTA	.	PASS	Atlas-SNP
LENG9	94059	hgsc.bcm.edu	37	19	54973307	54973307	+	Missense_Mutation	SNP	C	C	T	rs115799049	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	26	14	22	0	0.538462	0	C|0.977;T|0.023	0.023	strong	.	LENG9	46	.	NM_198988	exon1	c.G1469A	p.G490E	AAAGGCCCCCCTG	.	PASS	Atlas-SNP
JMJD7-PLA2G4B	8681	hgsc.bcm.edu	37	15	42138456	42138456	+	Silent	SNP	G	G	A	rs1197669	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68	68	86	0	1	0	G|0.725;A|0.275	0.275	strong	.	JMJD7-PLA2G4B	90	.	NM_005090	exon22	c.G2349A	p.R783R	CGGCAGGATAGCT	.	PASS	Atlas-SNP
KIF2B	84643	hgsc.bcm.edu	37	17	51900729	51900729	+	Missense_Mutation	SNP	C	C	T	rs3803824	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49	28	44	1	0.571429	0.0227273	C|0.741;T|0.259	0.259	strong	KIF2B,NS,carcinoma,+1,3	KIF2B	254	3	NM_032559	exon1	c.C335T	p.A112V	GTACCGCCACGAA	.	scavenged	Atlas-SNP
MS4A3	932	hgsc.bcm.edu	37	11	59837097	59837097	+	Silent	SNP	C	C	T	rs528823	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	160	84	166	0	0.525	0	C|0.734;T|0.266	0.266	strong	.	MS4A3	47	.	NM_006138	exon6	c.C564T	p.T188T	CGTAACCATCTCT	.	PASS	Atlas-SNP
MCMDC2	157777	hgsc.bcm.edu	37	8	67813482	67813482	+	Silent	SNP	G	G	A	rs139959817	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	171	65	180	0	0.380117	0	G|0.979;A|0.021	0.021	strong	.	MCMDC2	84	.	NM_173518	exon13	c.G1668A	p.L556L	CAGCTTGGAAGCA	.	PASS	Atlas-SNP
TSNARE1	203062	hgsc.bcm.edu	37	8	143396446	143396446	+	Missense_Mutation	SNP	C	C	T	rs62000450	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	129	69	123	0	0.534884	0	C|0.975;T|0.025	0.025	strong	.	TSNARE1	59	.	NM_145003	exon8	c.G992A	p.R331H	TGCAGACGCTCCT	.	PASS	Atlas-SNP
PARP4	143	hgsc.bcm.edu	37	13	25058867	25058867	+	Missense_Mutation	SNP	C	C	T	rs201518768	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	101	16	90	1	0.158416	0.0111111	.	.	weak	PARP4,NS,carcinoma,0,5	PARP4	142	5	NM_006437	exon12	c.G1372A	p.V458I	CCACTACTTTGGG	.	scavenged	Atlas-SNP
FAT2	2196	hgsc.bcm.edu	37	5	150948016	150948016	+	Silent	SNP	C	C	T	rs3734062	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	180	99	183	0	0.55	0	C|0.944;T|0.056	0.056	strong	.	FAT2	465	.	NM_001447	exon1	c.G477A	p.E159E	CATGTCCTCAGAG	.	PASS	Atlas-SNP
SLC4A5	57835	hgsc.bcm.edu	37	2	74466594	74466594	+	Silent	SNP	G	G	A	rs4853018	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	60	108	0	0.967742	0	G|0.694;A|0.306	0.306	strong	SLC4A5_ENST00000377634,colon,carcinoma,0,2	SLC4A5	215	2	NM_021196	exon16	c.C2187T	p.G729G	GCGCCCGCCGTAG	.	PASS	Atlas-SNP
SERPINB2	5055	hgsc.bcm.edu	37	18	61564394	61564394	+	Missense_Mutation	SNP	A	A	G	rs6098	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	103	56	76	0	0.543689	0	A|0.695;C|0.002	.	strong	.	SERPINB2	63	.	NM_002575	exon4	c.A358G	p.N120D	ACAGGGAATTATT	.	PASS	Atlas-SNP
OR10A4	283297	hgsc.bcm.edu	37	11	6898758	6898758	+	Silent	SNP	A	A	C	rs7102808	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85	34	78	0	0.4	0	A|0.839;C|0.161	0.161	strong	.	OR10A4	65	.	NM_207186	exon1	c.A880C	p.R294R	AGCTCAAGGAATA	.	PASS	Atlas-SNP
VPS13A	23230	hgsc.bcm.edu	37	9	79946961	79946961	+	Silent	SNP	C	C	T	rs17424026	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	161	93	135	0	0.57764	0	C|0.918;T|0.082	0.082	strong	.	VPS13A	735	.	NM_001018038	exon46	c.C6027T	p.Y2009Y	TGTTTACGAAGGG	.	PASS	Atlas-SNP
SEMA4D	10507	hgsc.bcm.edu	37	9	92003679	92003679	+	Missense_Mutation	SNP	C	C	T	rs11526468	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	21	11	26	0	0.52381	0	C|0.774;T|0.226	0.226	strong	.	SEMA4D	81	.	NM_006378	exon13	c.G979A	p.A327T	TGTAGGCGCACAC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195505763	195505763	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	58	4	90	0	0.0689655	0	.	.	none	MUC4_ENST00000463781,NS,carcinoma,0,4	MUC4	1505	4	NM_018406	exon2	c.C12688T	p.L4230F	AGGAAAGGCTGGT	.	scavenged	Atlas-SNP
FAM131C	348487	hgsc.bcm.edu	37	1	16386065	16386065	+	Silent	SNP	T	T	A	rs61769893	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	271	40	174	18	0.147601	0.103448	T|0.958;A|0.042	0.042	strong	FAM131C,caecum,carcinoma,0,1	FAM131C	21	1	NM_182623	exon6	c.A486T	p.T162T	GCTCAGTGTGGCC	.	scavenged	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179396354	179396354	+	Silent	SNP	G	G	A	rs3829748	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	109	48	115	0	0.440367	0	G|0.790;A|0.210	0.210	strong	.	TTN	18412	.	NM_001267550	exon358	c.C104988T	p.V34996V	GGTGAGGACTCCA	.	PASS	Atlas-SNP
KIAA0922	23240	hgsc.bcm.edu	37	4	154519764	154519764	+	Missense_Mutation	SNP	A	A	G	rs72729691	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	34	77	0	0.453333	0	A|0.994;G|0.006	0.006	strong	.	KIAA0922	214	.	NM_001131007	exon21	c.A2146G	p.M716V	ATTGACATGATTG	.	PASS	Atlas-SNP
CAD	790	hgsc.bcm.edu	37	2	27462076	27462076	+	Silent	SNP	C	C	T	rs3739092	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	30	66	0	0.47619	0	C|0.773;T|0.227	0.227	strong	.	CAD	199	.	NM_004341	exon32	c.C5229T	p.P1743P	CCTGCCCCCGCAG	.	PASS	Atlas-SNP
DMWD	1762	hgsc.bcm.edu	37	19	46289509	46289509	+	Silent	SNP	G	G	A	rs11545326	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49	21	42	0	0.428571	0	G|0.917;A|0.083	0.083	strong	.	DMWD	46	.	NM_004943	exon3	c.C1245T	p.G415G	CGGGGCGCCCCCG	.	PASS	Atlas-SNP
BSCL2	26580	hgsc.bcm.edu	37	11	62458275	62458275	+	Missense_Mutation	SNP	T	T	C	rs6856	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	22	64	0	0.407407	0	T|0.825;C|0.175	0.175	strong	.	BSCL2	35	.	NM_001130702	exon8	c.A803G	p.K268R	GGGATCTTCAGGG	.	PASS	Atlas-SNP
LONP1	9361	hgsc.bcm.edu	37	19	5693616	5693616	+	Silent	SNP	C	C	T	rs35804229	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	151	44	168	0	0.291391	0	C|0.988;T|0.012	0.012	strong	LONP1,colon,carcinoma,0,1	LONP1	66	1	NM_004793	exon16	c.A2485A	p.I829I	CGGGGGCGTGCTG	.	PASS	Atlas-SNP
SAMD9L	219285	hgsc.bcm.edu	37	7	92760738	92760738	+	Missense_Mutation	SNP	T	T	G	rs10282508	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	167	102	216	0	0.610778	0	T|0.887;G|0.113	0.113	strong	.	SAMD9L	227	.	NM_152703	exon5	c.A4547C	p.N1516T	ACTTCATTTTTTT	.	PASS	Atlas-SNP
ZNF749	388567	hgsc.bcm.edu	37	19	57955244	57955244	+	Missense_Mutation	SNP	A	A	G	rs12986235	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	77	39	70	0	0.506494	0	A|0.771;G|0.229	0.229	strong	.	ZNF749	75	.	NM_001023561	exon3	c.A728G	p.Q243R	AATATCAGCAAAA	.	PASS	Atlas-SNP
HYDIN	54768	hgsc.bcm.edu	37	16	71025245	71025245	+	Silent	SNP	C	C	T	rs1774516	bycluster;byfrequency;by2hit2allele;byhapmap	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	130	15	94	0	0.115385	0	C|0.977;T|0.023	0.023	strong	LOC652153,NS,carcinoma,-1,2	HYDIN	788	2	NM_001270974	exon25	c.G3840A	p.T1280T	AGCTTTCGTTTTT	.	scavenged	Atlas-SNP
MDN1	23195	hgsc.bcm.edu	37	6	90371202	90371202	+	Silent	SNP	G	G	A	rs9444701	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	183	182	184	0	0.994536	0	G|0.286;A|0.714	0.714	strong	.	MDN1	478	.	NM_014611	exon88	c.C14661T	p.L4887L	ACTGTCGAGGTTC	.	PASS	Atlas-SNP
ALMS1	7840	hgsc.bcm.edu	37	2	73679990	73679990	+	Missense_Mutation	SNP	T	T	A	rs6724782	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	43	76	0	0.704918	0	T|0.691;A|0.309	0.309	strong	.	ALMS1	384	.	NM_015120	exon8	c.T6333A	p.S2111R	AGGTAGTCATGTA	.	PASS	Atlas-SNP
TRIM3	10612	hgsc.bcm.edu	37	11	6478619	6478619	+	Silent	SNP	G	G	A	rs16913748	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	25	49	0	0.531915	0	G|0.791;A|0.209	0.209	strong	.	TRIM3	67	.	NM_001248006	exon5	c.C603T	p.I201I	TGCACTGATCTGG	.	PASS	Atlas-SNP
SIGLEC5	8778	hgsc.bcm.edu	37	19	52132668	52132668	+	Missense_Mutation	SNP	T	T	C	rs34553740	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	570	8	541	2	0.0140351	0.00369686	.	.	weak	SIGLEC5,NS,carcinoma,0,1	SIGLEC5	67	1	NM_003830	exon3	c.A643G	p.M215V	GTTTCATCTGACA	.	scavenged	Atlas-SNP
PCDHAC1	56135	hgsc.bcm.edu	37	5	140306924	140306924	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	15	95	0	0.211268	0	.	.	none	.	PCDHAC1	141	.	NM_031882	exon1	c.A447T	p.Q149H	TGCCCAAGATGAC	.	PASS	Atlas-SNP
NMI	9111	hgsc.bcm.edu	37	2	152132130	152132130	+	Silent	SNP	A	A	G	rs289834	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	114	25	142	0	0.219298	0	A|0.833;G|0.167	0.167	strong	.	NMI	21	.	NM_004688	exon6	c.T502C	p.L168L	CACGCAATGTGTC	.	PASS	Atlas-SNP
PCDHB11	56125	hgsc.bcm.edu	37	5	140580931	140580931	+	Missense_Mutation	SNP	C	C	G	rs799834	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	197	100	243	0	0.507614	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
GGA3	23163	hgsc.bcm.edu	37	17	73239557	73239557	+	Missense_Mutation	SNP	T	T	C	rs117805695	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	156	82	169	0	0.525641	0	T|0.998;C|0.002	0.002	strong	.	GGA3	54	.	NM_138619	exon5	c.A395G	p.K132R	GCGTCTTTGATCT	.	PASS	Atlas-SNP
MXD3	83463	hgsc.bcm.edu	37	5	176734855	176734855	+	Silent	SNP	G	G	C	rs4568379	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	18	10	33	0	0.555556	0	G|0.800;C|0.200	0.200	strong	.	MXD3	13	.	NM_001142935	exon5	c.C432G	p.A144A	CCGCTCGGCCGCC	.	PASS	Atlas-SNP
ARL17B	100506084	hgsc.bcm.edu	37	17	44430254	44430254	+	Missense_Mutation	SNP	G	G	C	rs35595570	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	532	322	396	0	0.605263	0	G|0.905;C|0.095	0.095	strong	ARL17B,NS,other,0,1	ARL17B	3	1	NM_001039083	exon3	c.C191G	p.A64G	CAGACAGCGAAGG	.	scavenged	Atlas-SNP
ZFP90	146198	hgsc.bcm.edu	37	16	68598023	68598023	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	70	14	79	0	0.2	0	.	.	none	ZFP90,NS,carcinoma,0,1	ZFP90	67	1	NM_133458	exon4	c.A1333G	p.T445A	ACTCTTACCGAAG	.	PASS	Atlas-SNP
SMCO4	0	hgsc.bcm.edu	37	11	93212245	93212245	+	Silent	SNP	C	C	T	rs3207348	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	62	49	0	0.96875	0	C|0.891;T|0.109	0.109	strong	.	.	.	.	NM_020179	exon3	c.G111A	p.T37T	GGCCAGCGTGGGC	.	PASS	Atlas-SNP
NRAP	4892	hgsc.bcm.edu	37	10	115409840	115409840	+	Missense_Mutation	SNP	C	C	T	rs2275799	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	28	90	0	0.424242	0	C|0.708;T|0.292	0.292	strong	.	NRAP	208	.	NM_001261463	exon9	c.G844A	p.A282T	CCTCAGCTCCAAT	.	PASS	Atlas-SNP
ATG16L1	55054	hgsc.bcm.edu	37	2	234183368	234183368	+	Missense_Mutation	SNP	A	A	G	rs2241880	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	103	103	136	0	1	0	G|0.422;N|0.000	0.422	strong	.	ATG16L1	83	.	NM_030803	exon9	c.A898G	p.T300A	GTGGATACTCATC	.	PASS	Atlas-SNP
ANKLE1	126549	hgsc.bcm.edu	37	19	17397244	17397244	+	Silent	SNP	C	C	T	rs10425939	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	106	65	108	0	0.613208	0	C|0.850;T|0.150	0.150	strong	.	ANKLE1	27	.	NM_152363	exon9	c.C1731T	p.G577G	GGCAGGCTGGCCA	.	PASS	Atlas-SNP
KCNAB1	7881	hgsc.bcm.edu	37	3	156249214	156249214	+	Silent	SNP	T	T	C	rs2280031	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	43	95	0	0.511905	0	T|0.756;C|0.244	0.244	strong	.	KCNAB1	176	.	NM_172160	exon13	c.T1098C	p.N366N	GAGAAATGAAGGT	.	PASS	Atlas-SNP
ELANE	1991	hgsc.bcm.edu	37	19	855966	855966	+	Silent	SNP	C	C	A	rs17216649	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	34	17	37	0	0.5	0	A|0.114;C|0.886;T|0.000	0.114	strong	ELANE,NS,carcinoma,0,1	ELANE	27	1	NM_001972	exon5	c.C606A	p.S202S	GGACTCCGGCAGC	.	PASS	Atlas-SNP
FFAR3	2865	hgsc.bcm.edu	37	19	35849926	35849926	+	Missense_Mutation	SNP	G	G	A	rs79251979	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	521	161	506	0	0.309021	0	G|0.800;A|0.200	0.200	strong	FFAR3,NS,carcinoma,0,1	FFAR3	40	1	NM_005304	exon2	c.G134A	p.R45H	TGCAGCGCCGCCC	.	PASS	Atlas-SNP
KRT33A	3883	hgsc.bcm.edu	37	17	39502917	39502917	+	Missense_Mutation	SNP	C	C	A	rs144588166	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73	30	92	0	0.410959	0	C|0.999;A|0.001	0.001	strong	.	KRT33A	53	.	NM_004138	exon6	c.G880T	p.D294Y	GAGAGTCTCGCTG	.	PASS	Atlas-SNP
ECE1	1889	hgsc.bcm.edu	37	1	21573722	21573722	+	Silent	SNP	G	G	A	rs2229450	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	125	50	115	0	0.4	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
MYOM1	8736	hgsc.bcm.edu	37	18	3188976	3188976	+	Missense_Mutation	SNP	A	A	G	rs1962519	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	39	104	0	0.58209	0	A|0.536;G|0.464	0.464	strong	.	MYOM1	192	.	NM_003803	exon4	c.T541C	p.S181P	GTTTAGATGTTGT	.	PASS	Atlas-SNP
ATP13A4	84239	hgsc.bcm.edu	37	3	193183817	193183817	+	Silent	SNP	A	A	G	rs3796181	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72	37	77	0	0.513889	0	A|0.474;G|0.526	0.526	strong	.	ATP13A4	154	.	NM_032279	exon11	c.T1269C	p.S423S	TACCCCACTAAGC	.	PASS	Atlas-SNP
WDFY4	57705	hgsc.bcm.edu	37	10	50034833	50034833	+	Missense_Mutation	SNP	G	G	A	rs6537579	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	171	94	153	0	0.549708	0	G|0.801;A|0.199	0.199	strong	WDFY4,NS,carcinoma,0,1	WDFY4	205	1	NM_020945	exon36	c.G6100A	p.G2034S	TGCCTCGGCCTTC	.	PASS	Atlas-SNP
NSUN2	54888	hgsc.bcm.edu	37	5	6600150	6600150	+	Silent	SNP	G	G	A	rs3822434	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91	52	80	0	0.571429	0	G|0.862;C|0.000;A|0.138	0.138	strong	NSUN2,colon,carcinoma,0,1	NSUN2	82	1	NM_017755	exon19	c.C2193T	p.D731D	AGTCACGTCATTG	.	PASS	Atlas-SNP
ZNF638	27332	hgsc.bcm.edu	37	2	71633389	71633389	+	Silent	SNP	C	C	T	rs6714975	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	65	85	0	0.984848	0	C|0.545;T|0.455	0.455	strong	.	ZNF638	179	.	NM_014497	exon19	c.C3132T	p.N1044N	TAGAAACAAGGTA	.	PASS	Atlas-SNP
NGEF	25791	hgsc.bcm.edu	37	2	233750074	233750074	+	Silent	SNP	C	C	T	rs2292725	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	48	71	0	0.551724	0	C|0.798;T|0.202	0.202	strong	.	NGEF	198	.	NM_019850	exon10	c.G1353A	p.V451V	TGCCTTCACCACC	.	PASS	Atlas-SNP
PAK6	56924	hgsc.bcm.edu	37	15	40564576	40564576	+	Missense_Mutation	SNP	C	C	T	rs3743137	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55	13	68	0	0.236364	0	C|0.904;T|0.096	0.096	strong	.	PAK6	49	.	NM_001128629	exon5	c.C1010T	p.P337L	CAGCCCCGGCCAC	.	PASS	Atlas-SNP
ZNF587B	100293516	hgsc.bcm.edu	37	19	58353003	58353003	+	Missense_Mutation	SNP	G	G	A	rs34871842	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	8	4	13	0	0.5	0	G|0.956;A|0.044	0.044	strong	.	.	.	.	NM_001204818	exon3	c.G961A	p.A321T	GTTCACGCTGGAA	.	PASS	Atlas-SNP
ZNF880	400713	hgsc.bcm.edu	37	19	52888210	52888210	+	Silent	SNP	T	T	C	rs56151179	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	38	35	57	0	0.921053	0	T|0.633;C|0.367	0.367	strong	.	ZNF880	45	.	NM_001145434	exon4	c.T1377C	p.T459T	TCATACTGGAGAG	.	PASS	Atlas-SNP
KIAA0825	285600	hgsc.bcm.edu	37	5	93722050	93722050	+	Silent	SNP	G	G	T	rs29913	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	109	49	118	0	0.449541	0	G|0.892;T|0.108	0.108	strong	.	KIAA0825	172	.	NM_001145678	exon19	c.C3516A	p.I1172I	AGGTCGGATGGGT	.	PASS	Atlas-SNP
TAF1C	9013	hgsc.bcm.edu	37	16	84215867	84215867	+	Missense_Mutation	SNP	C	C	T	rs79432776	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	33	81	0	0.434211	0	C|0.989;T|0.011	0.011	strong	.	TAF1C	60	.	NM_001243156	exon7	c.G662A	p.G221E	GTCCTTCCAGGAA	.	PASS	Atlas-SNP
ATP10A	57194	hgsc.bcm.edu	37	15	25924539	25924539	+	Silent	SNP	T	T	C	rs1047700	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	37	15	45	0	0.405405	0	T|0.749;C|0.251	0.251	strong	.	ATP10A	270	.	NM_024490	exon21	c.A4449G	p.Q1483Q	TGGCCCTTGAAGT	.	PASS	Atlas-SNP
SMTNL2	342527	hgsc.bcm.edu	37	17	4497160	4497160	+	Silent	SNP	T	T	C	rs8080130	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	119	119	106	0	1	0	T|0.350;C|0.650	0.650	strong	.	SMTNL2	57	.	NM_001114974	exon4	c.T774C	p.Y258Y	TGGCTATGGGGCA	.	PASS	Atlas-SNP
STK17A	9263	hgsc.bcm.edu	37	7	43664198	43664198	+	Silent	SNP	A	A	G	rs10233697	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	31	22	54	0	0.709677	0	A|0.868;G|0.132	0.132	strong	.	STK17A	31	.	NM_004760	exon7	c.A1002G	p.E334E	GATGGAAAAGGCA	.	PASS	Atlas-SNP
YME1L1	10730	hgsc.bcm.edu	37	10	27434483	27434483	+	Silent	SNP	G	G	A	rs2274634	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79	79	87	0	1	0	G|0.727;A|0.273	0.273	strong	.	YME1L1	71	.	NM_139312	exon4	c.C376T	p.L126L	TTTTTAGTTCAGA	.	PASS	Atlas-SNP
R3HCC1L	27291	hgsc.bcm.edu	37	10	99969475	99969475	+	Missense_Mutation	SNP	A	A	C	rs34494334	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49	25	74	0	0.510204	0	A|0.813;C|0.187	0.187	strong	.	R3HCC1L	3	.	NM_001256620	exon4	c.A1604C	p.D535A	AAGATGACTCAGG	.	PASS	Atlas-SNP
ITGA11	22801	hgsc.bcm.edu	37	15	68649587	68649587	+	Silent	SNP	G	G	A	rs12907890	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	45	15	65	0	0.333333	0	G|0.148;A|0.852	0.852	strong	.	ITGA11	110	.	NM_001004439	exon7	c.C651T	p.N217N	GTAGTCGTTGAGG	.	PASS	Atlas-SNP
XIRP2	129446	hgsc.bcm.edu	37	2	168115325	168115325	+	Missense_Mutation	SNP	A	A	G	rs3749005	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110	52	114	0	0.472727	0	A|0.928;G|0.072	0.072	strong	.	XIRP2	914	.	NM_001199143	exon11	c.A2368G	p.R790G	ACATCTAGAATCT	.	PASS	Atlas-SNP
RPAIN	84268	hgsc.bcm.edu	37	17	5326089	5326089	+	Silent	SNP	C	C	T	rs1071648	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	158	63	175	0	0.398734	0	C|0.689;T|0.311	0.311	strong	.	RPAIN	24	.	NM_001160246	exon3	c.C253T	p.L85L	TTCCAGCTGGAGG	.	PASS	Atlas-SNP
DMP1	1758	hgsc.bcm.edu	37	4	88583135	88583135	+	Missense_Mutation	SNP	A	A	T	rs10019009	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	168	79	174	0	0.470238	0	A|0.719;T|0.281	0.281	strong	.	DMP1	72	.	NM_004407	exon6	c.A205T	p.S69C	AGTGACAGCACTC	.	PASS	Atlas-SNP
UBD	10537	hgsc.bcm.edu	37	6	29523957	29523957	+	Silent	SNP	A	A	G	rs404240	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	158	129	193	0	0.816456	0	A|0.947;G|0.053	0.053	strong	.	UBD	13	.	NM_006398	exon2	c.T198C	p.Y66Y	AATGCCATAAGAT	.	PASS	Atlas-SNP
ND2	0	hgsc.bcm.edu	37	MT	5442	5442	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	17	17	8	0	1	0	.	.	none	.	.	.	.	ENST00000361453	exon1	c.T973C	p.F325L	ACCCCATTCCTCC	.	PASS	Atlas-SNP
KLK3	354	hgsc.bcm.edu	37	19	51362803	51362803	+	Silent	SNP	C	C	T	rs35192866	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93	35	101	0	0.376344	0	C|0.912;T|0.088	0.088	strong	.	KLK3	76	.	NM_001030047	exon5	c.C648T	p.T216T	GATCACCGAACTG	.	PASS	Atlas-SNP
P2RY2	5029	hgsc.bcm.edu	37	11	72946140	72946140	+	Missense_Mutation	SNP	G	G	C	rs3741156	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	45	6	54	0	0.133333	0	C|0.211;G|0.789	0.211	strong	.	P2RY2	54	.	NM_176071	exon3	c.G936C	p.R312S	GCAGAGGCTCGTA	.	PASS	Atlas-SNP
CYP2B6	1555	hgsc.bcm.edu	37	19	41497346	41497346	+	Missense_Mutation	SNP	A	A	G	rs35303484	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	32	16	28	0	0.5	0	A|0.997;G|0.003;T|0.000	0.003	strong	.	CYP2B6	79	.	NM_000767	exon1	c.A136G	p.M46V	CTGCAGATGGATA	.	PASS	Atlas-SNP
CYP4A22	284541	hgsc.bcm.edu	37	1	47608983	47608983	+	Missense_Mutation	SNP	G	G	T	rs4926581	bycluster;byfrequency;by2hit2allele;byhapmap	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	516	209	489	0	0.405039	0	G|0.849;T|0.151	0.151	strong	CYP4A22,colon,carcinoma,-2,1	CYP4A22	60	1	NM_001010969	exon5	c.G553T	p.V185F	CTGGAGGTCTTTC	.	PASS	Atlas-SNP
SAMD9	54809	hgsc.bcm.edu	37	7	92733766	92733766	+	Missense_Mutation	SNP	C	C	A	rs10279499	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	115	50	80	0	0.434783	0	C|0.882;A|0.118	0.118	strong	.	SAMD9	239	.	NM_001193307	exon2	c.G1645T	p.V549L	CATCCACAGAGGA	.	PASS	Atlas-SNP
IL17RA	23765	hgsc.bcm.edu	37	22	17589209	17589209	+	Missense_Mutation	SNP	C	C	T	rs879577	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	107	105	78	0	0.981308	0	C|0.709;T|0.291	0.291	strong	IL17RA,NS,carcinoma,0,1	IL17RA	62	1	NM_014339	exon13	c.C1100T	p.A367V	TGCCTGCGGCTGA	.	PASS	Atlas-SNP
CTSH	1512	hgsc.bcm.edu	37	15	79224747	79224747	+	Silent	SNP	C	C	T	rs13345	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	61	75	0	0.983871	0	C|0.720;T|0.280	0.280	strong	CTSH,NS,carcinoma,0,1	CTSH	23	1	NM_004390	exon6	c.G459A	p.A153A	GGCGATCGCAGAC	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	350	233	328	0	0.665714	0	T|0.791;C|0.209	0.209	strong	.	TCP10L	24	.	NM_144659	exon4	c.A434G	p.H145R	TTCTTGTGGCCAG	.	PASS	Atlas-SNP
CCDC63	160762	hgsc.bcm.edu	37	12	111342558	111342558	+	Silent	SNP	G	G	T	rs34300256	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	27	62	0	0.421875	0	G|0.810;T|0.190	0.190	strong	.	CCDC63	89	.	NM_152591	exon11	c.G1509T	p.V503V	CCCAGTGCTGGGG	.	PASS	Atlas-SNP
KIAA1551	55196	hgsc.bcm.edu	37	12	32135938	32135938	+	Silent	SNP	A	A	G	rs11051718	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	29	74	0	0.47541	0	A|0.920;G|0.080	0.080	strong	.	.	.	.	NM_018169	exon4	c.A2049G	p.Q683Q	AAAGCAACCTTCA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195515304	195515304	+	Silent	SNP	T	T	A	rs202019266		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	45	2	39	0	0.0444444	0	.	.	weak	MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	NM_018406	exon2	c.A3147T	p.A1049A	TGTGGATGCTGAG	.	scavenged	Atlas-SNP
TMEM60	85025	hgsc.bcm.edu	37	7	77423574	77423574	+	Silent	SNP	G	G	A	rs7953	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80	36	93	0	0.45	0	G|0.424;A|0.576	0.576	strong	.	TMEM60	24	.	NM_032936	exon2	c.C117T	p.F39F	TGGAATGAATATG	.	PASS	Atlas-SNP
GMPS	8833	hgsc.bcm.edu	37	3	155633817	155633817	+	Nonsense_Mutation	SNP	G	G	T	rs201869567	alternate_allele	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	4	70	0	0.0754717	0	G|0.999;A|0.001	.	alt	.	GMPS	70	.	NM_003875	exon9	c.G1048T	p.E350X	GCCAATGAAGTAA	.	PASS	Atlas-SNP
LILRB1	10859	hgsc.bcm.edu	37	19	55148031	55148031	+	Silent	SNP	T	T	C	rs637515		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	154	28	247	2	0.181818	0.00809717	.	.	weak	LILRB1,NS,carcinoma,+2,1	LILRB1	140	1	NM_001081637	exon14	c.T1740C	p.P580P	TCCTCCTTCCCCA	.	scavenged	Atlas-SNP
DUSP2	1844	hgsc.bcm.edu	37	2	96810609	96810609	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60	20	75	0	0.333333	0	.	.	none	.	DUSP2	20	.	NM_004418	exon2	c.G401A	p.G134D	TGGAAGCCGTCGA	.	PASS	Atlas-SNP
SMG5	23381	hgsc.bcm.edu	37	1	156233189	156233189	+	Silent	SNP	C	C	T	rs2273833	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	147	61	152	0	0.414966	0	C|0.798;T|0.202	0.202	strong	.	SMG5	98	.	NM_015327	exon13	c.G2028A	p.A676A	CACCTGCGCACAC	.	PASS	Atlas-SNP
CREB3L4	148327	hgsc.bcm.edu	37	1	153941842	153941842	+	Missense_Mutation	SNP	T	T	G	rs186432230	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	119	62	125	0	0.521008	0	T|1.000;G|0.000	0.000	strong	.	CREB3L4	36	.	NM_001255978	exon4	c.T454G	p.S152A	CCTGATTCCTGCA	.	PASS	Atlas-SNP
OR9Q1	219956	hgsc.bcm.edu	37	11	57947163	57947163	+	Missense_Mutation	SNP	G	G	A	rs111629598	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	210	105	175	0	0.5	0	G|0.976;A|0.024	0.024	strong	.	OR9Q1	60	.	NM_001005212	exon3	c.G247A	p.A83T	ATGCTGGCAGTGC	.	PASS	Atlas-SNP
STXBP5L	9515	hgsc.bcm.edu	37	3	121100283	121100283	+	Missense_Mutation	SNP	G	G	A	rs17740066	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	128	61	135	0	0.476562	0	G|0.930;A|0.070	0.070	strong	.	STXBP5L	159	.	NM_014980	exon23	c.G2563A	p.V855I	CTGTTCGTTGGAA	.	PASS	Atlas-SNP
UHRF1BP1	54887	hgsc.bcm.edu	37	6	34803947	34803947	+	Silent	SNP	C	C	T	rs4259246	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	41	5	47	0	0.121951	0	C|0.564;T|0.436	0.436	strong	.	UHRF1BP1	102	.	NM_017754	exon8	c.C855T	p.A285A	ACCAGCCCCCAGT	.	PASS	Atlas-SNP
HECTD1	25831	hgsc.bcm.edu	37	14	31598248	31598248	+	Silent	SNP	A	A	G	rs17097743	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	238	116	237	1	0.487395	0.00421941	A|0.888;G|0.112	0.112	strong	.	HECTD1	159	.	NM_015382	exon25	c.T4329C	p.S1443S	ACTGGAAGATGAC	.	PASS	Atlas-SNP
IGLL5	100423062	hgsc.bcm.edu	37	22	23230404	23230404	+	Missense_Mutation	SNP	A	A	C	rs115653109	byfrequency;by1000genomes;alternate_allele	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	41	12	141	0	0.292683	0	A|0.999;G|0.001	.	alt	.	IGLL5	26	.	NM_001256296	exon1	c.A65C	p.E22A	AGTTGGAAGCAGC	.	PASS	Atlas-SNP
RFC2	5982	hgsc.bcm.edu	37	7	73663362	73663362	+	Silent	SNP	T	T	C	rs1805395	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	30	12	40	0	0.4	0	T|0.971;C|0.029	0.029	strong	.	RFC2	27	.	NM_181471	exon4	c.A312G	p.E104E	ATTGAGTTCCAAC	.	PASS	Atlas-SNP
REG3A	5068	hgsc.bcm.edu	37	2	79385786	79385786	+	Silent	SNP	T	T	C	rs76653007	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91	11	135	0	0.120879	0	T|0.894;C|0.106	0.106	strong	.	REG3A	76	.	NM_138938	exon2	c.A186G	p.T62T	TGCATCTGTCCAG	.	PASS	Atlas-SNP
LAMA1	284217	hgsc.bcm.edu	37	18	6950847	6950847	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	103	27	110	0	0.262136	0	.	.	none	.	LAMA1	458	.	NM_005559	exon58	c.T8331G	p.F2777L	AAGGTCAAACATG	.	PASS	Atlas-SNP
GPR82	27197	hgsc.bcm.edu	37	X	41587218	41587218	+	Silent	SNP	T	T	C	rs1023065	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79	78	51	0	0.987342	0	T|0.167;C|0.833	0.833	strong	.	GPR82	52	.	NM_080817	exon3	c.T939C	p.D313D	ATTAGATAAAACA	.	PASS	Atlas-SNP
AKR1C3	8644	hgsc.bcm.edu	37	10	5138607	5138607	+	Silent	SNP	G	G	A	rs7741	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	141	72	147	0	0.510638	0	G|0.710;A|0.290	0.290	strong	.	AKR1C3	21	.	NM_001253908	exon2	c.G90A	p.P30P	GGTTCCGAGAAGT	.	PASS	Atlas-SNP
PARVG	64098	hgsc.bcm.edu	37	22	44586522	44586522	+	Silent	SNP	C	C	T	rs2272942	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	45	18	46	0	0.4	0	C|0.747;T|0.253	0.253	strong	.	PARVG	41	.	NM_001137606	exon7	c.C480T	p.V160V	CAACGTCCAGGTG	.	PASS	Atlas-SNP
ENTPD1	953	hgsc.bcm.edu	37	10	97599537	97599537	+	Silent	SNP	G	G	C	rs61731067	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	130	69	125	0	0.530769	0	G|0.945;C|0.055	0.055	strong	.	ENTPD1	44	.	NM_001164178	exon3	c.G270C	p.V90V	CGTGGTGCATCAA	.	PASS	Atlas-SNP
KIAA1804	0	hgsc.bcm.edu	37	1	233511675	233511675	+	Missense_Mutation	SNP	A	A	C	rs35758282	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	116	53	112	0	0.456897	0	A|0.998;C|0.002	0.002	strong	.	KIAA1804	129	.	NM_032435	exon7	c.A1689C	p.E563D	AGATGAAAGCAAT	.	PASS	Atlas-SNP
MYOF	26509	hgsc.bcm.edu	37	10	95107428	95107428	+	Missense_Mutation	SNP	G	G	A	rs11187393	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	129	67	148	0	0.51938	0	G|0.960;A|0.040	0.040	strong	.	MYOF	177	.	NM_013451	exon37	c.C4195T	p.R1399C	GAAAGCGGTCCAG	.	PASS	Atlas-SNP
MOB3C	148932	hgsc.bcm.edu	37	1	47078637	47078637	+	Silent	SNP	T	T	C	rs4660947	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	42	14	29	0	0.333333	0	T|0.452;C|0.548	0.548	strong	.	MOB3C	1	.	NM_145279	exon2	c.A513G	p.A171A	GAGCAATGCCATA	.	PASS	Atlas-SNP
ACAT1	38	hgsc.bcm.edu	37	11	108009660	108009660	+	Silent	SNP	C	C	A	rs35188041	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	119	17	115	0	0.142857	0	A|0.168;C|0.832;G|0.000	0.168	strong	ACAT1,colon,carcinoma,0,1	ACAT1	35	1	NM_000019	exon6	c.C471A	p.S157S	CATGTCCAATGTT	.	PASS	Atlas-SNP
NLRP11	204801	hgsc.bcm.edu	37	19	56297019	56297019	+	Missense_Mutation	SNP	G	G	A	rs11671248	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	232	96	248	0	0.413793	0	G|0.992;A|0.008	0.008	strong	.	NLRP11	139	.	NM_145007	exon12	c.C3074T	p.S1025L	GTATTTGACGTTC	.	PASS	Atlas-SNP
LMBRD2	92255	hgsc.bcm.edu	37	5	36143392	36143392	+	Silent	SNP	C	C	T	rs267766	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	144	73	187	0	0.506944	0	C|0.628;T|0.372	0.372	strong	LMBRD2,NS,carcinoma,0,1	LMBRD2	89	1	NM_001007527	exon2	c.G60A	p.L20L	ATGAAGCAGAAAT	.	PASS	Atlas-SNP
LILRB3	11025	hgsc.bcm.edu	37	19	54723030	54723030	+	Missense_Mutation	SNP	C	C	A	rs61734493	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	59	28	61	0	0.474576	0	C|0.956;A|0.044	0.044	strong	.	LILRB3	67	.	NM_006864	exon8	c.G1394T	p.R465L	TGACGTCGGAGGA	.	PASS	Atlas-SNP
CYP11B2	1585	hgsc.bcm.edu	37	8	143996539	143996539	+	Missense_Mutation	SNP	T	T	C	rs4539	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	125	50	138	0	0.4	0	T|0.648;C|0.352	0.352	strong	.	CYP11B2	107	.	NM_000498	exon3	c.A518G	p.K173R	TTCTTCTTCAGGG	.	PASS	Atlas-SNP
FYB	2533	hgsc.bcm.edu	37	5	39141240	39141240	+	Silent	SNP	G	G	A	rs3188386	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	168	74	208	0	0.440476	0	G|0.843;A|0.157	0.157	strong	.	FYB	354	.	NM_001243093	exon4	c.C1326T	p.S442S	GACAGGGCTTCTG	.	PASS	Atlas-SNP
ABCB4	5244	hgsc.bcm.edu	37	7	87092185	87092185	+	Silent	SNP	G	G	A	rs2302387	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	125	66	124	0	0.528	0	G|0.744;A|0.256	0.256	strong	.	ABCB4	177	.	NM_018850	exon4	c.C175T	p.L59L	TACCCAGCGACAT	.	PASS	Atlas-SNP
TAS2R14	50840	hgsc.bcm.edu	37	12	11091206	11091206	+	Missense_Mutation	SNP	G	G	A	rs35804287	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	77	42	78	0	0.545455	0	G|0.989;A|0.011	0.011	strong	.	TAS2R14	26	.	NM_023922	exon1	c.C601T	p.L201F	AGATGAGGAGAAG	.	PASS	Atlas-SNP
SPDEF	25803	hgsc.bcm.edu	37	6	34507305	34507305	+	Silent	SNP	C	C	T	rs374584207		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	190	34	217	0	0.178947	0	.	.	weak	.	SPDEF	34	.	NM_012391	exon4	c.G669A	p.A223A	GTGAATCGCCCCA	.	PASS	Atlas-SNP
IGHMBP2	3508	hgsc.bcm.edu	37	11	68705754	68705754	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	50	6	65	0	0.12	0	.	.	none	IGHMBP2,right_upper_lobe,carcinoma,0,1	IGHMBP2	83	1	NM_002180	exon14	c.G2716A	p.V906I	GCCGGCGTCACAA	.	PASS	Atlas-SNP
TTL	150465	hgsc.bcm.edu	37	2	113277949	113277949	+	Silent	SNP	T	T	C	rs62157538	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	96	95	162	0	0.989583	0	T|0.838;C|0.162	0.162	strong	TTL_ENST00000233336,colon,carcinoma,0,1	TTL	27	1	NM_153712	exon6	c.T966C	p.D322D	GGTCGATGAGGAG	.	PASS	Atlas-SNP
PCDHA7	56141	hgsc.bcm.edu	37	5	140214361	140214361	+	Silent	SNP	G	G	A	rs17844307	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	356	26	259	0	0.0730337	0	G|0.981;A|0.019	0.019	strong	PCDHA7_ENST00000525929,NS,carcinoma,+1,4	PCDHA7	367	4	NM_031852	exon1	c.G393A	p.P131P	CCCTCCGGTGTTC	.	PASS	Atlas-SNP
KLHL42	57542	hgsc.bcm.edu	37	12	27950775	27950775	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	17	60	0	0.326923	0	.	.	none	.	.	.	.	NM_020782	exon3	c.G1194A	p.G398G	GGGGGGGTGTCTC	.	PASS	Atlas-SNP
ERCC6L2	375748	hgsc.bcm.edu	37	9	98638288	98638288	+	Missense_Mutation	SNP	A	A	G	rs690528	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	30	12	41	0	0.4	0	A|0.717;G|0.283	0.283	strong	C9orf102,NS,carcinoma,0,2	.	.	2	NM_001010895	exon1	c.A1G	p.M1V	TGTTACATGCAGC	.	PASS	Atlas-SNP
LILRB3	11025	hgsc.bcm.edu	37	19	54722250	54722250	+	Missense_Mutation	SNP	T	T	C	rs1132610	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	143	69	152	0	0.482517	0	T|0.826;C|0.174	0.174	strong	LILRB3,colon,carcinoma,+2,1	LILRB3	67	1	NM_006864	exon11	c.A1573G	p.R525G	CCACCCTGTCCTC	.	PASS	Atlas-SNP
APOLD1	81575	hgsc.bcm.edu	37	12	12940402	12940402	+	Missense_Mutation	SNP	C	C	T	rs146348815		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80	30	87	0	0.375	0	C|1.000;T|0.000	0.000	weak	.	APOLD1	10	.	NM_001130415	exon2	c.C656T	p.T219I	GGGACACCAAGGT	.	PASS	Atlas-SNP
MDGA1	266727	hgsc.bcm.edu	37	6	37605158	37605158	+	Missense_Mutation	SNP	C	C	T	rs201115181	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	101	20	127	0	0.19802	0	C|0.999;T|0.001	0.001	strong	MDGA1,NS,carcinoma,+2,1	MDGA1	104	1	NM_153487	exon17	c.G2854A	p.A952T	GCAACGCCAAGAG	.	PASS	Atlas-SNP
HIST1H2BL	8340	hgsc.bcm.edu	37	6	27775367	27775367	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94	29	115	0	0.308511	0	.	.	none	.	HIST1H2BL	48	.	NM_003519	exon1	c.G318A	p.E106E	GGCCAGCTCCCCC	.	PASS	Atlas-SNP
ZNF831	128611	hgsc.bcm.edu	37	20	57768655	57768655	+	Missense_Mutation	SNP	G	G	A	rs61743779	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	30	61	0	0.566038	0	G|0.996;A|0.004	0.004	strong	.	ZNF831	287	.	NM_178457	exon1	c.G2581A	p.D861N	GATGCCGATCCCG	.	PASS	Atlas-SNP
EYS	346007	hgsc.bcm.edu	37	6	66005857	66005857	+	Missense_Mutation	SNP	T	T	A	rs17411795	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98	48	100	0	0.489796	0	A|0.141;N|0.000	0.141	strong	EYS_ENST00000370621,NS,carcinoma,0,1	EYS	527	1	NM_001142800	exon12	c.A1922T	p.E641V	TCTATCTCACAGA	.	PASS	Atlas-SNP
CCDC132	55610	hgsc.bcm.edu	37	7	92970847	92970847	+	Silent	SNP	C	C	T	rs2106432	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	105	105	102	0	1	0	C|0.433;T|0.567	0.567	strong	.	CCDC132	136	.	NM_017667	exon23	c.C2167T	p.L723L	GATACGCTGTATG	.	PASS	Atlas-SNP
ZNF716	441234	hgsc.bcm.edu	37	7	57529392	57529392	+	Missense_Mutation	SNP	A	A	C	rs13235676	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	22	11	17	0	0.5	0	A|0.591;C|0.409	0.409	strong	.	ZNF716	207	.	NM_001159279	exon4	c.A1225C	p.K409Q	CCCTACAAATGTG	.	PASS	Atlas-SNP
FRG1	2483	hgsc.bcm.edu	37	4	190878569	190878569	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	105	5	80	5	0.047619	0.0625	.	.	none	FRG1,NS,carcinoma,0,2	FRG1	76	2	NM_004477	exon6	c.T449C	p.L150S	CTTTGTTGGCCTC	.	scavenged	Atlas-SNP
MSH4	4438	hgsc.bcm.edu	37	1	76345823	76345823	+	Missense_Mutation	SNP	A	A	G	rs5745459	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	221	115	236	0	0.520362	0	A|0.993;G|0.007	0.007	strong	.	MSH4	147	.	NM_002440	exon13	c.A1766G	p.Y589C	AAATCTATCACAT	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	118	9	91	0	0.0762712	0	C|0.724;T|0.276	0.276	strong	.	ZDHHC11	97	.	NM_024786	exon8	c.G1022A	p.R341Q	CTTACCCGTGCCG	.	PASS	Atlas-SNP
TIGD2	166815	hgsc.bcm.edu	37	4	90034450	90034450	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	7	63	0	0.0921053	0	.	.	none	.	TIGD2	36	.	NM_145715	exon1	c.T325C	p.F109L	AAGTTCTTTTTTG	.	PASS	Atlas-SNP
NSUN4	387338	hgsc.bcm.edu	37	1	46827485	46827485	+	Silent	SNP	C	C	T	rs1053624	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	218	91	186	0	0.417431	0	C|0.804;T|0.196	0.196	strong	.	NSUN4	26	.	NM_199044	exon6	c.C1122T	p.P374P	TGGCCCCATGTAC	.	PASS	Atlas-SNP
OR10A6	390093	hgsc.bcm.edu	37	11	7950024	7950024	+	Silent	SNP	A	A	G	rs12272735	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	215	107	193	0	0.497674	0	A|0.658;G|0.342	0.342	strong	.	OR10A6	49	.	NM_001004461	exon1	c.T186C	p.F62F	CAGGAGAAACAGG	.	PASS	Atlas-SNP
ATM	472	hgsc.bcm.edu	37	11	108124761	108124761	+	Missense_Mutation	SNP	T	T	C	rs4986761	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	41	32	53	0	0.780488	0	T|0.993;C|0.007	0.007	strong	ATM,NS,carcinoma,0,2	ATM	1657	2	NM_000051	exon13	c.T2119C	p.S707P	TACTCATCTGAGG	.	PASS	Atlas-SNP
CCDC38	120935	hgsc.bcm.edu	37	12	96260947	96260947	+	Silent	SNP	A	A	G	rs7960706	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	154	63	161	0	0.409091	0	A|0.677;G|0.323	0.323	strong	.	CCDC38	45	.	NM_182496	exon16	c.T1599C	p.F533F	TGAATGAAAGACA	.	PASS	Atlas-SNP
TPX2	22974	hgsc.bcm.edu	37	20	30381758	30381758	+	Silent	SNP	G	G	C	rs1062794	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	141	67	153	0	0.475177	0	G|0.637;C|0.363	0.363	strong	.	TPX2	61	.	NM_012112	exon14	c.G1617C	p.S539S	TTTCTCGTTTGAT	.	PASS	Atlas-SNP
RNF123	63891	hgsc.bcm.edu	37	3	49738945	49738945	+	Silent	SNP	C	C	T	rs6804655	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	88	57	87	0	0.647727	0	C|0.749;N|0.001	.	strong	.	RNF123	100	.	NM_022064	exon16	c.C1299T	p.V433V	CTCCGTCGTCTTC	.	PASS	Atlas-SNP
SERTAD1	29950	hgsc.bcm.edu	37	19	40929363	40929363	+	Missense_Mutation	SNP	T	T	C	rs268687	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	25	67	0	0.462963	0	T|0.444;C|0.556	0.556	strong	.	SERTAD1	18	.	NM_013376	exon2	c.A91G	p.T31A	CCGCTGTGTGGCC	.	PASS	Atlas-SNP
NCKAP5L	57701	hgsc.bcm.edu	37	12	50189807	50189807	+	Silent	SNP	C	C	A	rs2720298	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	31	47	0	0.596154	0	C|0.433;A|0.567	0.567	strong	.	NCKAP5L	142	.	NM_001037806	exon8	c.G1836T	p.S612S	GGGGTACGATTCT	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51	27	43	0	0.529412	0	A|0.618;C|0.382	0.382	strong	.	NAV2	255	.	NM_001244963	exon29	c.A5682C	p.S1894S	AATTTCAGAATGC	.	PASS	Atlas-SNP
DMBX1	127343	hgsc.bcm.edu	37	1	46978076	46978076	+	Silent	SNP	C	C	A	rs11211298	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	33	74	0	0.532258	0	C|0.938;A|0.062	0.062	strong	.	DMBX1	50	.	NM_147192	exon4	c.C1059A	p.T353T	AGCTACCCTGAAC	.	PASS	Atlas-SNP
OR2T34	127068	hgsc.bcm.edu	37	1	248737293	248737293	+	Missense_Mutation	SNP	G	G	A	rs5014952		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	262	70	199	0	0.267176	0	.	.	weak	.	OR2T34	72	.	NM_001001821	exon1	c.C766T	p.L256F	CGAAGAGCAGCAG	.	PASS	Atlas-SNP
PSG7	5676	hgsc.bcm.edu	37	19	43433805	43433805	+	Silent	SNP	A	A	G	rs1065178	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98	58	90	0	0.591837	0	A|0.622;G|0.378	0.378	strong	.	.	.	.	NM_001206650	exon2	c.T132C	p.I44I	GGTTAAAATCACA	.	PASS	Atlas-SNP
SUPT6H	6830	hgsc.bcm.edu	37	17	27014483	27014483	+	Silent	SNP	C	C	A	rs28588628	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	28	16	40	0	0.571429	0	C|0.897;A|0.103	0.103	strong	.	SUPT6H	165	.	NM_003170	exon23	c.C3000A	p.L1000L	CCACCTCCTGAAG	.	PASS	Atlas-SNP
ARHGAP24	83478	hgsc.bcm.edu	37	4	86915848	86915848	+	Silent	SNP	T	T	C	rs10003909	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	135	65	152	0	0.481481	0	T|0.690;C|0.310	0.310	strong	.	ARHGAP24	116	.	NM_001025616	exon9	c.T1041C	p.N347N	CAACAATGAAATT	.	PASS	Atlas-SNP
WDR62	284403	hgsc.bcm.edu	37	19	36549684	36549684	+	Silent	SNP	G	G	A	rs61742664	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	40	22	48	0	0.55	0	G|0.947;A|0.053	0.053	strong	.	WDR62	102	.	NM_173636	exon2	c.G180A	p.V60V	GCAGGTGTCACTC	.	PASS	Atlas-SNP
STAB2	55576	hgsc.bcm.edu	37	12	104153004	104153004	+	Missense_Mutation	SNP	C	C	G	rs2271637	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	59	29	58	0	0.491525	0	C|0.734;G|0.266	0.266	strong	.	STAB2	370	.	NM_017564	exon65	c.C7201G	p.L2401V	ACGAGGCTGGGAA	.	PASS	Atlas-SNP
VGLL2	245806	hgsc.bcm.edu	37	6	117586990	117586990	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68	24	53	0	0.352941	0	.	.	none	.	VGLL2	18	.	NM_182645	exon1	c.T64G	p.Y22D	GCCGCCTACACCC	.	PASS	Atlas-SNP
OR2T2	401992	hgsc.bcm.edu	37	1	248616401	248616401	+	Silent	SNP	G	G	A	rs77680148	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	673	135	824	1	0.200594	0.00121359	G|0.913;A|0.087	0.087	strong	.	OR2T2	73	.	NM_001004136	exon1	c.G303A	p.Q101Q	AGTTCAGATCTTC	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110	110	95	0	1	0	A|0.515;G|0.485	0.485	strong	.	CAMKV	84	.	NM_024046	exon8	c.T651C	p.N217N	AGGTGGATTGCCT	.	PASS	Atlas-SNP
FAM71D	161142	hgsc.bcm.edu	37	14	67675021	67675021	+	Silent	SNP	C	C	T	rs35680137	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	103	51	102	0	0.495146	0	C|0.983;T|0.017	0.017	strong	.	FAM71D	33	.	NM_173526	exon6	c.C1015T	p.L339L	ATAACACTGACTT	.	PASS	Atlas-SNP
KRTAP19-5	337972	hgsc.bcm.edu	37	21	31874240	31874240	+	Missense_Mutation	SNP	T	T	C	rs117415039	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	65	24	57	0	0.369231	0	T|0.975;C|0.025	0.025	strong	.	KRTAP19-5	32	.	NM_181611	exon1	c.A169G	p.S57G	GGCAGCTGCGGTA	.	PASS	Atlas-SNP
ADARB2	105	hgsc.bcm.edu	37	10	1246060	1246060	+	Silent	SNP	C	C	T	rs138375235	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44	31	47	0	0.704545	0	C|0.997;T|0.003	0.003	strong	.	ADARB2	95	.	NM_018702	exon8	c.G1710A	p.A570A	CAGGAGCGCGCCC	.	PASS	Atlas-SNP
OR1S1	219959	hgsc.bcm.edu	37	11	57982726	57982726	+	Silent	SNP	G	G	T	rs1993089	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	114	114	200	0	1	0	G|0.609;T|0.391	0.391	strong	OR1S1,NS,carcinoma,0,1	OR1S1	139	1	NM_001004458	exon1	c.G510T	p.L170L	TGCTCTGACACAC	.	PASS	Atlas-SNP
OR2T8	343172	hgsc.bcm.edu	37	1	248084470	248084470	+	Missense_Mutation	SNP	C	C	T	rs140846339	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	417	49	369	0	0.117506	0	.	.	weak	OR2T8,rectum,carcinoma,0,2	OR2T8	67	2	NM_001005522	exon1	c.C151T	p.H51Y	TGGGACCACCGGC	.	scavenged	Atlas-SNP
ASPSCR1	79058	hgsc.bcm.edu	37	17	79941511	79941511	+	Silent	SNP	C	C	T	rs11539917	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	29	59	0	0.617021	0	C|0.988;T|0.012	0.012	strong	ASPSCR1_ENST00000306729,colon,carcinoma,0,1	ASPSCR1	27	1	NM_001251888	exon3	c.C240T	p.P80P	GGTGCCCGCTTCC	.	PASS	Atlas-SNP
FRY	10129	hgsc.bcm.edu	37	13	32752503	32752503	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	146	77	137	0	0.527397	0	.	.	none	.	FRY	312	.	NM_023037	exon21	c.A2611G	p.T871A	TGCCCCACAGCCC	.	PASS	Atlas-SNP
ZNF792	126375	hgsc.bcm.edu	37	19	35449760	35449760	+	Silent	SNP	G	G	C	rs2651080	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	61	62	0	1	0	G|0.671;C|0.329	0.329	strong	ZNF792,NS,carcinoma,-1,2	ZNF792	46	2	NM_175872	exon4	c.C999G	p.T333T	TTCACCGGTGTGA	.	PASS	Atlas-SNP
DOCK1	1793	hgsc.bcm.edu	37	10	129216658	129216658	+	Silent	SNP	T	T	C	rs2229600	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	52	56	0	0.981132	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
NOSTRIN	115677	hgsc.bcm.edu	37	2	169681151	169681151	+	Silent	SNP	C	C	T	rs3732031	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	367	168	421	0	0.457766	0	C|0.900;T|0.100	0.100	strong	NOSTRIN_ENST00000444448,NS,carcinoma,0,2	NOSTRIN	68	2	NM_001039724	exon3	c.C121T	p.L41L	GCAAACCTGGAAA	.	PASS	Atlas-SNP
DYX1C1	161582	hgsc.bcm.edu	37	15	55789910	55789910	+	Missense_Mutation	SNP	C	C	T	rs17819126	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	29	49	0	0.617021	0	C|0.959;T|0.041	0.041	strong	.	DYX1C1	54	.	NM_001033560	exon3	c.G271A	p.V91I	ACTTACCACCCGT	.	PASS	Atlas-SNP
MADD	8567	hgsc.bcm.edu	37	11	47303275	47303275	+	Silent	SNP	T	T	C	rs326217	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	77	42	91	0	0.545455	0	T|0.698;C|0.302	0.302	strong	.	MADD	172	.	NM_130474	exon8	c.T1440C	p.N480N	TGGCAATGATGTG	.	PASS	Atlas-SNP
TSNARE1	203062	hgsc.bcm.edu	37	8	143427178	143427178	+	Missense_Mutation	SNP	C	C	G	rs33970858	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	140	70	136	3	0.5	0.0220588	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	.	scavenged	Atlas-SNP
DOK3	79930	hgsc.bcm.edu	37	5	176931594	176931594	+	Missense_Mutation	SNP	G	G	C	rs61749657	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	14	6	21	0	0.428571	0	G|0.965;C|0.035	0.035	strong	.	DOK3	41	.	NM_024872	exon6	c.C881G	p.P294R	GCACAGGGGGTGC	.	PASS	Atlas-SNP
ENTPD7	57089	hgsc.bcm.edu	37	10	101445591	101445591	+	Silent	SNP	A	A	C	rs3740078	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110	53	99	0	0.481818	0	A|0.734;C|0.266	0.266	strong	.	ENTPD7	44	.	NM_020354	exon6	c.A591C	p.P197P	TTTACCACTGGAG	.	PASS	Atlas-SNP
PRR14L	253143	hgsc.bcm.edu	37	22	32110163	32110163	+	Missense_Mutation	SNP	G	G	A	rs140078	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	115	52	118	0	0.452174	0	G|0.689;A|0.311	0.311	strong	.	PRR14L	198	.	NM_173566	exon4	c.C3662T	p.S1221L	GACATCGACTCTT	.	PASS	Atlas-SNP
FANCI	55215	hgsc.bcm.edu	37	15	89836228	89836228	+	Missense_Mutation	SNP	G	G	C	rs2283432	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	143	66	189	0	0.461538	0	G|0.715;C|0.285	0.285	strong	FANCI_ENST00000310775,NS,adenoma,0,2	FANCI	129	2	NM_001113378	exon22	c.G2225C	p.C742S	ATATCTGTGCTTT	.	PASS	Atlas-SNP
ARSE	415	hgsc.bcm.edu	37	X	2856155	2856155	+	Missense_Mutation	SNP	C	C	T	rs35143646	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	176	47	119	0	0.267045	0	C|0.503;T|0.497	0.497	strong	.	ARSE	43	.	NM_000047	exon9	c.G1270A	p.G424S	CCTCGCCGCCCGC	.	PASS	Atlas-SNP
TAS1R2	80834	hgsc.bcm.edu	37	1	19181279	19181279	+	Missense_Mutation	SNP	G	G	A	rs140330444	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	39	14	53	0	0.358974	0	G|1.000;A|0.000	0.000	weak	.	TAS1R2	134	.	NM_152232	exon3	c.C685T	p.R229W	CGCGCCGGGCCAC	.	PASS	Atlas-SNP
TRPA1	8989	hgsc.bcm.edu	37	8	72948588	72948588	+	Silent	SNP	C	C	T	rs13280644	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	189	109	204	0	0.57672	0	C|0.934;T|0.066	0.066	strong	.	TRPA1	256	.	NM_007332	exon21	c.G2490A	p.L830L	CCACTGCAGATGA	.	PASS	Atlas-SNP
BMS1	9790	hgsc.bcm.edu	37	10	43281089	43281089	+	Silent	SNP	T	T	C	rs7074877	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	128	59	126	0	0.460938	0	T|0.503;C|0.497	0.497	strong	.	BMS1	132	.	NM_014753	exon3	c.T336C	p.T112T	GTTGACTGAGATC	.	PASS	Atlas-SNP
IPO4	79711	hgsc.bcm.edu	37	14	24653954	24653954	+	Missense_Mutation	SNP	G	G	A	rs7146310	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	190	114	194	0	0.6	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
TACC2	10579	hgsc.bcm.edu	37	10	123845897	123845897	+	Silent	SNP	G	G	C	rs1106992	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	43	18	42	0	0.418605	0	G|0.758;C|0.242	0.242	strong	.	TACC2	271	.	NM_206862	exon4	c.G3882C	p.L1294L	CCCCCTGTTGCAA	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	122	120	147	0	0.983607	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
GABRA6	2559	hgsc.bcm.edu	37	5	161119125	161119125	+	Silent	SNP	C	C	G	rs13184586	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	99	53	122	0	0.535354	0	C|0.535;G|0.465	0.465	strong	.	GABRA6	139	.	NM_000811	exon8	c.C1005G	p.A335A	GAAGGCCAAAAGG	.	PASS	Atlas-SNP
TET2	54790	hgsc.bcm.edu	37	4	106196829	106196829	+	Missense_Mutation	SNP	T	T	G	rs34402524	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	137	71	156	0	0.518248	0	T|0.903;G|0.097	0.097	strong	TET2,NS,haematopoietic_neoplasm,0,1	TET2	1762	1	NM_001127208	exon11	c.T5162G	p.L1721W	GGAAATTGCCTCC	.	PASS	Atlas-SNP
TRPM5	29850	hgsc.bcm.edu	37	11	2432666	2432666	+	Missense_Mutation	SNP	C	C	T	rs34364959	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48	21	72	0	0.4375	0	C|0.930;T|0.070	0.070	strong	.	TRPM5	86	.	NM_014555	exon18	c.G2698A	p.G900S	GGCGGCCGTCATG	.	PASS	Atlas-SNP
DDX51	317781	hgsc.bcm.edu	37	12	132626425	132626425	+	Missense_Mutation	SNP	G	G	A	rs60927391	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	120	59	106	0	0.491667	0	G|0.765;A|0.235	0.235	strong	.	DDX51	33	.	NM_175066	exon6	c.C965T	p.A322V	TCCTTGGCCAGAG	.	PASS	Atlas-SNP
RBAK	57786	hgsc.bcm.edu	37	7	5105133	5105133	+	Silent	SNP	C	C	T	rs12334144	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72	71	85	0	0.986111	0	C|0.426;G|0.000;T|0.574	0.574	strong	RBAK_ENST00000396912,colon,carcinoma,0,1	RBAK	82	1	NM_001204456	exon6	c.C2046T	p.N682N	ATGTAACGAGTGT	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179634961	179634961	+	Missense_Mutation	SNP	C	C	A	rs33917087	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	127	62	115	0	0.488189	0	C|0.985;A|0.015	0.015	strong	.	TTN	18412	.	NM_001267550	exon36	c.G8467T	p.V2823F	CTGGAACAGTGTC	.	PASS	Atlas-SNP
ZNF578	147660	hgsc.bcm.edu	37	19	53014787	53014787	+	Missense_Mutation	SNP	A	A	G	rs35356792	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44	22	42	0	0.5	0	A|0.938;G|0.062	0.062	strong	.	.	.	.	NM_001099694	exon6	c.A1153G	p.T385A	AATTCAACCCTTG	.	PASS	Atlas-SNP
SEC24D	9871	hgsc.bcm.edu	37	4	119736796	119736796	+	Silent	SNP	A	A	C	rs2389688	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	129	61	93	0	0.472868	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
ALMS1	7840	hgsc.bcm.edu	37	2	73677898	73677898	+	Missense_Mutation	SNP	G	G	C	rs6546837	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	65	41	105	0	0.630769	0	G|0.697;C|0.303	0.303	strong	.	ALMS1	384	.	NM_015120	exon8	c.G4241C	p.G1414A	GACCAGGTGACCG	.	PASS	Atlas-SNP
CARD14	79092	hgsc.bcm.edu	37	17	78157995	78157995	+	Silent	SNP	G	G	A	rs4889990	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	62	61	0	0.96875	0	G|0.641;A|0.359	0.359	strong	.	CARD14	98	.	NM_024110	exon4	c.G633A	p.E211E	GCAGGAGAAGGAG	.	PASS	Atlas-SNP
C2orf42	54980	hgsc.bcm.edu	37	2	70377653	70377653	+	Silent	SNP	G	G	A	rs12989348	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	31	9	47	0	0.290323	0	G|0.920;A|0.080	0.080	strong	.	C2orf42	30	.	NM_017880	exon10	c.C1560T	p.I520I	CCACTCGATGATG	.	PASS	Atlas-SNP
LAMA5	3911	hgsc.bcm.edu	37	20	60898891	60898891	+	Silent	SNP	C	C	T	rs138911913	byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51	23	78	0	0.45098	0	C|0.999;T|0.001	0.001	strong	.	LAMA5	268	.	NM_005560	exon44	c.G5790A	p.L1930L	GCCTCGCAGGACA	.	PASS	Atlas-SNP
TUBA3E	112714	hgsc.bcm.edu	37	2	130951949	130951949	+	Missense_Mutation	SNP	G	G	A	rs76125467	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	180	38	189	0	0.211111	0	G|0.500;A|0.500	0.500	weak	TUBA3E,NS,carcinoma,+2,1	TUBA3E	73	1	NM_207312	exon4	c.C466T	p.R156W	AGAGCCGCTCCAT	.	PASS	Atlas-SNP
ITK	3702	hgsc.bcm.edu	37	5	156671437	156671437	+	Silent	SNP	G	G	T	rs17595896	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	142	66	156	0	0.464789	0	G|0.994;T|0.006	0.006	strong	.	ITK	136	.	NM_005546	exon13	c.G1398T	p.V466V	GGATGTGTGTGAG	.	PASS	Atlas-SNP
SIGLEC10	89790	hgsc.bcm.edu	37	19	51918112	51918112	+	Silent	SNP	A	A	G	rs3810099	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85	44	89	0	0.517647	0	A|0.791;G|0.209	0.209	strong	SIGLEC12_ENST00000439889,NS,carcinoma,-1,4	SIGLEC10	112	4	NM_033130	exon8	c.T1581C	p.H527H	GGCCCCATGGACG	.	PASS	Atlas-SNP
SLC38A10	124565	hgsc.bcm.edu	37	17	79244802	79244802	+	Silent	SNP	T	T	C	rs2292184	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	28	105	0	0.345679	0	T|0.518;C|0.482	0.482	strong	SLC38A10_ENST00000374759,NS,carcinoma,0,2	SLC38A10	133	2	NM_001037984	exon10	c.A1047G	p.T349T	CGCTCCTGTGAGG	.	PASS	Atlas-SNP
COL4A3	1285	hgsc.bcm.edu	37	2	228121101	228121101	+	Missense_Mutation	SNP	G	G	T	rs55703767	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	37	14	41	0	0.378378	0	G|0.828;T|0.172	0.172	strong	.	COL4A3	293	.	NM_000091	exon17	c.G976T	p.D326Y	GGTGAAGATGGCA	.	PASS	Atlas-SNP
PLEK2	26499	hgsc.bcm.edu	37	14	67862269	67862269	+	Missense_Mutation	SNP	G	G	A	rs34300264	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110	47	121	0	0.427273	0	G|0.983;A|0.017	0.017	strong	.	PLEK2	23	.	NM_016445	exon3	c.C239T	p.T80M	TACTCCGTGGATG	.	PASS	Atlas-SNP
CTSL1	1514	hgsc.bcm.edu	37	9	90343505	90343505	+	Silent	SNP	G	G	A	rs11541204	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	77	36	83	0	0.467532	0	G|0.968;A|0.032	0.032	strong	.	CTSL1	43	.	NM_145918	exon5	c.G402A	p.Q134Q	GGGTCAGTGTGGT	.	PASS	Atlas-SNP
DYNC2LI1	51626	hgsc.bcm.edu	37	2	44021826	44021826	+	Missense_Mutation	SNP	T	T	A	rs9309107	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	180	179	189	0	0.994444	0	A|0.389;N|0.001	0.389	strong	.	DYNC2LI1	46	.	NM_015522	exon6	c.T551A	p.F184Y	TCCCATTTATAGT	.	PASS	Atlas-SNP
SSX3	10214	hgsc.bcm.edu	37	X	48213499	48213499	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	278	109	187	0	0.392086	0	.	.	none	.	SSX3	64	.	NM_021014	exon4	c.G215A	p.R72H	TTATTACGCATGA	.	PASS	Atlas-SNP
NOTCH4	4855	hgsc.bcm.edu	37	6	32168996	32168996	+	Missense_Mutation	SNP	C	C	G	rs8192573	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	14	117	0	0.162791	0	C|0.984;G|0.016	0.016	strong	NOTCH4,right_upper_lobe,carcinoma,-1,1	NOTCH4	201	1	NM_004557	exon22	c.G4037C	p.R1346P	TCAGCCCGGGCCC	.	PASS	Atlas-SNP
REP15	387849	hgsc.bcm.edu	37	12	27850113	27850113	+	Missense_Mutation	SNP	A	A	T	rs12819160	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	58	31	48	0	0.534483	0	A|0.877;T|0.123	0.123	strong	.	REP15	13	.	NM_001029874	exon1	c.A618T	p.E206D	AACTGAAGATTGT	.	PASS	Atlas-SNP
DYNC1H1	1778	hgsc.bcm.edu	37	14	102516487	102516487	+	Silent	SNP	G	G	A	rs35079638	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91	52	87	0	0.571429	0	G|0.998;A|0.002	0.002	strong	.	DYNC1H1	395	.	NM_001376	exon77	c.G13764A	p.T4588T	CCTGACGCAGCTG	.	PASS	Atlas-SNP
OTOGL	283310	hgsc.bcm.edu	37	12	80750659	80750659	+	Missense_Mutation	SNP	G	G	A	rs11836060	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	109	62	162	0	0.568807	0	G|0.823;A|0.177	0.177	strong	.	OTOGL	235	.	NM_173591	exon48	c.G5957A	p.R1986Q	AAGTTCGACAGGA	.	PASS	Atlas-SNP
PALD1	27143	hgsc.bcm.edu	37	10	72298745	72298745	+	Missense_Mutation	SNP	C	C	T	rs117244352	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	99	49	115	0	0.494949	0	C|0.990;T|0.010	0.010	strong	.	.	.	.	NM_014431	exon13	c.C1550T	p.T517M	ACGGCACGGCCCA	.	PASS	Atlas-SNP
FTSJD1	55783	hgsc.bcm.edu	37	16	71318001	71318001	+	Missense_Mutation	SNP	G	G	T	rs3096381	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60	30	71	0	0.5	0	G|0.883;T|0.117	0.117	strong	.	FTSJD1	70	.	NM_018348	exon3	c.C1823A	p.T608K	AAAGTTGTGAGTT	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179397561	179397561	+	Missense_Mutation	SNP	C	C	T	rs3829747	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	172	83	144	0	0.482558	0	C|0.813;T|0.187	0.187	strong	TTN_ENST00000359218,caecum,carcinoma,-1,7	TTN	18412	7	NM_001267550	exon358	c.G103781A	p.R34594H	CGGATGCGCTTGG	.	PASS	Atlas-SNP
OR13C9	286362	hgsc.bcm.edu	37	9	107380215	107380215	+	Missense_Mutation	SNP	T	T	A	rs993658	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	296	138	327	0	0.466216	0	T|0.743;A|0.257	0.257	strong	OR13C9,colon,carcinoma,+2,1	OR13C9	42	1	NM_001001956	exon1	c.A271T	p.T91S	AAATGGTCTTTCT	.	PASS	Atlas-SNP
SPPL2C	162540	hgsc.bcm.edu	37	17	43924200	43924200	+	Missense_Mutation	SNP	C	C	G	rs12373142	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60	59	56	0	0.983333	0	C|0.473;G|0.527	0.527	strong	.	.	.	.	NM_175882	exon1	c.C1928G	p.P643R	TGCCCCCGCCCTC	.	PASS	Atlas-SNP
ZNF462	58499	hgsc.bcm.edu	37	9	109687288	109687288	+	Silent	SNP	T	T	C	rs1000152	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72	36	66	0	0.5	0	T|0.801;C|0.199	0.199	strong	ZNF462,colon,carcinoma,0,1	ZNF462	322	1	NM_021224	exon3	c.T1095C	p.Y365Y	CCGTTATGGAATG	.	PASS	Atlas-SNP
SLC6A17	388662	hgsc.bcm.edu	37	1	110709720	110709720	+	Missense_Mutation	SNP	G	G	A	rs12737742	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	25	66	0	0.396825	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
KRBA2	124751	hgsc.bcm.edu	37	17	8272767	8272767	+	Silent	SNP	G	G	A	rs2430949	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	39	18	48	0	0.461538	0	G|0.834;A|0.166	0.166	strong	KRBA2,NS,carcinoma,0,1	KRBA2	34	1	NM_213597	exon2	c.C1164T	p.L388L	GAATCGGAGGCCT	.	PASS	Atlas-SNP
TMEM144	55314	hgsc.bcm.edu	37	4	159161513	159161513	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	89	46	117	0	0.516854	0	.	.	none	.	TMEM144	34	.	NM_018342	exon10	c.G745A	p.A249T	TTTCTGGCCTACT	.	PASS	Atlas-SNP
EGFL8	80864	hgsc.bcm.edu	37	6	32134510	32134510	+	Missense_Mutation	SNP	G	G	A	rs3096697	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	92	70	76	0	0.76087	0	G|0.830;A|0.170	0.170	strong	.	EGFL8	15	.	NM_030652	exon4	c.G257A	p.R86K	AGGTGAGGCGGGA	.	PASS	Atlas-SNP
DGCR2	9993	hgsc.bcm.edu	37	22	19028744	19028744	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72	4	72	0	0.0555556	0	.	.	none	.	DGCR2	45	.	NM_005137	exon9	c.C1223T	p.T408M	AGGCCCGTGCCAA	.	PASS	Atlas-SNP
CLIC5	53405	hgsc.bcm.edu	37	6	45882076	45882076	+	Missense_Mutation	SNP	C	C	A	rs148377014	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93	49	112	0	0.526882	0	C|0.998;A|0.002	0.002	strong	.	CLIC5	48	.	NM_001114086	exon5	c.G954T	p.E318D	GTCAATCTCCTCT	.	PASS	Atlas-SNP
TCEB3C	162699	hgsc.bcm.edu	37	18	44555147	44555147	+	Missense_Mutation	SNP	T	T	G	rs139717358	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	317	17	34	0	0.0536278	0	T|0.924;G|0.076	0.076	strong	TCEB3C,NS,carcinoma,0,1	TCEB3C	49	1	NM_145653	exon1	c.A1067C	p.E356A	ACCCCTTCCACGT	.	scavenged	Atlas-SNP
LRIT2	340745	hgsc.bcm.edu	37	10	85981889	85981889	+	Silent	SNP	G	G	A	rs12218853	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	50	26	38	0	0.52	0	G|0.817;A|0.183	0.183	strong	.	LRIT2	81	.	NM_001017924	exon3	c.C1440T	p.G480G	ATAGGCGCCCACA	.	PASS	Atlas-SNP
SF3B14	0	hgsc.bcm.edu	37	2	24291323	24291323	+	Silent	SNP	G	G	A	rs41281479	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100	49	110	0	0.49	0	G|0.997;A|0.003	0.003	strong	.	SF3B14	6	.	NM_016047	exon3	c.C156T	p.N52N	AGGTGTGTTCCCC	.	PASS	Atlas-SNP
DAGLB	221955	hgsc.bcm.edu	37	7	6456347	6456347	+	Silent	SNP	G	G	T	rs1055428	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	43	36	0	0.826923	0	G|0.843;T|0.157	0.157	strong	.	DAGLB	74	.	NM_139179	exon11	c.C1338A	p.G446G	CGCCCCGCCCCCG	.	PASS	Atlas-SNP
MRPL35	51318	hgsc.bcm.edu	37	2	86433240	86433240	+	Missense_Mutation	SNP	C	C	T	rs10901	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	205	204	287	0	0.995122	0	T|0.269;G|0.143	0.269	strong	MRPL35,NS,adenoma,0,2	MRPL35	23	2	NM_016622	exon2	c.C55T	p.P19S	CTACGGCCCCTGA	.	PASS	Atlas-SNP
ZNF860	344787	hgsc.bcm.edu	37	3	32031024	32031024	+	Silent	SNP	C	C	T	rs4449357	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	131	130	117	0	0.992366	0	C|0.655;T|0.345	0.345	strong	.	ZNF860	96	.	NM_001137674	exon2	c.C453T	p.I151I	GCCTATCAAAGAT	.	PASS	Atlas-SNP
SLC5A8	160728	hgsc.bcm.edu	37	12	101573812	101573812	+	Silent	SNP	A	A	G	rs61738704	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	38	21	39	0	0.552632	0	A|0.978;G|0.022	0.022	strong	.	SLC5A8	102	.	NM_145913	exon10	c.T1228C	p.L410L	CCTGCAACAAAGC	.	PASS	Atlas-SNP
TRIM32	22954	hgsc.bcm.edu	37	9	119461275	119461275	+	Silent	SNP	G	G	A	rs1661300	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69	31	75	0	0.449275	0	G|0.896;A|0.104	0.104	strong	.	TRIM32	67	.	NM_012210	exon2	c.G1254A	p.V418V	CTTTGTGCTAAGC	.	PASS	Atlas-SNP
KCNJ2	3759	hgsc.bcm.edu	37	17	68172326	68172326	+	Silent	SNP	C	C	T	rs173135	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	29	51	0	0.460317	0	C|0.867;T|0.133	0.133	strong	.	KCNJ2	74	.	NM_000891	exon2	c.C1146T	p.L382L	TGCCCTCACAAGC	.	PASS	Atlas-SNP
RSF1	51773	hgsc.bcm.edu	37	11	77378505	77378505	+	Silent	SNP	A	A	G	rs28930682	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51	43	41	0	0.843137	0	A|0.816;G|0.184	0.184	strong	.	RSF1	105	.	NM_016578	exon16	c.T3783C	p.D1261D	TAGCTCATCATCT	.	PASS	Atlas-SNP
TMEM2	23670	hgsc.bcm.edu	37	9	74349846	74349846	+	Missense_Mutation	SNP	A	A	T	rs25695	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	118	51	141	0	0.432203	0	A|0.936;T|0.064	0.064	strong	.	TMEM2	112	.	NM_013390	exon6	c.T1269A	p.D423E	ACTAACATCATCT	.	PASS	Atlas-SNP
SERPINF2	5345	hgsc.bcm.edu	37	17	1648502	1648502	+	Missense_Mutation	SNP	C	C	T	rs2070863	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	32	14	37	0	0.4375	0	C|0.794;T|0.206	0.206	strong	.	SERPINF2	33	.	NM_000934	exon3	c.C97T	p.R33W	TTGGGCCGGCAGG	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	32	67	0	0.5	0	C|0.359;T|0.641	0.641	strong	.	VPS33B	42	.	NM_018668	exon20	c.G1540A	p.G514S	CACCACCGAAGAC	.	PASS	Atlas-SNP
IPO4	79711	hgsc.bcm.edu	37	14	24654489	24654489	+	Silent	SNP	T	T	C	rs2025258	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	104	49	138	0	0.471154	0	T|0.551;C|0.448	0.448	strong	.	IPO4	74	.	NM_024658	exon14	c.A1308G	p.V436V	TGGCATTACCTCC	.	PASS	Atlas-SNP
TAS2R43	259289	hgsc.bcm.edu	37	12	11244194	11244194	+	Missense_Mutation	SNP	T	T	C	rs71443637	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	103	87	27	0	0.84466	0	T|0.599;C|0.401	0.401	strong	TAS2R43,NS,carcinoma,0,2	TAS2R43	19	2	NM_176884	exon1	c.A635G	p.H212R	TTACCATGGAGCT	.	PASS	Atlas-SNP
PML	5371	hgsc.bcm.edu	37	15	74336633	74336633	+	Missense_Mutation	SNP	T	T	C	rs5742915	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	38	18	38	0	0.473684	0	T|0.714;C|0.286	0.286	strong	.	PML	169	.	NM_033238	exon9	c.T1933C	p.F645L	GAAGCCTTCTTCA	.	PASS	Atlas-SNP
ZNF302	55900	hgsc.bcm.edu	37	19	35175749	35175749	+	Silent	SNP	C	C	G	rs10401309	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	30	51	0	0.576923	0	C|0.915;G|0.085	0.085	strong	.	ZNF302	27	.	NM_018443	exon5	c.C807G	p.G269G	CCATGGCTCATCA	.	PASS	Atlas-SNP
SAA1	6288	hgsc.bcm.edu	37	11	18291321	18291321	+	Silent	SNP	T	T	C	rs12218	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	174	79	163	1	0.454023	0.00613497	T|0.648;C|0.352	0.352	strong	SAA1,NS,carcinoma,0,1	SAA1	14	1	NM_199161	exon4	c.T288C	p.A96A	GCTGGCTGATCAG	.	scavenged	Atlas-SNP
CCL14	6358	hgsc.bcm.edu	37	17	34313674	34313674	+	Silent	SNP	G	G	A	rs113937434	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	111	59	79	0	0.531532	0	G|0.977;A|0.023	0.023	strong	.	CCL14	22	.	NM_032962	exon1	c.C12T	p.S4S	AGCCACGGAGATC	.	PASS	Atlas-SNP
RGAG1	57529	hgsc.bcm.edu	37	X	109696758	109696758	+	Silent	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	24	62	0	0.338028	0	.	.	none	.	RGAG1	168	.	NM_020769	exon3	c.T2913G	p.A971A	CATGGCTTCTGGA	.	PASS	Atlas-SNP
SLC12A7	10723	hgsc.bcm.edu	37	5	1057615	1057615	+	Silent	SNP	A	A	G	rs2241606	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57	32	71	0	0.561404	0	A|0.485;G|0.515	0.515	strong	SLC12A7,NS,carcinoma,-1,1	SLC12A7	97	1	NM_006598	exon22	c.T2997C	p.S999S	GAAACCAGATAGG	.	PASS	Atlas-SNP
SPTBN5	51332	hgsc.bcm.edu	37	15	42171462	42171462	+	Missense_Mutation	SNP	C	C	T	rs12708402	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	39	24	53	0	0.615385	0	C|0.800;T|0.200	0.200	strong	.	SPTBN5	171	.	NM_016642	exon16	c.G3073A	p.V1025I	ACTTTACGACCAC	.	PASS	Atlas-SNP
HECTD1	25831	hgsc.bcm.edu	37	14	31578762	31578762	+	Silent	SNP	C	C	T	rs17097735	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	131	64	130	0	0.48855	0	C|0.750;T|0.250	0.250	strong	.	HECTD1	159	.	NM_015382	exon36	c.G6321A	p.E2107E	CGTTCGCTCCACA	.	PASS	Atlas-SNP
KHK	3795	hgsc.bcm.edu	37	2	27315252	27315252	+	Missense_Mutation	SNP	G	G	A	rs2304681	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	23	48	0	0.489362	0	G|0.649;A|0.351	0.351	strong	KHK_ENST00000260598,colon,carcinoma,0,2	KHK	60	2	NM_006488	exon2	c.G145A	p.V49I	TGCACCGTTCTCT	.	PASS	Atlas-SNP
THUMPD1	55623	hgsc.bcm.edu	37	16	20748331	20748331	+	Missense_Mutation	SNP	C	C	A	rs11074471	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	228	129	210	0	0.565789	0	C|0.868;A|0.132	0.132	strong	.	THUMPD1	33	.	NM_017736	exon4	c.G933T	p.E311D	AGTATTCTCTGGT	.	PASS	Atlas-SNP
PSAPL1	768239	hgsc.bcm.edu	37	4	7436486	7436486	+	Missense_Mutation	SNP	C	C	A	rs11548325	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	103	102	142	0	0.990291	0	C|0.820;A|0.180	0.180	strong	.	PSAPL1	51	.	NM_001085382	exon1	c.G121T	p.A41S	ACCTGGCAGCTGT	.	PASS	Atlas-SNP
HRNR	388697	hgsc.bcm.edu	37	1	152187588	152187588	+	Missense_Mutation	SNP	C	C	T	rs201071455	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	263	25	132	0	0.095057	0	C|0.806;T|0.194	0.194	strong	HRNR,NS,carcinoma,0,2	HRNR	403	2	NM_001009931	exon3	c.G6517A	p.G2173S	GTCGGCCGTGGCC	.	scavenged	Atlas-SNP
C6orf15	29113	hgsc.bcm.edu	37	6	31080016	31080016	+	Missense_Mutation	SNP	C	C	G	rs2233974	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	92	76	71	0	0.826087	0	C|0.832;G|0.168	0.168	strong	.	C6orf15	29	.	NM_014070	exon2	c.G120C	p.L40F	GGTCCCCAAGTTT	.	PASS	Atlas-SNP
RAMP1	10267	hgsc.bcm.edu	37	2	238820380	238820380	+	Silent	SNP	G	G	A	rs61752232	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	223	98	231	0	0.439462	0	G|0.994;A|0.006	0.006	strong	.	RAMP1	10	.	NM_005855	exon3	c.G402A	p.T134T	GGTGACGGCACTG	.	PASS	Atlas-SNP
USP37	57695	hgsc.bcm.edu	37	2	219360656	219360656	+	Silent	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	59	21	77	0	0.355932	0	.	.	none	.	USP37	76	.	NM_020935	exon14	c.A1299G	p.L433L	CTGACTTAAAAAT	.	PASS	Atlas-SNP
SARDH	1757	hgsc.bcm.edu	37	9	136599146	136599146	+	Silent	SNP	C	C	T	rs573904	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	39	98	0	0.481481	0	C|0.776;T|0.224	0.224	strong	.	SARDH	112	.	NM_007101	exon2	c.G150A	p.Q50Q	GGTGCCCTGTCCC	.	PASS	Atlas-SNP
RFC1	5981	hgsc.bcm.edu	37	4	39302029	39302029	+	Silent	SNP	T	T	C	rs2066786	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	105	43	94	0	0.409524	0	T|0.557;C|0.443	0.443	strong	.	RFC1	114	.	NM_001204747	exon20	c.A2544G	p.P848P	ATCAAATGGGCCC	.	PASS	Atlas-SNP
ATP13A2	23400	hgsc.bcm.edu	37	1	17314702	17314702	+	Silent	SNP	C	C	T	rs3738815	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	105	51	132	0	0.485714	0	C|0.770;T|0.230	0.230	strong	ATP13A2,NS,carcinoma,-1,1	ATP13A2	85	1	NM_022089	exon25	c.G2790A	p.S930S	GCTGAACGAAGTG	.	PASS	Atlas-SNP
SLC1A6	6511	hgsc.bcm.edu	37	19	15083693	15083693	+	Silent	SNP	C	C	A	rs3746295	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49	15	31	0	0.306122	0	C|0.450;A|0.550	0.550	strong	SLC1A6,NS,carcinoma,0,2	SLC1A6	111	2	NM_001272087	exon4	c.G30T	p.L10L	CTCCCGCAGGAAC	.	PASS	Atlas-SNP
TCTE3	6991	hgsc.bcm.edu	37	6	170144228	170144228	+	Missense_Mutation	SNP	C	C	A	rs2027063	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73	34	72	0	0.465753	0	C|0.862;A|0.138	0.138	strong	.	TCTE3	13	.	NM_174910	exon2	c.G263T	p.R88I	TCCATTCTATATG	.	PASS	Atlas-SNP
DNAH3	55567	hgsc.bcm.edu	37	16	20966362	20966362	+	Missense_Mutation	SNP	T	T	C	rs34051490	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	43	90	0	0.573333	0	T|0.927;C|0.073	0.073	strong	.	DNAH3	1142	.	NM_017539	exon55	c.A10844G	p.Y3615C	GATGGATAGCTGG	.	PASS	Atlas-SNP
B4GALNT4	338707	hgsc.bcm.edu	37	11	372700	372700	+	Silent	SNP	G	G	C	rs35475866	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	59	57	53	0	0.966102	0	G|0.714;C|0.286	0.286	strong	B4GALNT4,rectum,carcinoma,0,1	B4GALNT4	83	1	NM_178537	exon3	c.G294C	p.G98G	TGGGGGGGCTGGG	.	PASS	Atlas-SNP
KRTAP3-1	83896	hgsc.bcm.edu	37	17	39165174	39165174	+	Silent	SNP	G	G	A	rs112432710	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	161	75	150	0	0.465839	0	G|0.925;A|0.075	0.075	strong	.	KRTAP3-1	11	.	NM_031958	exon1	c.C153T	p.C51C	TGGGGGGCAGGTG	.	PASS	Atlas-SNP
ZNF335	63925	hgsc.bcm.edu	37	20	44590732	44590732	+	Silent	SNP	G	G	A	rs16990964	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	35	97	0	0.406977	0	G|0.963;A|0.037	0.037	strong	.	ZNF335	115	.	NM_022095	exon10	c.C1623T	p.H541H	AGCGGCGTGCCGA	.	PASS	Atlas-SNP
TARBP1	6894	hgsc.bcm.edu	37	1	234564951	234564951	+	Missense_Mutation	SNP	A	A	T	rs12135427	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	106	49	97	0	0.462264	0	A|0.988;T|0.012	0.012	strong	.	TARBP1	111	.	NM_005646	exon17	c.T2991A	p.F997L	AAAAACAAACTGA	.	PASS	Atlas-SNP
TSEN15	116461	hgsc.bcm.edu	37	1	184023529	184023529	+	Missense_Mutation	SNP	A	A	C	rs1046934	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	77	45	110	0	0.584416	0	A|0.705;C|0.295	0.295	strong	.	TSEN15	19	.	NM_001127394	exon2	c.A177C	p.Q59H	CACCCAAGTTTAT	.	PASS	Atlas-SNP
OBP2A	29991	hgsc.bcm.edu	37	9	138440641	138440641	+	Missense_Mutation	SNP	T	T	C	rs2853652	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	96	96	74	0	1	0	T|0.207;C|0.793	0.793	strong	.	OBP2A	21	.	NM_014582	exon5	c.T476C	p.M159T	TTTTCATGCCCCT	.	PASS	Atlas-SNP
TBC1D4	9882	hgsc.bcm.edu	37	13	76055820	76055820	+	Silent	SNP	G	G	C	rs7327548	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80	50	49	0	0.625	0	G|0.616;C|0.384	0.384	strong	.	TBC1D4	142	.	NM_014832	exon1	c.C84G	p.P28P	CTTCCCGGGGCCG	.	PASS	Atlas-SNP
DPF3	8110	hgsc.bcm.edu	37	14	73220020	73220020	+	Silent	SNP	A	A	G	rs3742836	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	39	23	27	0	0.589744	0	A|0.773;G|0.227	0.227	strong	.	DPF3	117	.	NM_012074	exon3	c.T253C	p.L85L	GGTGCAATCGTCT	.	PASS	Atlas-SNP
LRRC52	440699	hgsc.bcm.edu	37	1	165533005	165533005	+	Silent	SNP	C	C	A	rs453717	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	88	48	87	1	0.545455	0.0114943	C|0.692;A|0.308	0.308	strong	LRRC52,caecum,carcinoma,0,1	LRRC52	50	1	NM_001005214	exon2	c.C886A	p.R296R	GTCAGCCGGCGGA	.	scavenged	Atlas-SNP
ATP9B	374868	hgsc.bcm.edu	37	18	77097360	77097360	+	Missense_Mutation	SNP	A	A	T	rs585033	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	36	17	49	0	0.472222	0	A|0.943;T|0.057	0.057	strong	.	ATP9B	96	.	NM_198531	exon19	c.A2194T	p.M732L	AGGGAGATGGAAC	.	PASS	Atlas-SNP
RSF1	51773	hgsc.bcm.edu	37	11	77409568	77409568	+	Silent	SNP	T	T	C	rs4945203	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	309	237	307	0	0.76699	0	T|0.813;C|0.187	0.187	strong	.	RSF1	105	.	NM_016578	exon7	c.A2679G	p.P893P	TTTGCATGGTTCA	.	PASS	Atlas-SNP
CR1	1378	hgsc.bcm.edu	37	1	207737312	207737312	+	Silent	SNP	T	T	C	rs77529679		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	6	5	392	0	0.833333	0	C|1.000;|0.000	1.000	weak	CR1_ENST00000367049,NS,carcinoma,0,2	CR1	354	2	NM_000651	exon22	c.T3690C	p.Y1230Y	CGGCTATGACCTC	.	scavenged	Atlas-SNP
HP	3240	hgsc.bcm.edu	37	16	72094348	72094348	+	Silent	SNP	G	G	A	rs5475	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	153	78	165	0	0.509804	0	G|0.978;A|0.022	0.022	strong	.	HP	27	.	NM_005143	exon7	c.G780A	p.E260E	TAATGAGAGAGTG	.	PASS	Atlas-SNP
LAMA5	3911	hgsc.bcm.edu	37	20	60895697	60895697	+	Missense_Mutation	SNP	C	C	T	rs2297587	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51	24	48	0	0.470588	0	C|0.805;T|0.195	0.195	strong	.	LAMA5	268	.	NM_005560	exon50	c.G6677A	p.R2226H	TCATGGCGGGGGC	.	PASS	Atlas-SNP
KNDC1	85442	hgsc.bcm.edu	37	10	135027195	135027195	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	10	61	0	0.192308	0	.	.	none	.	KNDC1	155	.	NM_152643	exon25	c.C4490T	p.A1497V	CACGGGCCCTGGG	.	PASS	Atlas-SNP
METTL11B	149281	hgsc.bcm.edu	37	1	170135669	170135669	+	Silent	SNP	C	C	T	rs6427234	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60	33	47	0	0.55	0	C|0.725;T|0.275	0.275	strong	.	METTL11B	18	.	NM_001136107	exon3	c.C357T	p.C119C	AGACTGCGCCTTG	.	PASS	Atlas-SNP
ATP2A3	489	hgsc.bcm.edu	37	17	3846802	3846802	+	Silent	SNP	A	A	G	rs758641	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83	31	94	0	0.373494	0	A|0.605;G|0.395	0.395	strong	.	ATP2A3	148	.	NM_174956	exon11	c.T1302C	p.Y434Y	CTTCTCATACACA	.	PASS	Atlas-SNP
LRRN1	57633	hgsc.bcm.edu	37	3	3887093	3887093	+	Silent	SNP	A	A	G	rs9844909	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51	31	65	0	0.607843	0	A|0.775;G|0.225	0.225	strong	.	LRRN1	82	.	NM_020873	exon2	c.A768G	p.Q256Q	CCCTCAACTTGCC	.	PASS	Atlas-SNP
TAP2	6891	hgsc.bcm.edu	37	6	32802938	32802938	+	Missense_Mutation	SNP	C	C	T	rs140654840	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	143	26	153	0	0.181818	0	C|0.986;T|0.014	0.014	strong	.	TAP2	98	.	NM_018833	exon5	c.G938A	p.R313H	TGATGGCGGGTGT	.	PASS	Atlas-SNP
HSPG2	3339	hgsc.bcm.edu	37	1	22174518	22174518	+	Silent	SNP	G	G	T	rs12737091	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	89	43	97	0	0.483146	0	G|0.964;T|0.036	0.036	strong	.	HSPG2	311	.	NM_005529	exon60	c.C7806A	p.V2602V	GTTACTGACGTGA	.	PASS	Atlas-SNP
OR2M5	127059	hgsc.bcm.edu	37	1	248309356	248309356	+	Missense_Mutation	SNP	A	A	G	rs73141283	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	140	68	139	0	0.485714	0	A|0.942;G|0.058	0.058	strong	.	OR2M5	117	.	NM_001004690	exon1	c.A907G	p.K303E	CTCAGGAAAGTGT	.	PASS	Atlas-SNP
RECQL5	9400	hgsc.bcm.edu	37	17	73657118	73657118	+	Silent	SNP	C	C	T	rs149970344		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	155	61	152	0	0.393548	0	C|1.000;T|0.000	0.000	weak	.	RECQL5	77	.	NM_001003715	exon6	c.G903A	p.V301V	GTTCTGCACCAGC	.	PASS	Atlas-SNP
OR10H4	126541	hgsc.bcm.edu	37	19	16059846	16059846	+	Missense_Mutation	SNP	C	C	G	rs117192411	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79	32	102	0	0.405063	0	C|0.982;G|0.018	0.018	strong	.	OR10H4	48	.	NM_001004465	exon1	c.C29G	p.S10C	TCATATCTGAATT	.	PASS	Atlas-SNP
IPP	3652	hgsc.bcm.edu	37	1	46195375	46195375	+	Missense_Mutation	SNP	T	T	C	rs28375469	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	125	56	125	0	0.448	0	T|0.709;C|0.291	0.291	strong	IPP,NS,carcinoma,0,1	IPP	66	1	NM_001145349	exon4	c.A791G	p.K264R	GGAGATTTGCATA	.	PASS	Atlas-SNP
TMEM99	147184	hgsc.bcm.edu	37	17	38991053	38991053	+	Silent	SNP	T	T	A	rs3169915	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	148	146	144	0	0.986486	0	T|0.873;A|0.127	0.127	strong	.	TMEM99	21	.	NM_001195386	exon3	c.T285A	p.L95L	AGGACTTCTTCTT	.	PASS	Atlas-SNP
ANK3	288	hgsc.bcm.edu	37	10	61831744	61831744	+	Silent	SNP	A	A	G	rs10740006	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60	31	83	0	0.516667	0	A|0.834;G|0.166	0.166	strong	.	ANK3	703	.	NM_020987	exon37	c.T8895C	p.A2965A	CTCATCAGCAACT	.	PASS	Atlas-SNP
WDR11	55717	hgsc.bcm.edu	37	10	122624679	122624679	+	Silent	SNP	G	G	A	rs10886789	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	113	57	117	0	0.504425	0	G|0.708;A|0.292	0.292	strong	WDR11,NS,carcinoma,0,1	WDR11	95	1	NM_018117	exon6	c.G834A	p.T278T	TCAGACGGTGGGT	.	PASS	Atlas-SNP
IL10RA	3587	hgsc.bcm.edu	37	11	117869670	117869670	+	Missense_Mutation	SNP	A	A	G	rs2229113	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	46	53	0	0.884615	0	A|0.247;G|0.753	0.753	strong	.	IL10RA	46	.	NM_001558	exon7	c.A1051G	p.R351G	GGAAACAGGGAGC	.	PASS	Atlas-SNP
PKN3	29941	hgsc.bcm.edu	37	9	131469190	131469190	+	Missense_Mutation	SNP	C	C	A	rs56251280	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60	33	49	0	0.55	0	C|0.996;A|0.004	0.004	strong	.	PKN3	62	.	NM_013355	exon5	c.C539A	p.A180E	TGCTGGCGGAGGA	.	PASS	Atlas-SNP
FAM21B	55747	hgsc.bcm.edu	37	10	47915898	47915898	+	Silent	SNP	A	A	G	rs61856727	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	605	68	149	0	0.112397	0	A|0.375;G|0.625	0.625	strong	FAM21B_ENST00000358474,NS,carcinoma,0,1	FAM21B	31	1	NM_018232	exon15	c.A1305G	p.K435K	CAGCAAAAATCTC	.	scavenged	Atlas-SNP
KRT32	3882	hgsc.bcm.edu	37	17	39619115	39619115	+	Missense_Mutation	SNP	G	G	A	rs2071563	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	25	62	0	0.462963	0	G|0.611;A|0.389	0.389	strong	.	KRT32	57	.	NM_002278	exon6	c.C1184T	p.T395M	CGGTACGTGTTGA	.	PASS	Atlas-SNP
PDGFRB	5159	hgsc.bcm.edu	37	5	149499672	149499672	+	Silent	SNP	T	T	C	rs246395	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	56	27	39	0	0.482143	0	T|0.745;C|0.255	0.255	strong	PDGFRB,NS,carcinoma,0,1	PDGFRB	142	1	NM_002609	exon19	c.A2601G	p.L867L	CCACTTTAAAGGC	.	PASS	Atlas-SNP
SH2D4A	63898	hgsc.bcm.edu	37	8	19221700	19221700	+	Missense_Mutation	SNP	G	G	A	rs34608771	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	59	36	51	0	0.610169	0	G|0.764;A|0.236	0.236	strong	.	SH2D4A	49	.	NM_022071	exon7	c.G824A	p.S275N	TGCAAAGCCCCTT	.	PASS	Atlas-SNP
BCL2A1	597	hgsc.bcm.edu	37	15	80263051	80263051	+	Silent	SNP	G	G	A	rs147879852		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	187	94	160	0	0.502674	0	G|1.000;A|0.000	0.000	weak	BCL2A1,colon,carcinoma,0,1	BCL2A1	28	1	NM_001114735	exon1	c.C411T	p.N137N	GCCTCCGTTTTGC	.	PASS	Atlas-SNP
ATP10A	57194	hgsc.bcm.edu	37	15	25926186	25926186	+	Silent	SNP	G	G	A	rs2076743	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	103	103	100	0	1	0	G|0.329;A|0.671	0.671	strong	.	ATP10A	270	.	NM_024490	exon18	c.C3528T	p.A1176A	GGCGTCGGCCATG	.	PASS	Atlas-SNP
XIRP2	129446	hgsc.bcm.edu	37	2	168099738	168099738	+	Silent	SNP	T	T	C	rs10497323	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	217	120	279	0	0.552995	0	T|0.689;C|0.311	0.311	strong	.	XIRP2	914	.	NM_152381	exon9	c.T1836C	p.G612G	TGGTGGTGATGTG	.	PASS	Atlas-SNP
ARSB	411	hgsc.bcm.edu	37	5	78181477	78181477	+	Missense_Mutation	SNP	C	C	T	rs1065757	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	58	58	67	0	1	0	T|0.311;C|0.689	0.311	strong	.	ARSB	47	.	NM_198709	exon6	c.G1072A	p.V358M	GCTTCACGAGTGT	.	PASS	Atlas-SNP
TGIF2LX	90316	hgsc.bcm.edu	37	X	89177673	89177673	+	Missense_Mutation	SNP	G	G	A	rs2290380	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	207	150	165	0	0.724638	0	G|0.234;A|0.766	0.766	strong	.	TGIF2LX	84	.	NM_138960	exon2	c.G589A	p.V197I	GTTTCTGTCACAT	.	PASS	Atlas-SNP
ZNF138	7697	hgsc.bcm.edu	37	7	64291987	64291987	+	Missense_Mutation	SNP	G	G	A	rs35742014	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	65	24	38	0	0.369231	0	G|0.953;A|0.047	0.047	strong	.	ZNF138	43	.	NM_001271639	exon4	c.G367A	p.G123S	CAAGGAGGTTTTA	.	PASS	Atlas-SNP
DNAH5	1767	hgsc.bcm.edu	37	5	13788927	13788927	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	199	37	207	0	0.18593	0	.	.	none	.	DNAH5	868	.	NM_001369	exon51	c.A8545C	p.S2849R	CCAAACTTACTAA	.	PASS	Atlas-SNP
DHX32	55760	hgsc.bcm.edu	37	10	127548215	127548215	+	Missense_Mutation	SNP	G	G	A	rs201005566	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	34	84	0	0.515152	0	.	.	weak	.	DHX32	67	.	NM_018180	exon3	c.C806T	p.S269L	TCACCCGAGTGGT	.	PASS	Atlas-SNP
PM20D1	148811	hgsc.bcm.edu	37	1	205810947	205810947	+	Missense_Mutation	SNP	C	C	T	rs11240573	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	260	132	251	0	0.507692	0	C|0.906;T|0.094	0.094	strong	.	PM20D1	56	.	NM_152491	exon9	c.G1036A	p.G346R	TGACCCCTGCTTT	.	PASS	Atlas-SNP
CNR1	1268	hgsc.bcm.edu	37	6	88853635	88853635	+	Silent	SNP	C	C	T	rs1049353	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	139	67	133	0	0.482014	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
GPR78	27201	hgsc.bcm.edu	37	4	8588950	8588950	+	Missense_Mutation	SNP	C	C	T	rs61746144	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	136	79	191	1	0.580882	0.0052356	C|0.986;T|0.014	0.014	strong	.	GPR78	58	.	NM_080819	exon3	c.C952T	p.R318C	ACCCCGCGCCCAG	.	PASS	Atlas-SNP
FAM200B	285550	hgsc.bcm.edu	37	4	15689632	15689632	+	Silent	SNP	G	G	A	rs11729955	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	156	155	224	2	0.99359	0.00892857	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
THEM6	51337	hgsc.bcm.edu	37	8	143808951	143808951	+	Silent	SNP	C	C	T	rs2585138	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	8	7	10	0	0.875	0	C|0.510;T|0.490	0.490	strong	.	.	.	.	NM_016647	exon1	c.C187T	p.L63L	CTGCTGCTGCACA	.	PASS	Atlas-SNP
AKNAD1	254268	hgsc.bcm.edu	37	1	109363232	109363232	+	Silent	SNP	T	T	C	rs1333130	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	41	22	77	0	0.536585	0	T|0.694;C|0.306	0.306	strong	.	AKNAD1	83	.	NM_152763	exon14	c.A2184G	p.K728K	GATCCGTTTGGGT	.	PASS	Atlas-SNP
CCDC174	51244	hgsc.bcm.edu	37	3	14712473	14712473	+	Silent	SNP	G	G	A	rs1901	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	143	57	135	0	0.398601	0	G|0.630;A|0.370	0.370	strong	.	.	.	.	NM_016474	exon11	c.G1176A	p.P392P	TGCCCCGCCGTCA	.	PASS	Atlas-SNP
CARKD	55739	hgsc.bcm.edu	37	13	111287893	111287893	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55	40	91	0	0.727273	0	.	.	none	.	CARKD	36	.	NM_018210	exon8	c.G730C	p.V244L	ACGGTGGTCCAGA	.	PASS	Atlas-SNP
ZNF671	79891	hgsc.bcm.edu	37	19	58233008	58233008	+	Missense_Mutation	SNP	G	G	A	rs3746207	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	137	58	114	0	0.423358	0	G|0.819;A|0.181	0.181	strong	.	ZNF671	55	.	NM_024833	exon4	c.C446T	p.A149V	ACTCCTGCTACAA	.	PASS	Atlas-SNP
PLA2G2A	5320	hgsc.bcm.edu	37	1	20304962	20304962	+	Silent	SNP	C	C	G	rs2236771	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	40	22	41	0	0.55	0	C|0.904;G|0.096	0.096	strong	.	PLA2G2A	14	.	NM_001161729	exon3	c.G96C	p.T32T	TCCTGTCGTCAAC	.	PASS	Atlas-SNP
OR6K3	391114	hgsc.bcm.edu	37	1	158687224	158687224	+	Missense_Mutation	SNP	G	G	A	rs857703	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85	38	79	0	0.447059	0	G|0.696;A|0.304	0.304	strong	OR6K3,NS,carcinoma,0,1	OR6K3	101	1	NM_001005327	exon1	c.C682T	p.P228S	AAGAGGGAATCCT	.	PASS	Atlas-SNP
CBLB	868	hgsc.bcm.edu	37	3	105439026	105439026	+	Silent	SNP	G	G	A	rs2305035	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	132	59	124	0	0.44697	0	G|0.787;A|0.213	0.213	strong	.	CBLB	118	.	NM_170662	exon10	c.C1272T	p.D424D	AAAGGGGTCCACG	.	PASS	Atlas-SNP
KRTAP10-2	386679	hgsc.bcm.edu	37	21	45971162	45971162	+	Silent	SNP	C	C	T	rs76415521		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	10	76	0	0.16129	0	.	.	weak	KRTAP10-2,colon,carcinoma,0,1	KRTAP10-2	21	1	NM_198693	exon1	c.G180A	p.A60A	ACAGGCCGCCTGG	.	scavenged	Atlas-SNP
WDR62	284403	hgsc.bcm.edu	37	19	36594369	36594369	+	Silent	SNP	C	C	T	rs45470992	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91	46	78	0	0.505495	0	C|0.963;T|0.037	0.037	strong	.	WDR62	102	.	NM_001083961	exon30	c.C3639T	p.S1213S	CCCCTCCACCTGT	.	PASS	Atlas-SNP
SENP1	29843	hgsc.bcm.edu	37	12	48477422	48477422	+	Silent	SNP	A	A	G	rs886588	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	140	63	120	0	0.45	0	A|0.817;G|0.183	0.183	strong	SENP1,NS,carcinoma,0,1	SENP1	44	1	NM_001267594	exon6	c.T504C	p.L168L	GCTCAAAAGACTT	.	PASS	Atlas-SNP
VWF	7450	hgsc.bcm.edu	37	12	6105387	6105387	+	Silent	SNP	G	G	A	rs216902	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	25	78	0	0.462963	0	G|0.580;A|0.420	0.420	strong	.	VWF	338	.	NM_000552	exon35	c.C5844T	p.C1948C	GCACACGCCTGGA	.	PASS	Atlas-SNP
C12orf40	283461	hgsc.bcm.edu	37	12	40041723	40041723	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	103	56	118	1	0.543689	0.00847458	.	.	none	C12orf40,NS,carcinoma,-1,1	C12orf40	118	1	NM_001031748	exon6	c.T514A	p.S172T	TTCACATCTGGAA	.	scavenged	Atlas-SNP
ABCA7	10347	hgsc.bcm.edu	37	19	1049269	1049269	+	Silent	SNP	G	G	A	rs4147914	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	167	74	132	0	0.443114	0	G|0.831;A|0.169	0.169	strong	ABCA7,NS,carcinoma,0,1	ABCA7	174	1	NM_019112	exon18	c.G2385A	p.L795L	AGTGCTGGTAGAA	.	PASS	Atlas-SNP
MBP	4155	hgsc.bcm.edu	37	18	74728823	74728823	+	Missense_Mutation	SNP	C	C	T	rs61742988	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49	48	50	0	0.979592	0	C|0.979;T|0.021	0.021	strong	.	MBP	45	.	NM_001025100	exon4	c.G541A	p.G181S	TGTCACCGCCAAA	.	PASS	Atlas-SNP
ABCA13	154664	hgsc.bcm.edu	37	7	48317708	48317708	+	Missense_Mutation	SNP	A	A	C	rs78334925	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	34	29	57	0	0.852941	0	A|0.900;C|0.100	0.100	strong	.	ABCA13	1192	.	NM_152701	exon18	c.A6917C	p.K2306T	AAGATAAAATTCT	.	PASS	Atlas-SNP
CXCL16	58191	hgsc.bcm.edu	37	17	4638484	4638484	+	Silent	SNP	T	T	C	rs1876444	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	89	49	79	0	0.550562	0	T|0.485;C|0.515	0.515	strong	CXCL16_ENST00000293778,NS,carcinoma,0,1	CXCL16	30	1	NM_022059	exon4	c.A678G	p.P226P	CAGGACTGGCACT	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72	35	61	0	0.486111	0	G|0.921;C|0.079	0.079	strong	.	TSHZ2	209	.	NM_173485	exon2	c.G339C	p.R113S	CGTCAGGCTTCCA	.	PASS	Atlas-SNP
TBX1	6899	hgsc.bcm.edu	37	22	19766782	19766782	+	Missense_Mutation	SNP	C	C	T	rs4819522	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	24	60	0	0.45283	0	C|0.829;T|0.171	0.171	strong	TBX1_ENST00000329705,colon,carcinoma,0,1	TBX1	62	1	NM_080646	exon9	c.C1049T	p.T350M	CTGAGACGTCTAG	.	PASS	Atlas-SNP
MYO3A	53904	hgsc.bcm.edu	37	10	26463130	26463130	+	Missense_Mutation	SNP	C	C	A	rs1999240	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	105	105	107	0	1	0	C|0.401;A|0.599	0.599	strong	MYO3A,colon,carcinoma,-1,1	MYO3A	371	1	NM_017433	exon30	c.C3937A	p.R1313S	ACCCAGCGTGCAC	.	PASS	Atlas-SNP
CDH22	64405	hgsc.bcm.edu	37	20	44806727	44806727	+	Silent	SNP	G	G	A	rs35585191	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	124	53	119	0	0.427419	0	G|0.914;A|0.086	0.086	strong	.	CDH22	112	.	NM_021248	exon11	c.C1773T	p.S591S	GCCTGTGCTGCTC	.	PASS	Atlas-SNP
CACNA1F	778	hgsc.bcm.edu	37	X	49071964	49071964	+	Silent	SNP	A	A	G	rs2075866	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	96	21	70	0	0.21875	0	0|0.014;T|0.004	.	strong	.	CACNA1F	218	.	NM_005183	exon28	c.T3309C	p.H1103H	GGGGCCATGGTCC	.	PASS	Atlas-SNP
TPST2	8459	hgsc.bcm.edu	37	22	26936897	26936897	+	Silent	SNP	G	G	A	rs12169509	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	29	76	0	0.432836	0	G|0.823;A|0.177	0.177	strong	.	TPST2	23	.	NM_001008566	exon3	c.C700T	p.L234L	CAGGCAGGCACTT	.	PASS	Atlas-SNP
TLR1	7096	hgsc.bcm.edu	37	4	38799710	38799710	+	Missense_Mutation	SNP	T	T	C	rs4833095	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	31	71	0	0.43662	0	T|0.512;C|0.488	0.488	strong	.	TLR1	70	.	NM_003263	exon4	c.A743G	p.N248S	GTAAGATTTGATA	.	PASS	Atlas-SNP
ATL1	51062	hgsc.bcm.edu	37	14	51054598	51054598	+	Silent	SNP	A	A	G	rs35014209	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	33	89	0	0.464789	0	A|0.807;G|0.193	0.193	strong	.	ATL1	46	.	NM_015915	exon2	c.A84G	p.P28P	GGAGCCAGTGAAA	.	PASS	Atlas-SNP
TACC1	6867	hgsc.bcm.edu	37	8	38677932	38677932	+	Silent	SNP	A	A	G	rs2013586	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93	51	126	0	0.548387	0	A|0.696;G|0.304	0.304	strong	TACC1_ENST00000317827,NS,carcinoma,0,1	TACC1	98	1	NM_006283	exon3	c.A1170G	p.E390E	GTGGGAAAGCCCC	.	PASS	Atlas-SNP
NEU4	129807	hgsc.bcm.edu	37	2	242758326	242758326	+	Silent	SNP	G	G	A	rs2293761	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	31	8	48	0	0.258065	0	G|0.618;A|0.382	0.382	strong	NEU4,rectum,carcinoma,0,1	NEU4	39	1	NM_001167599	exon4	c.G1446A	p.K482K	CCCCAAGCCGCCC	.	scavenged	Atlas-SNP
TRANK1	9881	hgsc.bcm.edu	37	3	36873866	36873866	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	270	153	273	0	0.566667	0	.	.	none	.	TRANK1	398	.	NM_014831	exon21	c.A7076T	p.H2359L	CACAGGTGGGTCT	.	PASS	Atlas-SNP
CAPN12	147968	hgsc.bcm.edu	37	19	39228244	39228244	+	Missense_Mutation	SNP	T	T	C	rs73038948	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	150	67	186	0	0.446667	0	T|0.867;C|0.133	0.133	strong	CAPN12,NS,carcinoma,0,1	CAPN12	43	1	NM_144691	exon9	c.A1000G	p.T334A	GCACGGTGTCGAA	.	PASS	Atlas-SNP
LRP2	4036	hgsc.bcm.edu	37	2	170063380	170063380	+	Missense_Mutation	SNP	T	T	C	rs35413340	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79	36	85	0	0.455696	0	T|0.999;C|0.001	0.001	strong	.	LRP2	751	.	NM_004525	exon39	c.A6850G	p.T2284A	AAACAGTGATGCC	.	PASS	Atlas-SNP
SLCO1C1	53919	hgsc.bcm.edu	37	12	20905250	20905250	+	Missense_Mutation	SNP	C	C	T	rs6487138	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	126	51	137	0	0.404762	0	C|0.547;T|0.453	0.453	strong	.	SLCO1C1	216	.	NM_001145946	exon16	c.C2030T	p.S677F	ATATATCTGGGAC	.	PASS	Atlas-SNP
XRRA1	143570	hgsc.bcm.edu	37	11	74559481	74559481	+	Silent	SNP	C	C	T	rs4944961	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	67	72	0	1	0	C|0.687;T|0.313	0.313	strong	.	XRRA1	46	.	NM_182969	exon15	c.G1383A	p.P461P	CTGCTTCGGCACC	.	PASS	Atlas-SNP
KCNH5	27133	hgsc.bcm.edu	37	14	63174960	63174960	+	Missense_Mutation	SNP	C	C	T	rs4902176	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	126	69	111	0	0.547619	0	C|0.730;T|0.270	0.270	strong	.	KCNH5	320	.	NM_139318	exon11	c.G2233A	p.A745T	TGGAGGCTCCATT	.	PASS	Atlas-SNP
P2RX6	9127	hgsc.bcm.edu	37	22	21377301	21377301	+	Silent	SNP	C	C	A	rs1548411	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	124	124	125	1	1	0.008	C|0.383;A|0.617	0.617	strong	.	.	.	.	NM_005446	exon5	c.C534A	p.P178P	GTGCCCCGTGGAG	.	PASS	Atlas-SNP
ZBTB7C	201501	hgsc.bcm.edu	37	18	45566276	45566276	+	Silent	SNP	G	G	A	rs80109066	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	16	8	31	0	0.5	0	G|0.804;A|0.196	0.196	strong	.	ZBTB7C	73	.	NM_001039360	exon2	c.C1203T	p.F401F	CCTGGTGAAGCGG	.	PASS	Atlas-SNP
TMPRSS9	360200	hgsc.bcm.edu	37	19	2396611	2396611	+	Missense_Mutation	SNP	C	C	T	rs17685098	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	36	99	0	0.418605	0	C|0.673;T|0.327	0.327	strong	.	TMPRSS9	79	.	NM_182973	exon2	c.C217T	p.R73W	AGTTTGCGGCGGG	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82	40	74	0	0.487805	0	C|0.742;G|0.258	0.258	strong	.	FRMD4B	90	.	NM_015123	exon6	c.G519C	p.E173D	TTCGCTCTCTACT	.	PASS	Atlas-SNP
POLQ	10721	hgsc.bcm.edu	37	3	121206402	121206402	+	Silent	SNP	C	C	T	rs369852464	alternate_allele	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	193	2	181	0	0.0103627	0	.	.	alt	POLQ,NS,carcinoma,-1,1	POLQ	273	1	NM_199420	exon16	c.G5376A	p.G1792G	TTTGAACCCATTT	.	scavenged	Atlas-SNP
BCAR1	9564	hgsc.bcm.edu	37	16	75269477	75269477	+	Silent	SNP	A	A	C	rs61729595	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	26	26	64	0	1	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
PTPN5	84867	hgsc.bcm.edu	37	11	18764026	18764026	+	Missense_Mutation	SNP	G	G	C	rs4757707	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49	48	47	0	0.979592	0	G|0.702;C|0.298	0.298	strong	PTPN5_ENST00000358540,caecum,carcinoma,0,3	PTPN5	163	3	NM_032781	exon7	c.C508G	p.P170A	GCTCTGGGGGTGT	.	PASS	Atlas-SNP
TSPYL6	388951	hgsc.bcm.edu	37	2	54482989	54482989	+	Silent	SNP	C	C	T	rs6740641	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	29	62	0	0.460317	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
CX3CR1	1524	hgsc.bcm.edu	37	3	39307256	39307256	+	Missense_Mutation	SNP	C	C	T	rs3732379	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	131	60	128	0	0.458015	0	C|0.832;T|0.168	0.168	strong	.	CX3CR1	91	.	NM_001171174	exon2	c.G841A	p.V281I	TCATAACGTTGTA	.	PASS	Atlas-SNP
SPRR3	6707	hgsc.bcm.edu	37	1	152975739	152975739	+	Silent	SNP	T	T	A	rs17851565	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	56	4	68	0	0.0714286	0	A|0.010;C|0.001;T|0.988	0.010	strong	SPRR3,colon,carcinoma,0,4	SPRR3	45	4	NM_001097589	exon2	c.T243A	p.G81G	GCCAGGTTGTACC	.	PASS	Atlas-SNP
CRHR1	1394	hgsc.bcm.edu	37	17	43907896	43907896	+	Silent	SNP	T	T	C	rs16940665	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	63	64	0	1	0	T|0.862;C|0.138	0.138	strong	.	CRHR1	48	.	NM_001145146	exon8	c.T756C	p.T252T	CTCCACTGACCGG	.	PASS	Atlas-SNP
TTC12	54970	hgsc.bcm.edu	37	11	113222885	113222885	+	Missense_Mutation	SNP	A	A	T	rs35852218	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	202	167	193	0	0.826733	0	A|0.989;T|0.011	0.011	strong	.	TTC12	66	.	NM_017868	exon16	c.A1402T	p.M468L	AGACACATGGCGG	.	PASS	Atlas-SNP
USP40	55230	hgsc.bcm.edu	37	2	234394487	234394487	+	Missense_Mutation	SNP	G	G	A	rs1048603	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	150	149	168	0	0.993333	0	G|0.604;T|0.006	.	strong	.	USP40	174	.	NM_018218	exon28	c.C3367T	p.R1123C	GAAGACGATAGAA	.	PASS	Atlas-SNP
DHX33	56919	hgsc.bcm.edu	37	17	5347576	5347576	+	Silent	SNP	G	G	A	rs2074438	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	46	91	0	0.567901	0	G|0.837;A|0.163	0.163	strong	.	DHX33	41	.	NM_020162	exon12	c.C2073T	p.Y691Y	AGCCTCGTACAGC	.	PASS	Atlas-SNP
NEBL	10529	hgsc.bcm.edu	37	10	21139389	21139389	+	Missense_Mutation	SNP	T	T	C	rs4025981	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79	30	58	0	0.379747	0	T|0.942;C|0.058	0.058	strong	NEBL,NS,carcinoma,0,1	NEBL	199	1	NM_006393	exon11	c.A1051G	p.M351V	CAAGCATTGGCTT	.	PASS	Atlas-SNP
CAT	847	hgsc.bcm.edu	37	11	34482908	34482908	+	Silent	SNP	C	C	T	rs769217	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	105	105	86	0	1	0	C|0.745;T|0.255	0.255	strong	.	CAT	42	.	NM_001752	exon9	c.C1167T	p.D389D	GCGTGACGGCCCG	.	PASS	Atlas-SNP
DDX11	1663	hgsc.bcm.edu	37	12	31256615	31256615	+	Missense_Mutation	SNP	C	C	A	rs3893680	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	108	6	120	0	0.0555556	0	.	.	weak	DDX11,lower_third,carcinoma,-2,1	DDX11	188	1	NM_030653	exon26	c.C2641A	p.R881S	CGAGCCCGTGTGG	.	scavenged	Atlas-SNP
RFX8	731220	hgsc.bcm.edu	37	2	102019129	102019129	+	Silent	SNP	C	C	T	rs201832728	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	89	42	81	0	0.47191	0	.	.	weak	.	RFX8	16	.	NM_001145664	exon11	c.G1014A	p.E338E	CATGTCCTCCTCC	.	PASS	Atlas-SNP
SYNC	81493	hgsc.bcm.edu	37	1	33161264	33161264	+	Silent	SNP	C	C	T	rs74519835	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	303	134	257	1	0.442244	0.00389105	C|0.942;T|0.058	0.058	strong	.	SYNC	36	.	NM_001161708	exon2	c.G435A	p.R145R	CTCCGCCCTTGTG	.	PASS	Atlas-SNP
SLC6A3	6531	hgsc.bcm.edu	37	5	1443199	1443199	+	Silent	SNP	G	G	A	rs6350	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	99	57	90	0	0.575758	0	G|0.943;A|0.057	0.057	strong	.	SLC6A3	102	.	NM_001044	exon2	c.C114T	p.N38N	CACTCCGTTCTGC	.	PASS	Atlas-SNP
PAQR7	164091	hgsc.bcm.edu	37	1	26189517	26189517	+	Missense_Mutation	SNP	C	C	T	rs6689014	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	113	57	101	0	0.504425	0	C|0.995;T|0.005	0.005	strong	.	PAQR7	23	.	NM_178422	exon2	c.G814A	p.G272R	CCTGCCCGAAGAC	.	PASS	Atlas-SNP
CDON	50937	hgsc.bcm.edu	37	11	125848261	125848261	+	Silent	SNP	C	C	T	rs3740904	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	4	49	0	0.0625	0	C|0.626;T|0.374	0.374	strong	CDON,NS,carcinoma,0,1	CDON	137	1	NM_016952	exon18	c.G3294A	p.T1098T	CACGGCCGTGTAC	.	scavenged	Atlas-SNP
HIST4H4	121504	hgsc.bcm.edu	37	12	14923887	14923887	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83	5	71	0	0.060241	0	.	.	none	.	HIST4H4	13	.	NM_175054	exon1	c.C132T	p.V44V	GCGCTTGACGCCC	.	PASS	Atlas-SNP
OR2T8	343172	hgsc.bcm.edu	37	1	248084471	248084471	+	Missense_Mutation	SNP	A	A	G	rs149623571	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	418	51	369	2	0.12201	0.00542005	A|0.875;G|0.125	0.125	strong	OR2T8,rectum,carcinoma,+1,2	OR2T8	67	2	NM_001005522	exon1	c.A152G	p.H51R	GGGACCACCGGCT	.	scavenged	Atlas-SNP
ZGLP1	100125288	hgsc.bcm.edu	37	19	10419130	10419130	+	Silent	SNP	C	C	T	rs281417	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	39	18	31	0	0.461538	0	C|0.758;T|0.242	0.242	strong	ZGLP1_ENST00000403903,NS,lymphoid_neoplasm,0,2	ZGLP1	18	2	NM_001103167	exon1	c.G228A	p.P76P	CAGGACCGGGGTG	.	PASS	Atlas-SNP
DNMBP	23268	hgsc.bcm.edu	37	10	101639796	101639796	+	Silent	SNP	G	G	A	rs2255901	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	223	223	256	1	1	0.00390625	G|0.502;A|0.498	0.498	strong	DNMBP,NS,adenoma,0,1	DNMBP	173	1	NM_015221	exon16	c.C4320T	p.S1440S	GGAGGTGGAGTCT	.	PASS	Atlas-SNP
HSPG2	3339	hgsc.bcm.edu	37	1	22154387	22154387	+	Silent	SNP	G	G	A	rs11552570	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	42	18	41	0	0.428571	0	G|0.971;C|0.000;A|0.029	0.029	strong	.	HSPG2	311	.	NM_005529	exon91	c.C12558T	p.S4186S	CCAGTCGGACTCT	.	PASS	Atlas-SNP
OSCAR	126014	hgsc.bcm.edu	37	19	54599222	54599222	+	Silent	SNP	G	G	T	rs61742144	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	40	18	54	0	0.45	0	G|0.886;T|0.114	0.114	strong	OSCAR_ENST00000356532,NS,carcinoma,0,2	OSCAR	22	2	NM_130771	exon5	c.C582A	p.P194P	GGTGCCGGGGGCG	.	PASS	Atlas-SNP
CSMD1	64478	hgsc.bcm.edu	37	8	2800096	2800096	+	Missense_Mutation	SNP	C	C	T	rs11984691	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48	22	72	0	0.458333	0	C|0.939;T|0.061	0.061	strong	.	CSMD1	1469	.	NM_033225	exon69	c.G10433A	p.S3478N	TAATGACTGGAAG	.	PASS	Atlas-SNP
PNMAL2	57469	hgsc.bcm.edu	37	19	46998236	46998236	+	Missense_Mutation	SNP	C	C	T	rs4803967	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	32	15	37	0	0.46875	0	C|0.876;T|0.124	0.124	strong	.	PNMAL2	44	.	NM_020709	exon1	c.G487A	p.G163S	TGCGACCCCGACG	.	PASS	Atlas-SNP
TMEM69	51249	hgsc.bcm.edu	37	1	46159157	46159157	+	Silent	SNP	C	C	T	rs61735666	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	92	38	84	0	0.413043	0	C|0.996;T|0.004	0.004	strong	.	TMEM69	20	.	NM_016486	exon3	c.C324T	p.F108F	CCCCTTCGTTGCT	.	PASS	Atlas-SNP
SYNCRIP	10492	hgsc.bcm.edu	37	6	86332210	86332210	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	113	6	93	0	0.0530973	0	.	.	none	.	SYNCRIP	80	.	NM_006372	exon8	c.T998G	p.V333G	GCCATAACCTCAG	.	PASS	Atlas-SNP
DENND1C	79958	hgsc.bcm.edu	37	19	6468331	6468331	+	Missense_Mutation	SNP	T	T	C	rs62107586	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	155	155	161	0	1	0	A|0.000;C|0.295;G|0.000;T|0.705	0.295	strong	.	DENND1C	93	.	NM_024898	exon22	c.A1705G	p.M569V	CTCCCATGCTAAG	.	PASS	Atlas-SNP
CLOCK	9575	hgsc.bcm.edu	37	4	56325365	56325365	+	Missense_Mutation	SNP	G	G	C	rs34897046	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	133	65	150	0	0.488722	0	G|0.964;C|0.036	0.036	strong	.	CLOCK	81	.	NM_004898	exon10	c.C623G	p.S208C	TAGGTAGATGGCT	.	PASS	Atlas-SNP
ZNF653	115950	hgsc.bcm.edu	37	19	11598483	11598483	+	Silent	SNP	T	T	C	rs311805	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	165	79	160	0	0.478788	0	T|0.731;C|0.269	0.269	strong	ZNF653,NS,carcinoma,0,2	ZNF653	48	2	NM_138783	exon4	c.A795G	p.P265P	GCCTGCTGGGTTG	.	PASS	Atlas-SNP
ZNF318	24149	hgsc.bcm.edu	37	6	43305991	43305991	+	Silent	SNP	A	A	T	rs374528550		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	102	58	96	0	0.568627	0	.	.	weak	.	ZNF318	175	.	NM_014345	exon10	c.T5745A	p.V1915V	ACTAACAACTGAA	.	PASS	Atlas-SNP
SLCO6A1	133482	hgsc.bcm.edu	37	5	101724448	101724448	+	Missense_Mutation	SNP	G	G	C	rs10055840	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	180	91	225	0	0.505556	0	G|0.778;C|0.222	0.222	strong	.	SLCO6A1	153	.	NM_173488	exon12	c.C1961G	p.T654R	CGTCCTGTGTGTC	.	PASS	Atlas-SNP
CACNA1A	773	hgsc.bcm.edu	37	19	13482554	13482554	+	Silent	SNP	C	C	T	rs41276894	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	113	49	97	0	0.433628	0	C|0.994;T|0.006	0.006	strong	.	CACNA1A	715	.	NM_001127221	exon4	c.G579A	p.T193T	CCTCAGCGTCCGT	.	PASS	Atlas-SNP
SYDE2	84144	hgsc.bcm.edu	37	1	85656421	85656421	+	Missense_Mutation	SNP	C	C	T	rs192842795	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91	42	90	0	0.461538	0	C|0.998;T|0.002	0.002	strong	.	SYDE2	135	.	NM_032184	exon2	c.G760A	p.A254T	CATAGGCATTTTC	.	PASS	Atlas-SNP
OR2T4	127074	hgsc.bcm.edu	37	1	248525071	248525071	+	Silent	SNP	T	T	C	rs28499298	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	521	29	527	0	0.0556622	0	T|0.769;C|0.231	0.231	strong	OR2T4,NS,carcinoma,0,1	OR2T4	126	1	NM_001004696	exon1	c.T189C	p.I63I	GGTCATTTTTGTG	.	scavenged	Atlas-SNP
CHRNG	1146	hgsc.bcm.edu	37	2	233410294	233410294	+	Silent	SNP	C	C	T	rs2099489	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	38	16	52	0	0.421053	0	C|0.836;T|0.164	0.164	strong	.	CHRNG	54	.	NM_005199	exon12	c.C1422T	p.R474R	GGACCGCGTCTGC	.	PASS	Atlas-SNP
CCDC65	85478	hgsc.bcm.edu	37	12	49314862	49314862	+	Silent	SNP	C	C	A	rs10875894	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	46	21	61	0	0.456522	0	C|0.681;A|0.319	0.319	strong	CCDC65,NS,carcinoma,+1,2	CCDC65	41	2	NM_033124	exon7	c.C1176A	p.T392T	GCTCACCAAGGTA	.	PASS	Atlas-SNP
GBP1	2633	hgsc.bcm.edu	37	1	89523844	89523844	+	Silent	SNP	G	G	A	rs141095851	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	125	62	106	0	0.496	0	G|0.999;A|0.001	0.001	strong	.	GBP1	68	.	NM_002053	exon6	c.C705T	p.C235C	GACAAAGCATTTT	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1268481	1268481	+	Silent	SNP	G	G	A	rs186744090	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	390	109	402	0	0.279487	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
GPRC6A	222545	hgsc.bcm.edu	37	6	117130544	117130544	+	Missense_Mutation	SNP	A	A	C	rs28360548	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	101	101	89	0	1	0	A|0.747;C|0.253	0.253	strong	.	GPRC6A	152	.	NM_148963	exon2	c.T431G	p.I144R	GAACCTATGACAG	.	PASS	Atlas-SNP
HIST1H2AC	8334	hgsc.bcm.edu	37	6	26124610	26124610	+	Silent	SNP	G	G	A	rs139293879	alternate_allele	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	92	24	100	0	0.26087	0	G|1.000;C|0.000	.	alt	.	HIST1H2AC	29	.	NM_003512	exon1	c.G150A	p.V50V	GCCGGTGTACCTG	.	PASS	Atlas-SNP
PNPLA1	285848	hgsc.bcm.edu	37	6	36269675	36269675	+	Silent	SNP	T	T	A	rs201231660	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	61	108	0	0.701149	0	T|1.000;A|0.000	0.000	strong	.	PNPLA1	92	.	NM_001145717	exon6	c.T813A	p.I271I	AGTGATTTTCCCC	.	PASS	Atlas-SNP
GABRD	2563	hgsc.bcm.edu	37	1	1961466	1961466	+	Silent	SNP	C	C	T	rs28398772	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	137	75	132	0	0.547445	0	C|0.971;T|0.029	0.029	strong	.	GABRD	49	.	NM_000815	exon9	c.C1104T	p.A368A	TGCTGCCGGCGTC	.	PASS	Atlas-SNP
ATPIF1	93974	hgsc.bcm.edu	37	1	28564279	28564279	+	Missense_Mutation	SNP	A	A	G	rs9508	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	113	49	115	0	0.433628	0	A|0.626;G|0.374	0.374	strong	.	ATPIF1	7	.	NM_178190	exon3	c.A187G	p.R63G	CATTACAGGTTAT	.	PASS	Atlas-SNP
ZHX2	22882	hgsc.bcm.edu	37	8	123964431	123964431	+	Silent	SNP	G	G	A	rs3204141	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	109	54	78	0	0.495413	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
OTC	5009	hgsc.bcm.edu	37	X	38268220	38268220	+	Missense_Mutation	SNP	A	A	G	rs1800328	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	129	83	92	0	0.643411	0	A|0.970;G|0.030	0.030	strong	.	OTC	60	.	NM_000531	exon8	c.A809G	p.Q270R	TGGGACAAGAAGA	.	PASS	Atlas-SNP
ADAMTSL4	54507	hgsc.bcm.edu	37	1	150526044	150526044	+	Missense_Mutation	SNP	G	G	C	rs41317515	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110	110	123	0	1	0	G|0.456;C|0.544	0.544	strong	.	ADAMTSL4	101	.	NM_019032	exon6	c.G577C	p.A193P	GAAGAGGCTATTC	.	PASS	Atlas-SNP
TLR3	7098	hgsc.bcm.edu	37	4	187004078	187004078	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	26	101	0	0.302326	0	.	.	none	.	TLR3	83	.	NM_003265	exon4	c.A1238C	p.N413T	TACTCAACCTAAC	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	133	67	122	0	0.503759	0	G|0.621;A|0.379	0.379	strong	.	PTK2B	304	.	NM_173174	exon8	c.G330A	p.T110T	GATGACGGTGGGT	.	PASS	Atlas-SNP
OR2D3	120775	hgsc.bcm.edu	37	11	6942628	6942628	+	Silent	SNP	A	A	C	rs11605995	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	191	85	233	0	0.445026	0	A|0.655;C|0.345	0.345	strong	.	OR2D3	51	.	NM_001004684	exon1	c.A396C	p.A132A	GCTGGCAGTGATG	.	PASS	Atlas-SNP
ABLIM3	22885	hgsc.bcm.edu	37	5	148626067	148626067	+	Silent	SNP	G	G	A	rs61999264	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	103	49	63	0	0.475728	0	G|0.989;A|0.011	0.011	strong	.	ABLIM3	91	.	NM_014945	exon17	c.G1509A	p.S503S	GTTCTCGTCTGGA	.	PASS	Atlas-SNP
POLR1A	25885	hgsc.bcm.edu	37	2	86317012	86317012	+	Missense_Mutation	SNP	C	C	G	rs146078741	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69	18	152	0	0.26087	0	C|0.991;G|0.009	0.009	strong	.	POLR1A	137	.	NM_015425	exon4	c.G473C	p.R158P	TCCTCCCGAATTT	.	PASS	Atlas-SNP
PPP2R1B	5519	hgsc.bcm.edu	37	11	111637049	111637049	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	35	17	24	0	0.485714	0	.	.	none	.	PPP2R1B	44	.	NM_001177562	exon1	c.G37A	p.A13T	CCGCTGCTCCTGG	.	PASS	Atlas-SNP
SPRR4	163778	hgsc.bcm.edu	37	1	152944594	152944594	+	Silent	SNP	C	C	T	rs3170863	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	113	53	139	0	0.469027	0	C|0.355;T|0.645	0.645	strong	.	SPRR4	8	.	NM_173080	exon2	c.C228T	p.S76S	CAAGAGCAAACAG	.	PASS	Atlas-SNP
PCDHGA3	56112	hgsc.bcm.edu	37	5	140723835	140723835	+	Missense_Mutation	SNP	C	C	T	rs11575947	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	43	66	0	0.511905	0	C|0.935;T|0.065	0.065	strong	PCDHGA3_ENST00000253812,NS,carcinoma,-2,3	PCDHGA3	246	3	NM_032011	exon1	c.C235T	p.P79S	CTGAATCCGCAAA	.	PASS	Atlas-SNP
KIF13A	63971	hgsc.bcm.edu	37	6	17764755	17764755	+	Silent	SNP	T	T	C	rs2296197	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	116	96	130	0	0.827586	0	A|0.000;C|0.183;T|0.817	0.183	strong	.	KIF13A	276	.	NM_022113	exon39	c.A5004G	p.P1668P	CTTGAGTGGCACC	.	PASS	Atlas-SNP
CCDC102A	92922	hgsc.bcm.edu	37	16	57555076	57555076	+	Silent	SNP	C	C	T	rs28446687	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	86	65	0	1	0	C|0.768;T|0.232	0.232	strong	.	CCDC102A	22	.	NM_033212	exon4	c.G825A	p.A275A	GCTCAACGCCAGT	.	PASS	Atlas-SNP
ST6GALNAC2	10610	hgsc.bcm.edu	37	17	74570559	74570559	+	Silent	SNP	C	C	T	rs17513606	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	146	79	123	0	0.541096	0	C|0.975;T|0.025	0.025	strong	.	ST6GALNAC2	29	.	NM_006456	exon3	c.G249A	p.L83L	ATTGAACAGGCCA	.	PASS	Atlas-SNP
PVRL1	5818	hgsc.bcm.edu	37	11	119548402	119548402	+	Missense_Mutation	SNP	C	C	T	rs78809001	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	208	34	192	0	0.163462	0	C|0.991;T|0.009	0.009	strong	.	PVRL1	133	.	NM_002855	exon3	c.G596A	p.R199Q	GGGTTCCGGATCT	.	PASS	Atlas-SNP
UGGT1	56886	hgsc.bcm.edu	37	2	128939799	128939799	+	Silent	SNP	C	C	T	rs17178720	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	88	66	123	0	0.75	0	C|0.882;T|0.118	0.118	strong	.	UGGT1	126	.	NM_020120	exon37	c.C4179T	p.D1393D	AATGGACGGCTAC	.	PASS	Atlas-SNP
CAV2	858	hgsc.bcm.edu	37	7	116146074	116146074	+	Missense_Mutation	SNP	C	C	G	rs8940	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	154	88	163	0	0.571429	0	C|0.830;G|0.170	0.170	strong	.	CAV2	10	.	NM_001233	exon3	c.C388G	p.Q130E	TCAGTGCAGACAA	.	PASS	Atlas-SNP
ANKRD53	79998	hgsc.bcm.edu	37	2	71211989	71211989	+	Silent	SNP	A	A	G	rs3796099	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69	16	121	0	0.231884	0	A|0.366;C|0.000;G|0.634	0.634	strong	.	ANKRD53	55	.	NM_001115116	exon6	c.A1152G	p.T384T	GCCCACAATGTGG	.	PASS	Atlas-SNP
ZNF3	7551	hgsc.bcm.edu	37	7	99669802	99669802	+	Missense_Mutation	SNP	A	A	G	rs11550034	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	31	60	0	0.484375	0	A|0.890;G|0.110	0.110	strong	.	ZNF3	54	.	NM_032924	exon6	c.T305C	p.I102T	TCAGAAATTTCTT	.	PASS	Atlas-SNP
CPB1	1360	hgsc.bcm.edu	37	3	148562310	148562310	+	Missense_Mutation	SNP	G	G	A	rs1059502	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	134	134	185	1	1	0.00540541	G|0.743;A|0.257	0.257	strong	.	CPB1	74	.	NM_001871	exon7	c.G622A	p.D208N	CTTCTCGACAAGT	.	PASS	Atlas-SNP
MTOR	2475	hgsc.bcm.edu	37	1	11181327	11181327	+	Silent	SNP	C	C	T	rs11121691	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68	28	44	0	0.411765	0	C|0.721;T|0.279	0.279	strong	.	MTOR	327	.	NM_004958	exon49	c.G6909A	p.L2303L	CAGCCACAGCAGC	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179444939	179444939	+	Missense_Mutation	SNP	C	C	T	rs2303838	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	77	49	77	0	0.636364	0	C|0.677;T|0.323	0.323	strong	.	TTN	18412	.	NM_001267550	exon318	c.G67075A	p.V22359I	CATTGACAGGTGG	.	PASS	Atlas-SNP
DENND4A	10260	hgsc.bcm.edu	37	15	65994733	65994733	+	Silent	SNP	C	C	T	rs17810074	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	170	86	184	0	0.505882	0	C|0.761;T|0.239	0.239	strong	.	DENND4A	217	.	NM_001144823	exon17	c.G2340A	p.V780V	GACTTTCACATAA	.	PASS	Atlas-SNP
GPR162	27239	hgsc.bcm.edu	37	12	6933787	6933787	+	Silent	SNP	A	A	G	rs1051409	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	26	61	0	0.481481	0	A|0.507;G|0.493	0.493	strong	.	GPR162	55	.	NM_019858	exon2	c.A723G	p.V241V	TGAGGTACCAGCC	.	PASS	Atlas-SNP
ALPPL2	251	hgsc.bcm.edu	37	2	233273011	233273011	+	Missense_Mutation	SNP	C	C	G	rs75920311	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	190	59	333	0	0.310526	0	C|0.910;G|0.090	0.090	strong	.	ALPPL2	36	.	NM_031313	exon6	c.C683G	p.P228R	TGTTTCCCATGGG	.	PASS	Atlas-SNP
KDM2B	84678	hgsc.bcm.edu	37	12	121878659	121878659	+	Silent	SNP	C	C	T	rs1064951	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82	44	73	0	0.536585	0	C|0.667;T|0.333	0.333	strong	.	KDM2B	218	.	NM_032590	exon21	c.G3570A	p.Q1190Q	CCGCATCTGGGCA	.	PASS	Atlas-SNP
CORO1B	57175	hgsc.bcm.edu	37	11	67209515	67209515	+	Silent	SNP	C	C	T	rs111451405	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	42	4	62	0	0.0952381	0	C|0.986;T|0.014	0.014	strong	CORO1B,NS,carcinoma,-1,1	CORO1B	30	1	NM_020441	exon3	c.G246A	p.T82T	AGGTCCCGTGTGC	.	PASS	Atlas-SNP
ABCC4	10257	hgsc.bcm.edu	37	13	95715014	95715014	+	Silent	SNP	A	A	G	rs11568655	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	43	71	0	0.530864	0	A|0.966;G|0.034	0.034	strong	.	ABCC4	248	.	NM_005845	exon26	c.T3310C	p.L1104L	TTGTCAAGATCTT	.	PASS	Atlas-SNP
PLCB1	23236	hgsc.bcm.edu	37	20	8770822	8770822	+	Nonsense_Mutation	SNP	C	C	T	rs2294597	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	31	89	0	0.407895	0	C|0.774;T|0.226	0.226	strong	.	PLCB1	394	.	NM_182734	exon31	c.G3337T	p.G1113X	TTATAGCTAGAAG	.	PASS	Atlas-SNP
ADIPOQ	9370	hgsc.bcm.edu	37	3	186572089	186572089	+	Missense_Mutation	SNP	T	T	C	rs17366743	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	173	69	159	0	0.398844	0	T|0.981;C|0.019	0.019	strong	.	ADIPOQ	35	.	NM_001177800	exon4	c.T331C	p.Y111H	TATGTATACCGCT	.	PASS	Atlas-SNP
RAET1L	154064	hgsc.bcm.edu	37	6	150342155	150342155	+	Missense_Mutation	SNP	C	C	T	rs148198102	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	297	144	307	1	0.484848	0.00325733	C|0.994;T|0.006	0.006	strong	.	RAET1L	21	.	NM_130900	exon3	c.G517A	p.E173K	CATTCTCCCACTT	.	PASS	Atlas-SNP
SP140L	93349	hgsc.bcm.edu	37	2	231222655	231222655	+	Silent	SNP	G	G	T	rs10498250	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79	41	95	0	0.518987	0	G|0.883;T|0.117	0.117	strong	SP140L_ENST00000415673,NS,carcinoma,+2,2	SP140L	68	2	NM_138402	exon3	c.G243T	p.R81R	CGATCGGGAACTC	.	PASS	Atlas-SNP
PPP2R3B	28227	hgsc.bcm.edu	37	X	322294	322294	+	Missense_Mutation	SNP	G	G	A	rs200157354	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	241	161	310	0	0.66805	0	.	.	weak	.	PPP2R3B	43	.	NM_013239	exon2	c.C356T	p.P119L	GTGGCCGGGGGCA	.	PASS	Atlas-SNP
HNRNPCL1	343069	hgsc.bcm.edu	37	1	12907449	12907449	+	Missense_Mutation	SNP	C	C	G	rs78163065	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	249	68	167	0	0.273092	0	C|0.961;G|0.039	0.039	strong	HNRNPCL1,NS,carcinoma,0,1	HNRNPCL1	68	1	NM_001013631	exon2	c.G694C	p.D232H	TCTCATCTTTCTT	.	PASS	Atlas-SNP
CCDC114	93233	hgsc.bcm.edu	37	19	48800914	48800914	+	Missense_Mutation	SNP	G	G	A	rs35461177	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	95	43	82	0	0.452632	0	G|0.793;A|0.207	0.207	strong	CCDC114,NS,carcinoma,0,1	CCDC114	100	1	NM_144577	exon13	c.C1403T	p.P468L	AAACCCGGGGGGT	.	PASS	Atlas-SNP
KIR3DL1	3811	hgsc.bcm.edu	37	19	55329892	55329892	+	Missense_Mutation	SNP	A	A	G	rs149123986	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	26	24	74	0	0.923077	0	A|0.860;G|0.140	0.140	strong	.	KIR3DL1	174	.	NM_013289	exon3	c.A193G	p.R65G	GAAGACAGAATCC	.	PASS	Atlas-SNP
CHI3L2	1117	hgsc.bcm.edu	37	1	111778325	111778325	+	Missense_Mutation	SNP	C	C	T	rs11556868	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	146	86	126	0	0.589041	0	C|0.915;T|0.085	0.085	strong	.	CHI3L2	38	.	NM_004000	exon6	c.C545T	p.A182V	TGACTGCGGGCGT	.	PASS	Atlas-SNP
RP1	6101	hgsc.bcm.edu	37	8	55541617	55541617	+	Silent	SNP	A	A	G	rs441800	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	123	123	125	0	1	0	A|0.776;G|0.224	0.224	strong	.	RP1	429	.	NM_006269	exon4	c.A5175G	p.Q1725Q	AAAACAAAATGAT	.	PASS	Atlas-SNP
MICALL2	79778	hgsc.bcm.edu	37	7	1486451	1486451	+	Missense_Mutation	SNP	G	G	A	rs75056037	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55	24	48	0	0.436364	0	G|0.901;A|0.099	0.099	strong	MICALL2,NS,carcinoma,0,2	MICALL2	63	2	NM_182924	exon5	c.C539T	p.A180V	CTGCCCGCCAATG	.	PASS	Atlas-SNP
PTK2	5747	hgsc.bcm.edu	37	8	141711117	141711117	+	Missense_Mutation	SNP	G	G	C	rs185796736	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	140	67	131	0	0.478571	0	G|0.999;C|0.001	0.001	strong	.	PTK2	311	.	NM_005607	exon26	c.C2438G	p.S813C	ACTGTAGAGTCCT	.	PASS	Atlas-SNP
PDZD7	79955	hgsc.bcm.edu	37	10	102782113	102782113	+	Missense_Mutation	SNP	A	A	T	rs118098246	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	130	66	122	0	0.507692	0	A|0.996;T|0.004	0.004	strong	.	PDZD7	101	.	NM_001195263	exon5	c.T572A	p.V191E	TTCTCCACTACCA	.	PASS	Atlas-SNP
HNF1A	6927	hgsc.bcm.edu	37	12	121416650	121416650	+	Missense_Mutation	SNP	A	A	C	rs1169288	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	136	136	133	0	1	0	T|0.002;G|0.007	.	strong	HNF1A,NS,carcinoma,0,1	HNF1A	302	1	NM_000545	exon1	c.A79C	p.I27L	GCACTGATCCAGG	.	PASS	Atlas-SNP
RTP4	64108	hgsc.bcm.edu	37	3	187088612	187088612	+	Silent	SNP	C	C	T	rs33927333	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	190	94	142	0	0.494737	0	C|0.885;T|0.115	0.115	strong	.	RTP4	20	.	NM_022147	exon2	c.C192T	p.S64S	GGCTTCCGCCCAA	.	PASS	Atlas-SNP
EMC10	284361	hgsc.bcm.edu	37	19	50983930	50983930	+	Silent	SNP	C	C	T	rs10409679	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	43	43	47	0	1	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
WRN	7486	hgsc.bcm.edu	37	8	30973957	30973957	+	Silent	SNP	G	G	T	rs1800392	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	97	45	110	0	0.463918	0	G|0.509;T|0.491	0.491	strong	.	WRN	116	.	NM_000553	exon20	c.G2361T	p.L787L	GAAACTGAATCTA	.	PASS	Atlas-SNP
TMC4	147798	hgsc.bcm.edu	37	19	54665970	54665970	+	Silent	SNP	C	C	T	rs36655	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	34	20	29	0	0.588235	0	C|0.743;T|0.257	0.257	strong	.	TMC4	89	.	NM_001145303	exon11	c.G1572A	p.Q524Q	GAACTCCTGGGTC	.	PASS	Atlas-SNP
OGDHL	55753	hgsc.bcm.edu	37	10	50960209	50960209	+	Silent	SNP	G	G	A	rs1258184	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	71	53	0	1	0	G|0.567;A|0.433	0.433	strong	.	OGDHL	149	.	NM_018245	exon5	c.C564T	p.L188L	CAGAGAGAGGGTG	.	PASS	Atlas-SNP
SLC24A2	25769	hgsc.bcm.edu	37	9	19786217	19786217	+	Silent	SNP	G	G	A	rs1536517	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	59	20	69	1	0.338983	0.0144928	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	.	scavenged	Atlas-SNP
CNDP2	55748	hgsc.bcm.edu	37	18	72168608	72168608	+	Silent	SNP	G	G	A	rs2303463	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	133	60	140	0	0.451128	0	G|0.791;A|0.209	0.209	strong	CNDP2,caecum,carcinoma,0,2	CNDP2	55	2	NM_001168499	exon2	c.G105A	p.P35P	GTGGCCGGAGAAG	.	PASS	Atlas-SNP
NIPSNAP3B	55335	hgsc.bcm.edu	37	9	107533175	107533175	+	Missense_Mutation	SNP	C	C	G	rs3739741	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	136	65	132	0	0.477941	0	C|0.851;G|0.149	0.149	strong	NIPSNAP3B,NS,carcinoma,0,1	NIPSNAP3B	22	1	NM_018376	exon4	c.C476G	p.A159G	GGCCAGCTCTGTG	.	PASS	Atlas-SNP
LTF	4057	hgsc.bcm.edu	37	3	46484964	46484964	+	Silent	SNP	G	G	A	rs1042073	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	102	51	123	0	0.5	0	G|0.597;A|0.403	0.403	strong	.	LTF	98	.	NM_002343	exon13	c.C1623T	p.N541N	TCTCTCGTTGCTG	.	PASS	Atlas-SNP
LRWD1	222229	hgsc.bcm.edu	37	7	102112980	102112980	+	Silent	SNP	G	G	A	rs3800987	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	10	7	23	0	0.7	0	G|0.476;A|0.524	0.524	strong	LRWD1,NS,carcinoma,0,1	LRWD1	41	1	NM_152892	exon13	c.G1614A	p.T538T	GTCCACGGTGGCA	.	scavenged	Atlas-SNP
CHRNB3	1142	hgsc.bcm.edu	37	8	42587659	42587659	+	Silent	SNP	G	G	C	rs4953	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	34	79	0	0.447368	0	G|0.959;C|0.041	0.041	strong	CHRNB3,NS,carcinoma,0,1	CHRNB3	74	1	NM_000749	exon5	c.G1209C	p.S403S	CATTTCGAGACAT	.	PASS	Atlas-SNP
LOXHD1	125336	hgsc.bcm.edu	37	18	44104437	44104437	+	Missense_Mutation	SNP	T	T	C	rs12606417	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	95	43	84	0	0.452632	0	T|0.934;C|0.066	0.066	strong	.	LOXHD1	367	.	NM_144612	exon31	c.A4868G	p.E1623G	GGGCCCTCTTGAA	.	PASS	Atlas-SNP
HK1	3098	hgsc.bcm.edu	37	10	71103597	71103597	+	Silent	SNP	C	C	G	rs1133189	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85	47	85	0	0.552941	0	C|0.651;G|0.349	0.349	strong	.	HK1	170	.	NM_033498	exon5	c.C90G	p.L30L	GTATCTCTATGCC	.	PASS	Atlas-SNP
RBM19	9904	hgsc.bcm.edu	37	12	114377877	114377877	+	Missense_Mutation	SNP	T	T	C	rs2290789	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	19	78	0	0.311475	0	T|0.830;C|0.170	0.170	strong	.	RBM19	117	.	NM_001146699	exon15	c.A1826G	p.H609R	CCAAAATGGCCGA	.	PASS	Atlas-SNP
PGLYRP4	57115	hgsc.bcm.edu	37	1	153317723	153317723	+	Missense_Mutation	SNP	T	T	C	rs3006453	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	56	29	52	0	0.517857	0	T|0.964;C|0.036	0.036	strong	.	PGLYRP4	45	.	NM_020393	exon4	c.A275G	p.Q92R	ACTGTCTGGTCGT	.	PASS	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149492640	149492640	+	Silent	SNP	G	G	A	rs372238122		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	109	58	115	0	0.53211	0	.	.	weak	.	.	.	.	NM_198455	exon43	c.G6420A	p.P2140P	AGTGCCGGAGACT	.	PASS	Atlas-SNP
COL5A1	1289	hgsc.bcm.edu	37	9	137711997	137711997	+	Silent	SNP	G	G	C	rs2228560	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	77	41	70	0	0.532468	0	A|0.009;C|0.408;G|0.583	0.408	strong	.	COL5A1	323	.	NM_000093	exon58	c.G4482C	p.P1494P	TCCTCCGGGTGAA	.	PASS	Atlas-SNP
ADD1	118	hgsc.bcm.edu	37	4	2916762	2916762	+	Missense_Mutation	SNP	C	C	G	rs4963	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	16	92	0	0.301887	0	C|0.773;G|0.227;N|0.000	0.227	strong	.	ADD1	56	.	NM_176801	exon13	c.C1850G	p.S617C	AGGGCTCTGAAGG	.	PASS	Atlas-SNP
MARK1	4139	hgsc.bcm.edu	37	1	220804451	220804451	+	Silent	SNP	G	G	A	rs35322308	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	35	94	0	0.406977	0	G|0.985;A|0.015	0.015	strong	MARK1,NS,carcinoma,0,1	MARK1	161	1	NM_018650	exon10	c.G984A	p.P328P	TGATCCGGATTTC	.	PASS	Atlas-SNP
ATXN1	6310	hgsc.bcm.edu	37	6	16327912	16327912	+	Missense_Mutation	SNP	C	C	A	rs368218879		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44	6	34	1	0.136364	0.0294118	.	.	weak	ATXN1,colon,carcinoma,0,2	ATXN1	117	2	NM_001128164	exon7	c.G630T	p.Q210H	CTGATGCTGATGC	.	scavenged	Atlas-SNP
FAT4	79633	hgsc.bcm.edu	37	4	126411594	126411594	+	Silent	SNP	G	G	A	rs62312781	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	44	76	0	0.578947	0	G|0.825;A|0.175	0.175	strong	.	FAT4	1752	.	NM_024582	exon17	c.G13617A	p.E4539E	CAAAGAGGAGAAG	.	PASS	Atlas-SNP
ZBTB8OS	339487	hgsc.bcm.edu	37	1	33099637	33099637	+	Silent	SNP	A	A	G	rs704878	bycluster;byfrequency;bysubmitter;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	171	74	174	0	0.432749	0	A|0.831;G|0.169	0.169	strong	.	ZBTB8OS	9	.	NM_178547	exon3	c.T195C	p.F65F	TTGCTCAAATGCT	.	PASS	Atlas-SNP
UBR3	130507	hgsc.bcm.edu	37	2	170762566	170762566	+	Silent	SNP	A	A	T	rs10194785	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	34	100	0	0.478873	0	A|0.748;T|0.252	0.252	strong	.	UBR3	182	.	NM_172070	exon10	c.A1671T	p.L557L	AGAACTAAACGAG	.	PASS	Atlas-SNP
FMO1	2326	hgsc.bcm.edu	37	1	171252287	171252287	+	Silent	SNP	A	A	G	rs1126692	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	256	125	232	0	0.488281	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
ACP1	52	hgsc.bcm.edu	37	2	277003	277003	+	Missense_Mutation	SNP	A	A	G	rs79716074	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	117	51	144	0	0.435897	0	A|0.725;G|0.275	0.275	strong	ACP1_ENST00000272067,NS,carcinoma,+1,4	ACP1	42	4	NM_007099	exon5	c.A317G	p.Q106R	GTAATCAAGTTAA	.	PASS	Atlas-SNP
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32557510	32557510	+	Silent	SNP	G	G	A	rs201125976	byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	220	36	124	0	0.163636	0	G|0.981;A|0.019	0.019	strong	.	HLA-DRB1	41	.	NM_002124	exon1	c.C10T	p.L4L	GCTTCAGACACAC	.	PASS	Atlas-SNP
GM2A	2760	hgsc.bcm.edu	37	5	150639439	150639439	+	Missense_Mutation	SNP	A	A	G	rs153478	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	58	58	82	0	1	0	A|0.237;G|0.763	0.763	strong	.	GM2A	24	.	NM_001167607	exon2	c.A205G	p.M69V	AGTGTCATGGGCA	.	PASS	Atlas-SNP
ITGA11	22801	hgsc.bcm.edu	37	15	68654003	68654003	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57	5	37	0	0.0877193	0	.	.	none	.	ITGA11	110	.	NM_001004439	exon5	c.T397C	p.Y133H	TGTAGTAGGAGCT	.	PASS	Atlas-SNP
BTG2	7832	hgsc.bcm.edu	37	1	203274867	203274867	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	30	90	0	0.37037	0	.	.	none	BTG2,lymph_node,lymphoid_neoplasm,-1,2	BTG2	16	2	NM_006763	exon1	c.G133C	p.A45P	CAGGAGGCACTCA	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9083427	9083427	+	Silent	SNP	A	A	G	rs1609453	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	99	40	92	0	0.40404	0	A|0.789;G|0.211	0.211	strong	.	MUC16	4315	.	NM_024690	exon1	c.T8388C	p.A2796A	AGAGCTAGCCATA	.	PASS	Atlas-SNP
MKL1	57591	hgsc.bcm.edu	37	22	40814500	40814500	+	Missense_Mutation	SNP	T	T	C	rs878756	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	154	153	135	0	0.993506	0	T|0.474;C|0.526	0.526	strong	MKL1,NS,carcinoma,0,1	MKL1	69	1	NM_020831	exon12	c.A1942G	p.S648G	TGAGGCTGGGGCC	.	PASS	Atlas-SNP
KRTAP10-11	386678	hgsc.bcm.edu	37	21	46067180	46067180	+	Missense_Mutation	SNP	C	C	T	rs462007	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	97	38	74	0	0.391753	0	C|0.202;T|0.798	0.798	strong	.	KRTAP10-11	36	.	NM_198692	exon1	c.C805T	p.R269C	TGCTGCCGCCCGG	.	PASS	Atlas-SNP
OTOA	146183	hgsc.bcm.edu	37	16	21742174	21742174	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	794	11	737	5	0.0138539	0.00678426	.	.	none	OTOA,NS,carcinoma,-1,1	OTOA	144	1	NM_144672	exon20	c.A2224G	p.T742A	CACTGGACAGCCG	.	scavenged	Atlas-SNP
EFCAB7	84455	hgsc.bcm.edu	37	1	63999826	63999826	+	Missense_Mutation	SNP	C	C	T	rs6693255	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	125	76	148	0	0.608	0	C|0.857;T|0.143	0.143	strong	EFCAB7,NS,carcinoma,+1,1	EFCAB7	45	1	NM_032437	exon6	c.C743T	p.T248I	CCTTCACAGTTAC	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	232	231	258	0	0.99569	0	T|0.677;C|0.323	0.323	strong	.	BEND7	85	.	NM_001100912	exon6	c.A1011G	p.V337V	AATCTGTACCCAA	.	PASS	Atlas-SNP
FSHB	2488	hgsc.bcm.edu	37	11	30255185	30255185	+	Silent	SNP	C	C	T	rs6169	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49	21	70	0	0.428571	0	C|0.436;T|0.564	0.564	strong	.	FSHB	28	.	NM_000510	exon3	c.C228T	p.Y76Y	GGTATACGAAACA	.	PASS	Atlas-SNP
ZNF69	7620	hgsc.bcm.edu	37	19	11998777	11998777	+	Silent	SNP	C	C	T	rs3810314	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	39	86	0	0.481481	0	C|0.897;T|0.103	0.103	strong	.	ZNF69	27	.	NM_021915	exon1	c.C39T	p.P13P	GGACCCCGGGACA	.	PASS	Atlas-SNP
ANKRD30A	91074	hgsc.bcm.edu	37	10	37455583	37455583	+	Silent	SNP	G	G	A	rs75413857	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	301	7	470	6	0.0232558	0.012766	A|1.000;|0.000	1.000	weak	ANKRD30A,NS,haematopoietic_neoplasm,+1,1	ANKRD30A	448	1	NM_052997	exon19	c.G1947A	p.A649A	GGCTGCGCATCAA	.	scavenged	Atlas-SNP
SH3PXD2B	285590	hgsc.bcm.edu	37	5	171766135	171766135	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	113	28	100	0	0.247788	0	.	.	none	.	SH3PXD2B	91	.	NM_001017995	exon13	c.A1974C	p.E658D	TTGGTCTTCGCCC	.	PASS	Atlas-SNP
AFAP1	60312	hgsc.bcm.edu	37	4	7802292	7802292	+	Silent	SNP	G	G	A	rs11728778	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	108	107	149	0	0.990741	0	G|0.812;A|0.188	0.188	strong	.	AFAP1	93	.	NM_001134647	exon10	c.C1143T	p.T381T	CAGGTCGGTCCTG	.	PASS	Atlas-SNP
OR13C9	286362	hgsc.bcm.edu	37	9	107380414	107380414	+	Missense_Mutation	SNP	C	C	A	rs2900373	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	212	95	219	0	0.448113	0	A|0.365;C|0.635	0.365	strong	.	OR13C9	42	.	NM_001001956	exon1	c.G72T	p.E24D	GAGTAACTCAAGC	.	PASS	Atlas-SNP
GFM1	85476	hgsc.bcm.edu	37	3	158362441	158362441	+	Silent	SNP	T	T	C	rs1864507	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	134	61	132	0	0.455224	0	T|0.450;C|0.550	0.550	strong	.	GFM1	83	.	NM_024996	exon1	c.T18C	p.A6A	GGGAGCTGCAGCC	.	PASS	Atlas-SNP
SLC22A12	116085	hgsc.bcm.edu	37	11	64359274	64359274	+	Silent	SNP	C	C	T	rs3825017	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	35	17	39	0	0.485714	0	C|0.976;T|0.024	0.024	strong	.	SLC22A12	68	.	NM_144585	exon1	c.C246T	p.N82N	CCCCAACCAGAGG	.	PASS	Atlas-SNP
AASDH	132949	hgsc.bcm.edu	37	4	57211352	57211352	+	Missense_Mutation	SNP	T	T	C	rs12498340	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	123	66	130	0	0.536585	0	T|0.830;C|0.170	0.170	strong	.	AASDH	101	.	NM_181806	exon12	c.A2593G	p.T865A	CTGTGGTTGGATC	.	PASS	Atlas-SNP
CD83	9308	hgsc.bcm.edu	37	6	14131854	14131854	+	Missense_Mutation	SNP	A	A	G	rs35118414	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	113	20	134	0	0.176991	0	A|0.956;G|0.044	0.044	strong	.	CD83	23	.	NM_004233	exon3	c.A257G	p.N86S	CCCCCAATGAAAG	.	PASS	Atlas-SNP
CCDC170	80129	hgsc.bcm.edu	37	6	151894340	151894340	+	Missense_Mutation	SNP	C	C	T	rs12205837	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	123	56	111	0	0.455285	0	C|0.911;T|0.089	0.089	strong	.	.	.	.	NM_025059	exon6	c.C806T	p.A269V	AAGAAGCTCTTGA	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29910663	29910663	+	Missense_Mutation	SNP	G	G	A	rs707910	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	140	119	155	0	0.85	0	A|0.112;G|0.888	0.112	strong	.	HLA-A	89	.	NM_001242758	exon2	c.G203A	p.R68K	GCCAGAGGATGGA	.	PASS	Atlas-SNP
HSPG2	3339	hgsc.bcm.edu	37	1	22158157	22158157	+	Silent	SNP	A	A	G	rs2229488	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	174	78	186	0	0.448276	0	A|0.904;G|0.096	0.096	strong	.	HSPG2	311	.	NM_005529	exon82	c.T11340C	p.N3780N	GGTCCCATTGACC	.	PASS	Atlas-SNP
PCDHGB2	56103	hgsc.bcm.edu	37	5	140739874	140739874	+	Missense_Mutation	SNP	G	G	A	rs13171859	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	31	80	0	0.413333	0	G|0.930;A|0.070	0.070	strong	.	PCDHGB2	196	.	NM_018923	exon1	c.G172A	p.V58I	CTCAGCGTCCGGG	.	PASS	Atlas-SNP
OSBPL7	114881	hgsc.bcm.edu	37	17	45885756	45885756	+	Silent	SNP	C	C	T	rs9911983	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	113	51	104	0	0.451327	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
CCDC50	152137	hgsc.bcm.edu	37	3	191093053	191093053	+	Silent	SNP	T	T	C	rs2028572	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	163	85	152	0	0.521472	0	T|0.501;C|0.499	0.499	strong	.	CCDC50	39	.	NM_178335	exon6	c.T651C	p.H217H	TCCCCATATTAAC	.	PASS	Atlas-SNP
CTU2	348180	hgsc.bcm.edu	37	16	88779739	88779739	+	Missense_Mutation	SNP	A	A	G	rs11549837	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	32	70	0	0.450704	0	A|0.607;G|0.393	0.393	strong	.	CTU2	66	.	NM_001012759	exon8	c.A757G	p.M253V	CTCCACATGGCCC	.	PASS	Atlas-SNP
UBTF	7343	hgsc.bcm.edu	37	17	42287519	42287519	+	Silent	SNP	C	C	T	rs2071167	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	249	111	204	0	0.445783	0	C|0.599;T|0.401	0.401	strong	.	UBTF	65	.	NM_014233	exon15	c.G1599A	p.K533K	GGCTGCCTTCTTA	.	PASS	Atlas-SNP
NID2	22795	hgsc.bcm.edu	37	14	52509501	52509501	+	Silent	SNP	T	T	C	rs3818186	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93	51	87	0	0.548387	0	T|0.667;C|0.333	0.333	strong	.	NID2	201	.	NM_007361	exon6	c.A1578G	p.E526E	ATTACCTTCAGGC	.	PASS	Atlas-SNP
NRG3	10718	hgsc.bcm.edu	37	10	84744926	84744926	+	Missense_Mutation	SNP	C	C	A	rs17101193	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	77	43	75	0	0.558442	0	C|0.910;A|0.090	0.090	strong	.	NRG3	301	.	NM_001010848	exon9	c.C1656A	p.N552K	GACAAACCCCTAT	.	PASS	Atlas-SNP
ATF7	11016	hgsc.bcm.edu	37	12	53946410	53946410	+	Silent	SNP	G	G	A	rs33921258	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	116	65	116	0	0.560345	0	G|0.934;A|0.066	0.066	strong	.	ATF7	51	.	NM_001130060	exon3	c.C60T	p.N20N	GTCCTCGTTTGTA	.	PASS	Atlas-SNP
PDIA2	64714	hgsc.bcm.edu	37	16	334899	334899	+	Missense_Mutation	SNP	G	G	A	rs141542731	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82	44	82	0	0.536585	0	G|0.994;A|0.006	0.006	strong	PDIA2,NS,lymphoid_neoplasm,0,1	PDIA2	51	1	NM_006849	exon4	c.G562A	p.A188T	GACGTGGCCACCT	.	PASS	Atlas-SNP
MYO9B	4650	hgsc.bcm.edu	37	19	17318018	17318018	+	Silent	SNP	G	G	A	rs17535005	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	176	82	191	0	0.465909	0	G|0.955;A|0.045	0.045	strong	.	MYO9B	264	.	NM_001130065	exon35	c.G5589A	p.P1863P	GGACCCGCTGACC	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	141	140	105	0	0.992908	0	A|0.785;G|0.214	0.214	strong	.	CR1	354	.	NM_000651	exon30	c.A4973G	p.H1658R	GTGAGCATACCCC	.	PASS	Atlas-SNP
HTT	3064	hgsc.bcm.edu	37	4	3227419	3227419	+	Silent	SNP	A	A	G	rs362273	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	113	40	160	1	0.353982	0.00625	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	.	scavenged	Atlas-SNP
BIRC7	79444	hgsc.bcm.edu	37	20	61869826	61869826	+	Silent	SNP	C	C	T	rs2273487	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49	19	51	0	0.387755	0	C|0.554;T|0.446	0.446	strong	.	BIRC7	25	.	NM_139317	exon3	c.C528T	p.S176S	GGGCTCCTGGGTG	.	PASS	Atlas-SNP
DENND4C	55667	hgsc.bcm.edu	37	9	19346710	19346710	+	Missense_Mutation	SNP	A	A	G	rs17818730	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	88	40	90	0	0.454545	0	A|0.940;G|0.060	0.060	strong	.	DENND4C	120	.	NM_017925	exon22	c.A3796G	p.T1266A	GGCATGACTACTG	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1097794	1097794	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68	5	74	0	0.0735294	0	.	.	none	.	MUC2	614	.	NM_002457	exon37	c.A6875T	p.K2292M	CCTCCAAGCCACA	.	PASS	Atlas-SNP
CLN8	2055	hgsc.bcm.edu	37	8	1719450	1719450	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	160	18	140	0	0.1125	0	.	.	none	.	CLN8	64	.	NM_018941	exon2	c.G230C	p.S77T	TTCAGAGCACAGC	.	PASS	Atlas-SNP
GCSAM	257144	hgsc.bcm.edu	37	3	111842539	111842539	+	Silent	SNP	C	C	T	rs34879456	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	169	78	155	0	0.461538	0	C|0.979;T|0.021	0.021	strong	.	.	.	.	NM_001190259	exon6	c.G306A	p.G102G	AGAGTTCCCTGAT	.	PASS	Atlas-SNP
NACC2	138151	hgsc.bcm.edu	37	9	138905136	138905136	+	Silent	SNP	C	C	T	rs2280486	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	115	58	119	0	0.504348	0	C|0.543;T|0.457	0.457	strong	.	NACC2	16	.	NM_144653	exon5	c.G1164A	p.T388T	GGCCAGCGTGTTC	.	PASS	Atlas-SNP
CTAGE1	64693	hgsc.bcm.edu	37	18	19996011	19996011	+	Silent	SNP	G	G	A	rs7227477	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	140	67	180	0	0.478571	0	G|0.539;A|0.461	0.461	strong	.	CTAGE1	146	.	NM_172241	exon1	c.C1764T	p.L588L	TGGAGGGAGAGCT	.	PASS	Atlas-SNP
DDX11	1663	hgsc.bcm.edu	37	12	31237922	31237922	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	190	11	168	5	0.0578947	0.0297619	.	.	none	DDX11_ENST00000407793,right_upper_lobe,carcinoma,0,16	DDX11	188	16	NM_030653	exon5	c.G500C	p.R167T	AAGAAAGAGAGAA	.	scavenged	Atlas-SNP
ZNF577	84765	hgsc.bcm.edu	37	19	52375854	52375854	+	Silent	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73	18	63	0	0.246575	0	.	.	none	.	ZNF577	63	.	NM_032679	exon7	c.A1389C	p.T463T	TTCATTTGTGAGG	.	PASS	Atlas-SNP
NSF	4905	hgsc.bcm.edu	37	17	44828931	44828931	+	Silent	SNP	G	G	A	rs199533	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	130	129	105	0	0.992308	0	G|0.874;A|0.126	0.126	strong	.	NSF	27	.	NM_006178	exon19	c.G2106A	p.K702K	GAAGAAGGTCTGG	.	PASS	Atlas-SNP
KCNA1	3736	hgsc.bcm.edu	37	12	5021348	5021348	+	Silent	SNP	G	G	C	rs2227910	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	35	90	0	0.564516	0	G|0.461;C|0.539	0.539	strong	.	KCNA1	112	.	NM_000217	exon2	c.G804C	p.T268T	CATCACGCTGGGC	.	PASS	Atlas-SNP
BTN3A3	10384	hgsc.bcm.edu	37	6	26446209	26446209	+	Silent	SNP	C	C	T	rs3846848	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	122	26	112	0	0.213115	0	C|0.838;T|0.162	0.162	strong	.	BTN3A3	56	.	NM_006994	exon5	c.C711T	p.I237I	ATCCATCGCAGGT	.	PASS	Atlas-SNP
HDGF	3068	hgsc.bcm.edu	37	1	156713558	156713558	+	Missense_Mutation	SNP	G	G	A	rs4399146	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	89	52	64	0	0.58427	0	G|0.790;A|0.210	0.210	strong	.	HDGF	60	.	NM_001126050	exon5	c.C650T	p.P217L	TCAGAGGGGGTGC	.	PASS	Atlas-SNP
TARSL2	123283	hgsc.bcm.edu	37	15	102264476	102264476	+	Missense_Mutation	SNP	C	C	A	rs1143136	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	31	24	23	0	0.774194	0	C|0.794;A|0.206	0.206	strong	.	TARSL2	63	.	NM_152334	exon1	c.G115T	p.A39S	AGGGCGCGTTCAG	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1266561	1266561	+	Silent	SNP	G	G	A	rs200970694	byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	300	19	308	0	0.0633333	0	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
GPR56	9289	hgsc.bcm.edu	37	16	57689805	57689805	+	Missense_Mutation	SNP	A	A	C	rs1801255	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80	46	63	0	0.575	0	A|0.834;C|0.166	0.166	strong	.	GPR56	44	.	NM_001145773	exon7	c.A933C	p.Q311H	CAGCCAAGTCCTG	.	PASS	Atlas-SNP
LOXHD1	125336	hgsc.bcm.edu	37	18	44063598	44063598	+	Missense_Mutation	SNP	G	G	A	rs1377016	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	131	130	153	1	0.992366	0.00653595	G|0.598;A|0.402	0.402	strong	.	LOXHD1	367	.	NM_144612	exon39	c.C6107T	p.A2036V	TGCCAGGCAAGTT	.	PASS	Atlas-SNP
CEACAM5	1048	hgsc.bcm.edu	37	19	42213872	42213872	+	Missense_Mutation	SNP	T	T	C	rs35091611	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	168	90	177	0	0.535714	0	T|0.832;C|0.168	0.168	strong	.	CEACAM5	84	.	NM_004363	exon2	c.T338C	p.I113T	ACATCATCCAGAA	.	PASS	Atlas-SNP
LRP6	4040	hgsc.bcm.edu	37	12	12279735	12279735	+	Missense_Mutation	SNP	C	C	T	rs34815107	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93	46	110	0	0.494624	0	C|0.994;T|0.006	0.006	strong	.	LRP6	170	.	NM_002336	exon20	c.G4202A	p.R1401H	TTCATACGTGGAC	.	PASS	Atlas-SNP
XDH	7498	hgsc.bcm.edu	37	2	31593265	31593265	+	Missense_Mutation	SNP	T	T	C	rs17323225	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	96	46	73	0	0.479167	0	T|0.978;C|0.022	0.022	strong	.	XDH	191	.	NM_000379	exon18	c.A1936G	p.I646V	CAGTTATGTTACT	.	PASS	Atlas-SNP
IGF2BP3	10643	hgsc.bcm.edu	37	7	23353246	23353246	+	Missense_Mutation	SNP	A	A	C	rs199812608		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	2	89	0	0.0327869	0	.	.	weak	IGF2BP3,NS,carcinoma,0,1	IGF2BP3	71	1	NM_006547	exon13	c.T1422G	p.I474M	TTCTTTAATTTTT	.	scavenged	Atlas-SNP
NPHP4	261734	hgsc.bcm.edu	37	1	6012866	6012866	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	42	11	42	0	0.261905	0	.	.	none	.	NPHP4	119	.	NM_015102	exon7	c.A704C	p.K235T	ATGGGCTTCTGGA	.	PASS	Atlas-SNP
RBMXL1	494115	hgsc.bcm.edu	37	1	89449383	89449383	+	Missense_Mutation	SNP	G	G	A	rs71216132		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	244	66	257	2	0.270492	0.0077821	G|0.500;A|0.500	0.500	weak	CCBL2,NS,carcinoma,0,1	.	.	1	NM_001162536	exon3	c.C127T	p.R43C	TTTCACGGTCTTT	.	scavenged	Atlas-SNP
IAH1	285148	hgsc.bcm.edu	37	2	9616161	9616161	+	Missense_Mutation	SNP	C	C	G	rs61732203	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	179	178	170	0	0.994413	0	C|0.982;G|0.018	0.018	strong	.	IAH1	12	.	NM_001039613	exon2	c.C127G	p.L43V	GACAGGCTGGTCA	.	PASS	Atlas-SNP
PDE6A	5145	hgsc.bcm.edu	37	5	149323906	149323906	+	Silent	SNP	T	T	G	rs2277925	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	43	88	0	0.5	0	T|0.786;G|0.214	0.214	strong	PDE6A,NS,carcinoma,0,1	PDE6A	98	1	NM_000440	exon1	c.A331C	p.R111R	AAAGCCTGGTGGC	.	PASS	Atlas-SNP
WWC2	80014	hgsc.bcm.edu	37	4	184190233	184190233	+	Missense_Mutation	SNP	G	G	T	rs11941467	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	90	49	111	0	0.544444	0	G|0.917;T|0.083	0.083	strong	.	WWC2	78	.	NM_024949	exon15	c.G2317T	p.A773S	AGAGTCGCCATTT	.	PASS	Atlas-SNP
C17orf67	339210	hgsc.bcm.edu	37	17	54872439	54872439	+	Missense_Mutation	SNP	T	T	C	rs72837329	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	47	53	0	1	0	T|0.870;C|0.130	0.130	strong	.	C17orf67	13	.	NM_001085430	exon7	c.A259G	p.I87V	GATGAATCCTGTT	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179650408	179650408	+	Missense_Mutation	SNP	G	G	A	rs35813871	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	97	43	96	0	0.443299	0	G|0.827;A|0.173	0.173	strong	.	TTN	18412	.	NM_001267550	exon15	c.C2432T	p.T811I	CTAGCTGTGCGGG	.	PASS	Atlas-SNP
CCDC88B	283234	hgsc.bcm.edu	37	11	64110683	64110683	+	Silent	SNP	G	G	C	rs479552	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	18	10	26	0	0.555556	0	G|0.651;C|0.349	0.349	strong	CCDC88B,NS,carcinoma,0,1	CCDC88B	89	1	NM_032251	exon11	c.G1095C	p.A365A	GGAGGCGTCCAAG	.	PASS	Atlas-SNP
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32634303	32634303	+	Silent	SNP	G	G	A	rs1049061	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	13	8	11	0	0.615385	0	G|0.848;A|0.152	0.152	strong	.	HLA-DQB1	15	.	NM_002123	exon1	c.C82T	p.L28L	CCAGTAGGGAGCT	.	PASS	Atlas-SNP
CEP112	201134	hgsc.bcm.edu	37	17	63822357	63822357	+	Missense_Mutation	SNP	T	T	C	rs62065084	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	248	246	240	1	0.991935	0.00416667	T|0.765;C|0.235	0.235	strong	.	CEP112	192	.	NM_001037325	exon1	c.A61G	p.I21V	TCTCTATCAGTCT	.	PASS	Atlas-SNP
ATP8B3	148229	hgsc.bcm.edu	37	19	1789556	1789556	+	Silent	SNP	C	C	T	rs12978609	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	11	4	24	0	0.363636	0	C|0.670;T|0.330	0.330	strong	.	ATP8B3	108	.	NM_138813	exon23	c.G2649A	p.Q883Q	GGAGTCCTGGGCT	.	PASS	Atlas-SNP
MTMR9	66036	hgsc.bcm.edu	37	8	11162496	11162496	+	Silent	SNP	A	A	C	rs2164272	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98	44	100	0	0.44898	0	A|0.640;C|0.360	0.360	strong	.	MTMR9	58	.	NM_015458	exon4	c.A564C	p.L188L	AGTACTAAGCTAT	.	PASS	Atlas-SNP
ALK	238	hgsc.bcm.edu	37	2	29449819	29449819	+	Silent	SNP	C	C	T	rs2293563	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	119	60	126	0	0.504202	0	C|0.816;T|0.184	0.184	strong	ALK,NS,carcinoma,0,1	ALK	533	1	NM_004304	exon18	c.G3036A	p.T1012T	CAGCACCGTCCCG	.	PASS	Atlas-SNP
TEX15	56154	hgsc.bcm.edu	37	8	30702602	30702602	+	Missense_Mutation	SNP	T	T	C	rs323345	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	143	75	138	0	0.524476	0	T|0.707;C|0.293	0.293	strong	.	TEX15	350	.	NM_031271	exon1	c.A3932G	p.N1311S	ATAATGTTTTGTT	.	PASS	Atlas-SNP
GIMAP7	168537	hgsc.bcm.edu	37	7	150217248	150217248	+	Silent	SNP	A	A	G	rs3735081	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	30	52	0	0.566038	0	A|0.252;G|0.748	0.748	strong	GIMAP7,NS,carcinoma,+2,1	GIMAP7	47	1	NM_153236	exon2	c.A186G	p.V62V	TGTTGTAGACACT	.	PASS	Atlas-SNP
DYNC1I1	1780	hgsc.bcm.edu	37	7	95442624	95442624	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	7	62	0	0.111111	0	.	.	none	.	DYNC1I1	111	.	NM_004411	exon4	c.T340A	p.S114T	CAAGACTCAGGCG	.	PASS	Atlas-SNP
HIST1H1B	3009	hgsc.bcm.edu	37	6	27835218	27835218	+	Silent	SNP	G	G	A	rs17763089	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	111	88	113	0	0.792793	0	G|0.945;A|0.055	0.055	strong	.	HIST1H1B	54	.	NM_005322	exon1	c.C90T	p.G30G	GCCGGCGCCGGCA	.	PASS	Atlas-SNP
SLC18A1	6570	hgsc.bcm.edu	37	8	20036827	20036827	+	Missense_Mutation	SNP	C	C	G	rs2270637	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	130	129	150	0	0.992308	0	C|0.796;G|0.204	0.204	strong	SLC18A1,colon,carcinoma,0,1	SLC18A1	68	1	NM_001142324	exon4	c.G293C	p.S98T	ATTCCACTAGGTA	.	PASS	Atlas-SNP
PHLDB3	653583	hgsc.bcm.edu	37	19	43983740	43983740	+	Silent	SNP	T	T	C	rs1133929	bycluster;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	78	38	70	0	0.487179	0	T|0.268;C|0.732	0.732	strong	.	PHLDB3	30	.	NM_198850	exon14	c.A1491G	p.P497P	GGTGGGTGGGGCC	.	PASS	Atlas-SNP
LRRK2	120892	hgsc.bcm.edu	37	12	40713901	40713901	+	Missense_Mutation	SNP	T	T	A	rs11564148	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93	34	71	0	0.365591	0	A|0.266;N|0.000	0.266	strong	.	LRRK2	763	.	NM_198578	exon34	c.T4939A	p.S1647T	TACATGTCACAGT	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	41	98	0	0.471264	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
SNX21	90203	hgsc.bcm.edu	37	20	44469290	44469290	+	Missense_Mutation	SNP	G	G	A	rs4638862	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	18	59	0	0.253521	0	G|0.611;A|0.389	0.389	strong	.	SNX21	23	.	NM_033421	exon4	c.G460A	p.A154T	ACCCTCGCCGTGA	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9084183	9084183	+	Silent	SNP	G	G	A	rs1609460	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	197	194	200	0	0.984772	0	G|0.573;A|0.427	0.427	strong	.	MUC16	4315	.	NM_024690	exon1	c.C7632T	p.P2544P	GAGATGGGGAGTG	.	PASS	Atlas-SNP
TMEM54	113452	hgsc.bcm.edu	37	1	33361552	33361552	+	Missense_Mutation	SNP	C	C	T	rs139394643	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	37	15	32	0	0.405405	0	C|0.998;T|0.002	0.002	strong	.	TMEM54	12	.	NM_033504	exon3	c.G229A	p.A77T	TGGCTGCGATGCC	.	PASS	Atlas-SNP
SLC1A5	6510	hgsc.bcm.edu	37	19	47278938	47278938	+	Silent	SNP	G	G	A	rs1060043	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	143	66	146	0	0.461538	0	G|0.933;A|0.067	0.067	strong	.	SLC1A5	31	.	NM_005628	exon8	c.C1455T	p.Y485Y	GTCCACGTAATTT	.	PASS	Atlas-SNP
ELSPBP1	64100	hgsc.bcm.edu	37	19	48525466	48525466	+	Missense_Mutation	SNP	C	C	T	rs35700000	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	157	74	118	0	0.471338	0	C|0.980;T|0.020	0.020	strong	.	ELSPBP1	29	.	NM_022142	exon6	c.C554T	p.P185L	ACTTTCCGTTCAA	.	PASS	Atlas-SNP
SLCO6A1	133482	hgsc.bcm.edu	37	5	101834386	101834386	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	122	5	103	0	0.0409836	0	.	.	none	.	SLCO6A1	153	.	NM_173488	exon1	c.C163T	p.P55S	CCTCTGGAAGTAG	.	PASS	Atlas-SNP
DMP1	1758	hgsc.bcm.edu	37	4	88584148	88584148	+	Silent	SNP	C	C	T	rs2615498	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	106	57	100	0	0.537736	0	C|0.850;T|0.150	0.150	strong	.	DMP1	72	.	NM_004407	exon6	c.C1218T	p.S406S	AGACAGCGAATCC	.	PASS	Atlas-SNP
RXRG	6258	hgsc.bcm.edu	37	1	165398115	165398115	+	Silent	SNP	T	T	C	rs113471	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	99	50	112	0	0.50505	0	T|0.776;G|0.003	.	strong	RXRG,NS,carcinoma,-2,1	RXRG	91	1	NM_006917	exon2	c.A138G	p.T46T	GGTATCTGTGTAG	.	PASS	Atlas-SNP
TEKT1	83659	hgsc.bcm.edu	37	17	6716242	6716242	+	Missense_Mutation	SNP	G	G	A	rs3744395	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	123	57	97	0	0.463415	0	G|0.790;A|0.210	0.210	strong	.	TEKT1	49	.	NM_053285	exon6	c.C760T	p.R254C	GCTTGCGCAGATC	.	PASS	Atlas-SNP
CD200	4345	hgsc.bcm.edu	37	3	112063850	112063850	+	Missense_Mutation	SNP	C	C	A	rs2272022	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	95	42	78	0	0.442105	0	C|0.748;A|0.252	0.252	strong	.	CD200	33	.	NM_001004196	exon4	c.C211A	p.P71T	TACACACCTGCTT	.	PASS	Atlas-SNP
LOXHD1	125336	hgsc.bcm.edu	37	18	44149474	44149474	+	Silent	SNP	G	G	A	rs2086005	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	117	51	121	0	0.435897	0	G|0.917;A|0.083	0.083	strong	.	LOXHD1	367	.	NM_144612	exon16	c.C2175T	p.N725N	GAGGTTGTTGTCA	.	PASS	Atlas-SNP
ZFP36L2	678	hgsc.bcm.edu	37	2	43452334	43452334	+	Silent	SNP	G	G	A	rs8098	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	25	12	18	0	0.48	0	G|0.886;A|0.114	0.114	strong	.	ZFP36L2	56	.	NM_006887	exon2	c.C609T	p.I203I	GAAGCCGATGGTA	.	PASS	Atlas-SNP
SPNS3	201305	hgsc.bcm.edu	37	17	4352636	4352636	+	Missense_Mutation	SNP	G	G	A	rs34457931	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	42	12	31	0	0.285714	0	G|0.906;A|0.094	0.094	strong	.	SPNS3	52	.	NM_182538	exon7	c.G877A	p.G293R	GTTCACGGGCTGC	.	PASS	Atlas-SNP
DNAI2	64446	hgsc.bcm.edu	37	17	72301432	72301432	+	Silent	SNP	A	A	G	rs8073660	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110	46	105	0	0.418182	0	A|0.535;G|0.465	0.465	strong	.	DNAI2	102	.	NM_001172810	exon9	c.A1062G	p.E354E	AGCTGAAAAGATT	.	PASS	Atlas-SNP
AQP1	358	hgsc.bcm.edu	37	7	30961790	30961790	+	Missense_Mutation	SNP	G	G	A	rs28362731	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	42	29	50	0	0.690476	0	G|0.972;A|0.028	0.028	strong	.	AQP1	38	.	NM_198098	exon2	c.G494A	p.G165D	ACCTTGGTGGCTC	.	PASS	Atlas-SNP
CCDC114	93233	hgsc.bcm.edu	37	19	48807367	48807367	+	Silent	SNP	C	C	A	rs28582401	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	40	17	35	0	0.425	0	C|0.817;A|0.183	0.183	strong	.	CCDC114	100	.	NM_144577	exon7	c.G585T	p.L195L	CTCCCGCAGCAAG	.	PASS	Atlas-SNP
NPHS1	4868	hgsc.bcm.edu	37	19	36342212	36342212	+	Missense_Mutation	SNP	C	C	T	rs3814995	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	34	77	0	0.459459	0	C|0.735;T|0.265	0.265	strong	.	NPHS1	165	.	NM_004646	exon3	c.G349A	p.E117K	CCATCTCAGAGCG	.	PASS	Atlas-SNP
CCDC135	84229	hgsc.bcm.edu	37	16	57741404	57741404	+	Silent	SNP	C	C	T	rs114955852	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	99	41	102	0	0.414141	0	C|0.996;T|0.004	0.004	strong	.	CCDC135	97	.	NM_032269	exon7	c.C891T	p.H297H	CCTGCACGGCCTG	.	PASS	Atlas-SNP
NIPSNAP3B	55335	hgsc.bcm.edu	37	9	107531152	107531152	+	Missense_Mutation	SNP	G	G	C	rs10761084	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	104	50	115	0	0.480769	0	G|0.846;C|0.154	0.154	strong	NIPSNAP3B,NS,carcinoma,0,1	NIPSNAP3B	22	1	NM_018376	exon3	c.G280C	p.A94P	AATTTTGCTCATC	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105423809	105423809	+	Missense_Mutation	SNP	G	G	A	rs76650680	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49	20	37	0	0.408163	0	A|0.017;C|0.000;G|0.982	0.017	strong	.	AHNAK2	719	.	NM_138420	exon3	c.C151T	p.R51W	GCGGCCGTGGTCG	.	PASS	Atlas-SNP
SLC8A2	6543	hgsc.bcm.edu	37	19	47969394	47969394	+	Silent	SNP	G	G	A	rs12459087	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	170	92	147	0	0.541176	0	G|0.927;A|0.073	0.073	strong	.	SLC8A2	77	.	NM_015063	exon2	c.C267T	p.I89I	GTCGGCGATGATG	.	PASS	Atlas-SNP
ARHGEF25	115557	hgsc.bcm.edu	37	12	58010163	58010163	+	Missense_Mutation	SNP	A	A	G	rs1564374	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	60	36	0	0.983607	0	A|0.402;G|0.598;T|0.000	0.598	strong	.	ARHGEF25	111	.	NM_001111270	exon15	c.A1634G	p.Q545R	GAATTCAGCTTGG	.	PASS	Atlas-SNP
CCDC18	343099	hgsc.bcm.edu	37	1	93720070	93720070	+	Missense_Mutation	SNP	C	C	G	rs12030843	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	136	69	138	0	0.507353	0	C|0.809;G|0.191	0.191	strong	.	CCDC18	93	.	NM_206886	exon24	c.C3241G	p.L1081V	GAACAGCTTCGAG	.	PASS	Atlas-SNP
MICB	4277	hgsc.bcm.edu	37	6	31473957	31473957	+	Missense_Mutation	SNP	C	C	G	rs3134900	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	116	94	117	0	0.810345	0	C|0.918;G|0.082	0.082	strong	MICB,NS,neuroblastoma,0,2	MICB	26	2	NM_005931	exon3	c.C363G	p.I121M	TGAGATCCATGAA	.	PASS	Atlas-SNP
PLEC	5339	hgsc.bcm.edu	37	8	145001031	145001031	+	Missense_Mutation	SNP	T	T	C	rs55895668	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	30	69	1	0.37037	0.0144928	T|0.550;C|0.450	0.450	strong	PLEC_ENST00000436759,NS,carcinoma,0,2	PLEC	1144	2	NM_201380	exon30	c.A4376G	p.H1459R	CTGTAGTGCGTAC	.	scavenged	Atlas-SNP
FAHD1	81889	hgsc.bcm.edu	37	16	1877698	1877698	+	Silent	SNP	C	C	G	rs3743852	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44	25	72	0	0.568182	0	C|0.878;G|0.122	0.122	strong	FAHD1,colon,carcinoma,0,1	FAHD1	18	1	NM_031208	exon1	c.C468G	p.L156L	CGAACTCAGACAG	.	PASS	Atlas-SNP
GUCA1B	2979	hgsc.bcm.edu	37	6	42162388	42162388	+	Silent	SNP	A	A	G	rs3749921	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110	110	149	0	1	0	A|0.459;G|0.541	0.541	strong	.	GUCA1B	19	.	NM_002098	exon1	c.T171C	p.Y57Y	CTCTACATACTGG	.	PASS	Atlas-SNP
DPCD	25911	hgsc.bcm.edu	37	10	103368654	103368654	+	Missense_Mutation	SNP	T	T	C	rs7006	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82	45	69	0	0.548781	0	T|0.720;C|0.280	0.280	strong	.	DPCD	15	.	NM_015448	exon5	c.T467C	p.L156S	ACGCCTTGCTGAG	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100686777	100686777	+	Missense_Mutation	SNP	C	C	T	rs138142210	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	234	125	220	0	0.534188	0	C|0.983;T|0.017	0.017	strong	MUC17,NS,carcinoma,0,3	MUC17	804	3	NM_001040105	exon3	c.C12080T	p.T4027M	CATCAACGCTTTC	.	PASS	Atlas-SNP
MPP3	4356	hgsc.bcm.edu	37	17	41901366	41901366	+	Missense_Mutation	SNP	G	G	T	rs189143886	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	139	56	115	0	0.402878	0	G|0.996;T|0.004	0.004	strong	.	MPP3	42	.	NM_001932	exon10	c.C617A	p.S206Y	CCCTGGGACTGGG	.	PASS	Atlas-SNP
USP36	57602	hgsc.bcm.edu	37	17	76823425	76823425	+	Silent	SNP	G	G	T	rs143701541	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	38	22	27	0	0.578947	0	G|0.980;T|0.020	0.020	strong	.	USP36	243	.	NM_025090	exon6	c.C591A	p.I197I	TCGGGCGATCTCT	.	PASS	Atlas-SNP
GPATCH1	55094	hgsc.bcm.edu	37	19	33608733	33608733	+	Silent	SNP	C	C	A	rs2287681	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57	36	53	0	0.631579	0	C|0.699;A|0.301	0.301	strong	.	GPATCH1	79	.	NM_018025	exon16	c.C2199A	p.T733T	ACAGACCGTCAAC	.	PASS	Atlas-SNP
MAGEC2	51438	hgsc.bcm.edu	37	X	141290865	141290865	+	Silent	SNP	C	C	T	rs3765272	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	63	63	0	0.984375	0	C|0.316;T|0.684	0.684	strong	.	MAGEC2	102	.	NM_016249	exon3	c.G909A	p.P303P	GGCTCTCGGACCC	.	PASS	Atlas-SNP
OR2T4	127074	hgsc.bcm.edu	37	1	248525138	248525138	+	Missense_Mutation	SNP	C	C	T	rs75096121	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	540	101	448	0	0.187037	0	C|0.500;T|0.500	0.500	weak	.	OR2T4	126	.	NM_001004696	exon1	c.C256T	p.H86Y	GACGCCCACCTCC	.	PASS	Atlas-SNP
DSCAML1	57453	hgsc.bcm.edu	37	11	117303858	117303858	+	Silent	SNP	T	T	C	rs11216382	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	113	15	77	0	0.132743	0	T|0.826;C|0.174	0.174	strong	DSCAML1,NS,carcinoma,-2,1	DSCAML1	286	1	NM_020693	exon29	c.A5202G	p.Q1734Q	ACCCAGTTGCTTG	.	PASS	Atlas-SNP
MLPH	79083	hgsc.bcm.edu	37	2	238449108	238449108	+	Missense_Mutation	SNP	G	G	T	rs61737681	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	43	24	41	0	0.55814	0	C|0.000;G|0.952;T|0.047	0.047	strong	.	MLPH	41	.	NM_024101	exon10	c.G1222T	p.A408S	GAGGAAGCCAAGG	.	PASS	Atlas-SNP
DNMBP	23268	hgsc.bcm.edu	37	10	101716112	101716112	+	Missense_Mutation	SNP	G	G	C	rs35924554	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	78	33	79	0	0.423077	0	G|0.947;C|0.053	0.053	strong	.	DNMBP	173	.	NM_015221	exon4	c.C1119G	p.N373K	ATAAGAGTTTCTG	.	PASS	Atlas-SNP
FAM47A	158724	hgsc.bcm.edu	37	X	34149267	34149267	+	Missense_Mutation	SNP	C	C	A	rs1811716	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	101	62	67	0	0.613861	0	C|0.751;A|0.249	0.249	strong	.	FAM47A	249	.	NM_203408	exon1	c.G1129T	p.A377S	GCTCCGCGTGGAG	.	PASS	Atlas-SNP
IRF2BP1	26145	hgsc.bcm.edu	37	19	46387344	46387344	+	Silent	SNP	G	G	A	rs11550348	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	58	33	70	0	0.568965	0	G|0.836;A|0.164	0.164	strong	.	IRF2BP1	23	.	NM_015649	exon1	c.C1689T	p.F563F	CTGCATGAAGGCC	.	PASS	Atlas-SNP
MAGEB10	139422	hgsc.bcm.edu	37	X	27839572	27839572	+	Missense_Mutation	SNP	T	T	C	rs1368769	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	45	43	41	0	0.955556	0	0|0.029;C|0.421	0.421	strong	.	MAGEB10	107	.	NM_182506	exon3	c.T149C	p.F50S	ATGTTTTCCAGAG	.	PASS	Atlas-SNP
IKBKE	9641	hgsc.bcm.edu	37	1	206651107	206651107	+	Silent	SNP	G	G	A	rs2297545	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	101	53	83	0	0.524752	0	G|0.745;A|0.255	0.255	strong	IKBKE,NS,carcinoma,0,1	IKBKE	77	1	NM_001193322	exon8	c.G717A	p.T239T	CACCACGGAGAAG	.	PASS	Atlas-SNP
LAX1	54900	hgsc.bcm.edu	37	1	203743798	203743798	+	Missense_Mutation	SNP	C	C	T	rs41264261	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80	36	76	0	0.45	0	C|0.979;T|0.021	0.021	strong	.	LAX1	48	.	NM_017773	exon5	c.C1186T	p.P396S	CTCCTTCCTGATG	.	PASS	Atlas-SNP
KIAA0753	9851	hgsc.bcm.edu	37	17	6524298	6524298	+	Missense_Mutation	SNP	T	T	A	rs9889363	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	34	55	0	0.515152	0	T|0.697;A|0.303	0.303	strong	.	KIAA0753	63	.	NM_014804	exon7	c.A1125T	p.E375D	TTTCTTTTCCAGG	.	PASS	Atlas-SNP
PCDHB10	56126	hgsc.bcm.edu	37	5	140573439	140573439	+	Silent	SNP	G	G	C	rs610836	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	101	49	88	0	0.485149	0	G|0.551;C|0.449	0.449	strong	.	PCDHB10	177	.	NM_018930	exon1	c.G1314C	p.T438T	CATAACGGTCCTG	.	PASS	Atlas-SNP
SPATA31A6	389730	hgsc.bcm.edu	37	9	43625382	43625382	+	Missense_Mutation	SNP	G	G	A	rs77264639		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	75	191	2	0.925926	0.0104712	A|1.000;|0.000	1.000	weak	FAM75A6,NS,carcinoma,0,3	.	.	3	NM_001145196	exon4	c.C3305T	p.P1102L	TGAATAGGGGGAA	.	scavenged	Atlas-SNP
DRG2	1819	hgsc.bcm.edu	37	17	17997209	17997209	+	Silent	SNP	G	G	A	rs2230316	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	204	100	177	0	0.490196	0	G|0.609;A|0.391	0.391	strong	.	DRG2	27	.	NM_001388	exon2	c.G147A	p.S49S	GGCCTCGTCCAAA	.	PASS	Atlas-SNP
STPG2	285555	hgsc.bcm.edu	37	4	99049593	99049593	+	Missense_Mutation	SNP	A	A	G	rs17558193	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	177	77	179	0	0.435028	0	A|0.611;G|0.389	0.389	strong	.	.	.	.	NM_174952	exon3	c.T373C	p.Y125H	GTTTGTAGTATGC	.	PASS	Atlas-SNP
RNF213	57674	hgsc.bcm.edu	37	17	78337058	78337058	+	Missense_Mutation	SNP	G	G	C	rs35332090	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	27	63	0	0.421875	0	G|0.852;C|0.148	0.148	strong	.	RNF213	766	.	NM_001256071	exon40	c.G11512C	p.V3838L	CCTCAGGTTCTCC	.	PASS	Atlas-SNP
BPHL	670	hgsc.bcm.edu	37	6	3129402	3129402	+	Missense_Mutation	SNP	G	G	A	rs199698749	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	25	55	0	0.352113	0	G|1.000;A|0.000	0.000	strong	.	BPHL	32	.	NM_004332	exon4	c.G502A	p.V168I	GCCTACGTCACTG	.	PASS	Atlas-SNP
CYP11B2	1585	hgsc.bcm.edu	37	8	143996553	143996553	+	Silent	SNP	G	G	A	rs72552275	byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	129	54	143	0	0.418605	0	G|0.655;A|0.345	0.345	strong	CYP11B2,rectum,carcinoma,0,1	CYP11B2	107	1	NM_000498	exon3	c.C504T	p.F168F	CTGGGAGAAGTCC	.	PASS	Atlas-SNP
YWHAG	7532	hgsc.bcm.edu	37	7	75959188	75959188	+	Silent	SNP	G	G	A	rs2072435	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94	47	110	0	0.5	0	G|0.697;A|0.303	0.303	strong	.	YWHAG	24	.	NM_012479	exon2	c.C450T	p.S150S	CTTCTCGGAGGAC	.	PASS	Atlas-SNP
ZFHX3	463	hgsc.bcm.edu	37	16	72830539	72830539	+	Missense_Mutation	SNP	C	C	G	rs62051555	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	124	56	147	0	0.451613	0	C|0.973;G|0.027	0.027	strong	.	ZFHX3	404	.	NM_006885	exon9	c.G6042C	p.Q2014H	CTCGAGCTGTTTG	.	PASS	Atlas-SNP
EMR1	2015	hgsc.bcm.edu	37	19	6897464	6897464	+	Missense_Mutation	SNP	C	C	G	rs330880	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	154	89	201	0	0.577922	0	C|0.551;G|0.449	0.449	strong	.	EMR1	153	.	NM_001256253	exon5	c.C420G	p.S140R	CAGCAGCGTCTGC	.	PASS	Atlas-SNP
GJD4	219770	hgsc.bcm.edu	37	10	35896957	35896957	+	Silent	SNP	G	G	A	rs595652	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49	18	66	0	0.367347	0	G|0.825;A|0.175	0.175	strong	.	GJD4	38	.	NM_153368	exon2	c.G516A	p.K172K	GAAGAAGTTCCCT	.	PASS	Atlas-SNP
BTBD10	84280	hgsc.bcm.edu	37	11	13441250	13441250	+	Missense_Mutation	SNP	C	C	T	rs199534943		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	136	2	95	0	0.0147059	0	C|0.999;T|0.001	0.001	weak	BTBD10,NS,carcinoma,0,1	BTBD10	43	1	NM_032320	exon4	c.G341A	p.R114H	TGAGGACGCGGAC	.	scavenged	Atlas-SNP
PCK1	5105	hgsc.bcm.edu	37	20	56137834	56137834	+	Silent	SNP	A	A	G	rs1062601	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72	71	73	0	0.986111	0	A|0.609;G|0.391	0.391	strong	.	PCK1	95	.	NM_002591	exon4	c.A489G	p.S163S	GGATTCACCCTAC	.	PASS	Atlas-SNP
RABEP2	79874	hgsc.bcm.edu	37	16	28925694	28925694	+	Missense_Mutation	SNP	G	G	A	rs200278634		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	112	57	116	0	0.508929	0	.	.	weak	.	RABEP2	48	.	NM_024816	exon5	c.C757T	p.R253C	CCTGGCGGCTTTG	.	PASS	Atlas-SNP
FASTKD5	60493	hgsc.bcm.edu	37	20	3128578	3128578	+	Missense_Mutation	SNP	A	A	C	rs41304800	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	120	48	105	0	0.4	0	A|0.921;C|0.079	0.079	strong	FASTKD5,right_upper_lobe,carcinoma,-1,1	FASTKD5	63	1	NM_021826	exon2	c.T1139G	p.I380R	GGAGCTATCTCTC	.	PASS	Atlas-SNP
ZNF768	79724	hgsc.bcm.edu	37	16	30536918	30536918	+	Missense_Mutation	SNP	C	C	G	rs10871453	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	158	157	141	0	0.993671	0	C|0.640;G|0.360	0.360	strong	.	ZNF768	28	.	NM_024671	exon2	c.G543C	p.E181D	CTTTTCCTCGGGG	.	PASS	Atlas-SNP
ACAN	176	hgsc.bcm.edu	37	15	89417238	89417238	+	Missense_Mutation	SNP	A	A	G	rs1126823	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	28	42	0	0.538462	0	A|0.613;G|0.387	0.387	strong	.	ACAN	220	.	NM_013227	exon17	c.A7499G	p.Q2500R	AGCCTCAGATCAC	.	PASS	Atlas-SNP
TMPRSS15	5651	hgsc.bcm.edu	37	21	19756040	19756040	+	Missense_Mutation	SNP	C	C	G	rs2824790	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	148	92	124	0	0.621622	0	C|0.739;G|0.261	0.261	strong	.	TMPRSS15	189	.	NM_002772	exon4	c.G400C	p.E134Q	CATTTTCATCTGA	.	PASS	Atlas-SNP
CRB2	286204	hgsc.bcm.edu	37	9	126133497	126133497	+	Silent	SNP	C	C	T	rs13290763	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	137	134	137	1	0.978102	0.00729927	C|0.763;T|0.237	0.237	strong	.	CRB2	86	.	NM_173689	exon8	c.C2076T	p.S692S	TGACTCCGCAGCT	.	PASS	Atlas-SNP
ABLIM1	3983	hgsc.bcm.edu	37	10	116335246	116335246	+	Silent	SNP	G	G	A	rs985273	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	90	40	103	1	0.444444	0.00970874	G|0.719;A|0.281	0.281	strong	ABLIM1,NS,carcinoma,0,1	ABLIM1	131	1	NM_002313	exon3	c.C492T	p.F164F	CTCCACGAACTCC	.	scavenged	Atlas-SNP
MGME1	92667	hgsc.bcm.edu	37	20	17950545	17950545	+	Missense_Mutation	SNP	A	A	T	rs11551768	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	72	90	0	0.972973	0	A|0.900;T|0.100	0.100	strong	.	.	.	.	NM_052865	exon2	c.A43T	p.S15C	CTCAGGAGTTCAA	.	PASS	Atlas-SNP
KRT6B	3854	hgsc.bcm.edu	37	12	52844246	52844246	+	Silent	SNP	A	A	G	rs3194290		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	224	51	207	4	0.227679	0.0193237	.	.	weak	KRT6B,NS,carcinoma,0,1	KRT6B	90	1	NM_005555	exon2	c.T699C	p.G233G	CAGACGACCCCGT	.	scavenged	Atlas-SNP
ZNF285	26974	hgsc.bcm.edu	37	19	44891043	44891043	+	Missense_Mutation	SNP	G	G	T	rs77661661	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	92	8	82	2	0.0869565	0.0243902	.	.	weak	ZNF285,trunk,malignant_melanoma,0,1	ZNF285	86	1	NM_152354	exon4	c.C1364A	p.P455Q	TTGTATGGTTTCT	.	scavenged	Atlas-SNP
ZC3H4	23211	hgsc.bcm.edu	37	19	47588325	47588325	+	Silent	SNP	G	G	A	rs2287842	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	192	191	221	0	0.994792	0	G|0.775;A|0.225	0.225	strong	.	ZC3H4	96	.	NM_015168	exon8	c.C1095T	p.D365D	GTCCTCGTCATAG	.	PASS	Atlas-SNP
FBXO39	162517	hgsc.bcm.edu	37	17	6684003	6684003	+	Silent	SNP	C	C	G	rs17731806	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49	28	42	0	0.571429	0	C|0.963;G|0.037	0.037	strong	.	FBXO39	50	.	NM_153230	exon2	c.C816G	p.S272S	TATGTCCTGGGCC	.	PASS	Atlas-SNP
PRR22	163154	hgsc.bcm.edu	37	19	5783712	5783712	+	Silent	SNP	C	C	T	rs2446211	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	28	17	37	0	0.607143	0	C|0.689;T|0.311	0.311	strong	PRR22_ENST00000419421,NS,carcinoma,0,2	PRR22	25	2	NM_001134316	exon3	c.G546A	p.P182P	TGGCAGCGGGGCC	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9058624	9058624	+	Missense_Mutation	SNP	G	G	A	rs11878666	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	155	85	159	0	0.548387	0	G|0.785;A|0.215	0.215	strong	.	MUC16	4315	.	NM_024690	exon3	c.C28822T	p.P9608S	CAGAGGGCATCTT	.	PASS	Atlas-SNP
STPG2	285555	hgsc.bcm.edu	37	4	99027184	99027184	+	Missense_Mutation	SNP	T	T	C	rs2903150	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	31	78	0	0.382716	0	T|0.617;C|0.383	0.383	strong	.	.	.	.	NM_174952	exon5	c.A532G	p.I178V	TCTTGATGTTAAC	.	PASS	Atlas-SNP
TCF7	6932	hgsc.bcm.edu	37	5	133481467	133481467	+	Missense_Mutation	SNP	G	G	A	rs30489	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	88	48	67	0	0.545455	0	G|0.827;N|0.000	.	strong	.	TCF7	81	.	NM_001134851	exon9	c.G766A	p.G256R	GGTAATGGACAAG	.	PASS	Atlas-SNP
OR2A25	392138	hgsc.bcm.edu	37	7	143771408	143771408	+	Silent	SNP	G	G	C	rs59319753	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	133	70	164	0	0.526316	0	G|0.684;C|0.316	0.316	strong	.	OR2A25	66	.	NM_001004488	exon1	c.G96C	p.L32L	CTCCCTGTTCTAC	.	PASS	Atlas-SNP
CD82	3732	hgsc.bcm.edu	37	11	44636833	44636833	+	Silent	SNP	G	G	A	rs2303865	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	166	74	188	0	0.445783	0	G|0.866;A|0.134	0.134	strong	.	CD82	27	.	NM_002231	exon7	c.G348A	p.E116E	GCAGGAGATGGGC	.	PASS	Atlas-SNP
CNOT1	23019	hgsc.bcm.edu	37	16	58579274	58579274	+	Silent	SNP	C	C	T	rs246258	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	201	101	198	0	0.502488	0	C|0.754;T|0.246	0.246	strong	.	CNOT1	359	.	NM_206999	exon30	c.G4128A	p.L1376L	TGGATTCAGAGTA	.	PASS	Atlas-SNP
VWA5B2	90113	hgsc.bcm.edu	37	3	183953972	183953972	+	Silent	SNP	G	G	A	rs1709657	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	170	62	186	0	0.364706	0	G|0.823;A|0.177	0.177	strong	.	VWA5B2	47	.	NM_138345	exon8	c.G1134A	p.P378P	CCTCCCGCCCCAG	.	PASS	Atlas-SNP
HSPA9	3313	hgsc.bcm.edu	37	5	137902339	137902339	+	Silent	SNP	T	T	C	rs1042665	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	22	59	0	0.360656	0	T|0.686;C|0.314	0.314	strong	.	HSPA9	49	.	NM_004134	exon9	c.A948G	p.K316K	TTCACATTTAGCC	.	PASS	Atlas-SNP
OR10X1	128367	hgsc.bcm.edu	37	1	158549421	158549421	+	Missense_Mutation	SNP	G	G	A	rs77690058	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	125	47	144	0	0.376	0	G|0.926;A|0.074	0.074	strong	OR10X1,face,carcinoma,-1,1	OR10X1	96	1	NM_001004477	exon1	c.C269T	p.T90M	GTCAGCGTATAGC	.	PASS	Atlas-SNP
SLC35G2	80723	hgsc.bcm.edu	37	3	136574521	136574521	+	Silent	SNP	C	C	T	rs1052620	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	92	38	135	0	0.413043	0	C|0.857;T|0.143	0.143	strong	.	.	.	.	NM_025246	exon2	c.C1219T	p.L407L	GAAATACTAGACT	.	PASS	Atlas-SNP
KLK3	354	hgsc.bcm.edu	37	19	51361472	51361472	+	Missense_Mutation	SNP	C	C	A	rs2003783	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	27	57	0	0.509434	0	C|0.896;A|0.104	0.104	strong	.	KLK3	76	.	NM_001030047	exon3	c.C394A	p.L132I	GCCGAGCTCACGG	.	PASS	Atlas-SNP
EPHX2	2053	hgsc.bcm.edu	37	8	27396208	27396208	+	Silent	SNP	G	G	A	rs4149253	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51	24	62	0	0.470588	0	G|0.907;A|0.093	0.093	strong	.	EPHX2	57	.	NM_001979	exon14	c.G1275A	p.A425A	TGAAGCGGGTAAG	.	PASS	Atlas-SNP
PRDM9	56979	hgsc.bcm.edu	37	5	23527323	23527323	+	Missense_Mutation	SNP	C	C	G	rs200539936	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	18	63	5	0.24	0.0793651	C|0.934;G|0.066	0.066	strong	PRDM9,NS,carcinoma,0,1	PRDM9	344	1	NM_020227	exon11	c.C2126G	p.T709S	TCCTCACTCACCA	.	scavenged	Atlas-SNP
CD6	923	hgsc.bcm.edu	37	11	60777073	60777073	+	Missense_Mutation	SNP	G	G	A	rs12360861	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	29	14	27	0	0.482759	0	G|0.878;A|0.122	0.122	strong	CD6_ENST00000313421,rectum,carcinoma,0,2	CD6	122	2	NM_006725	exon5	c.G811A	p.A271T	GGGGGCGCTGACC	.	PASS	Atlas-SNP
C2orf73	129852	hgsc.bcm.edu	37	2	54587659	54587659	+	Missense_Mutation	SNP	G	G	C	rs13184	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93	39	110	0	0.419355	0	G|0.813;C|0.186	0.186	strong	.	C2orf73	17	.	NM_001100396	exon5	c.G824C	p.R275T	TCACTAGGCACAA	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	45	34	69	0	0.755556	0	A|0.663;G|0.337	0.337	strong	.	ALMS1	384	.	NM_015120	exon8	c.A5623G	p.I1875V	AAAGCAATAGGGG	.	PASS	Atlas-SNP
LPP	4026	hgsc.bcm.edu	37	3	188590446	188590446	+	Silent	SNP	A	A	G	rs1136644	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	191	83	141	0	0.434555	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
KCNJ18	100134444	hgsc.bcm.edu	37	17	21318770	21318770	+	Missense_Mutation	SNP	G	G	A	rs3752033	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	115	39	126	0	0.33913	0	G|0.743;A|0.257	0.257	strong	.	.	.	.	NM_001194958	exon3	c.G116A	p.R39Q	ACACGCGGCGCAG	.	PASS	Atlas-SNP
TMEM79	84283	hgsc.bcm.edu	37	1	156255456	156255456	+	Missense_Mutation	SNP	G	G	A	rs6684514	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	38	76	0	0.59375	0	G|0.784;A|0.216	0.216	strong	.	TMEM79	43	.	NM_032323	exon2	c.G439A	p.V147M	CTTATCGTGCGCT	.	PASS	Atlas-SNP
PON1	5444	hgsc.bcm.edu	37	7	94953765	94953765	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48	14	36	0	0.291667	0	.	.	none	.	PON1	55	.	NM_000446	exon1	c.C23G	p.T8S	AAGAGGGTGAGCG	.	PASS	Atlas-SNP
PTK7	5754	hgsc.bcm.edu	37	6	43109751	43109751	+	Silent	SNP	G	G	A	rs6905948	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	42	42	40	0	1	0	G|0.619;A|0.381	0.381	strong	PTK7,NS,carcinoma,+2,1	PTK7	101	1	NM_001270398	exon12	c.G1875A	p.G625G	CCAGGGGGACCCC	.	PASS	Atlas-SNP
CDHR3	222256	hgsc.bcm.edu	37	7	105658451	105658451	+	Missense_Mutation	SNP	G	G	A	rs6967330	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	38	22	48	0	0.578947	0	G|0.826;A|0.174	0.174	strong	.	CDHR3	153	.	NM_152750	exon12	c.G1586A	p.C529Y	TGGACTGTGAAAC	.	PASS	Atlas-SNP
PRKCD	5580	hgsc.bcm.edu	37	3	53220215	53220215	+	Silent	SNP	G	G	A	rs2230494	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	65	41	74	0	0.630769	0	A|0.289;C|0.000;G|0.710;N|0.000	0.289	strong	PRKCD_ENST00000394729,NS,adenoma,0,2	PRKCD	124	2	NM_212539	exon12	c.G1119A	p.E373E	AGGAGAGTACTTT	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	136	135	172	0	0.992647	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
SLC6A12	6539	hgsc.bcm.edu	37	12	319125	319125	+	Missense_Mutation	SNP	A	A	G	rs557881	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85	85	114	0	1	0	A|0.466;G|0.534	0.534	strong	.	SLC6A12	60	.	NM_001122848	exon3	c.T28C	p.C10R	GCCCACACTCTTG	.	PASS	Atlas-SNP
TTF1	7270	hgsc.bcm.edu	37	9	135277341	135277341	+	Missense_Mutation	SNP	C	C	A	rs8999	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	28	55	0	0.451613	0	C|0.878;A|0.122	0.122	strong	.	TTF1	82	.	NM_007344	exon2	c.G868T	p.A290S	CCAATGCCTCAAA	.	PASS	Atlas-SNP
ZNF117	51351	hgsc.bcm.edu	37	7	64439613	64439613	+	Missense_Mutation	SNP	T	T	G	rs3807068	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	38	14	67	0	0.368421	0	T|0.611;G|0.389	0.389	strong	ZNF117,NS,carcinoma,0,1	ZNF117	56	1	NM_015852	exon4	c.A336C	p.K112N	ACATTCTTTACAT	.	PASS	Atlas-SNP
EEFSEC	60678	hgsc.bcm.edu	37	3	128060346	128060346	+	Missense_Mutation	SNP	C	C	T	rs374389896		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	95	52	122	0	0.547368	0	.	.	weak	.	EEFSEC	53	.	NM_021937	exon5	c.C1057T	p.P353S	TTCAGTCCTGCTC	.	PASS	Atlas-SNP
C2CD3	26005	hgsc.bcm.edu	37	11	73806443	73806443	+	Missense_Mutation	SNP	C	C	T	rs11235995	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57	10	70	0	0.175439	0	C|0.780;N|0.000	.	strong	.	C2CD3	288	.	NM_015531	exon17	c.G2990A	p.R997Q	TTTCCTCGGTCCT	.	PASS	Atlas-SNP
PTPRD	5789	hgsc.bcm.edu	37	9	8376067	8376067	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	56	5	75	0	0.0892857	0	.	.	none	.	PTPRD	1348	.	NM_002839	exon39	c.A4530C	p.E1510D	TCTCACTTCTCTC	.	PASS	Atlas-SNP
SECISBP2	79048	hgsc.bcm.edu	37	9	91954848	91954848	+	Missense_Mutation	SNP	C	C	G	rs45452691	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	43	19	61	0	0.44186	0	C|0.961;G|0.039	0.039	strong	.	SECISBP2	64	.	NM_024077	exon9	c.C1282G	p.Q428E	AAATTTCAATCTA	.	PASS	Atlas-SNP
DNMT1	1786	hgsc.bcm.edu	37	19	10273372	10273372	+	Missense_Mutation	SNP	T	T	C	rs2228612	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	28	63	0	0.459016	0	T|0.712;G|0.042;C|0.092;A|0.154	0.092	strong	.	DNMT1	148	.	NM_001130823	exon13	c.A979G	p.I327V	CAGAAATCTGTGG	.	PASS	Atlas-SNP
DEGS2	123099	hgsc.bcm.edu	37	14	100625902	100625902	+	Missense_Mutation	SNP	C	C	T	rs7157599	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	9	6	19	0	0.666667	0	C|0.235;T|0.765	0.765	strong	.	DEGS2	25	.	NM_206918	exon1	c.G23A	p.S8N	AAGTCGCTGCGGC	.	PASS	Atlas-SNP
FBXO43	286151	hgsc.bcm.edu	37	8	101153024	101153024	+	Silent	SNP	G	G	A	rs1460934	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	107	45	119	0	0.420561	0	G|0.370;A|0.630	0.630	strong	.	FBXO43	155	.	NM_001029860	exon2	c.C1458T	p.I486I	CTTGCCGATCAGT	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	141	63	118	0	0.446809	0	C|0.882;G|0.118	0.118	strong	.	FAM46C	25	.	NM_017709	exon2	c.C87G	p.L29L	GGTCCTCACTGAA	.	PASS	Atlas-SNP
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32629155	32629155	+	Silent	SNP	C	C	A	rs1130431	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	45	23	5	0	0.511111	0	C|0.805;A|0.195	0.195	strong	.	HLA-DQB1	15	.	NM_002123	exon4	c.G741T	p.L247L	AAGGCCCAGCCCA	.	PASS	Atlas-SNP
PCDHA13	56136	hgsc.bcm.edu	37	5	140263210	140263210	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72	6	75	0	0.0833333	0	.	.	none	PCDHA13,NS,carcinoma,-2,1	PCDHA13	213	1	NM_031865	exon1	c.C1357G	p.P453A	AACGCGCCGGCGT	.	PASS	Atlas-SNP
HORMAD2	150280	hgsc.bcm.edu	37	22	30518155	30518155	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	107	52	106	0	0.485981	0	.	.	none	.	HORMAD2	12	.	NM_152510	exon10	c.C771T	p.I257I	TGAGATCGCCCAT	.	PASS	Atlas-SNP
PTPRB	5787	hgsc.bcm.edu	37	12	70988287	70988287	+	Silent	SNP	A	A	G	rs34615667	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	123	64	157	0	0.520325	0	A|0.905;G|0.095	0.095	strong	.	PTPRB	676	.	NM_001109754	exon6	c.T1476C	p.A492A	CCCTGCAGCCTCA	.	PASS	Atlas-SNP
CIT	11113	hgsc.bcm.edu	37	12	120222830	120222830	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91	25	107	0	0.274725	0	.	.	none	.	CIT	535	.	NM_001206999	exon11	c.C1335T	p.S445S	CATGGAGCTAGTC	.	PASS	Atlas-SNP
FAM83B	222584	hgsc.bcm.edu	37	6	54804798	54804798	+	Silent	SNP	T	T	C	rs9370340	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	65	37	47	0	0.569231	0	T|0.971;C|0.029	0.029	strong	FAM83B,colon,carcinoma,+1,1	FAM83B	186	1	NM_001010872	exon5	c.T1029C	p.Y343Y	GATATATACTTTA	.	PASS	Atlas-SNP
PRDM1	639	hgsc.bcm.edu	37	6	106555025	106555025	+	Silent	SNP	G	G	A	rs1010273	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	27	65	0	0.509434	0	G|0.910;A|0.090	0.090	strong	.	PRDM1	195	.	NM_001198	exon7	c.G2142A	p.P714P	GGCCCCGGCGCCT	.	PASS	Atlas-SNP
C7orf72	100130988	hgsc.bcm.edu	37	7	50175760	50175760	+	Missense_Mutation	SNP	T	T	G	rs149326344	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	114	28	177	0	0.245614	0	T|0.999;G|0.001	0.001	strong	.	C7orf72	26	.	NM_001161834	exon5	c.T934G	p.F312V	ATTAATTTGTAAG	.	PASS	Atlas-SNP
ANO4	121601	hgsc.bcm.edu	37	12	101336201	101336201	+	Missense_Mutation	SNP	G	G	C	rs34162417	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	41	67	0	0.546667	0	G|0.953;C|0.047	0.047	strong	ANO4,NS,carcinoma,0,1	ANO4	183	1	NM_178826	exon4	c.G239C	p.G80A	GAGATGGAAAGTG	.	PASS	Atlas-SNP
CDH23	64072	hgsc.bcm.edu	37	10	73270906	73270906	+	Silent	SNP	T	T	C	rs3802720	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	102	48	117	0	0.470588	0	T|0.244;C|0.756	0.756	strong	.	CDH23	365	.	NM_052836	exon6	c.T366C	p.V122V	CCAGGTTGGGGAT	.	PASS	Atlas-SNP
WDR90	197335	hgsc.bcm.edu	37	16	705344	705344	+	Silent	SNP	C	C	A	rs144704309	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	26	14	21	0	0.538462	0	C|0.999;A|0.001	0.001	strong	.	WDR90	107	.	NM_145294	exon15	c.C1594A	p.R532R	CTCTGGCGGCTGC	.	PASS	Atlas-SNP
SARDH	1757	hgsc.bcm.edu	37	9	136555629	136555629	+	Missense_Mutation	SNP	T	T	C	rs886016	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	29	15	22	0	0.517241	0	T|0.470;C|0.530	0.530	strong	.	SARDH	112	.	NM_007101	exon16	c.A1942G	p.M648V	CGCCCATGGCCAG	.	PASS	Atlas-SNP
ACTG1	71	hgsc.bcm.edu	37	17	79479099	79479099	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	37	10	74	0	0.27027	0	.	.	none	.	ACTG1	55	.	NM_001614	exon3	c.C193A	p.L65M	GGGTCAGGATGCC	.	PASS	Atlas-SNP
MYO18A	399687	hgsc.bcm.edu	37	17	27422053	27422053	+	Silent	SNP	C	C	T	rs2320786	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79	78	79	0	0.987342	0	C|0.497;T|0.503	0.503	strong	.	MYO18A	217	.	NM_078471	exon29	c.G4410A	p.A1470A	CTCATGCGCCTGC	.	PASS	Atlas-SNP
FSIP1	161835	hgsc.bcm.edu	37	15	39910052	39910052	+	Missense_Mutation	SNP	C	C	G	rs16969386	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	120	45	146	1	0.375	0.00684932	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	.	scavenged	Atlas-SNP
SORT1	6272	hgsc.bcm.edu	37	1	109897100	109897100	+	Silent	SNP	T	T	C	rs72646560	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	44	100	0	0.505747	0	T|0.955;C|0.045	0.045	strong	.	SORT1	48	.	NM_002959	exon5	c.A597G	p.R199R	TGATGATCTAAAG	.	PASS	Atlas-SNP
PRKCDBP	112464	hgsc.bcm.edu	37	11	6340706	6340706	+	Missense_Mutation	SNP	A	A	G	rs1051992	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	62	70	0	0.984127	0	A|0.509;G|0.491	0.491	strong	PRKCDBP,caecum,carcinoma,0,2	PRKCDBP	19	2	NM_145040	exon2	c.T473C	p.L158P	GCCTCCAGCTGCT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195510156	195510156	+	Silent	SNP	G	G	A	rs201141296	byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	16	54	1	0.242424	0.0185185	G|0.996;A|0.004	0.004	strong	MUC4_ENST00000463781,NS,carcinoma,0,4	MUC4	1505	4	NM_018406	exon2	c.C8295T	p.H2765H	GGTGGCGTGACCT	.	scavenged	Atlas-SNP
SLC25A10	1468	hgsc.bcm.edu	37	17	79682558	79682558	+	Silent	SNP	T	T	C	rs2072700	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	24	78	1	0.510638	0.0128205	T|0.579;C|0.421	0.421	strong	SLC25A10,NS,carcinoma,0,1	SLC25A10	24	1	NM_001270888	exon3	c.T264C	p.R88R	GGACCGTGTGGCC	.	scavenged	Atlas-SNP
USP53	54532	hgsc.bcm.edu	37	4	120214030	120214030	+	Missense_Mutation	SNP	T	T	G	rs3749591	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68	34	65	0	0.5	0	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	.	PASS	Atlas-SNP
IGSF10	285313	hgsc.bcm.edu	37	3	151154666	151154666	+	Silent	SNP	T	T	C	rs2172250	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	120	49	122	0	0.408333	0	T|0.152;C|0.848	0.848	strong	.	IGSF10	279	.	NM_178822	exon6	c.A7683G	p.T2561T	CTCCCATGTGATT	.	PASS	Atlas-SNP
ZNF79	7633	hgsc.bcm.edu	37	9	130191186	130191186	+	Missense_Mutation	SNP	C	C	T	rs13292096	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	39	69	0	0.52	0	C|0.414;T|0.586	0.586	strong	ZNF79,NS,carcinoma,+1,2	ZNF79	47	2	NM_007135	exon2	c.C92T	p.T31I	TCCTCACAGCTGG	.	PASS	Atlas-SNP
CCHCR1	54535	hgsc.bcm.edu	37	6	31110391	31110391	+	Missense_Mutation	SNP	G	G	C	rs1576	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	25	21	33	0	0.84	0	G|0.722;C|0.278	0.278	strong	.	CCHCR1	68	.	NM_001105564	exon18	c.C2594G	p.S865C	GGATTGGAGCTGG	.	PASS	Atlas-SNP
TMEM108	66000	hgsc.bcm.edu	37	3	133098806	133098806	+	Missense_Mutation	SNP	C	C	T	rs34111099	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	109	55	125	0	0.504587	0	C|0.952;T|0.048	0.048	strong	TMEM108,rectum,carcinoma,0,1	TMEM108	67	1	NM_023943	exon4	c.C251T	p.P84L	CAACACCGACACC	.	PASS	Atlas-SNP
PPP1R36	145376	hgsc.bcm.edu	37	14	65031534	65031534	+	Missense_Mutation	SNP	C	C	T	rs6573560	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	74	66	0	0.986667	0	C|0.407;N|0.000	.	strong	.	.	.	.	NM_172365	exon4	c.C248T	p.T83I	CAGAAACTGATGG	.	PASS	Atlas-SNP
ATF6	22926	hgsc.bcm.edu	37	1	161751741	161751741	+	Missense_Mutation	SNP	A	A	G	rs1058405	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	35	56	0	0.522388	0	A|0.793;G|0.207	0.207	strong	.	ATF6	84	.	NM_007348	exon3	c.A199G	p.M67V	GATTTGATGCCTT	.	PASS	Atlas-SNP
FCHO1	23149	hgsc.bcm.edu	37	19	17885270	17885270	+	Silent	SNP	A	A	G	rs2287859	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	20	72	0	0.384615	0	A|0.495;G|0.505	0.505	strong	.	FCHO1	69	.	NM_001161358	exon12	c.A903G	p.P301P	GGAGCCAGAGCCA	.	PASS	Atlas-SNP
DOCK10	55619	hgsc.bcm.edu	37	2	225684166	225684166	+	Silent	SNP	A	A	G	rs7572725	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	97	40	87	0	0.412371	0	A|0.757;G|0.243	0.243	strong	.	DOCK10	308	.	NM_014689	exon29	c.T3264C	p.L1088L	TACCTTAAGGTCA	.	PASS	Atlas-SNP
LMAN1	3998	hgsc.bcm.edu	37	18	57000469	57000469	+	Missense_Mutation	SNP	T	T	A	rs2298711	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100	100	124	1	1	0.00806452	T|0.893;A|0.107	0.107	strong	.	LMAN1	57	.	NM_005570	exon11	c.A1228T	p.M410L	CACTCATGGAATT	.	PASS	Atlas-SNP
PKHD1	5314	hgsc.bcm.edu	37	6	51613177	51613177	+	Silent	SNP	C	C	T	rs765525	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	65	40	91	0	0.615385	0	T|0.317;G|0.011	0.317	strong	.	PKHD1	927	.	NM_170724	exon58	c.G9237A	p.A3079A	GATTCCCGCCACC	.	PASS	Atlas-SNP
CCND3	896	hgsc.bcm.edu	37	6	41903782	41903782	+	Missense_Mutation	SNP	A	A	C	rs1051130	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	51	60	0	0.796875	0	T|0.000;G|0.000;C|0.610;A|0.389	0.610	strong	CCND3,NS,carcinoma,0,2	CCND3	40	2	NM_001760	exon5	c.T775G	p.S259A	TCTGAGAGGCTTC	.	PASS	Atlas-SNP
PNLIPRP1	5407	hgsc.bcm.edu	37	10	118364967	118364967	+	Missense_Mutation	SNP	G	G	C	rs2305204	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	111	57	110	0	0.513514	0	G|0.919;C|0.081	0.081	strong	.	PNLIPRP1	82	.	NM_006229	exon12	c.G1242C	p.E414D	AATTGAGAAAGTC	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	101	39	115	0	0.386139	0	T|0.339;C|0.661	0.661	strong	.	KRTAP10-9	24	.	NM_198690	exon1	c.T622C	p.L208L	TCCTCTTTGTGCT	.	PASS	Atlas-SNP
C5orf52	100190949	hgsc.bcm.edu	37	5	157102185	157102185	+	Missense_Mutation	SNP	A	A	G	rs6884959	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69	69	106	1	1	0.00943396	A|0.478;G|0.522	0.522	strong	.	C5orf52	17	.	NM_001145132	exon2	c.A298G	p.T100A	CGCATCACACAAC	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1093769	1093769	+	Missense_Mutation	SNP	G	G	A	rs41361144	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	37	70	0	0.5	0	G|0.937;A|0.063	0.063	strong	.	MUC2	614	.	NM_002457	exon31	c.G5576A	p.R1859Q	CCTCTCGGTCCAC	.	PASS	Atlas-SNP
ZNF202	7753	hgsc.bcm.edu	37	11	123598941	123598941	+	Silent	SNP	T	T	C	rs2282644	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	133	110	111	0	0.827068	0	T|0.784;C|0.216	0.216	strong	.	ZNF202	72	.	NM_003455	exon7	c.A732G	p.V244V	AAAGCATACGGCC	.	PASS	Atlas-SNP
RXFP2	122042	hgsc.bcm.edu	37	13	32360583	32360583	+	Silent	SNP	A	A	G	rs9549106	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	39	94	0	0.481481	0	A|0.860;G|0.140	0.140	strong	.	RXFP2	95	.	NM_130806	exon12	c.A993G	p.L331L	GCTTCTACAAAAG	.	PASS	Atlas-SNP
HAPLN3	145864	hgsc.bcm.edu	37	15	89421327	89421327	+	Silent	SNP	A	A	G	rs2280463	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	38	71	0	0.513514	0	A|0.561;G|0.439	0.439	strong	.	HAPLN3	43	.	NM_178232	exon5	c.T957C	p.G319G	GACGCTACCATCT	.	PASS	Atlas-SNP
POLR2J3	548644	hgsc.bcm.edu	37	7	102212939	102212939	+	Missense_Mutation	SNP	G	G	C	rs139049967	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	1070	129	1201	1	0.120561	0.000832639	G|0.980;C|0.020	0.020	strong	.	POLR2J3	2	.	NM_001097615	exon1	c.C30G	p.F10L	GAGCAAGAACGAC	.	PASS	Atlas-SNP
PLCB2	5330	hgsc.bcm.edu	37	15	40590134	40590134	+	Silent	SNP	G	G	A	rs2229690	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	66	83	0	0.985075	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
NUP88	4927	hgsc.bcm.edu	37	17	5290033	5290033	+	Silent	SNP	T	T	C	rs1071705	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	141	66	154	0	0.468085	0	T|0.566;C|0.434	0.434	strong	.	NUP88	47	.	NM_002532	exon16	c.A2157G	p.K719K	CTCCTCTTTCAGG	.	PASS	Atlas-SNP
NEFM	4741	hgsc.bcm.edu	37	8	24774646	24774646	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	140	79	148	0	0.564286	0	.	.	none	.	NEFM	115	.	NM_005382	exon3	c.C1278G	p.H426Q	TACACACCGACCC	.	PASS	Atlas-SNP
JPH2	57158	hgsc.bcm.edu	37	20	42747247	42747247	+	Missense_Mutation	SNP	C	C	T	rs3810510	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	21	16	15	0	0.761905	0	C|0.772;T|0.228	0.228	strong	JPH2,caecum,carcinoma,0,1	JPH2	86	1	NM_020433	exon3	c.G1186A	p.A396T	CTTTGGCCTTGGC	.	PASS	Atlas-SNP
SALL3	27164	hgsc.bcm.edu	37	18	76753491	76753491	+	Silent	SNP	C	C	T	rs7233194	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	46	21	55	0	0.456522	0	C|0.974;T|0.026	0.026	strong	.	SALL3	162	.	NM_171999	exon2	c.C1500T	p.G500G	CTACGGCATGTCG	.	PASS	Atlas-SNP
GCSAM	257144	hgsc.bcm.edu	37	3	111842431	111842431	+	Silent	SNP	T	T	C	rs16859261	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	220	103	239	0	0.468182	0	T|0.970;C|0.030	0.030	strong	.	.	.	.	NM_001190259	exon6	c.A414G	p.T138T	GGGGTCTGTAGAA	.	PASS	Atlas-SNP
ADCK1	57143	hgsc.bcm.edu	37	14	78390880	78390880	+	Silent	SNP	T	T	C	rs2302944	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	45	15	30	0	0.333333	0	T|0.791;C|0.209	0.209	strong	.	ADCK1	81	.	NM_020421	exon8	c.T939C	p.N313N	CGGCAATGTACTG	.	PASS	Atlas-SNP
PGM2	55276	hgsc.bcm.edu	37	4	37836302	37836302	+	Silent	SNP	T	T	C	rs3752683	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	235	117	219	0	0.497872	0	T|0.651;C|0.349	0.349	strong	.	PGM2	45	.	NM_018290	exon3	c.T312C	p.S104S	GATCAGTTTTGAC	.	PASS	Atlas-SNP
CRY1	1407	hgsc.bcm.edu	37	12	107395106	107395106	+	Silent	SNP	A	A	G	rs8192440	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	175	174	224	0	0.994286	0	A|0.264;G|0.736	0.736	strong	CRY1,NS,carcinoma,-2,1	CRY1	74	1	NM_004075	exon5	c.T636C	p.G212G	TTCTCCACCTGGC	.	PASS	Atlas-SNP
FAT1	2195	hgsc.bcm.edu	37	4	187629538	187629538	+	Missense_Mutation	SNP	C	C	T	rs3733413	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68	37	66	0	0.544118	0	C|0.650;T|0.350	0.350	strong	.	FAT1	500	.	NM_005245	exon2	c.G1444A	p.V482I	TCATGACAGTAGT	.	PASS	Atlas-SNP
KIAA1244	57221	hgsc.bcm.edu	37	6	138642258	138642258	+	Silent	SNP	C	C	T	rs17510658	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57	19	73	0	0.333333	0	C|0.957;T|0.043	0.043	strong	.	KIAA1244	236	.	NM_020340	exon29	c.C4662T	p.Y1554Y	CAGGTACGAGAGC	.	PASS	Atlas-SNP
SLC5A4	6527	hgsc.bcm.edu	37	22	32625210	32625210	+	Silent	SNP	C	C	T	rs5998322	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100	50	119	0	0.5	0	C|0.931;T|0.069	0.069	strong	SLC5A4,NS,lymphoid_neoplasm,-1,1	SLC5A4	82	1	NM_014227	exon11	c.G1251A	p.A417A	CTCCGACGCTTGC	.	PASS	Atlas-SNP
DOCK8	81704	hgsc.bcm.edu	37	9	399255	399255	+	Missense_Mutation	SNP	G	G	A	rs34627722	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	96	40	138	0	0.416667	0	G|0.945;A|0.055	0.055	strong	.	DOCK8	401	.	NM_203447	exon26	c.G3230A	p.S1077N	ATTGCAGCCAGGT	.	PASS	Atlas-SNP
SIPA1L3	23094	hgsc.bcm.edu	37	19	38652993	38652993	+	Silent	SNP	C	C	T	rs332864	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	136	135	177	0	0.992647	0	C|0.679;T|0.321	0.321	strong	SIPA1L3,NS,adenoma,0,1	SIPA1L3	150	1	NM_015073	exon14	c.C3762T	p.S1254S	AGATTCCCCCAAC	.	PASS	Atlas-SNP
FGF5	2250	hgsc.bcm.edu	37	4	81188221	81188221	+	Missense_Mutation	SNP	G	G	T	rs112475347	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	111	57	121	0	0.513514	0	G|0.998;T|0.002	0.002	strong	.	FGF5	49	.	NM_004464	exon1	c.G243T	p.W81C	CCAGTGGAGCCCC	.	PASS	Atlas-SNP
ZNF608	57507	hgsc.bcm.edu	37	5	123976967	123976967	+	Silent	SNP	C	C	T	rs7703447	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	27	51	0	0.409091	0	C|0.880;T|0.120	0.120	strong	ZNF608,NS,carcinoma,-1,1	ZNF608	117	1	NM_020747	exon7	c.G4428A	p.P1476P	TTGACCCGGGATT	.	PASS	Atlas-SNP
FEZ2	9637	hgsc.bcm.edu	37	2	36818109	36818109	+	Silent	SNP	T	T	C	rs117617575	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	197	92	176	0	0.467005	0	T|0.998;C|0.002	0.002	strong	.	FEZ2	13	.	NM_001042548	exon2	c.A312G	p.V104V	CCAGTCTACAGGC	.	PASS	Atlas-SNP
SGOL1	151648	hgsc.bcm.edu	37	3	20216519	20216519	+	Silent	SNP	T	T	A	rs61729306	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	151	77	195	0	0.509934	0	T|0.811;A|0.189	0.189	strong	.	SGOL1	55	.	NM_001199253	exon6	c.A504T	p.T168T	TCCCAGTGTGTCT	.	PASS	Atlas-SNP
FYB	2533	hgsc.bcm.edu	37	5	39110463	39110463	+	Silent	SNP	C	C	T	rs35970892	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	169	76	176	0	0.449704	0	C|0.985;T|0.015	0.015	strong	FYB_ENST00000540520,NS,carcinoma,-1,3	FYB	354	3	NM_001243093	exon17	c.G2460A	p.A820A	CTTGTCCGCTAGG	.	PASS	Atlas-SNP
CPA4	51200	hgsc.bcm.edu	37	7	129938598	129938598	+	Missense_Mutation	SNP	G	G	T	rs34587586	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	178	81	187	0	0.455056	0	G|0.630;T|0.370	0.370	strong	.	CPA4	47	.	NM_016352	exon2	c.G81T	p.L27F	AGTTTTGAGGATT	.	PASS	Atlas-SNP
OR2C1	4993	hgsc.bcm.edu	37	16	3406651	3406651	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	34	67	0	0.419753	0	.	.	none	.	OR2C1	38	.	NM_012368	exon1	c.G711A	p.A237A	AAAGGCGTTCAAT	.	PASS	Atlas-SNP
TRMT11	60487	hgsc.bcm.edu	37	6	126332554	126332554	+	Missense_Mutation	SNP	A	A	G	rs116913944	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	92	40	72	0	0.434783	0	A|0.966;G|0.034	0.034	strong	.	TRMT11	43	.	NM_001031712	exon9	c.A916G	p.I306V	GCAATCATTACTG	.	PASS	Atlas-SNP
SPATA16	83893	hgsc.bcm.edu	37	3	172835469	172835469	+	Missense_Mutation	SNP	T	T	C	rs115897458	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	210	92	231	1	0.438095	0.004329	T|0.996;C|0.004	0.004	strong	.	SPATA16	111	.	NM_031955	exon2	c.A53G	p.H18R	TGATCATGATAGA	.	PASS	Atlas-SNP
UNC79	57578	hgsc.bcm.edu	37	14	93943998	93943998	+	Silent	SNP	G	G	A	rs61992606	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	164	79	152	0	0.481707	0	G|0.684;A|0.316	0.316	strong	.	UNC79	366	.	NM_020818	exon4	c.G12A	p.T4T	ATCAACGTTGGCT	.	PASS	Atlas-SNP
NOC3L	64318	hgsc.bcm.edu	37	10	96104665	96104665	+	Missense_Mutation	SNP	T	T	G	rs3758526	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	40	70	0	0.645161	0	T|0.852;G|0.148	0.148	strong	.	NOC3L	67	.	NM_022451	exon12	c.A1415C	p.E472A	TCTCGCTCTAGTT	.	PASS	Atlas-SNP
AP2M1	1173	hgsc.bcm.edu	37	3	183899832	183899832	+	Silent	SNP	C	C	T	rs8478	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85	46	72	0	0.541176	0	C|0.853;T|0.147	0.147	strong	.	AP2M1	35	.	NM_001025205	exon8	c.C954T	p.I318I	GAAGATCGAGGTG	.	PASS	Atlas-SNP
TTC30A	92104	hgsc.bcm.edu	37	2	178482246	178482246	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	246	31	241	0	0.126016	0	.	.	none	.	TTC30A	60	.	NM_152275	exon1	c.A1184C	p.K395T	ACTTGCTTGGTGA	.	PASS	Atlas-SNP
FAT2	2196	hgsc.bcm.edu	37	5	150924769	150924769	+	Silent	SNP	G	G	A	rs998076	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	27	54	0	0.509434	0	G|0.887;A|0.113	0.113	strong	.	FAT2	465	.	NM_001447	exon9	c.C5919T	p.Y1973Y	TGCCCAGTAGACA	.	PASS	Atlas-SNP
KANSL1	284058	hgsc.bcm.edu	37	17	44110541	44110541	+	Silent	SNP	G	G	A	rs35833914	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	137	137	155	0	1	0	A|0.144;C|0.000;G|0.856;T|0.000	0.144	strong	.	.	.	.	NM_001193466	exon13	c.C2742T	p.D914D	GGCTGCGTCGGAT	.	PASS	Atlas-SNP
OR4D6	219983	hgsc.bcm.edu	37	11	59224608	59224608	+	Missense_Mutation	SNP	A	A	G	rs1453544	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	238	105	233	0	0.441176	0	A|0.815;G|0.185	0.185	strong	OR4D6,NS,adenoma,0,1	OR4D6	65	1	NM_001004708	exon1	c.A175G	p.M59V	ACTCCTATGTACT	.	PASS	Atlas-SNP
EPG5	57724	hgsc.bcm.edu	37	18	43490602	43490602	+	Silent	SNP	G	G	A	rs3744996	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57	31	62	0	0.54386	0	G|0.786;A|0.214	0.214	strong	.	EPG5	199	.	NM_020964	exon23	c.C4089T	p.H1363H	AGCATGGTGGAAG	.	PASS	Atlas-SNP
FAT4	79633	hgsc.bcm.edu	37	4	126329944	126329944	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	4	78	0	0.0645161	0	.	.	none	.	FAT4	1752	.	NM_024582	exon4	c.A5915T	p.D1972V	ATGCAGATGATGG	.	PASS	Atlas-SNP
OR2T4	127074	hgsc.bcm.edu	37	1	248525290	248525290	+	Silent	SNP	C	C	T	rs202028348	byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	655	19	657	1	0.0290076	0.00152207	C|0.840;T|0.160	0.160	strong	OR2T4,NS,carcinoma,0,1	OR2T4	126	1	NM_001004696	exon1	c.C408T	p.Y136Y	CTTCTACGTGACA	.	scavenged	Atlas-SNP
PLP1	5354	hgsc.bcm.edu	37	X	103042882	103042882	+	Silent	SNP	T	T	C	rs1126707	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	105	105	71	0	1	0	T|0.774;C|0.226	0.226	strong	.	PLP1	37	.	NM_001128834	exon5	c.T609C	p.D203D	TGCTGATGCCAGA	.	PASS	Atlas-SNP
CDC20B	166979	hgsc.bcm.edu	37	5	54420799	54420799	+	Silent	SNP	A	A	C	rs382402	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51	16	70	0	0.313726	0	A|0.851;C|0.149	0.149	strong	CDC20B,NS,carcinoma,0,1	CDC20B	61	1	NM_001170402	exon9	c.T1047G	p.V349V	TGTTCCAACATGA	.	PASS	Atlas-SNP
CD200R1L	344807	hgsc.bcm.edu	37	3	112546473	112546473	+	Silent	SNP	G	G	A	rs41511944		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	115	56	149	1	0.486957	0.00671141	.	.	weak	CD200R1L,colon,carcinoma,-2,1	CD200R1L	47	1	NM_001008784	exon3	c.C171T	p.I57I	TAATGCGATAGGA	.	scavenged	Atlas-SNP
CSMD2	114784	hgsc.bcm.edu	37	1	34238283	34238283	+	Missense_Mutation	SNP	T	T	C	rs474474	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	65	27	56	0	0.415385	0	T|0.662;C|0.338	0.338	strong	.	CSMD2	946	.	NM_052896	exon13	c.A1613G	p.H538R	CCGTGGTGAAACC	.	PASS	Atlas-SNP
CIITA	4261	hgsc.bcm.edu	37	16	11001914	11001914	+	Silent	SNP	G	G	A	rs2229321	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	91	43	108	0	0.472527	0	G|0.932;A|0.068	0.068	strong	.	CIITA	92	.	NM_000246	exon11	c.G2565A	p.A855A	GGCGGCGGGCCAA	.	PASS	Atlas-SNP
MAPT	4137	hgsc.bcm.edu	37	17	44073973	44073973	+	Silent	SNP	T	T	C	rs17652121	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	138	138	190	0	1	0	T|0.860;C|0.140	0.140	strong	.	MAPT	135	.	NM_001123066	exon11	c.T1770C	p.N590N	GAAGAATGTCAAG	.	PASS	Atlas-SNP
LYST	1130	hgsc.bcm.edu	37	1	235955150	235955150	+	Silent	SNP	G	G	A	rs11583387	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94	53	108	0	0.56383	0	G|0.905;A|0.095	0.095	strong	.	LYST	370	.	NM_000081	exon12	c.C4392T	p.N1464N	CCAGCAGTTTTGC	.	PASS	Atlas-SNP
CCBL2	56267	hgsc.bcm.edu	37	1	89426902	89426902	+	Silent	SNP	G	G	A	rs3738055	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60	28	68	0	0.466667	0	G|0.584;A|0.416	0.416	strong	CCBL2_ENST00000370491,NS,carcinoma,0,1	CCBL2	138	1	NM_001008661	exon8	c.C735T	p.S245S	CTCATCGCTGATG	.	PASS	Atlas-SNP
CD207	50489	hgsc.bcm.edu	37	2	71061108	71061108	+	Silent	SNP	G	G	A	rs17662453	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	21	93	0	0.33871	0	G|0.858;A|0.142	0.142	strong	.	CD207	47	.	NM_015717	exon3	c.C234T	p.V78V	CAACTGGACATTG	.	PASS	Atlas-SNP
PLCB3	5331	hgsc.bcm.edu	37	11	64023270	64023270	+	Silent	SNP	C	C	T	rs12419663	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79	35	78	0	0.443038	0	C|0.982;T|0.018	0.018	strong	.	PLCB3	103	.	NM_000932	exon8	c.C675T	p.D225D	GCCGGACATTGAC	.	PASS	Atlas-SNP
SERPINB2	5055	hgsc.bcm.edu	37	18	61570503	61570503	+	Missense_Mutation	SNP	C	C	G	rs6103	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	116	38	158	0	0.327586	0	C|0.647;G|0.353	0.353	strong	.	SERPINB2	63	.	NM_002575	exon8	c.C1212G	p.N404K	AACCAACTGCATT	.	PASS	Atlas-SNP
NRD1	4898	hgsc.bcm.edu	37	1	52266242	52266242	+	Silent	SNP	G	G	A	rs8375	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	228	104	238	0	0.45614	0	T|0.088;G|0.434;C|0.096;A|0.382	0.382	strong	.	NRD1	89	.	NM_002525	exon23	c.C2631T	p.P877P	AGTCTCGGGCTTG	.	PASS	Atlas-SNP
TRPV5	56302	hgsc.bcm.edu	37	7	142626549	142626549	+	Missense_Mutation	SNP	C	C	T	rs4236480	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	90	46	73	0	0.511111	0	C|0.656;T|0.344	0.344	strong	.	TRPV5	164	.	NM_019841	exon4	c.G461A	p.R154H	GGACTACGGCGGA	.	PASS	Atlas-SNP
FOLH1	2346	hgsc.bcm.edu	37	11	49204779	49204779	+	Missense_Mutation	SNP	C	C	T	rs116795343	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	123	16	114	0	0.130081	0	C|0.974;T|0.026	0.026	strong	FOLH1,NS,carcinoma,-1,2	FOLH1	141	2	NM_004476	exon7	c.G842A	p.R281H	ATTCCACGCCTAT	.	scavenged	Atlas-SNP
MYOM3	127294	hgsc.bcm.edu	37	1	24418768	24418768	+	Silent	SNP	T	T	C	rs7556176	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	41	96	0	0.476744	0	T|0.586;C|0.414	0.414	strong	.	MYOM3	131	.	NM_152372	exon11	c.A1128G	p.P376P	GTTCAGTGGGGAG	.	PASS	Atlas-SNP
ITGAE	3682	hgsc.bcm.edu	37	17	3649214	3649214	+	Silent	SNP	G	G	A	rs1183610	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	29	14	37	0	0.482759	0	G|0.215;A|0.785	0.785	strong	.	ITGAE	96	.	NM_002208	exon18	c.C2163T	p.R721R	TGCCTCGCGGAGG	.	PASS	Atlas-SNP
TNXB	7148	hgsc.bcm.edu	37	6	32029205	32029205	+	Silent	SNP	G	G	A	rs1150757	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	67	104	0	0.797619	0	G|0.959;A|0.041	0.041	strong	.	TNXB	553	.	NM_019105	exon21	c.C7461T	p.R2487R	GCCCACGCGCCGC	.	PASS	Atlas-SNP
GPBP1L1	60313	hgsc.bcm.edu	37	1	46094027	46094027	+	Silent	SNP	A	A	G	rs1250	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48	23	60	0	0.479167	0	A|0.704;G|0.296	0.296	strong	GPBP1L1,NS,carcinoma,0,1	GPBP1L1	43	1	NM_021639	exon13	c.T1326C	p.S442S	GAACAGACTGGAA	.	PASS	Atlas-SNP
NLRC5	84166	hgsc.bcm.edu	37	16	57075406	57075406	+	Silent	SNP	T	T	C	rs56171037	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	28	80	0	0.528302	0	T|0.932;C|0.068	0.068	strong	.	NLRC5	186	.	NM_032206	exon17	c.T2949C	p.H983H	GACACATTGTGGC	.	PASS	Atlas-SNP
ASS1	445	hgsc.bcm.edu	37	9	133364757	133364757	+	Silent	SNP	T	T	C	rs1057484	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	41	24	29	0	0.585366	0	T|0.900;C|0.100	0.100	strong	.	ASS1	37	.	NM_054012	exon12	c.T876C	p.H292H	TTACCATGCTCAT	.	PASS	Atlas-SNP
BAALC	79870	hgsc.bcm.edu	37	8	104153137	104153137	+	Silent	SNP	C	C	T	rs3736043	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	22	13	17	0	0.590909	0	C|0.958;T|0.042	0.042	strong	.	BAALC	15	.	NM_001024372	exon1	c.C12T	p.G4G	CTGCGGCGGGAGC	.	PASS	Atlas-SNP
ZNF407	55628	hgsc.bcm.edu	37	18	72344553	72344553	+	Silent	SNP	G	G	A	rs7227391	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	106	48	92	0	0.45283	0	G|0.907;A|0.093	0.093	strong	.	ZNF407	231	.	NM_001146190	exon1	c.G1578A	p.T526T	TCAGACGTTGTGT	.	PASS	Atlas-SNP
KCNV2	169522	hgsc.bcm.edu	37	9	2718654	2718654	+	Silent	SNP	G	G	A	rs7859993	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	23	109	0	0.442308	0	G|0.957;A|0.043	0.043	strong	.	KCNV2	72	.	NM_133497	exon1	c.G915A	p.V305V	GCACGTGGAGATG	.	PASS	Atlas-SNP
CEL	1056	hgsc.bcm.edu	37	9	135942008	135942008	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	26	33	0	0.5	0	.	.	none	.	CEL	71	.	NM_001807	exon5	c.C639T	p.L213L	CACGCTCTTCGGG	.	PASS	Atlas-SNP
FAM114A1	92689	hgsc.bcm.edu	37	4	38930921	38930921	+	Silent	SNP	A	A	G	rs3188469	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	50	33	76	0	0.66	0	A|0.887;G|0.113	0.113	strong	.	FAM114A1	42	.	NM_138389	exon10	c.A1128G	p.L376L	TGAATTACATGTG	.	PASS	Atlas-SNP
STRA8	346673	hgsc.bcm.edu	37	7	134925411	134925411	+	Silent	SNP	G	G	A	rs7805859	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	154	150	175	0	0.974026	0	G|0.591;A|0.409	0.409	strong	.	STRA8	39	.	NM_182489	exon2	c.G201A	p.A67A	GGCAGCGCTCTTC	.	PASS	Atlas-SNP
WRN	7486	hgsc.bcm.edu	37	8	31024654	31024654	+	Missense_Mutation	SNP	T	T	C	rs1346044	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	123	62	107	0	0.504065	0	T|0.798;C|0.202	0.202	strong	.	WRN	116	.	NM_000553	exon34	c.T4099C	p.C1367R	CCTTCATGTGATG	.	PASS	Atlas-SNP
OR4A47	403253	hgsc.bcm.edu	37	11	48511105	48511105	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	106	8	89	0	0.0754717	0	.	.	none	.	OR4A47	72	.	NM_001005512	exon1	c.T761G	p.F254C	GTATTTTTATGTA	.	PASS	Atlas-SNP
INPP4A	3631	hgsc.bcm.edu	37	2	99193496	99193496	+	Silent	SNP	C	C	T	rs2230388	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	197	87	188	0	0.441624	0	C|0.753;T|0.247	0.247	strong	.	INPP4A	205	.	NM_001134224	exon25	c.C2691T	p.S897S	CAAGAGCGCTAAG	.	PASS	Atlas-SNP
SERPINB2	5055	hgsc.bcm.edu	37	18	61570529	61570529	+	Missense_Mutation	SNP	C	C	G	rs6104	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	21	122	0	0.295775	0	C|0.705;G|0.295	0.295	strong	.	SERPINB2	63	.	NM_002575	exon8	c.C1238G	p.S413C	GATTTTCCTCACC	.	PASS	Atlas-SNP
LANCL2	55915	hgsc.bcm.edu	37	7	55459563	55459563	+	Silent	SNP	A	A	G	rs2049497	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	32	13	40	0	0.40625	0	A|0.628;G|0.372	0.372	strong	.	LANCL2	54	.	NM_018697	exon2	c.A282G	p.T94T	GAAGACAGCTGAT	.	PASS	Atlas-SNP
SLC25A29	123096	hgsc.bcm.edu	37	14	100759277	100759277	+	Silent	SNP	C	C	T	rs3742379	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	83	85	0	0.988095	0	C|0.688;G|0.000;T|0.312	0.312	strong	SLC25A29,NS,carcinoma,0,1	SLC25A29	14	1	NM_001039355	exon4	c.G255A	p.R85R	CAGGGCCCGGAGG	.	PASS	Atlas-SNP
MED13L	23389	hgsc.bcm.edu	37	12	116408538	116408538	+	Silent	SNP	A	A	G	rs2304460	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	45	107	0	0.517241	0	A|0.842;G|0.158	0.158	strong	MED13L,NS,carcinoma,0,1	MED13L	193	1	NM_015335	exon27	c.T5928C	p.T1976T	CAGTGCAGTACTT	.	PASS	Atlas-SNP
AP1M1	8907	hgsc.bcm.edu	37	19	16318904	16318904	+	Silent	SNP	G	G	C	rs143435975	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	112	58	109	0	0.517857	0	G|0.996;C|0.004	0.004	strong	.	AP1M1	48	.	NM_001130524	exon4	c.G342C	p.L114L	GCTGCTGGACGAG	.	PASS	Atlas-SNP
NUP210	23225	hgsc.bcm.edu	37	3	13407556	13407556	+	Missense_Mutation	SNP	T	T	C	rs3732671	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	21	68	0	0.313433	0	T|0.368;C|0.631	0.631	strong	.	NUP210	182	.	NM_024923	exon14	c.A1822G	p.I608V	CCCGGATGCCGCT	.	PASS	Atlas-SNP
FAT1	2195	hgsc.bcm.edu	37	4	187541971	187541971	+	Silent	SNP	G	G	A	rs372720339	alternate_allele	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	119	62	135	0	0.521008	0	.	.	alt	.	FAT1	500	.	NM_005245	exon10	c.C5769T	p.I1923I	CTCCCCGATGTTG	.	PASS	Atlas-SNP
RERGL	79785	hgsc.bcm.edu	37	12	18234256	18234256	+	Missense_Mutation	SNP	T	T	C	rs941048	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	88	52	126	0	0.590909	0	T|0.897;C|0.103	0.103	strong	.	RERGL	66	.	NM_024730	exon6	c.A487G	p.M163V	ACATCATTTCCAC	.	PASS	Atlas-SNP
ANP32C	23520	hgsc.bcm.edu	37	4	165118253	165118253	+	Missense_Mutation	SNP	T	T	C	rs2288676	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	159	77	165	8	0.484277	0.0484848	T|0.938;C|0.062	0.062	strong	ANP32C,NS,carcinoma,-1,1	ANP32C	59	1	NM_012403	exon1	c.A611G	p.E204G	TCCTCCTCGTCCC	.	scavenged	Atlas-SNP
ESR1	2099	hgsc.bcm.edu	37	6	152201863	152201863	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	50	4	59	0	0.08	0	.	.	none	.	ESR1	94	.	NM_000125	exon3	c.C717T	p.A239A	CCAGGCCTGCCGG	.	PASS	Atlas-SNP
CCDC171	203238	hgsc.bcm.edu	37	9	15591372	15591372	+	Missense_Mutation	SNP	T	T	A	rs4741510	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	119	119	102	0	1	0	T|0.666;A|0.334	0.334	strong	C9orf93,NS,carcinoma,0,1	.	.	1	NM_173550	exon5	c.T361A	p.S121T	CAGAATTCAGAAC	.	PASS	Atlas-SNP
KDM6B	23135	hgsc.bcm.edu	37	17	7754993	7754993	+	Silent	SNP	G	G	A	rs12939056	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	34	12	38	0	0.352941	0	A|0.324;C|0.000;G|0.675	0.324	strong	.	KDM6B	95	.	NM_001080424	exon17	c.G4044A	p.L1348L	GCTGCTGAAGCTG	.	PASS	Atlas-SNP
LILRA6	79168	hgsc.bcm.edu	37	19	54745907	54745907	+	Missense_Mutation	SNP	A	A	G	rs77267627		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	369	105	380	1	0.284553	0.00263158	A|0.250;G|0.750	0.750	weak	LILRA6,NS,neuroblastoma,0,2	LILRA6	75	2	NM_024318	exon3	c.T350C	p.M117T	CCTGTCATCACCA	.	PASS	Atlas-SNP
SIGLEC8	27181	hgsc.bcm.edu	37	19	51960940	51960940	+	Missense_Mutation	SNP	A	A	G	rs10409962	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	32	64	0	0.484848	0	A|0.783;G|0.217	0.217	strong	SIGLEC8,colon,carcinoma,+1,2	SIGLEC8	130	2	NM_014442	exon2	c.T508C	p.S170P	TCCTGGAGTGGCC	.	PASS	Atlas-SNP
SNAI1	6615	hgsc.bcm.edu	37	20	48600557	48600557	+	Silent	SNP	T	T	C	rs4647959	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	65	29	43	0	0.446154	0	T|0.712;C|0.288	0.288	strong	.	SNAI1	28	.	NM_005985	exon2	c.T279C	p.D93D	GTCAGATGAGGAC	.	PASS	Atlas-SNP
DHX57	90957	hgsc.bcm.edu	37	2	39090515	39090515	+	Missense_Mutation	SNP	T	T	G	rs199537184	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	58	30	46	0	0.517241	0	.	.	weak	.	DHX57	127	.	NM_198963	exon3	c.A371C	p.D124A	CCAGCATCAGCAT	.	PASS	Atlas-SNP
C10orf54	64115	hgsc.bcm.edu	37	10	73521371	73521371	+	Silent	SNP	C	C	T	rs3747867	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	25	55	0	0.462963	0	C|0.779;T|0.221	0.221	strong	.	C10orf54	29	.	NM_022153	exon2	c.G495A	p.E165E	CTGCAGCTCCATG	.	PASS	Atlas-SNP
FNDC3B	64778	hgsc.bcm.edu	37	3	171969077	171969077	+	Missense_Mutation	SNP	C	C	G	rs7652177	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	78	26	78	0	0.333333	0	C|0.384;G|0.616	0.616	strong	FNDC3B,NS,carcinoma,0,1	FNDC3B	118	1	NM_001135095	exon6	c.C536G	p.T179S	TGTCAACCTACAT	.	PASS	Atlas-SNP
FAM114A1	92689	hgsc.bcm.edu	37	4	38945169	38945169	+	Silent	SNP	A	A	G	rs1060582	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	161	160	160	1	0.993789	0.00625	A|0.883;G|0.117	0.117	strong	.	FAM114A1	42	.	NM_138389	exon15	c.A1683G	p.A561A	GAAAGCACAGCCG	.	PASS	Atlas-SNP
SPRY2	10253	hgsc.bcm.edu	37	13	80911525	80911525	+	Missense_Mutation	SNP	G	G	A	rs504122	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	95	27	92	0	0.284211	0	G|0.726;N|0.000	.	strong	.	SPRY2	28	.	NM_005842	exon2	c.C316T	p.P106S	ACAGAGGGGCTCG	.	PASS	Atlas-SNP
ZNF417	147687	hgsc.bcm.edu	37	19	58420167	58420167	+	Silent	SNP	T	T	C	rs17852300	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	138	47	217	1	0.34058	0.00460829	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	.	scavenged	Atlas-SNP
ZRANB2	9406	hgsc.bcm.edu	37	1	71538191	71538191	+	Silent	SNP	A	A	G	rs11556475	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	268	129	203	0	0.481343	0	A|0.898;G|0.102	0.102	strong	.	ZRANB2	75	.	NM_203350	exon5	c.T342C	p.Y114Y	TTCTATATATTCA	.	PASS	Atlas-SNP
C3	718	hgsc.bcm.edu	37	19	6709848	6709848	+	Silent	SNP	C	C	T	rs2230204	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	41	53	0	0.554054	0	C|0.634;N|0.001	.	strong	.	C3	192	.	NM_000064	exon14	c.G1692A	p.V564V	TTTTACCACCAGC	.	PASS	Atlas-SNP
SLC9C1	285335	hgsc.bcm.edu	37	3	111887788	111887788	+	Missense_Mutation	SNP	A	A	G	rs73853324	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	42	85	0	0.488372	0	A|0.946;G|0.054	0.054	strong	.	.	.	.	NM_183061	exon25	c.T3173C	p.V1058A	TCTTCTACAGCTC	.	PASS	Atlas-SNP
KIAA1143	57456	hgsc.bcm.edu	37	3	44794955	44794955	+	Missense_Mutation	SNP	T	T	C	rs138479225	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	140	72	110	0	0.514286	0	T|0.997;C|0.003	0.003	strong	.	KIAA1143	10	.	NM_020696	exon3	c.A343G	p.S115G	TTGAGCTTGCTGT	.	PASS	Atlas-SNP
UGT2B7	7364	hgsc.bcm.edu	37	4	69962610	69962610	+	Silent	SNP	A	A	G	rs28365063	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	130	68	122	0	0.523077	0	A|0.850;G|0.150	0.150	strong	.	UGT2B7	79	.	NM_001074	exon1	c.A372G	p.R124R	AACTAGAAAGTTC	.	PASS	Atlas-SNP
CEP120	153241	hgsc.bcm.edu	37	5	122685727	122685727	+	Missense_Mutation	SNP	C	C	G	rs1047437	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	311	155	304	0	0.498392	0	C|0.836;G|0.164	0.164	strong	.	CEP120	72	.	NM_153223	exon20	c.G2637C	p.Q879H	TCTCATCTGTTCC	.	PASS	Atlas-SNP
GRIK2	2898	hgsc.bcm.edu	37	6	102074485	102074485	+	Missense_Mutation	SNP	G	G	A	rs201893729	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	107	60	96	0	0.560748	0	G|0.999;A|0.001	0.001	weak	GRIK2_ENST00000421544,NS,carcinoma,0,2	GRIK2	487	2	NM_021956	exon3	c.G514A	p.V172I	AAAACCGTCACGG	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	137	86	180	0	0.627737	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
PASD1	139135	hgsc.bcm.edu	37	X	150840916	150840916	+	Silent	SNP	C	C	T	rs41299110	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	181	173	148	1	0.955801	0.00675676	C|0.803;T|0.197	0.197	strong	.	PASD1	286	.	NM_173493	exon14	c.C1699T	p.L567L	CAGCAGCTGCAAG	.	PASS	Atlas-SNP
HSPA8	3312	hgsc.bcm.edu	37	11	122929407	122929407	+	Silent	SNP	T	T	G	rs1064585	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	62	68	0	1	0	T|0.770;G|0.230	0.230	strong	.	HSPA8	168	.	NM_006597	exon7	c.A1455C	p.I485I	ATTGAGTATACCA	.	PASS	Atlas-SNP
DNAI2	64446	hgsc.bcm.edu	37	17	72295966	72295966	+	Silent	SNP	C	C	T	rs34159194	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	33	18	39	0	0.545455	0	C|0.883;T|0.117	0.117	strong	.	DNAI2	102	.	NM_001172810	exon7	c.C834T	p.T278T	GGGCACCGAGTGC	.	PASS	Atlas-SNP
PALD1	27143	hgsc.bcm.edu	37	10	72289701	72289701	+	Silent	SNP	G	G	A	rs2275059	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69	31	54	0	0.449275	0	G|0.845;A|0.155	0.155	strong	.	.	.	.	NM_014431	exon4	c.G345A	p.V115V	CACCGTGGGAAGC	.	PASS	Atlas-SNP
TMCC2	9911	hgsc.bcm.edu	37	1	205240251	205240251	+	Silent	SNP	C	C	T	rs1668867	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	43	19	40	0	0.44186	0	C|0.762;T|0.238	0.238	strong	.	TMCC2	89	.	NM_014858	exon4	c.C1686T	p.Y562Y	CAGGTACGAGCGG	.	PASS	Atlas-SNP
ANKRD66	100287718	hgsc.bcm.edu	37	6	46721588	46721588	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	109	7	115	0	0.0642202	0	.	.	none	.	.	.	.	NM_001162435	exon4	c.C458T	p.A153V	TCCATGCATTGCA	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228482028	228482028	+	Silent	SNP	G	G	C	rs4653547	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	157	76	178	0	0.484076	0	G|0.788;C|0.212	0.212	strong	.	OBSCN	2142	.	NM_001271223	exon47	c.G12594C	p.L4198L	TGAGCTGCAGATC	.	PASS	Atlas-SNP
SUSD2	56241	hgsc.bcm.edu	37	22	24582041	24582041	+	Missense_Mutation	SNP	A	A	G	rs8141797	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	129	64	128	0	0.496124	0	A|0.901;G|0.099	0.099	strong	.	SUSD2	68	.	NM_019601	exon9	c.A1397G	p.N466S	CATTCAATGGGCG	.	PASS	Atlas-SNP
BEND2	139105	hgsc.bcm.edu	37	X	18230715	18230715	+	Missense_Mutation	SNP	A	A	C	rs17274127	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	77	52	68	0	0.675325	0	A|0.766;0|0.015	.	strong	.	BEND2	108	.	NM_001184767	exon4	c.T462G	p.F154L	TTTTGGAAAATCC	.	PASS	Atlas-SNP
KCNMB3	27094	hgsc.bcm.edu	37	3	178962370	178962370	+	Silent	SNP	C	C	T	rs139532669	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	197	97	177	0	0.492386	0	C|0.994;T|0.006	0.006	strong	.	KCNMB3	46	.	NM_014407	exon3	c.G372A	p.P124P	AAGACACGGGTAC	.	PASS	Atlas-SNP
ARMC3	219681	hgsc.bcm.edu	37	10	23297252	23297252	+	Missense_Mutation	SNP	G	G	A	rs10828395	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	88	41	67	0	0.465909	0	G|0.805;A|0.194	0.194	strong	.	ARMC3	102	.	NM_173081	exon15	c.G1877A	p.R626Q	ATGGACGAAGTAT	.	PASS	Atlas-SNP
LMOD1	25802	hgsc.bcm.edu	37	1	201869257	201869257	+	Missense_Mutation	SNP	G	G	A	rs2820312	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	238	127	226	1	0.533613	0.00442478	G|0.763;A|0.237	0.237	strong	.	LMOD1	59	.	NM_012134	exon2	c.C884T	p.T295M	CTGGGCGTCTGTT	.	PASS	Atlas-SNP
KIAA1804	0	hgsc.bcm.edu	37	1	233514934	233514934	+	Missense_Mutation	SNP	G	G	A	rs3795375	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	38	20	38	0	0.526316	0	G|0.789;A|0.211	0.211	strong	KIAA1804,NS,carcinoma,0,1	KIAA1804	129	1	NM_032435	exon9	c.G2182A	p.V728I	TGCACCGTCCTTC	.	PASS	Atlas-SNP
WWC1	23286	hgsc.bcm.edu	37	5	167868779	167868779	+	Silent	SNP	A	A	G	rs3733981	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	119	68	151	0	0.571429	0	A|0.525;G|0.475	0.475	strong	.	WWC1	98	.	NM_015238	exon16	c.A2373G	p.K791K	GAAGAAACAGAGC	.	PASS	Atlas-SNP
RNF123	63891	hgsc.bcm.edu	37	3	49749979	49749979	+	Missense_Mutation	SNP	C	C	T	rs201817210		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110	45	126	0	0.409091	0	C|0.999;T|0.001	0.001	weak	.	RNF123	100	.	NM_022064	exon27	c.C2564T	p.T855I	ATCGCACAGGGTC	.	PASS	Atlas-SNP
SHD	56961	hgsc.bcm.edu	37	19	4288332	4288332	+	Missense_Mutation	SNP	A	A	G	rs888930	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	36	25	63	0	0.694444	0	A|0.552;G|0.446	0.446	strong	SHD,NS,carcinoma,0,3	SHD	33	3	NM_020209	exon5	c.A809G	p.N270S	AGACCAACCCCCA	.	PASS	Atlas-SNP
UTS2B	257313	hgsc.bcm.edu	37	3	190999917	190999917	+	Missense_Mutation	SNP	C	C	A	rs6788319	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	172	69	182	0	0.401163	0	C|0.495;A|0.505	0.505	strong	UTS2D,NS,carcinoma,0,1	.	.	1	NM_198152	exon5	c.G62T	p.S21I	AAAAAACTCAACA	.	PASS	Atlas-SNP
OR4L1	122742	hgsc.bcm.edu	37	14	20528528	20528528	+	Missense_Mutation	SNP	G	G	A	rs2775254	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	43	118	0	0.494253	0	G|0.625;A|0.375	0.375	strong	.	OR4L1	98	.	NM_001004717	exon1	c.G325A	p.G109S	TTTGGGGGTGCTG	.	PASS	Atlas-SNP
ELP2	55250	hgsc.bcm.edu	37	18	33739735	33739735	+	Silent	SNP	G	G	C	rs139343265	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	78	38	74	0	0.487179	0	G|0.996;C|0.004	0.004	strong	.	ELP2	70	.	NM_001242875	exon16	c.G1767C	p.L589L	GGAGCTGTTAACT	.	PASS	Atlas-SNP
BRAT1	221927	hgsc.bcm.edu	37	7	2578924	2578924	+	Silent	SNP	G	G	A	rs61746940	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	162	70	122	0	0.432099	0	G|0.998;A|0.002	0.002	strong	.	BRAT1	57	.	NM_152743	exon13	c.C1659T	p.L553L	CTGGAGGAGCTGC	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	38	20	37	0	0.526316	0	G|0.817;N|0.000	.	strong	.	SDK2	219	.	NM_001144952	exon12	c.C1577A	p.T526N	CTGATGGTTACTC	.	PASS	Atlas-SNP
ZZEF1	23140	hgsc.bcm.edu	37	17	4016096	4016096	+	Silent	SNP	T	T	C	rs74887186	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	29	66	0	0.47541	0	T|0.978;C|0.022	0.022	strong	.	ZZEF1	195	.	NM_015113	exon5	c.A873G	p.K291K	CTTCATTTTTAAA	.	PASS	Atlas-SNP
PLXDC1	57125	hgsc.bcm.edu	37	17	37262117	37262117	+	Silent	SNP	C	C	T	rs17705646	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	37	62	0	0.578125	0	C|0.974;T|0.026	0.026	strong	.	PLXDC1	45	.	NM_020405	exon7	c.G801A	p.P267P	CACATCCGGGGAT	.	PASS	Atlas-SNP
ACTG1	71	hgsc.bcm.edu	37	17	79479108	79479108	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	37	9	69	0	0.243243	0	.	.	none	.	ACTG1	55	.	NM_001614	exon3	c.C184T	p.R62C	TGCCACGCTTGCT	.	PASS	Atlas-SNP
BCCIP	56647	hgsc.bcm.edu	37	10	127541743	127541743	+	Silent	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	28	79	0	0.459016	0	.	.	none	.	BCCIP	48	.	NM_016567	exon8	c.A900G	p.L300L	TGGACTAATTCAA	.	PASS	Atlas-SNP
SPTA1	6708	hgsc.bcm.edu	37	1	158597507	158597507	+	Missense_Mutation	SNP	G	G	C	rs3737515	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	38	14	50	0	0.368421	0	G|0.758;C|0.242	0.242	strong	.	SPTA1	720	.	NM_003126	exon40	c.C5572G	p.L1858V	TCATTAGCAAGCT	.	PASS	Atlas-SNP
CCHCR1	54535	hgsc.bcm.edu	37	6	31112737	31112737	+	Missense_Mutation	SNP	C	C	A	rs130079	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	35	26	40	0	0.742857	0	C|0.801;A|0.199	0.199	strong	.	CCHCR1	68	.	NM_001105564	exon14	c.G1990T	p.G664C	GCTGGCCCTGGCG	.	PASS	Atlas-SNP
JAK1	3716	hgsc.bcm.edu	37	1	65313232	65313232	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	126	39	135	0	0.309524	0	.	.	none	.	JAK1	209	.	NM_002227	exon13	c.C1882T	p.H628Y	CCCTGTGGCTGGG	.	PASS	Atlas-SNP
MEIOB	254528	hgsc.bcm.edu	37	16	1912021	1912021	+	Missense_Mutation	SNP	T	T	G	rs1657125	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	97	48	96	1	0.494845	0.0104167	T|0.820;G|0.180	0.180	strong	C16orf73_ENST00000412554,caecum,carcinoma,0,1	.	.	1	NM_001163560	exon4	c.A224C	p.K75T	AGAGACTTGATGT	.	scavenged	Atlas-SNP
MOV10	4343	hgsc.bcm.edu	37	1	113243048	113243048	+	Silent	SNP	C	C	T	rs6679	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	153	80	155	0	0.522876	0	C|0.753;T|0.247	0.247	strong	.	MOV10	74	.	NM_020963	exon21	c.C2931T	p.S977S	CCACAGCCATGAC	.	PASS	Atlas-SNP
HDAC10	83933	hgsc.bcm.edu	37	22	50684256	50684256	+	Missense_Mutation	SNP	T	T	C	rs75596977	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44	25	51	0	0.568182	0	T|0.966;C|0.034	0.034	strong	.	HDAC10	29	.	NM_032019	exon19	c.A1834G	p.N612D	TGGAGTTCTGGAC	.	PASS	Atlas-SNP
PDS5B	23047	hgsc.bcm.edu	37	13	33232435	33232435	+	Silent	SNP	A	A	G	rs2301393	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	117	49	107	0	0.418803	0	A|0.686;G|0.314	0.314	strong	.	PDS5B	141	.	NM_015032	exon4	c.A372G	p.Q124Q	CCCACAATTCAAT	.	PASS	Atlas-SNP
SEMA5B	54437	hgsc.bcm.edu	37	3	122646734	122646734	+	Silent	SNP	C	C	T	rs2276775	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80	38	64	0	0.475	0	C|0.906;T|0.094	0.094	strong	.	SEMA5B	303	.	NM_001256347	exon8	c.G915A	p.T305T	GATGACCGTGGCT	.	PASS	Atlas-SNP
MTCH2	23788	hgsc.bcm.edu	37	11	47640429	47640429	+	Missense_Mutation	SNP	G	G	C	rs1064608	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	32	17	33	0	0.53125	0	G|0.727;C|0.273	0.273	strong	MTCH2,NS,carcinoma,0,1	MTCH2	25	1	NM_014342	exon13	c.C868G	p.P290A	CAAAGGGGACCTT	.	PASS	Atlas-SNP
SGK1	6446	hgsc.bcm.edu	37	6	134494280	134494280	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	96	20	96	0	0.208333	0	.	.	none	.	SGK1	387	.	NM_001143676	exon8	c.A715T	p.M239L	CCGACATAATATG	.	PASS	Atlas-SNP
FMN2	56776	hgsc.bcm.edu	37	1	240370985	240370985	+	Missense_Mutation	SNP	C	C	T	rs111896385	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	38	12	74	0	0.315789	0	C|0.803;T|0.197	0.197	strong	.	FMN2	451	.	NM_020066	exon5	c.C2873T	p.P958L	CGCCCCCTCTTCC	.	PASS	Atlas-SNP
HSPA8	3312	hgsc.bcm.edu	37	11	122928622	122928622	+	Silent	SNP	A	A	G	rs4802	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	46	46	48	0	1	0	A|0.653;G|0.347	0.347	strong	.	HSPA8	168	.	NM_006597	exon9	c.T1761C	p.A587A	CTTCTCAGCAGTC	.	PASS	Atlas-SNP
C5orf20	140947	hgsc.bcm.edu	37	5	134782396	134782396	+	Missense_Mutation	SNP	T	T	A	rs67187482	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79	31	76	0	0.392405	0	T|0.905;A|0.095	0.095	strong	.	C5orf20	16	.	NM_130848	exon1	c.A403T	p.S135C	TGAAACTACAAAC	.	PASS	Atlas-SNP
SYNE3	161176	hgsc.bcm.edu	37	14	95884294	95884294	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	7	98	0	0.0864198	0	.	.	none	.	SYNE3	130	.	NM_152592	exon17	c.C2797T	p.L933F	GCAGAAGCAGCTG	.	PASS	Atlas-SNP
ZNF423	23090	hgsc.bcm.edu	37	16	49671177	49671177	+	Missense_Mutation	SNP	T	T	C	rs34214571	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	108	54	134	0	0.5	0	T|0.972;C|0.028	0.028	strong	.	ZNF423	463	.	NM_015069	exon4	c.A1886G	p.N629S	TCCCCATTGGAGA	.	PASS	Atlas-SNP
ARAP3	64411	hgsc.bcm.edu	37	5	141052986	141052986	+	Missense_Mutation	SNP	C	C	T	rs150744263	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	224	104	259	1	0.464286	0.003861	C|0.997;T|0.003	0.003	strong	.	ARAP3	139	.	NM_022481	exon6	c.G954A	p.M318I	AAAGTACATCAGA	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9077581	9077581	+	Missense_Mutation	SNP	G	G	T	rs73011014	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	366	209	370	0	0.571038	0	G|0.809;T|0.191	0.191	strong	.	MUC16	4315	.	NM_024690	exon3	c.C9865A	p.P3289T	CAGGTGGGGATGG	.	PASS	Atlas-SNP
GNRH1	2796	hgsc.bcm.edu	37	8	25280800	25280800	+	Missense_Mutation	SNP	C	C	G	rs6185	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	48	23	43	0	0.479167	0	C|0.738;G|0.262	0.262	strong	.	GNRH1	8	.	NM_000825	exon1	c.G59C	p.W20S	ACGCACCAAGTCA	.	PASS	Atlas-SNP
QRICH2	84074	hgsc.bcm.edu	37	17	74287204	74287204	+	Missense_Mutation	SNP	C	C	G	rs2279052	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	90	37	92	0	0.411111	0	C|0.613;G|0.387	0.387	strong	.	QRICH2	143	.	NM_032134	exon4	c.G3106C	p.E1036Q	TGAGCTCTCCCAT	.	PASS	Atlas-SNP
C14orf105	55195	hgsc.bcm.edu	37	14	57947421	57947421	+	Nonsense_Mutation	SNP	G	G	A	rs34960436	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	143	68	141	0	0.475524	0	G|0.976;A|0.024	0.024	strong	.	C14orf105	26	.	NM_018168	exon5	c.C547T	p.Q183X	GACTTTGCTTATT	.	PASS	Atlas-SNP
ADCY9	115	hgsc.bcm.edu	37	16	4164337	4164337	+	Silent	SNP	C	C	T	rs887248	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80	34	93	0	0.425	0	C|0.956;T|0.044	0.044	strong	.	ADCY9	151	.	NM_001116	exon2	c.G1107A	p.R369R	TTTCTTCCTGTTC	.	PASS	Atlas-SNP
EMILIN3	90187	hgsc.bcm.edu	37	20	39990700	39990700	+	Silent	SNP	T	T	C	rs41278104	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	37	68	0	0.521127	0	T|0.802;C|0.198	0.198	strong	.	EMILIN3	63	.	NM_052846	exon4	c.A1509G	p.V503V	TGTCTGTACAAGG	.	PASS	Atlas-SNP
MYADML2	255275	hgsc.bcm.edu	37	17	79898933	79898933	+	Missense_Mutation	SNP	G	G	A	rs62077244	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	77	43	90	0	0.558442	0	G|0.981;A|0.019	0.019	strong	.	MYADML2	11	.	NM_001145113	exon3	c.C685T	p.R229W	CCAGCCGGTCAAA	.	PASS	Atlas-SNP
KRTAP1-3	81850	hgsc.bcm.edu	37	17	39191027	39191027	+	Missense_Mutation	SNP	G	G	A	rs140428118	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	145	76	166	0	0.524138	0	G|0.997;A|0.003	0.003	strong	.	KRTAP1-3	18	.	NM_030966	exon1	c.C47T	p.T16I	CCACTGGTGGAGC	.	PASS	Atlas-SNP
KRT16	3868	hgsc.bcm.edu	37	17	39767744	39767744	+	Silent	SNP	A	A	G	rs4796681	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	106	54	136	0	0.509434	0	A|0.328;G|0.672	0.672	strong	.	KRT16	45	.	NM_005557	exon3	c.T624C	p.H208H	CAGTTCATGCTCA	.	PASS	Atlas-SNP
KIAA1328	57536	hgsc.bcm.edu	37	18	34647323	34647323	+	Silent	SNP	T	T	A	rs3747896	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	143	68	167	0	0.475524	0	A|0.237;G|0.031;T|0.732	0.237	strong	.	KIAA1328	39	.	NM_020776	exon7	c.T1047A	p.G349G	TGGTGGTGGGGCA	.	PASS	Atlas-SNP
ZFYVE20	64145	hgsc.bcm.edu	37	3	15126313	15126313	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	123	58	119	0	0.471545	0	.	.	none	.	ZFYVE20	61	.	NM_022340	exon8	c.G527A	p.R176H	TGGTGGCGGCGGT	.	PASS	Atlas-SNP
NCR2	9436	hgsc.bcm.edu	37	6	41309552	41309552	+	Missense_Mutation	SNP	T	T	C	rs2236369	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55	50	49	2	0.909091	0.0408163	A|0.004;C|0.466	0.466	strong	NCR2,colon,carcinoma,0,1	NCR2	44	1	NM_004828	exon3	c.T415C	p.S139P	CAGACCTCCTGGA	.	scavenged	Atlas-SNP
PKD1	5310	hgsc.bcm.edu	37	16	2167594	2167594	+	Silent	SNP	C	C	T	rs141553109	byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	189	99	253	0	0.52381	0	C|0.999;T|0.001	0.001	strong	.	PKD1	184	.	NM_000296	exon6	c.G1281A	p.A427A	CCAGGCCGCCTTC	.	PASS	Atlas-SNP
UHRF2	115426	hgsc.bcm.edu	37	9	6413643	6413643	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	14	5	22	0	0.357143	0	.	.	none	.	UHRF2	50	.	NM_152896	exon1	c.G153A	p.Q51Q	CAAGCAGGTGAGG	.	PASS	Atlas-SNP
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32549563	32549563	+	Silent	SNP	G	G	A	rs77689370	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	132	72	192	0	0.545455	0	A|0.051;C|0.002;G|0.947	0.051	strong	.	HLA-DRB1	41	.	NM_002124	exon3	c.C423T	p.H141H	GAGGTTGTGGTGC	.	PASS	Atlas-SNP
ASB1	51665	hgsc.bcm.edu	37	2	239353001	239353001	+	Silent	SNP	C	C	T	rs2290075	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94	41	92	0	0.43617	0	C|0.937;T|0.063	0.063	strong	.	ASB1	25	.	NM_001040445	exon4	c.C513T	p.D171D	TGTTGACGTCAAC	.	PASS	Atlas-SNP
LILRB3	11025	hgsc.bcm.edu	37	19	54725980	54725980	+	Silent	SNP	G	G	A	rs150024950	byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	95	7	185	1	0.0736842	0.00540541	G|0.947;A|0.053	0.053	strong	LILRB3,NS,carcinoma,0,1	LILRB3	67	1	NM_006864	exon4	c.C378T	p.L126L	GGCTGAGAGGGTG	.	scavenged	Atlas-SNP
KRTAP12-2	353323	hgsc.bcm.edu	37	21	46086718	46086718	+	Missense_Mutation	SNP	G	G	C	rs7276859	bycluster;by2hit2allele;alternate_allele	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72	21	86	0	0.291667	0	.	.	alt	.	KRTAP12-2	10	.	NM_181684	exon1	c.C86G	p.S29C	TGGCAGGAGCTGG	.	PASS	Atlas-SNP
ANKRD50	57182	hgsc.bcm.edu	37	4	125592188	125592188	+	Silent	SNP	G	G	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	115	2	134	1	0.0173913	0.00746269	.	.	none	ANKRD50,NS,carcinoma,-1,1	ANKRD50	136	1	NM_020337	exon4	c.C2244A	p.G748G	AGTCATGCCATCT	.	scavenged	Atlas-SNP
SREK1	140890	hgsc.bcm.edu	37	5	65455141	65455141	+	Silent	SNP	G	G	A	rs72770236	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	45	25	64	0	0.555556	0	G|0.990;A|0.010	0.010	strong	SREK1_ENST00000334121,NS,carcinoma,0,4	SREK1	58	4	NM_001077199	exon3	c.G390A	p.P130P	AATACCGACCCCA	.	PASS	Atlas-SNP
CIITA	4261	hgsc.bcm.edu	37	16	11001694	11001694	+	Missense_Mutation	SNP	T	T	C	rs13336804	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44	21	47	0	0.477273	0	T|0.935;C|0.065	0.065	strong	.	CIITA	92	.	NM_000246	exon11	c.T2345C	p.V782A	CCTCGGTGGACAG	.	PASS	Atlas-SNP
SULT1C2	6819	hgsc.bcm.edu	37	2	108922036	108922036	+	Missense_Mutation	SNP	T	T	G	rs17036104	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	116	48	93	0	0.413793	0	T|0.948;G|0.052	0.052	strong	.	SULT1C2	82	.	NM_176825	exon8	c.T796G	p.S266A	ATTTCCTCCTTCA	.	PASS	Atlas-SNP
NDST4	64579	hgsc.bcm.edu	37	4	115749005	115749005	+	Silent	SNP	C	C	T	rs6843860	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44	19	66	0	0.431818	0	C|0.735;T|0.265	0.265	strong	.	NDST4	193	.	NM_022569	exon14	c.G2586A	p.S862S	CAGCCACGATGGC	.	PASS	Atlas-SNP
C6orf118	168090	hgsc.bcm.edu	37	6	165712942	165712942	+	Missense_Mutation	SNP	G	G	C	rs61733397	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	59	31	70	0	0.525424	0	G|0.968;C|0.032	0.032	strong	.	C6orf118	116	.	NM_144980	exon4	c.C926G	p.A309G	TACTGTGCTGCAG	.	PASS	Atlas-SNP
PLEK2	26499	hgsc.bcm.edu	37	14	67878765	67878765	+	Silent	SNP	G	G	A	rs115017102	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	24	7	24	0	0.291667	0	G|0.976;A|0.024	0.024	strong	.	PLEK2	23	.	NM_016445	exon1	c.C12T	p.G4G	GAGCACGCCGTCC	.	PASS	Atlas-SNP
CYP1B1	1545	hgsc.bcm.edu	37	2	38298150	38298150	+	Silent	SNP	A	A	G	rs1056837	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	134	133	148	0	0.992537	0	G|0.522;A|0.478	0.522	strong	.	CYP1B1	39	.	NM_000104	exon3	c.T1347C	p.D449D	GAGGCCATCCTTG	.	PASS	Atlas-SNP
ZBBX	79740	hgsc.bcm.edu	37	3	167023624	167023624	+	Missense_Mutation	SNP	A	A	G	rs35190925	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	137	60	135	0	0.437956	0	A|0.918;G|0.082	0.082	strong	.	ZBBX	299	.	NM_024687	exon17	c.T1532C	p.I511T	AAACCTATATTTT	.	PASS	Atlas-SNP
PCDHB7	56129	hgsc.bcm.edu	37	5	140552975	140552975	+	Missense_Mutation	SNP	G	G	A	rs17096946	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	108	54	125	0	0.5	0	G|0.932;A|0.068	0.068	strong	.	PCDHB7	231	.	NM_018940	exon1	c.G559A	p.E187K	AGCGGGGAGGGGA	.	PASS	Atlas-SNP
HNRNPCL1	343069	hgsc.bcm.edu	37	1	12907848	12907848	+	Missense_Mutation	SNP	G	G	C	rs140567799	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	236	29	234	1	0.122881	0.0042735	.	.	weak	HNRNPCL1,NS,carcinoma,0,1	HNRNPCL1	68	1	NM_001013631	exon2	c.C295G	p.R99G	CTGATCGTTTCAC	.	scavenged	Atlas-SNP
LOXL4	84171	hgsc.bcm.edu	37	10	100013438	100013438	+	Silent	SNP	C	C	T	rs17524355	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	43	71	0	0.511905	0	C|0.826;T|0.174	0.174	strong	LOXL4,caecum,carcinoma,-1,2	LOXL4	60	2	NM_032211	exon11	c.G1707A	p.A569A	GTGATCCGCAGAC	.	PASS	Atlas-SNP
DMD	1756	hgsc.bcm.edu	37	X	31697636	31697636	+	Silent	SNP	A	A	G	rs1801188	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	81	81	65	0	1	0	0|0.002;G|0.185	0.185	strong	.	DMD	2127	.	NM_004006	exon53	c.T7728C	p.N2576N	CATTTCATTCAAC	.	PASS	Atlas-SNP
ZNF211	10520	hgsc.bcm.edu	37	19	58152817	58152817	+	Silent	SNP	G	G	C	rs11880050	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	41	21	44	0	0.512195	0	G|0.804;C|0.196	0.196	strong	.	ZNF211	78	.	NM_001265597	exon5	c.G1158C	p.S386S	GAAATCGTTTAGT	.	PASS	Atlas-SNP
PIM3	415116	hgsc.bcm.edu	37	22	50354819	50354819	+	Silent	SNP	C	C	A	rs11541025	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	22	12	26	0	0.545455	0	C|0.669;A|0.331	0.331	strong	.	PIM3	15	.	NM_001001852	exon2	c.C132A	p.A44A	GGGCGCCGTGCTG	.	PASS	Atlas-SNP
TFDP3	51270	hgsc.bcm.edu	37	X	132352230	132352230	+	Missense_Mutation	SNP	C	C	G	rs28455963	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	134	52	66	0	0.38806	0	C|0.877;G|0.123	0.123	strong	.	TFDP3	92	.	NM_016521	exon1	c.G58C	p.E20Q	GGTTCTCGTCCAT	.	PASS	Atlas-SNP
GCNT2	2651	hgsc.bcm.edu	37	6	10556872	10556872	+	Silent	SNP	C	C	T	rs2230906	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	115	23	124	0	0.2	0	C|0.905;T|0.095	0.095	strong	.	GCNT2	123	.	NM_001491	exon1	c.C216T	p.C72C	TTCTTGCAAGGAA	.	PASS	Atlas-SNP
NEK1	4750	hgsc.bcm.edu	37	4	170482883	170482883	+	Silent	SNP	A	A	G	rs56064008	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	294	135	306	0	0.459184	0	A|0.953;G|0.047	0.047	strong	.	NEK1	203	.	NM_001199399	exon15	c.T1146C	p.I382I	TAAACTAATAATC	.	PASS	Atlas-SNP
OR1S1	219959	hgsc.bcm.edu	37	11	57982584	57982584	+	Missense_Mutation	SNP	T	T	C	rs1966835	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	211	211	253	1	1	0.00395257	T|0.569;C|0.431	0.431	strong	.	OR1S1	139	.	NM_001004458	exon1	c.T368C	p.I123T	TCGTCATTGACAA	.	PASS	Atlas-SNP
LDHAL6A	160287	hgsc.bcm.edu	37	11	18485611	18485611	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	25	56	0	0.373134	0	.	.	none	.	LDHAL6A	35	.	NM_144972	exon2	c.T230C	p.I77T	CAAATATTGTCTC	.	PASS	Atlas-SNP
ZNF470	388566	hgsc.bcm.edu	37	19	57088850	57088850	+	Silent	SNP	T	T	C	rs3752180	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44	21	34	0	0.477273	0	T|0.693;C|0.307	0.307	strong	.	ZNF470	103	.	NM_001001668	exon6	c.T1053C	p.D351D	TAGTGATTGCTCA	.	PASS	Atlas-SNP
ZNF180	7733	hgsc.bcm.edu	37	19	45001346	45001346	+	Missense_Mutation	SNP	G	G	A	rs2571108	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	20	20	25	0	1	0	G|0.703;A|0.297	0.297	strong	ZNF180,colon,carcinoma,0,1	ZNF180	103	1	NM_013256	exon2	c.C122T	p.A41V	GCACAGGCCTTCG	.	PASS	Atlas-SNP
EPX	8288	hgsc.bcm.edu	37	17	56271094	56271094	+	Missense_Mutation	SNP	G	G	C	rs11652709	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	193	93	208	1	0.481865	0.00480769	G|0.745;C|0.254	0.254	strong	.	EPX	95	.	NM_000502	exon4	c.G366C	p.Q122H	ACCACAGCTGCGG	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57	27	71	0	0.473684	0	G|0.251;T|0.749	0.749	strong	.	CEP192	340	.	NM_032142	exon43	c.G7346T	p.R2449L	GGTTCCGGCCGAC	.	PASS	Atlas-SNP
OR9Q2	219957	hgsc.bcm.edu	37	11	57958775	57958775	+	Silent	SNP	C	C	T	rs7120468	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	111	110	100	0	0.990991	0	C|0.651;T|0.349	0.349	strong	OR9Q2,NS,carcinoma,0,1	OR9Q2	78	1	NM_001005283	exon1	c.C813T	p.D271D	GGGAGACCGAGTG	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	192	99	172	0	0.515625	0	T|0.705;C|0.295	0.295	strong	.	.	.	.	NM_183061	exon8	c.A856G	p.I286V	CTTCAATTGCTGC	.	PASS	Atlas-SNP
PLXNC1	10154	hgsc.bcm.edu	37	12	94673277	94673277	+	Silent	SNP	G	G	A	rs2230760	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	22	66	0	0.349206	0	G|0.888;A|0.112	0.112	strong	PLXNC1,NS,carcinoma,0,1	PLXNC1	135	1	NM_005761	exon22	c.G3627A	p.P1209P	AATCCCGGAAAAC	.	PASS	Atlas-SNP
AZI1	22994	hgsc.bcm.edu	37	17	79170576	79170576	+	Silent	SNP	C	C	T	rs1542961	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	97	48	100	0	0.494845	0	C|0.699;T|0.301	0.301	strong	AZI1_ENST00000450824,NS,carcinoma,0,2	AZI1	145	2	NM_014984	exon15	c.G1824A	p.A608A	GCTCAGCGCCTTC	.	PASS	Atlas-SNP
TMC4	147798	hgsc.bcm.edu	37	19	54676763	54676763	+	Missense_Mutation	SNP	C	C	T	rs641738	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60	29	65	0	0.483333	0	C|0.615;T|0.385	0.385	strong	.	TMC4	89	.	NM_001145303	exon1	c.G50A	p.G17E	AGCCACCCCCTAG	.	PASS	Atlas-SNP
SERPINH1	871	hgsc.bcm.edu	37	11	75279846	75279846	+	Silent	SNP	C	C	T	rs649257	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	92	22	93	0	0.23913	0	C|0.660;T|0.340	0.340	strong	SERPINH1,NS,carcinoma,0,1	SERPINH1	33	1	NM_001235	exon3	c.C693T	p.T231T	CTATACCGTGGGT	.	PASS	Atlas-SNP
HSPG2	3339	hgsc.bcm.edu	37	1	22167605	22167605	+	Missense_Mutation	SNP	C	C	T	rs2228349	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	174	84	185	0	0.482759	0	C|0.909;T|0.091	0.091	strong	.	HSPG2	311	.	NM_005529	exon71	c.G9502A	p.A3168T	GCACCGCGTGGCT	.	PASS	Atlas-SNP
USH2A	7399	hgsc.bcm.edu	37	1	216496947	216496947	+	Silent	SNP	G	G	A	rs1805050	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	89	41	100	0	0.460674	0	G|0.716;A|0.284	0.284	strong	.	USH2A	1168	.	NM_007123	exon8	c.C1419T	p.T473T	AGATGGGGTATTA	.	PASS	Atlas-SNP
TAF1C	9013	hgsc.bcm.edu	37	16	84218565	84218565	+	Silent	SNP	T	T	C	rs2230126	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	35	79	0	0.522388	0	T|0.829;C|0.171	0.171	strong	.	TAF1C	60	.	NM_001243156	exon2	c.A30G	p.A10A	AAACAATGCAGGG	.	PASS	Atlas-SNP
PAK2	5062	hgsc.bcm.edu	37	3	196544948	196544948	+	Silent	SNP	T	T	C	rs56172538	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57	23	62	0	0.403509	0	T|0.896;C|0.104	0.104	strong	.	PAK2	113	.	NM_002577	exon12	c.T1074C	p.F358F	GGAGTTTTTACAT	.	PASS	Atlas-SNP
PEG3	5178	hgsc.bcm.edu	37	19	57335022	57335022	+	Silent	SNP	G	G	A	rs1860565	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69	34	76	0	0.492754	0	G|0.798;A|0.202	0.202	strong	.	PEG3	414	.	NM_001146184	exon4	c.C420T	p.S140S	GTCGTCGCTGGTC	.	PASS	Atlas-SNP
TMEM71	137835	hgsc.bcm.edu	37	8	133759318	133759318	+	Silent	SNP	A	A	G	rs74775484	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	36	88	0	0.545455	0	A|0.937;G|0.063	0.063	strong	TMEM71_ENST00000377901,right_upper_lobe,carcinoma,0,1	TMEM71	55	1	NM_001145153	exon5	c.T357C	p.S119S	GAAGAGAGAAGAA	.	PASS	Atlas-SNP
RNF213	57674	hgsc.bcm.edu	37	17	78327358	78327358	+	Silent	SNP	G	G	A	rs7216493	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	65	64	83	0	0.984615	0	G|0.313;A|0.687	0.687	strong	RNF213_ENST00000411702,NS,carcinoma,0,2	RNF213	766	2	NM_001256071	exon34	c.G10470A	p.E3490E	GATGGAGACGGAG	.	PASS	Atlas-SNP
PKD1L2	114780	hgsc.bcm.edu	37	16	81242198	81242198	+	Nonsense_Mutation	SNP	G	G	A	rs7499011	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	34	11	21	0	0.323529	0	G|0.742;A|0.258	0.258	strong	.	PKD1L2	361	.	NM_001076780	exon4	c.C658T	p.Q220X	GCTCCTGGCACTG	.	PASS	Atlas-SNP
HMCN1	83872	hgsc.bcm.edu	37	1	186121995	186121995	+	Missense_Mutation	SNP	A	A	T	rs114364265	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	169	72	158	0	0.426035	0	A|0.996;T|0.004	0.004	strong	.	HMCN1	797	.	NM_031935	exon96	c.A15010T	p.T5004S	GAAGTCACTGTAA	.	PASS	Atlas-SNP
NRBP2	340371	hgsc.bcm.edu	37	8	144917880	144917880	+	Silent	SNP	G	G	A	rs72693365	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44	22	36	0	0.5	0	G|0.942;A|0.058	0.058	strong	.	NRBP2	20	.	NM_178564	exon18	c.C1458T	p.A486A	GAAGGCGGCCAGC	.	PASS	Atlas-SNP
HCFC1	3054	hgsc.bcm.edu	37	X	153223257	153223257	+	Silent	SNP	C	C	T	rs3027888	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98	22	66	0	0.22449	0	C|0.998;T|0.002	0.002	strong	.	HCFC1	284	.	NM_005334	exon12	c.G2109A	p.T703T	AGGACCCGTGGAC	.	PASS	Atlas-SNP
FBF1	85302	hgsc.bcm.edu	37	17	73926121	73926121	+	Missense_Mutation	SNP	C	C	A	rs1135889	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	46	46	30	0	1	0	C|0.810;A|0.190	0.190	strong	FBF1_ENST00000319129,NS,carcinoma,0,1	FBF1	48	1	NM_001080542	exon6	c.G194T	p.G65V	GAGATACCTGAAA	.	PASS	Atlas-SNP
OR2A2	442361	hgsc.bcm.edu	37	7	143806688	143806688	+	Missense_Mutation	SNP	C	C	A	rs10230228	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	172	76	152	1	0.44186	0.00657895	C|0.826;A|0.174	0.174	strong	OR2A2,rectum,carcinoma,-2,1	OR2A2	48	1	NM_001005480	exon1	c.C13A	p.Q5K	GGCAACCAGACAT	.	scavenged	Atlas-SNP
MARC2	54996	hgsc.bcm.edu	37	1	220928313	220928313	+	Silent	SNP	T	T	C	rs12044903	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	102	42	100	0	0.411765	0	T|0.984;C|0.016	0.016	strong	.	.	.	.	NM_017898	exon2	c.T297C	p.D99D	GGAAGATGGACAC	.	PASS	Atlas-SNP
COL3A1	1281	hgsc.bcm.edu	37	2	189864080	189864080	+	Missense_Mutation	SNP	G	G	A	rs1800255	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51	51	60	0	1	0	G|0.808;A|0.192	0.192	strong	.	COL3A1	292	.	NM_000090	exon30	c.G2092A	p.A698T	GGTGGAGCTGGTC	.	PASS	Atlas-SNP
OR10A2	341276	hgsc.bcm.edu	37	11	6891528	6891528	+	Silent	SNP	C	C	G	rs7117739	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	161	66	184	0	0.409938	0	C|0.680;G|0.320	0.320	strong	.	OR10A2	55	.	NM_001004460	exon1	c.C543G	p.L181L	AGCACTCTTTGAG	.	PASS	Atlas-SNP
HSPA4L	22824	hgsc.bcm.edu	37	4	128741710	128741710	+	Missense_Mutation	SNP	T	T	C	rs35518193	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	107	47	117	0	0.439252	0	T|0.967;C|0.033	0.033	strong	HSPA4L,NS,carcinoma,-1,2	HSPA4L	82	2	NM_014278	exon14	c.T1802C	p.I601T	GCTACATTGAAAA	.	PASS	Atlas-SNP
RPS6KB2	6199	hgsc.bcm.edu	37	11	67200819	67200819	+	Silent	SNP	C	C	T	rs4930427	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	35	33	49	0	0.942857	0	A|0.000;C|0.599;T|0.400	0.400	strong	RPS6KB2_ENST00000312629,NS,carcinoma,0,1	RPS6KB2	92	1	NM_003952	exon10	c.C807T	p.F269F	GCCCTTCACCGCA	.	PASS	Atlas-SNP
GZMB	3002	hgsc.bcm.edu	37	14	25102160	25102160	+	Missense_Mutation	SNP	C	C	T	rs8192917	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	53	70	0	1	0	C|0.297;T|0.703	0.703	strong	.	GZMB	73	.	NM_004131	exon2	c.G164A	p.R55Q	TCGTCTCGTATCA	.	PASS	Atlas-SNP
PCDHB15	56121	hgsc.bcm.edu	37	5	140625629	140625629	+	Silent	SNP	C	C	T	rs150283740	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	40	102	0	0.47619	0	C|0.994;T|0.006	0.006	strong	PCDHB15,NS,carcinoma,+2,1	PCDHB15	138	1	NM_018935	exon1	c.C483T	p.D161D	CTTGGACGTGGGC	.	PASS	Atlas-SNP
MATN1	4146	hgsc.bcm.edu	37	1	31188089	31188089	+	Silent	SNP	C	C	T	rs1065755	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	196	104	190	0	0.530612	0	C|0.696;T|0.304	0.304	strong	.	MATN1	28	.	NM_002379	exon6	c.G1275A	p.E425E	CACAGGCTCTGAG	.	PASS	Atlas-SNP
FLRT2	23768	hgsc.bcm.edu	37	14	86089315	86089315	+	Missense_Mutation	SNP	G	G	A	rs17646457	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	221	96	237	0	0.434389	0	G|0.899;A|0.101	0.101	strong	FLRT2,NS,carcinoma,0,1	FLRT2	168	1	NM_013231	exon2	c.G1457A	p.R486Q	AGCCCCGATCCAC	.	PASS	Atlas-SNP
RORA	6095	hgsc.bcm.edu	37	15	61521304	61521304	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	45	18	49	0	0.4	0	.	.	none	.	RORA	114	.	NM_134261	exon1	c.G114A	p.K38K	CTCGCTCTTGCGG	.	PASS	Atlas-SNP
DRAXIN	374946	hgsc.bcm.edu	37	1	11771988	11771988	+	Silent	SNP	A	A	G	rs17037327	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	50	30	52	0	0.6	0	A|0.885;G|0.115	0.115	strong	.	.	.	.	NM_198545	exon4	c.A723G	p.L241L	AGACTTAAAACCT	.	PASS	Atlas-SNP
TMEM155	132332	hgsc.bcm.edu	37	4	122682720	122682720	+	Missense_Mutation	SNP	C	C	T	rs138330999	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	243	125	261	0	0.514403	0	C|0.995;T|0.005	0.005	strong	TMEM155,NS,carcinoma,0,1	TMEM155	17	1	NM_152399	exon5	c.G185A	p.R62H	TGCAAGCGAACCA	.	PASS	Atlas-SNP
BEGAIN	57596	hgsc.bcm.edu	37	14	101005215	101005215	+	Silent	SNP	T	T	C	rs12893951	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	27	11	49	0	0.407407	0	T|0.388;C|0.612	0.612	strong	.	BEGAIN	32	.	NM_020836	exon7	c.A873G	p.A291A	TGAGCCTGCGTAG	.	PASS	Atlas-SNP
TMTC1	83857	hgsc.bcm.edu	37	12	29736480	29736480	+	Silent	SNP	A	A	G	rs2113879	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	116	56	131	0	0.482759	0	A|0.662;G|0.338	0.338	strong	.	TMTC1	147	.	NM_001193451	exon8	c.T1278C	p.H426H	CAGTCCATGCACA	.	PASS	Atlas-SNP
ENGASE	64772	hgsc.bcm.edu	37	17	77075670	77075670	+	Silent	SNP	C	C	T	rs3744184	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	15	67	0	0.319149	0	C|0.738;T|0.262	0.262	strong	ENGASE,upper_leg,malignant_melanoma,+1,1	ENGASE	55	1	NM_001042573	exon4	c.C516T	p.P172P	CATTCCCCCAGTG	.	PASS	Atlas-SNP
KIR3DL1	3811	hgsc.bcm.edu	37	19	55340906	55340906	+	Missense_Mutation	SNP	G	G	A	rs45542639	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	8	8	21	0	1	0	G|0.875;A|0.125	0.125	strong	KIR3DL1_ENST00000391728,NS,carcinoma,+1,1	KIR3DL1	174	1	NM_013289	exon7	c.G1091A	p.C364Y	TCTGGTGCTCCAA	.	PASS	Atlas-SNP
OR2G6	391211	hgsc.bcm.edu	37	1	248685719	248685719	+	Missense_Mutation	SNP	A	A	T	rs9330305	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	119	57	101	0	0.478992	0	A|0.832;T|0.168	0.168	strong	OR2G6,NS,carcinoma,0,1	OR2G6	124	1	NM_001013355	exon1	c.A772T	p.M258L	ATATTCATGTACC	.	PASS	Atlas-SNP
WDR25	79446	hgsc.bcm.edu	37	14	100847437	100847437	+	Missense_Mutation	SNP	A	A	G	rs2273801	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	40	85	0	0.540541	0	A|0.948;G|0.052	0.052	strong	.	WDR25	37	.	NM_001161476	exon2	c.A176G	p.K59R	TGCCCAAAGCAGG	.	PASS	Atlas-SNP
CEP170B	283638	hgsc.bcm.edu	37	14	105350178	105350178	+	Silent	SNP	C	C	T	rs45449696	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	35	13	54	0	0.371429	0	C|0.760;T|0.240	0.240	strong	.	.	.	.	NM_001112726	exon9	c.C1062T	p.H354H	CAAGCACGAGGAC	.	PASS	Atlas-SNP
COL6A1	1291	hgsc.bcm.edu	37	21	47423636	47423636	+	Silent	SNP	C	C	T	rs1053320	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	180	119	135	0	0.661111	0	C|0.700;T|0.300	0.300	strong	COL6A1,NS,carcinoma,0,1	COL6A1	101	1	NM_001848	exon35	c.C2796T	p.S932S	CTCGTCCGGCGCT	.	PASS	Atlas-SNP
ZNF577	84765	hgsc.bcm.edu	37	19	52375907	52375907	+	Silent	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	17	83	0	0.223684	0	.	.	none	ZNF577,colon,carcinoma,+1,1	ZNF577	63	1	NM_032679	exon7	c.A1336C	p.R446R	GATTTCTTGGAAA	.	PASS	Atlas-SNP
FANCI	55215	hgsc.bcm.edu	37	15	89858602	89858602	+	Silent	SNP	T	T	C	rs1138465	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82	30	124	0	0.365854	0	T|0.586;C|0.414	0.414	strong	.	FANCI	129	.	NM_001113378	exon37	c.T3906C	p.G1302G	GGATGGTGAAGAT	.	PASS	Atlas-SNP
HIST1H2AD	3013	hgsc.bcm.edu	37	6	26199193	26199193	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	164	31	182	0	0.189024	0	.	.	none	HIST1H2AD,NS,lymphoid_neoplasm,0,1	HIST1H2AD	20	1	NM_021065	exon1	c.G279A	p.E93E	GTTTAGCTCCTCG	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44	29	61	0	0.659091	0	G|0.663;T|0.337	0.337	strong	.	ALMS1	384	.	NM_015120	exon10	c.G8478T	p.R2826S	TACCAGGGCAAAT	.	PASS	Atlas-SNP
SPTBN5	51332	hgsc.bcm.edu	37	15	42150888	42150888	+	Missense_Mutation	SNP	G	G	A	rs890503	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	75	89	1	0.986842	0.011236	G|0.757;T|0.009	.	strong	SPTBN5,NS,carcinoma,0,3	SPTBN5	171	3	NM_016642	exon49	c.C8033T	p.T2678I	ATGGCTGTGTCCA	.	scavenged	Atlas-SNP
POTEC	388468	hgsc.bcm.edu	37	18	14542949	14542949	+	Missense_Mutation	SNP	T	T	C	rs9807555	bycluster;by2hit2allele;byhapmap	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	254	42	252	0	0.165354	0	T|1.000;|0.000	.	weak	POTEC,right_upper_lobe,carcinoma,+1,1	POTEC	129	1	NM_001137671	exon1	c.A197G	p.H66R	CAGTGGTGGCAAC	.	scavenged	Atlas-SNP
SAMD9	54809	hgsc.bcm.edu	37	7	92734051	92734051	+	Missense_Mutation	SNP	C	C	T	rs117649834	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	77	41	103	0	0.532468	0	C|0.965;T|0.035	0.035	strong	.	SAMD9	239	.	NM_001193307	exon2	c.G1360A	p.A454T	TGTAAGCTTTGAC	.	PASS	Atlas-SNP
WDPCP	51057	hgsc.bcm.edu	37	2	63660902	63660902	+	Missense_Mutation	SNP	C	C	T	rs17617459	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	17	53	0	0.269841	0	C|0.970;T|0.030	0.030	strong	.	WDPCP	79	.	NM_015910	exon9	c.G802A	p.G268S	CATAACCCAGGAG	.	PASS	Atlas-SNP
ASB10	136371	hgsc.bcm.edu	37	7	150873754	150873754	+	Missense_Mutation	SNP	G	G	A	rs62489646	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	137	68	126	0	0.49635	0	G|0.909;A|0.091	0.091	strong	.	ASB10	99	.	NM_001142459	exon4	c.C1114T	p.R372C	TCCAGCGCTCCAG	.	PASS	Atlas-SNP
HSPG2	3339	hgsc.bcm.edu	37	1	22154845	22154845	+	Silent	SNP	A	A	G	rs2228347	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73	39	76	0	0.534247	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
MYH4	4622	hgsc.bcm.edu	37	17	10348354	10348354	+	Missense_Mutation	SNP	T	T	C	rs2277649	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	157	69	159	0	0.43949	0	T|0.644;C|0.356	0.356	strong	.	MYH4	349	.	NM_017533	exon37	c.A5405G	p.D1802G	GCCTCATCCAGAC	.	PASS	Atlas-SNP
TAAR1	134864	hgsc.bcm.edu	37	6	132966279	132966279	+	Silent	SNP	T	T	C	rs8192620	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	164	88	189	0	0.536585	0	T|0.792;C|0.208	0.208	strong	.	TAAR1	41	.	NM_138327	exon1	c.A864G	p.V288V	AATCAATACATCA	.	PASS	Atlas-SNP
UNC13D	201294	hgsc.bcm.edu	37	17	73824121	73824121	+	Silent	SNP	T	T	C	rs7210574	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	178	177	191	0	0.994382	0	T|0.444;C|0.556	0.556	strong	.	UNC13D	68	.	NM_199242	exon32	c.A3198G	p.E1066E	CTGGGCTTCTCGG	.	PASS	Atlas-SNP
ANKRD61	100310846	hgsc.bcm.edu	37	7	6071115	6071115	+	Missense_Mutation	SNP	A	A	G	rs12334093	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	150	48	106	0	0.32	0	A|0.885;G|0.115	0.115	strong	.	.	.	.	NM_001271700	exon1	c.A109G	p.M37V	GCCATCATGAGAG	.	PASS	Atlas-SNP
EHBP1	23301	hgsc.bcm.edu	37	2	63176139	63176139	+	Missense_Mutation	SNP	A	A	C	rs17432615	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	173	172	198	0	0.99422	0	A|0.917;C|0.083	0.083	strong	.	EHBP1	127	.	NM_015252	exon14	c.A2263C	p.K755Q	ATCAAAAAAACAA	.	PASS	Atlas-SNP
LZTS1	11178	hgsc.bcm.edu	37	8	20110641	20110641	+	Silent	SNP	C	C	T	rs2645386	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	21	53	0	0.446809	0	C|0.631;T|0.369	0.369	strong	.	LZTS1	72	.	NM_021020	exon2	c.G801A	p.E267E	CTTCTGCTCCAGC	.	PASS	Atlas-SNP
MRPL38	64978	hgsc.bcm.edu	37	17	73900688	73900688	+	Silent	SNP	T	T	C	rs3744015	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	21	21	25	0	1	0	T|0.523;C|0.477	0.477	strong	.	MRPL38	26	.	NM_032478	exon2	c.A180G	p.R60R	CTCTGCTCGGCGC	.	PASS	Atlas-SNP
CDH2	1000	hgsc.bcm.edu	37	18	25543387	25543387	+	Silent	SNP	G	G	A	rs1041985	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	92	91	119	0	0.98913	0	G|0.706;A|0.294	0.294	strong	CDH2,colon,carcinoma,-2,2	CDH2	194	2	NM_001792	exon15	c.C2448T	p.A816A	GGGCTCGGCGTGG	.	PASS	Atlas-SNP
HDAC10	83933	hgsc.bcm.edu	37	22	50687595	50687595	+	Silent	SNP	A	A	G	rs75455741	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	138	64	123	0	0.463768	0	A|0.958;G|0.042	0.042	strong	.	HDAC10	29	.	NM_032019	exon8	c.T693C	p.V231V	CATCCCAACCTGG	.	PASS	Atlas-SNP
ABCA13	154664	hgsc.bcm.edu	37	7	48528923	48528923	+	Missense_Mutation	SNP	G	G	C	rs73694648	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	132	35	166	0	0.265152	0	G|0.951;C|0.049	0.049	strong	.	ABCA13	1192	.	NM_152701	exon48	c.G13273C	p.V4425L	CCTACTGTGGACT	.	PASS	Atlas-SNP
KIAA1984	84960	hgsc.bcm.edu	37	9	139693596	139693596	+	Missense_Mutation	SNP	T	T	C	rs945386	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	88	53	98	0	0.602273	0	T|0.759;C|0.241	0.241	strong	.	KIAA1984	39	.	NM_001039374	exon2	c.T113C	p.M38T	AGAATATGGACCA	.	PASS	Atlas-SNP
PLD1	5337	hgsc.bcm.edu	37	3	171404478	171404478	+	Missense_Mutation	SNP	C	C	A	rs2290480	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	154	154	171	0	1	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
PLEKHG1	57480	hgsc.bcm.edu	37	6	151152250	151152250	+	Missense_Mutation	SNP	A	A	G	rs148178393	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	35	55	0	0.492958	0	A|0.991;G|0.009	0.009	strong	.	PLEKHG1	97	.	NM_001029884	exon16	c.A2003G	p.D668G	ATGAGGACTTAAA	.	PASS	Atlas-SNP
C1orf172	126695	hgsc.bcm.edu	37	1	27278521	27278521	+	Silent	SNP	G	G	A	rs3010110	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	149	84	179	0	0.563758	0	G|0.848;A|0.152	0.152	strong	.	C1orf172	38	.	NM_152365	exon2	c.C351T	p.D117D	AGTGGAGTCCTCA	.	PASS	Atlas-SNP
SLC44A1	23446	hgsc.bcm.edu	37	9	108147763	108147763	+	Missense_Mutation	SNP	T	T	G	rs3199966	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	25	45	0	0.531915	0	T|0.803;G|0.197	0.197	strong	.	SLC44A1	61	.	NM_080546	exon15	c.T1930G	p.S644A	GCTGATTCCAGAG	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73	73	66	0	1	0	A|0.462;G|0.538	0.538	strong	.	ARHGAP42	32	.	NM_152432	exon20	c.A2004G	p.P668P	AACCCCATCATCT	.	PASS	Atlas-SNP
CYP2C19	1557	hgsc.bcm.edu	37	10	96602622	96602622	+	Silent	SNP	C	C	T	rs3758580	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	96	52	89	0	0.541667	0	C|0.826;T|0.174	0.174	strong	CYP2C19,colon,carcinoma,0,1	CYP2C19	88	1	NM_000769	exon7	c.C990T	p.V330V	ACGTGTCGTTGGC	.	PASS	Atlas-SNP
CCNL1	57018	hgsc.bcm.edu	37	3	156877707	156877707	+	Silent	SNP	A	A	T	rs9814142	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100	54	120	0	0.54	0	A|0.954;T|0.046	0.046	strong	CCNL1,NS,carcinoma,0,1	CCNL1	53	1	NM_020307	exon1	c.T177A	p.I59I	CTCCGGAATCAGA	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1080576	1080576	+	Silent	SNP	G	G	A	rs41349846	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	195	95	232	0	0.487179	0	G|0.804;A|0.196	0.196	strong	.	MUC2	614	.	NM_002457	exon9	c.G1218A	p.T406T	GAAGACGTACACC	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	50	27	53	0	0.54	0	G|0.519;N|0.001	0.519	strong	.	ZNF462	322	.	NM_021224	exon3	c.A5483G	p.N1828S	GAGGCAACTTTGA	.	PASS	Atlas-SNP
TUBA3E	112714	hgsc.bcm.edu	37	2	130951581	130951581	+	Silent	SNP	A	A	G	rs16848443	byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	108	21	160	0	0.194444	0	A|0.790;G|0.210	0.210	strong	.	TUBA3E	73	.	NM_207312	exon4	c.T834C	p.A278A	CTTCTCAGCTGAG	.	PASS	Atlas-SNP
GPR128	84873	hgsc.bcm.edu	37	3	100328750	100328750	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	254	113	225	0	0.444882	0	.	.	none	.	GPR128	126	.	NM_032787	exon1	c.G50A	p.C17Y	TCGTGTGTGGACT	.	PASS	Atlas-SNP
NBEA	26960	hgsc.bcm.edu	37	13	35692378	35692378	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	3	79	0	0.0394737	0	.	.	none	NBEA,NS,carcinoma,-1,1	NBEA	340	1	NM_015678	exon15	c.A2096C	p.K699T	GGGTCAAGGAAGA	.	scavenged	Atlas-SNP
PRPF4	9128	hgsc.bcm.edu	37	9	116044998	116044998	+	Silent	SNP	A	A	G	rs11552582	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	103	56	112	0	0.543689	0	A|0.602;G|0.398	0.398	strong	.	PRPF4	56	.	NM_004697	exon4	c.A468G	p.K156K	GTCTAAAAAGTCC	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1088835	1088835	+	Missense_Mutation	SNP	C	C	T	rs41389046	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	65	27	55	0	0.415385	0	C|0.932;T|0.068	0.068	strong	MUC2_ENST00000441003,colon,carcinoma,0,2	MUC2	614	2	NM_002457	exon26	c.C3620T	p.T1207I	AGGAGACCTGCAA	.	PASS	Atlas-SNP
ASCC2	84164	hgsc.bcm.edu	37	22	30189642	30189642	+	Missense_Mutation	SNP	C	C	T	rs61736786	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	59	30	36	0	0.508475	0	C|0.974;T|0.026	0.026	strong	.	ASCC2	53	.	NM_032204	exon16	c.G1712A	p.R571Q	AAACTCCGCGTGT	.	PASS	Atlas-SNP
OR5P2	120065	hgsc.bcm.edu	37	11	7817665	7817665	+	Silent	SNP	T	T	C	rs72484720	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	171	170	165	1	0.994152	0.00606061	T|0.738;C|0.262	0.262	strong	.	OR5P2	68	.	NM_153444	exon1	c.A825G	p.T275T	CACCACTGTGTAC	.	PASS	Atlas-SNP
RBMS1	5937	hgsc.bcm.edu	37	2	161174693	161174693	+	Silent	SNP	C	C	T	rs1430	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	30	21	66	3	0.7	0.0454545	C|0.733;T|0.267	0.267	strong	RBMS1_ENST00000348849,caecum,carcinoma,0,1	RBMS1	34	1	NM_016836	exon3	c.G297A	p.T99T	TTTGTTCGTTGTC	.	scavenged	Atlas-SNP
ACADSB	36	hgsc.bcm.edu	37	10	124806770	124806770	+	Missense_Mutation	SNP	A	A	G	rs1131430	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	26	54	0	0.553191	0	A|0.935;G|0.065	0.065	strong	.	ACADSB	45	.	NM_001609	exon8	c.A946G	p.I316V	CCATATATTAAAG	.	PASS	Atlas-SNP
ZP1	22917	hgsc.bcm.edu	37	11	60638461	60638461	+	Silent	SNP	C	C	T	rs10897122	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94	50	79	0	0.531915	0	C|0.776;N|0.000	.	strong	.	ZP1	69	.	NM_207341	exon5	c.C858T	p.F286F	CTACTTCGTCCTC	.	PASS	Atlas-SNP
COL20A1	57642	hgsc.bcm.edu	37	20	61943089	61943089	+	Missense_Mutation	SNP	G	G	A	rs6089877	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	30	48	0	0.491803	0	G|0.985;A|0.015	0.015	strong	.	COL20A1	137	.	NM_020882	exon13	c.G1652A	p.R551H	GCATCCGTGCCAG	.	PASS	Atlas-SNP
PRKAA1	5562	hgsc.bcm.edu	37	5	40798278	40798278	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	117	22	83	0	0.188034	0	.	.	none	.	PRKAA1	27	.	NM_006251	exon1	c.G14A	p.S5N	CAGGAACTGAGTC	.	PASS	Atlas-SNP
TSPYL5	85453	hgsc.bcm.edu	37	8	98289714	98289714	+	Missense_Mutation	SNP	G	G	C	rs2635164	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	43	74	0	0.511905	0	G|0.810;C|0.190	0.190	strong	.	TSPYL5	48	.	NM_033512	exon1	c.C359G	p.T120S	AAGACAGTGTCTG	.	PASS	Atlas-SNP
CXCR5	643	hgsc.bcm.edu	37	11	118765231	118765231	+	Silent	SNP	C	C	T	rs12795395	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	58	12	41	0	0.206897	0	C|0.980;T|0.020	0.020	strong	.	CXCR5	34	.	NM_001716	exon2	c.C978T	p.G326G	CGCCGGCGTGAAG	.	PASS	Atlas-SNP
ZNF205	7755	hgsc.bcm.edu	37	16	3165425	3165425	+	Missense_Mutation	SNP	A	A	G	rs909410	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85	85	96	0	1	0	A|0.601;G|0.399	0.399	strong	.	ZNF205	42	.	NM_003456	exon3	c.A127G	p.T43A	GGGGACACTCAGG	.	PASS	Atlas-SNP
ZNF485	220992	hgsc.bcm.edu	37	10	44104101	44104101	+	Missense_Mutation	SNP	C	C	T	rs45545532	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	220	111	222	0	0.504545	0	C|0.915;T|0.085	0.085	strong	.	ZNF485	102	.	NM_145312	exon3	c.C64T	p.R22W	TTTACCCGGATTG	.	PASS	Atlas-SNP
OR8B2	26595	hgsc.bcm.edu	37	11	124252417	124252417	+	Missense_Mutation	SNP	C	C	G	rs139038842	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	242	42	160	0	0.173554	0	C|0.997;G|0.003	0.003	strong	.	OR8B2	42	.	NM_001005468	exon1	c.G823C	p.V275L	AGAAAACAGAAGA	.	PASS	Atlas-SNP
CPO	130749	hgsc.bcm.edu	37	2	207824384	207824384	+	Missense_Mutation	SNP	T	T	G	rs11903403	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	178	84	186	0	0.47191	0	T|0.526;G|0.474	0.474	strong	CPO,NS,carcinoma,+2,1	CPO	42	1	NM_173077	exon5	c.T402G	p.S134R	CTCAAGTATACGC	.	PASS	Atlas-SNP
KRT6C	286887	hgsc.bcm.edu	37	12	52863038	52863038	+	Silent	SNP	G	G	A	rs410562	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80	25	79	0	0.3125	0	G|0.731;A|0.269	0.269	strong	.	KRT6C	55	.	NM_173086	exon9	c.C1503T	p.S501S	GACACCGCTGGCA	.	PASS	Atlas-SNP
GIMAP4	55303	hgsc.bcm.edu	37	7	150269542	150269542	+	Missense_Mutation	SNP	G	G	T	rs2293172	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	121	61	120	0	0.504132	0	G|0.866;T|0.134	0.134	strong	.	GIMAP4	61	.	NM_018326	exon3	c.G384T	p.E128D	CACTGAGGAAGAG	.	PASS	Atlas-SNP
DNAJA1	3301	hgsc.bcm.edu	37	9	33026572	33026572	+	Silent	SNP	T	T	C	rs20583	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	78	78	90	0	1	0	A|0.004;C|0.607	0.607	strong	.	DNAJA1	26	.	NM_001539	exon2	c.T90C	p.A30A	ACTGGCTTTGAAG	.	PASS	Atlas-SNP
CSPG4	1464	hgsc.bcm.edu	37	15	75982072	75982072	+	Missense_Mutation	SNP	G	G	A	rs77681934	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	149	16	123	0	0.107383	0	G|0.918;A|0.082	0.082	strong	CSPG4,NS,carcinoma,0,1	CSPG4	175	1	NM_001897	exon3	c.C1334T	p.A445V	AGCCAGGCTGTGC	.	PASS	Atlas-SNP
SPTA1	6708	hgsc.bcm.edu	37	1	158606449	158606449	+	Silent	SNP	G	G	T	rs3738791	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	112	61	87	0	0.544643	0	G|0.676;T|0.324	0.324	strong	.	SPTA1	720	.	NM_003126	exon37	c.C5292A	p.A1764A	CTCATGGGCCACC	.	PASS	Atlas-SNP
IL17RA	23765	hgsc.bcm.edu	37	22	17589567	17589567	+	Silent	SNP	C	C	T	rs879575	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	18	18	16	0	1	0	C|0.809;T|0.191	0.191	strong	.	IL17RA	62	.	NM_014339	exon13	c.C1458T	p.I486I	CATGATCCTCCCG	.	PASS	Atlas-SNP
SP140L	93349	hgsc.bcm.edu	37	2	231248261	231248261	+	Missense_Mutation	SNP	C	C	T	rs28497362	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	185	81	169	0	0.437838	0	C|0.819;T|0.181	0.181	strong	.	SP140L	68	.	NM_138402	exon8	c.C674T	p.T225M	TGGGAACGAGAAC	.	PASS	Atlas-SNP
ATXN1L	342371	hgsc.bcm.edu	37	16	71885423	71885423	+	Missense_Mutation	SNP	A	A	G	rs61747555	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	29	66	0	0.557692	0	A|0.828;G|0.172	0.172	strong	.	ATXN1L	18	.	NM_001137675	exon3	c.A1780G	p.S594G	CAGGCCAGCTGTG	.	PASS	Atlas-SNP
CCHCR1	54535	hgsc.bcm.edu	37	6	31116210	31116210	+	Silent	SNP	G	G	A	rs130071	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	144	115	99	0	0.798611	0	G|0.746;A|0.254	0.254	strong	.	CCHCR1	68	.	NM_001105564	exon10	c.C1552T	p.L518L	GCCTCAGCTGCTC	.	PASS	Atlas-SNP
VPS13C	54832	hgsc.bcm.edu	37	15	62223303	62223303	+	Missense_Mutation	SNP	C	C	G	rs78071599	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	29	68	0	0.460317	0	C|0.986;G|0.014	0.014	strong	.	VPS13C	506	.	NM_020821	exon50	c.G6024C	p.E2008D	TGCTCTCTCAATT	.	PASS	Atlas-SNP
ELF1	1997	hgsc.bcm.edu	37	13	41515118	41515118	+	Missense_Mutation	SNP	C	C	T	rs34905611	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	131	82	76	0	0.625954	0	C|0.989;T|0.011	0.011	strong	.	ELF1	65	.	NM_172373	exon8	c.G1195A	p.E399K	CTGCTTCTCCCTC	.	PASS	Atlas-SNP
PLP2	5355	hgsc.bcm.edu	37	X	49029758	49029758	+	Silent	SNP	G	G	A	rs145837656		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60	24	38	0	0.4	0	G|1.000;A|0.000	0.000	weak	.	PLP2	25	.	NM_002668	exon3	c.G273A	p.A91A	CATAGCGGCAATC	.	PASS	Atlas-SNP
LTA	4049	hgsc.bcm.edu	37	6	31540784	31540784	+	Missense_Mutation	SNP	C	C	A	rs1041981	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72	60	66	0	0.833333	0	C|0.603;A|0.397	0.397	strong	.	LTA	18	.	NM_001159740	exon3	c.C179A	p.T60N	ACAGCACCCTCAA	.	PASS	Atlas-SNP
MYBPC2	4606	hgsc.bcm.edu	37	19	50965272	50965272	+	Silent	SNP	T	T	C	rs25668	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	66	78	0	1	0	T|0.231;C|0.769	0.769	strong	.	MYBPC2	103	.	NM_004533	exon26	c.T3207C	p.C1069C	CAACTGTGCTGTC	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	17	10	11	0	0.588235	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
SCARF2	91179	hgsc.bcm.edu	37	22	20784050	20784050	+	Missense_Mutation	SNP	T	T	A	rs2241230	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	124	58	114	0	0.467742	0	T|0.861;A|0.139	0.139	strong	.	SCARF2	23	.	NM_182895	exon7	c.A1273T	p.T425S	CGCACGTGTCCTC	.	PASS	Atlas-SNP
GPRC5D	55507	hgsc.bcm.edu	37	12	13102605	13102605	+	Silent	SNP	G	G	A	rs4630382	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	102	51	93	0	0.5	0	G|0.739;A|0.261	0.261	strong	.	GPRC5D	23	.	NM_018654	exon1	c.C714T	p.D238D	CGGGTCGTCCCAC	.	PASS	Atlas-SNP
CCDC41	51134	hgsc.bcm.edu	37	12	94769769	94769769	+	Missense_Mutation	SNP	G	G	A	rs74340001	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	40	20	45	0	0.5	0	G|0.962;A|0.038	0.038	strong	.	CCDC41	59	.	NM_016122	exon8	c.C826T	p.R276W	CTGCCCGTAAATT	.	PASS	Atlas-SNP
CDHR4	389118	hgsc.bcm.edu	37	3	49836707	49836707	+	Silent	SNP	G	G	A	rs7629936	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	169	86	160	0	0.508876	0	G|0.775;A|0.225	0.225	strong	CDHR4,caecum,carcinoma,0,1	CDHR4	37	1	NM_001007540	exon2	c.C213T	p.A71A	CCACCTGGCCAAG	.	PASS	Atlas-SNP
LY6G5C	80741	hgsc.bcm.edu	37	6	31647044	31647044	+	Silent	SNP	A	A	G	rs143778717	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69	18	80	0	0.26087	0	A|0.999;G|0.001	0.001	strong	.	LY6G5C	8	.	NM_025262	exon2	c.T123C	p.G41G	AAACTTACCTAGA	.	PASS	Atlas-SNP
KIR3DL1	3811	hgsc.bcm.edu	37	19	55329854	55329854	+	Missense_Mutation	SNP	G	G	A	rs144994606	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	20	20	71	0	1	0	G|0.854;A|0.146	0.146	strong	.	KIR3DL1	174	.	NM_013289	exon3	c.G155A	p.R52H	ACTATCGTCATAG	.	PASS	Atlas-SNP
HLA-DOA	3111	hgsc.bcm.edu	37	6	32974934	32974934	+	Silent	SNP	G	G	A	rs378352	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	184	139	166	0	0.755435	0	G|0.833;A|0.167	0.167	strong	.	HLA-DOA	22	.	NM_002119	exon4	c.C672T	p.G224G	GGCCAGGCCCAGG	.	PASS	Atlas-SNP
C9orf114	51490	hgsc.bcm.edu	37	9	131585086	131585086	+	Silent	SNP	G	G	C	rs35677895	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	119	63	97	0	0.529412	0	G|0.990;C|0.010	0.010	strong	.	C9orf114	28	.	NM_016390	exon12	c.C1089G	p.A363A	CTGCAGGGCGGCC	.	PASS	Atlas-SNP
DHX33	56919	hgsc.bcm.edu	37	17	5364393	5364393	+	Missense_Mutation	SNP	A	A	G	rs141223137	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	70	28	61	0	0.4	0	A|0.996;G|0.004	0.004	strong	DHX33,NS,carcinoma,+2,3	DHX33	41	3	NM_020162	exon4	c.T715C	p.F239L	GAGAGAACAGGTC	.	PASS	Atlas-SNP
PKD1L1	168507	hgsc.bcm.edu	37	7	47851623	47851623	+	Missense_Mutation	SNP	C	C	T	rs73692834	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60	49	69	0	0.816667	0	C|0.871;T|0.129	0.129	strong	.	PKD1L1	328	.	NM_138295	exon50	c.G7373A	p.R2458Q	CTGAGTCGGGACA	.	PASS	Atlas-SNP
PARVB	29780	hgsc.bcm.edu	37	22	44489868	44489868	+	Missense_Mutation	SNP	T	T	C	rs1983609	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	47	62	0	1	0	T|0.150;C|0.850	0.850	strong	.	PARVB	44	.	NM_001003828	exon3	c.T272C	p.V91A	CCCTGGTGGATGT	.	PASS	Atlas-SNP
SLC22A15	55356	hgsc.bcm.edu	37	1	116609185	116609185	+	Silent	SNP	G	G	A	rs3748742	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	106	42	96	0	0.396226	0	G|0.891;A|0.109	0.109	strong	.	SLC22A15	65	.	NM_018420	exon11	c.G1410A	p.T470T	AGCCACGGGTCTG	.	PASS	Atlas-SNP
GRM1	2911	hgsc.bcm.edu	37	6	146755140	146755140	+	Silent	SNP	G	G	A	rs2942	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	45	17	51	0	0.377778	0	G|0.481;A|0.519	0.519	strong	.	GRM1	419	.	NM_000838	exon9	c.G2793A	p.K931K	CATCAAGCCCCTC	.	PASS	Atlas-SNP
DSC3	1825	hgsc.bcm.edu	37	18	28574150	28574150	+	Silent	SNP	T	T	C	rs114143100	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	182	83	192	0	0.456044	0	T|0.989;C|0.011	0.011	strong	.	DSC3	225	.	NM_001941	exon16	c.A2682G	p.T894T	TCTCTTTGTGCAT	.	PASS	Atlas-SNP
SPATA31D1	389763	hgsc.bcm.edu	37	9	84610059	84610059	+	Silent	SNP	T	T	C	rs200816660	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	18	11	29	0	0.611111	0	T|0.999;C|0.001	0.001	strong	.	.	.	.	NM_001001670	exon4	c.T4674C	p.T1558T	CCTAACTGGACAG	.	PASS	Atlas-SNP
CSPG4	1464	hgsc.bcm.edu	37	15	75982239	75982239	+	Silent	SNP	G	G	A	rs148229217	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83	35	95	0	0.421687	0	G|0.899;A|0.101	0.101	strong	CSPG4,NS,carcinoma,0,2	CSPG4	175	2	NM_001897	exon3	c.C1167T	p.D389D	GGCATCGTCCTCA	.	PASS	Atlas-SNP
MDN1	23195	hgsc.bcm.edu	37	6	90390443	90390443	+	Missense_Mutation	SNP	C	C	A	rs9353689	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	41	18	29	0	0.439024	0	C|0.413;A|0.587	0.587	strong	.	MDN1	478	.	NM_014611	exon74	c.G12130T	p.A4044S	GAGCAGCGCCCTG	.	PASS	Atlas-SNP
ZC3H3	23144	hgsc.bcm.edu	37	8	144620183	144620183	+	Missense_Mutation	SNP	T	T	C	rs4874147	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	79	34	90	0	0.43038	0	T|0.251;C|0.749	0.749	strong	.	ZC3H3	75	.	NM_015117	exon2	c.A1354G	p.S452G	TGCTGCTGCGTCT	.	PASS	Atlas-SNP
ARHGEF28	64283	hgsc.bcm.edu	37	5	73090261	73090261	+	Silent	SNP	T	T	C	rs7716253	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	52	79	0	0.597701	0	T|0.404;C|0.596	0.596	strong	.	.	.	.	NM_001080479	exon8	c.T945C	p.A315A	AGCAGCTGAAAAG	.	PASS	Atlas-SNP
DYNC1H1	1778	hgsc.bcm.edu	37	14	102446161	102446161	+	Silent	SNP	G	G	A	rs3818188	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	135	50	106	0	0.37037	0	G|0.812;A|0.188	0.188	strong	.	DYNC1H1	395	.	NM_001376	exon4	c.G624A	p.P208P	CCTGCCGATTCAT	.	PASS	Atlas-SNP
LIPI	149998	hgsc.bcm.edu	37	21	15558346	15558346	+	Silent	SNP	G	G	A	rs397517	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83	37	35	0	0.445783	0	G|0.827;A|0.173	0.173	strong	.	LIPI	95	.	NM_198996	exon3	c.C540T	p.S180S	CCCTAAGCTCACA	.	PASS	Atlas-SNP
LCA5L	150082	hgsc.bcm.edu	37	21	40778182	40778182	+	Missense_Mutation	SNP	C	C	T	rs11558767	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	206	69	167	2	0.334951	0.011976	C|0.932;T|0.068	0.068	strong	LCA5L,NS,carcinoma,+2,2	LCA5L	57	2	NM_152505	exon10	c.G1639A	p.G547S	TGTTGCCGGCATT	.	scavenged	Atlas-SNP
CHRNB3	1142	hgsc.bcm.edu	37	8	42587065	42587065	+	Silent	SNP	C	C	T	rs4952	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	101	53	99	0	0.524752	0	C|0.968;T|0.032	0.032	strong	.	CHRNB3	74	.	NM_000749	exon5	c.C615T	p.N205N	ACTGAACGCAAAG	.	PASS	Atlas-SNP
NRP1	8829	hgsc.bcm.edu	37	10	33469181	33469181	+	Silent	SNP	A	A	G	rs1048804	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	244	123	217	3	0.504098	0.0138249	A|0.634;G|0.366	0.366	strong	NRP1,NS,carcinoma,0,1	NRP1	126	1	NM_003873	exon17	c.T2595C	p.S865S	CAGGGCACTCATG	.	scavenged	Atlas-SNP
PAMR1	25891	hgsc.bcm.edu	37	11	35492351	35492351	+	Silent	SNP	G	G	A	rs16927500	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83	37	102	0	0.445783	0	G|0.906;A|0.094	0.094	strong	.	PAMR1	85	.	NM_001001991	exon5	c.C510T	p.S170S	CTCCAGGCTCAAC	.	PASS	Atlas-SNP
TH	7054	hgsc.bcm.edu	37	11	2190951	2190951	+	Missense_Mutation	SNP	C	C	T	rs6356	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	117	54	141	0	0.461538	0	C|0.652;T|0.348	0.348	strong	.	TH	43	.	NM_199292	exon3	c.G334A	p.V112M	TTAGCACGGCCTT	.	PASS	Atlas-SNP
TRIM65	201292	hgsc.bcm.edu	37	17	73888423	73888423	+	Silent	SNP	A	A	G	rs7222755	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	41	41	31	0	1	0	A|0.591;G|0.409	0.409	strong	.	TRIM65	23	.	NM_001256124	exon3	c.T669C	p.H223H	CTCCAAATGGACC	.	PASS	Atlas-SNP
ZBTB7C	201501	hgsc.bcm.edu	37	18	45555829	45555829	+	Silent	SNP	T	T	C	rs7231151	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	25	8	29	0	0.32	0	T|0.652;C|0.348	0.348	strong	.	ZBTB7C	73	.	NM_001039360	exon3	c.A1662G	p.T554T	CATCTGTGTCTCC	.	PASS	Atlas-SNP
DUSP8	1850	hgsc.bcm.edu	37	11	1580172	1580172	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	121	34	119	0	0.280992	0	.	.	none	.	DUSP8	22	.	NM_004420	exon4	c.A484T	p.T162S	TGCGGGTCAGGCC	.	PASS	Atlas-SNP
KCNQ4	9132	hgsc.bcm.edu	37	1	41285553	41285553	+	Silent	SNP	T	T	C	rs55737429	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	154	86	183	0	0.558442	0	T|0.959;C|0.041	0.041	strong	.	KCNQ4	58	.	NM_004700	exon6	c.T841C	p.L281L	ATTACATTGACAA	.	PASS	Atlas-SNP
COL11A2	1302	hgsc.bcm.edu	37	6	33144243	33144243	+	Silent	SNP	T	T	A	rs1799908	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	78	14	71	0	0.179487	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
VPS13C	54832	hgsc.bcm.edu	37	15	62202482	62202482	+	Missense_Mutation	SNP	C	C	T	rs10851704	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	38	38	56	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
ZNF407	55628	hgsc.bcm.edu	37	18	72344238	72344238	+	Silent	SNP	C	C	T	rs17817969	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	33	82	0	0.44	0	C|0.907;T|0.093	0.093	strong	.	ZNF407	231	.	NM_001146190	exon1	c.C1263T	p.L421L	TATTCTCGTGTTG	.	PASS	Atlas-SNP
DDX20	11218	hgsc.bcm.edu	37	1	112308953	112308953	+	Missense_Mutation	SNP	T	T	C	rs197412	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55	23	75	0	0.418182	0	C|0.483;N|0.000	0.483	strong	DDX20,NS,carcinoma,+1,1	DDX20	50	1	NM_007204	exon11	c.T1907C	p.I636T	AAGTTATTGAACA	.	PASS	Atlas-SNP
NLRC5	84166	hgsc.bcm.edu	37	16	57111232	57111232	+	Silent	SNP	C	C	T	rs11864231	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	46	117	0	0.528736	0	C|0.819;T|0.181	0.181	strong	.	NLRC5	186	.	NM_032206	exon40	c.C4860T	p.D1620D	TGGAGACGCTGGT	.	PASS	Atlas-SNP
CD276	80381	hgsc.bcm.edu	37	15	74000729	74000729	+	Silent	SNP	G	G	C	rs2291012	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	38	54	0	0.452381	0	G|0.817;C|0.183	0.183	strong	.	CD276	29	.	NM_001024736	exon7	c.G1419C	p.L473L	GGGGCTGTCTGTC	.	PASS	Atlas-SNP
PCDHB6	56130	hgsc.bcm.edu	37	5	140530852	140530852	+	Silent	SNP	G	G	C	rs246708	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	142	81	197	0	0.570423	0	G|0.747;C|0.253	0.253	strong	PCDHB6,NS,carcinoma,+2,1	PCDHB6	161	1	NM_018939	exon1	c.G1014C	p.V338V	GGACGTGAATGAC	.	PASS	Atlas-SNP
EGFR	1956	hgsc.bcm.edu	37	7	55238874	55238874	+	Silent	SNP	T	T	A	rs2227984	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	40	14	59	0	0.35	0	T|0.645;A|0.355	0.355	strong	.	EGFR	20426	.	NM_005228	exon16	c.T1887A	p.T629T	ATGCACTGGGCCA	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	90	88	80	0	0.977778	0	C|0.801;T|0.199	0.199	strong	.	ALLC	61	.	NM_018436	exon6	c.C329T	p.T110I	GAGGAACCAGGAC	.	PASS	Atlas-SNP
CDKL5	6792	hgsc.bcm.edu	37	X	18638082	18638082	+	Missense_Mutation	SNP	A	A	C	rs35478150	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	25	30	0	0.531915	0	A|0.976;C|0.024	0.024	strong	.	CDKL5	124	.	NM_003159	exon16	c.A2372C	p.Q791P	AATCTCAAACAGT	.	PASS	Atlas-SNP
SIRPD	128646	hgsc.bcm.edu	37	20	1538266	1538266	+	Silent	SNP	G	G	A	rs11697395	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68	32	83	0	0.470588	0	G|0.853;A|0.147	0.147	strong	.	SIRPD	34	.	NM_178460	exon1	c.C34T	p.L12L	AAGGCAGAGGTGG	.	PASS	Atlas-SNP
CYP26A1	1592	hgsc.bcm.edu	37	10	94835624	94835624	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94	4	75	0	0.0425532	0	.	.	none	.	CYP26A1	59	.	NM_000783	exon5	c.C906T	p.H302H	AGGACACGAAACC	.	PASS	Atlas-SNP
POLE	5426	hgsc.bcm.edu	37	12	133219831	133219831	+	Silent	SNP	T	T	C	rs5744944	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	63	63	64	0	1	0	T|0.448;C|0.552	0.552	strong	.	POLE	416	.	NM_006231	exon35	c.A4530G	p.A1510A	GACGGATGCCCTG	.	PASS	Atlas-SNP
TNK2	10188	hgsc.bcm.edu	37	3	195594931	195594931	+	Silent	SNP	C	C	T	rs200272067	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	45	21	50	0	0.466667	0	C|0.997;T|0.003	0.003	strong	.	TNK2	246	.	NM_001010938	exon13	c.G2427A	p.P809P	ACCCCCCGGGCTG	.	PASS	Atlas-SNP
ITGB4	3691	hgsc.bcm.edu	37	17	73750859	73750859	+	Silent	SNP	C	C	G	rs8669	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	137	136	129	0	0.992701	0	C|0.640;G|0.360	0.360	strong	.	ITGB4	165	.	NM_000213	exon34	c.C4521G	p.P1507P	ACTGCCCAGGGAC	.	PASS	Atlas-SNP
AQP10	89872	hgsc.bcm.edu	37	1	154293675	154293675	+	Missense_Mutation	SNP	G	G	A	rs6668968	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	41	15	46	0	0.365854	0	G|0.718;A|0.282	0.282	strong	.	AQP10	44	.	NM_080429	exon1	c.G44A	p.R15Q	ACCTCCGGATACG	.	PASS	Atlas-SNP
TMPRSS15	5651	hgsc.bcm.edu	37	21	19704490	19704490	+	Missense_Mutation	SNP	G	G	A	rs146718638	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	36	62	0	0.428571	0	G|1.000;A|0.000	0.000	weak	.	TMPRSS15	189	.	NM_002772	exon14	c.C1565T	p.T522M	CAGTCCGCTGAAA	.	PASS	Atlas-SNP
CHMP1A	5119	hgsc.bcm.edu	37	16	89715813	89715813	+	Missense_Mutation	SNP	C	C	T	rs201479143	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80	44	92	0	0.55	0	C|0.999;T|0.001	0.001	strong	.	CHMP1A	15	.	NM_001083314	exon3	c.G178A	p.V60I	GCGGGACGCCATC	.	PASS	Atlas-SNP
ADAMTS14	140766	hgsc.bcm.edu	37	10	72513682	72513682	+	Silent	SNP	C	C	T	rs2587475	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	33	10	39	0	0.30303	0	C|0.469;T|0.531	0.531	strong	.	ADAMTS14	148	.	NM_139155	exon19	c.C2865T	p.C955C	AGCCTGCGCCGGG	.	PASS	Atlas-SNP
KCNQ2	3785	hgsc.bcm.edu	37	20	62038277	62038277	+	Missense_Mutation	SNP	T	T	G	rs1801475	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	29	11	20	0	0.37931	0	T|0.412;G|0.578	0.578	strong	.	KCNQ2	201	.	NM_172107	exon17	c.A2339C	p.N780T	CGCAGGTTCCCCT	.	PASS	Atlas-SNP
TNMD	64102	hgsc.bcm.edu	37	X	99849017	99849017	+	Silent	SNP	G	G	A	rs2073162	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	207	135	140	0	0.652174	0	0|0.015;A|0.433	0.433	strong	.	TNMD	40	.	NM_022144	exon3	c.G306A	p.V102V	GGAAGTGCACGAC	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55	25	57	0	0.454545	0	T|0.505;C|0.495	0.495	strong	.	SETX	234	.	NM_015046	exon26	c.A7759G	p.I2587V	GCTGTATATGGCT	.	PASS	Atlas-SNP
HIST1H2AI	8329	hgsc.bcm.edu	37	6	27776002	27776002	+	Silent	SNP	C	C	T	rs493283	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	214	42	184	0	0.196262	0	C|0.988;T|0.012	0.012	strong	.	HIST1H2AI	9	.	NM_003509	exon1	c.C15T	p.G5G	GCGTGGCAAGCAG	.	PASS	Atlas-SNP
TENC1	23371	hgsc.bcm.edu	37	12	53442956	53442956	+	Missense_Mutation	SNP	G	G	C	rs12369033	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	39	22	38	0	0.564103	0	G|0.494;C|0.506	0.506	strong	.	TENC1	148	.	NM_015319	exon1	c.G29C	p.R10T	TTGGGAGGGGGGA	.	PASS	Atlas-SNP
GJA9	81025	hgsc.bcm.edu	37	1	39340862	39340862	+	Silent	SNP	A	A	G	rs874243	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	231	114	199	0	0.493506	0	G|0.140;N|0.000	0.140	strong	.	GJA9	55	.	NM_030772	exon2	c.T909C	p.S303S	TACAGAAGATGAA	.	PASS	Atlas-SNP
CDC27	996	hgsc.bcm.edu	37	17	45214643	45214643	+	Silent	SNP	A	A	T	rs138020641		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	18	6	10	0	0.333333	0	.	.	weak	.	CDC27	337	.	NM_001114091	exon14	c.T1806A	p.V602V	TGGATCAACTTGG	.	PASS	Atlas-SNP
SCAF8	22828	hgsc.bcm.edu	37	6	155114112	155114112	+	Splice_Site	SNP	T	T	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	26	84	0	0.42623	0	.	.	none	.	SCAF8	122	.	NM_014892	exon5	c.475+2T>A	.	TCCAGGTATGTTG	.	PASS	Atlas-SNP
KRTAP9-2	83899	hgsc.bcm.edu	37	17	39383217	39383217	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	132	42	148	0	0.318182	0	.	.	none	.	KRTAP9-2	24	.	NM_031961	exon1	c.G311A	p.S104N	GGTCCAGCTGTGG	.	PASS	Atlas-SNP
DNMT3L	29947	hgsc.bcm.edu	37	21	45670790	45670790	+	Missense_Mutation	SNP	C	C	T	rs113593938	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	159	88	110	0	0.553459	0	C|0.996;T|0.004	0.004	strong	.	DNMT3L	33	.	NM_013369	exon10	c.G812A	p.R271Q	TTGGGCCGTGCGT	.	PASS	Atlas-SNP
MAML2	84441	hgsc.bcm.edu	37	11	95713077	95713077	+	Missense_Mutation	SNP	C	C	T	rs34520053	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	191	37	149	0	0.193717	0	C|0.986;T|0.014	0.014	strong	.	MAML2	94	.	NM_032427	exon5	c.G2506A	p.V836I	TTGAAACTGGGTT	.	PASS	Atlas-SNP
KRTAP19-8	728299	hgsc.bcm.edu	37	21	32410600	32410600	+	Missense_Mutation	SNP	C	C	T	rs200348786	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	106	2	53	0	0.0188679	0	.	.	weak	KRTAP19-8,caecum,carcinoma,0,1	KRTAP19-8	9	1	NM_001099219	exon1	c.G163A	p.G55R	ATCCTCCGTAGTA	.	scavenged	Atlas-SNP
KRT32	3882	hgsc.bcm.edu	37	17	39616453	39616453	+	Missense_Mutation	SNP	G	G	A	rs146527191	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	149	71	130	0	0.47651	0	G|0.999;A|0.001	0.001	strong	.	KRT32	57	.	NM_002278	exon7	c.C1256T	p.T419I	ACACAGGTGGTGC	.	PASS	Atlas-SNP
IQSEC1	9922	hgsc.bcm.edu	37	3	12962074	12962074	+	Missense_Mutation	SNP	G	G	A	rs35319679	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	109	50	101	0	0.458716	0	G|0.898;A|0.102	0.102	strong	.	IQSEC1	88	.	NM_014869	exon6	c.C1918T	p.P640S	CCCCAGGGTTGCA	.	PASS	Atlas-SNP
SERPINA10	51156	hgsc.bcm.edu	37	14	94750408	94750408	+	Missense_Mutation	SNP	A	A	C	rs117152910	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	42	60	0	0.488372	0	A|0.993;C|0.007	0.007	strong	SERPINA10,caecum,carcinoma,+1,1	SERPINA10	83	1	NM_001100607	exon5	c.T1229G	p.M410R	GGAGGCATGGAAT	.	PASS	Atlas-SNP
CRMP1	1400	hgsc.bcm.edu	37	4	5841350	5841350	+	Silent	SNP	A	A	G	rs16837723	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	33	11	37	0	0.333333	0	A|0.731;G|0.269	0.269	strong	.	CRMP1	118	.	NM_001014809	exon9	c.T1209C	p.H403H	CCAGTAATGGGTG	.	PASS	Atlas-SNP
PSMA6	5687	hgsc.bcm.edu	37	14	35783656	35783656	+	Silent	SNP	A	A	G	rs13393	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	222	101	245	0	0.454955	0	A|0.955;G|0.045	0.045	strong	.	PSMA6	18	.	NM_002791	exon6	c.A678G	p.K226K	TCCTAAATTCAGG	.	PASS	Atlas-SNP
FAM131C	348487	hgsc.bcm.edu	37	1	16385131	16385131	+	Missense_Mutation	SNP	C	C	A	rs1832151	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	452	236	339	0	0.522124	0	C|0.837;A|0.163	0.163	strong	.	FAM131C	21	.	NM_182623	exon7	c.G644T	p.S215I	GAGGGGCTGGGCG	.	PASS	Atlas-SNP
HMCN1	83872	hgsc.bcm.edu	37	1	186031041	186031041	+	Silent	SNP	C	C	T	rs7522627	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	30	65	0	0.344828	0	C|0.372;T|0.628	0.628	strong	.	HMCN1	797	.	NM_031935	exon47	c.C7371T	p.C2457C	TACTTGCGTTGTA	.	PASS	Atlas-SNP
OR52E8	390079	hgsc.bcm.edu	37	11	5877979	5877979	+	Missense_Mutation	SNP	T	T	A	rs12419602	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	99	40	73	0	0.40404	0	T|0.599;A|0.401	0.401	strong	.	OR52E8	54	.	NM_001005168	exon1	c.A954T	p.X318Y	AACTGGTTAGTGA	.	PASS	Atlas-SNP
SALL1	6299	hgsc.bcm.edu	37	16	51172677	51172677	+	Silent	SNP	G	G	A	rs11645288	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	148	73	141	0	0.493243	0	G|0.822;A|0.178	0.178	strong	.	SALL1	301	.	NM_002968	exon2	c.C3456T	p.H1152H	TCTCTCGTGAATC	.	PASS	Atlas-SNP
RABEP1	9135	hgsc.bcm.edu	37	17	5284698	5284698	+	Silent	SNP	A	A	G	rs1143206	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69	32	60	0	0.463768	0	A|0.519;G|0.481	0.481	strong	.	RABEP1	59	.	NM_004703	exon17	c.A2385G	p.Q795Q	TGAACAACTAATG	.	PASS	Atlas-SNP
HDX	139324	hgsc.bcm.edu	37	X	83723541	83723541	+	Missense_Mutation	SNP	A	A	G	rs35161124	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	142	104	87	0	0.732394	0	A|0.879;G|0.121	0.121	strong	.	HDX	124	.	NM_144657	exon3	c.T1190C	p.F397S	GGAGAAAAATTAC	.	PASS	Atlas-SNP
MATN4	8785	hgsc.bcm.edu	37	20	43926573	43926573	+	Missense_Mutation	SNP	C	C	T	rs2227275	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	78	44	78	0	0.564103	0	C|0.757;T|0.243	0.243	strong	.	MATN4	57	.	NM_003833	exon8	c.G1564A	p.G522S	TGCTGCCTCTGAG	.	PASS	Atlas-SNP
CYP2D6	1565	hgsc.bcm.edu	37	22	42523558	42523558	+	Missense_Mutation	SNP	T	T	C	rs202102799	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	193	7	224	4	0.0362694	0.0178571	T|0.999;C|0.001	0.001	weak	CYP2D6_ENST00000360608,NS,carcinoma,0,2	CYP2D6	104	2	NM_000106	exon7	c.A1064G	p.Y355C	GTGGTGTAGGGCA	.	scavenged	Atlas-SNP
CABP5	56344	hgsc.bcm.edu	37	19	48537585	48537585	+	Missense_Mutation	SNP	A	A	G	rs3745746	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	65	31	68	0	0.476923	0	G|0.275;N|0.000	0.275	strong	.	CABP5	28	.	NM_019855	exon5	c.T383C	p.V128A	AGCTCCACCAGGG	.	PASS	Atlas-SNP
BDKRB2	624	hgsc.bcm.edu	37	14	96707457	96707457	+	Silent	SNP	A	A	G	rs5224	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	59	59	54	0	1	0	A|0.123;G|0.877	0.877	strong	BDKRB2,NS,carcinoma,+1,1	BDKRB2	56	1	NM_000623	exon3	c.A792G	p.T264T	CCAGACAGAGAGG	.	PASS	Atlas-SNP
ADAMTS7	11173	hgsc.bcm.edu	37	15	79067063	79067063	+	Silent	SNP	A	A	G	rs117662146	byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72	10	96	2	0.138889	0.0208333	A|0.998;G|0.002	0.002	strong	ADAMTS7,NS,carcinoma,0,2	ADAMTS7	142	2	NM_014272	exon12	c.T1779C	p.P593P	GCCAGCAGGGCAG	.	scavenged	Atlas-SNP
SUN2	25777	hgsc.bcm.edu	37	22	39134207	39134207	+	Missense_Mutation	SNP	C	C	T	rs2072797	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	85	42	68	1	0.494118	0.0147059	C|0.906;T|0.094	0.094	strong	SUN2,NS,carcinoma,0,1	SUN2	59	1	NM_001199579	exon17	c.G2074A	p.G692S	GCTCGCCGTCCTG	.	scavenged	Atlas-SNP
COG5	10466	hgsc.bcm.edu	37	7	106897237	106897237	+	Silent	SNP	A	A	C	rs17349904	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	32	67	0	0.680851	0	A|0.851;C|0.149	0.149	strong	.	COG5	78	.	NM_006348	exon16	c.T1782G	p.V594V	GGAAACAACCTAG	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9066874	9066874	+	Missense_Mutation	SNP	G	G	T	rs12609150	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	322	159	321	1	0.493789	0.00311526	G|0.786;T|0.214	0.214	strong	.	MUC16	4315	.	NM_024690	exon3	c.C20572A	p.P6858T	AATTTGGAGGTGA	.	PASS	Atlas-SNP
ACAT2	39	hgsc.bcm.edu	37	6	160196343	160196343	+	Missense_Mutation	SNP	A	A	G	rs25683	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	40	40	62	0	1	0	A|0.593;G|0.407	0.407	strong	.	ACAT2	32	.	NM_005891	exon5	c.A632G	p.K211R	CTAGAAAAGGTGA	.	PASS	Atlas-SNP
ZNF639	51193	hgsc.bcm.edu	37	3	179051472	179051472	+	Silent	SNP	A	A	G	rs35983049	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68	27	80	0	0.397059	0	A|0.877;G|0.123	0.123	strong	.	ZNF639	45	.	NM_016331	exon7	c.A720G	p.E240E	CAAGGAAAGTTTC	.	PASS	Atlas-SNP
GALNT4	8693	hgsc.bcm.edu	37	12	89917037	89917037	+	Silent	SNP	G	G	A	rs2230282	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	30	65	0	0.422535	0	G|0.924;A|0.076	0.076	strong	.	GALNT4	38	.	NM_003774	exon1	c.C1290T	p.N430N	AAAAACGTTTTTC	.	PASS	Atlas-SNP
FDFT1	2222	hgsc.bcm.edu	37	8	11689119	11689119	+	Silent	SNP	G	G	C	rs9205	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	42	94	0	0.482759	0	G|0.773;C|0.227	0.227	strong	.	FDFT1	25	.	NM_004462	exon7	c.G972C	p.L324L	GACCCTGATGATG	.	PASS	Atlas-SNP
SFSWAP	6433	hgsc.bcm.edu	37	12	132241162	132241162	+	Missense_Mutation	SNP	A	A	G	rs145713017	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	34	16	31	0	0.470588	0	A|0.997;G|0.003	0.003	strong	.	SFSWAP	69	.	NM_001261411	exon11	c.A1693G	p.T565A	AGTAAGACCGTCC	.	PASS	Atlas-SNP
IFNB1	3456	hgsc.bcm.edu	37	9	21077716	21077716	+	Silent	SNP	G	G	A	rs1051922	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	113	60	94	0	0.530973	0	G|0.656;N|0.000	.	strong	.	IFNB1	33	.	NM_002176	exon1	c.C153T	p.Y51Y	GAGGCAGTATTCA	.	PASS	Atlas-SNP
STK32A	202374	hgsc.bcm.edu	37	5	146619206	146619206	+	Silent	SNP	G	G	C	rs4705132	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	102	53	147	0	0.519608	0	G|0.476;C|0.523	0.523	strong	.	STK32A	54	.	NM_145001	exon2	c.G9C	p.A3A	GGGAGCGAACACT	.	PASS	Atlas-SNP
ARHGEF28	64283	hgsc.bcm.edu	37	5	73144845	73144845	+	Silent	SNP	A	A	G	rs2973568	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	36	79	0	0.48	0	A|0.346;G|0.654	0.654	strong	NP_001073948_1,NS,carcinoma,+1,2	.	.	2	NM_001080479	exon13	c.A1680G	p.S560S	TTGCTCATCACCC	.	PASS	Atlas-SNP
SERPINA1	5265	hgsc.bcm.edu	37	14	94849201	94849201	+	Missense_Mutation	SNP	C	C	T	rs709932	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	22	57	0	0.360656	0	T|0.129;G|0.004	0.129	strong	.	SERPINA1	51	.	NM_001127701	exon4	c.G374A	p.R125H	AGGGTACGGAGGA	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	150	60	161	0	0.4	0	G|0.555;A|0.445	0.445	strong	.	TTC21A	96	.	NM_145755	exon8	c.G869A	p.R290K	AGACAAGGGAACC	.	PASS	Atlas-SNP
SCG2	7857	hgsc.bcm.edu	37	2	224463164	224463164	+	Silent	SNP	G	G	A	rs16864975	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	219	105	210	0	0.479452	0	G|0.956;A|0.044	0.044	strong	.	SCG2	99	.	NM_003469	exon2	c.C837T	p.N279N	CTCATCGTTGATT	.	PASS	Atlas-SNP
WT1	7490	hgsc.bcm.edu	37	11	32417945	32417945	+	Silent	SNP	T	T	C	rs16754	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	40	18	39	0	0.45	0	T|0.782;C|0.218	0.218	strong	WT1_ENST00000379079,colon,carcinoma,0,7	WT1	744	7	NM_024424	exon7	c.A1107G	p.R369R	CACACGTCGCACA	.	PASS	Atlas-SNP
OR1S1	219959	hgsc.bcm.edu	37	11	57982763	57982763	+	Missense_Mutation	SNP	A	A	G	rs61763008	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	62	193	0	1	0	A|0.671;G|0.329	0.329	strong	OR1S1,NS,carcinoma,0,2	OR1S1	139	2	NM_001004458	exon1	c.A547G	p.N183D	TTCTGTAACCACA	.	PASS	Atlas-SNP
GPR20	2843	hgsc.bcm.edu	37	8	142367087	142367087	+	Missense_Mutation	SNP	C	C	T	rs34591516	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80	36	103	0	0.45	0	C|0.934;T|0.066	0.066	strong	.	GPR20	43	.	NM_005293	exon2	c.G937A	p.G313S	GCTGGCCGAAGAG	.	PASS	Atlas-SNP
RNMTL1	55178	hgsc.bcm.edu	37	17	685640	685640	+	Missense_Mutation	SNP	G	G	T	rs2273454	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	18	12	34	0	0.666667	0	G|0.803;T|0.197	0.197	strong	RNMTL1,NS,carcinoma,-1,1	RNMTL1	25	1	NM_018146	exon1	c.G22T	p.A8S	AGACCCGCGAGGT	.	PASS	Atlas-SNP
MTHFR	4524	hgsc.bcm.edu	37	1	11854476	11854476	+	Missense_Mutation	SNP	T	T	G	rs1801131	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	65	77	0	0.984848	0	T|0.722;G|0.238	0.238	strong	.	MTHFR	65	.	NM_005957	exon8	c.A1286C	p.E429A	ACACTTTCTTCAC	.	PASS	Atlas-SNP
DMRT3	58524	hgsc.bcm.edu	37	9	990235	990235	+	Missense_Mutation	SNP	C	C	T	rs61737966	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	29	16	35	0	0.551724	0	C|0.995;T|0.005	0.005	strong	.	DMRT3	83	.	NM_021240	exon2	c.C649T	p.R217C	GAGAGCCGCCCTG	.	PASS	Atlas-SNP
NBEAL2	23218	hgsc.bcm.edu	37	3	47046485	47046485	+	Silent	SNP	C	C	T	rs141569354	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	39	84	0	0.453488	0	C|0.995;T|0.005	0.005	strong	.	NBEAL2	267	.	NM_015175	exon39	c.C6318T	p.Y2106Y	GGACTACGTGTCC	.	PASS	Atlas-SNP
NEUROG3	50674	hgsc.bcm.edu	37	10	71332204	71332204	+	Missense_Mutation	SNP	A	A	G	rs4536103	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	15	9	7	0	0.6	0	A|0.573;G|0.427	0.427	strong	.	NEUROG3	33	.	NM_020999	exon2	c.T596C	p.F199S	GCGGAAAAGGTGG	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	105	105	101	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
TTLL2	83887	hgsc.bcm.edu	37	6	167754702	167754702	+	Silent	SNP	C	C	T	rs909546	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	86	73	0	0.988506	0	C|0.503;A|0.003	.	strong	TTLL2,NS,carcinoma,0,1	TTLL2	82	1	NM_031949	exon3	c.C1314T	p.D438D	CATCGACGCTGCA	.	PASS	Atlas-SNP
FEM1A	55527	hgsc.bcm.edu	37	19	4793128	4793128	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	20	43	0	0.384615	0	.	.	none	.	FEM1A	41	.	NM_018708	exon1	c.A1262C	p.Q421P	TGCAACAGAGCAA	.	PASS	Atlas-SNP
FAM186A	121006	hgsc.bcm.edu	37	12	50727706	50727706	+	Missense_Mutation	SNP	G	G	C	rs6580741	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	216	102	217	0	0.472222	0	G|0.688;C|0.312	0.312	strong	.	FAM186A	181	.	NM_001145475	exon5	c.C6684G	p.H2228Q	GAATACGTGTATC	.	PASS	Atlas-SNP
HSP90B1	7184	hgsc.bcm.edu	37	12	104341103	104341103	+	Silent	SNP	C	C	T	rs7645	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	184	183	186	0	0.994565	0	C|0.550;T|0.450	0.450	strong	.	HSP90B1	72	.	NM_003299	exon17	c.C2277T	p.P759P	AGAGCCCGAAGAA	.	PASS	Atlas-SNP
OR1S2	219958	hgsc.bcm.edu	37	11	57971195	57971195	+	Silent	SNP	G	G	A	rs11229279	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	147	130	199	0	0.884354	0	G|0.677;A|0.323	0.323	strong	OR1S2,caecum,carcinoma,-2,2	OR1S2	119	2	NM_001004459	exon1	c.C459T	p.F153F	AGTGCCGAACCTG	.	PASS	Atlas-SNP
MLL4	8085	hgsc.bcm.edu	37	19	36224161	36224161	+	Silent	SNP	C	C	A	rs112013670	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	42	22	36	0	0.52381	0	C|0.894;A|0.106	0.106	strong	.	MLL4	229	.	NM_014727	exon28	c.C6711A	p.G2237G	CCCAGGCCCCCTC	.	PASS	Atlas-SNP
VWF	7450	hgsc.bcm.edu	37	12	6138595	6138595	+	Silent	SNP	C	C	T	rs1800380	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68	30	77	0	0.441176	0	C|0.766;T|0.234	0.234	strong	.	VWF	338	.	NM_000552	exon22	c.G2880A	p.R960R	GATGTACCGGCCA	.	PASS	Atlas-SNP
TCEB3C	162699	hgsc.bcm.edu	37	18	44555232	44555232	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	222	6	56	0	0.027027	0	.	.	none	TCEB3C,NS,carcinoma,+1,1	TCEB3C	49	1	NM_145653	exon1	c.C982G	p.P328A	AGGCAGGCCTGGA	.	scavenged	Atlas-SNP
HEATR5B	54497	hgsc.bcm.edu	37	2	37241050	37241050	+	Silent	SNP	G	G	A	rs17020125	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	113	62	92	0	0.548673	0	G|0.798;A|0.202	0.202	strong	.	HEATR5B	185	.	NM_019024	exon27	c.C4218T	p.S1406S	CTGGCTGGAAGAT	.	PASS	Atlas-SNP
AAK1	22848	hgsc.bcm.edu	37	2	69741609	69741609	+	Silent	SNP	C	C	T	rs2276689	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	8	51	0	0.153846	0	C|0.642;T|0.358	0.358	strong	.	AAK1	121	.	NM_014911	exon13	c.G1770A	p.E590E	CGCTGGCTCCTGG	.	PASS	Atlas-SNP
HDAC10	83933	hgsc.bcm.edu	37	22	50684747	50684747	+	Missense_Mutation	SNP	C	C	T	rs76578729	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	27	53	0	0.574468	0	C|0.981;G|0.000;T|0.019	0.019	strong	.	HDAC10	29	.	NM_032019	exon17	c.G1630A	p.V544I	TGGAGACATGGAA	.	PASS	Atlas-SNP
MED16	10025	hgsc.bcm.edu	37	19	872089	872089	+	Silent	SNP	A	A	G	rs72984031	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	90	89	54	0	0.988889	0	A|0.775;G|0.225	0.225	strong	.	MED16	61	.	NM_005481	exon12	c.T1935C	p.F645F	CCGCAGAAAGCTG	.	PASS	Atlas-SNP
ZNF239	8187	hgsc.bcm.edu	37	10	44052903	44052903	+	Missense_Mutation	SNP	A	A	C	rs2230661	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	90	43	89	0	0.477778	0	A|0.480;C|0.520	0.520	strong	.	ZNF239	45	.	NM_001099283	exon2	c.T625G	p.C209G	GACTACATTCGTA	.	PASS	Atlas-SNP
IL7R	3575	hgsc.bcm.edu	37	5	35871273	35871273	+	Silent	SNP	C	C	T	rs2228141	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	64	22	77	0	0.34375	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
PPYR1	5540	hgsc.bcm.edu	37	10	47087501	47087501	+	Missense_Mutation	SNP	C	C	T	rs3824733	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	56	27	44	0	0.482143	0	C|0.702;T|0.298	0.298	strong	PPYR1,rectum,carcinoma,-1,1	PPYR1	54	1	NM_005972	exon3	c.C718T	p.R240C	TACCGGCGCCTGC	.	PASS	Atlas-SNP
ZNF672	79894	hgsc.bcm.edu	37	1	249142169	249142169	+	Silent	SNP	C	C	T	rs58906520	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	22	12	30	0	0.545455	0	C|0.902;T|0.098	0.098	strong	.	ZNF672	32	.	NM_024836	exon4	c.C696T	p.C232C	GGAGTGCGGCAAG	.	PASS	Atlas-SNP
TLCD1	116238	hgsc.bcm.edu	37	17	27052358	27052358	+	Silent	SNP	C	C	T	rs2288595	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	118	46	113	0	0.38983	0	C|0.894;T|0.106	0.106	strong	.	TLCD1	15	.	NM_138463	exon3	c.G324A	p.T108T	GGCTCGCGTCTGT	.	PASS	Atlas-SNP
ELAC2	60528	hgsc.bcm.edu	37	17	12898295	12898295	+	Silent	SNP	T	T	C	rs17552022	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	146	69	159	0	0.472603	0	T|0.921;C|0.079	0.079	strong	.	ELAC2	48	.	NM_018127	exon20	c.A1893G	p.T631T	ATCACATGTTCGC	.	PASS	Atlas-SNP
RTN4IP1	84816	hgsc.bcm.edu	37	6	107019880	107019880	+	Silent	SNP	A	A	G	rs9486410	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	93	93	115	0	1	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
ECE2	9718	hgsc.bcm.edu	37	3	183976108	183976108	+	Silent	SNP	T	T	C	rs902415	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	107	56	104	0	0.523364	0	T|0.697;C|0.303	0.303	strong	.	ECE2	303	.	NM_032331	exon3	c.T513C	p.F171F	CCGGTTTATCTCA	.	PASS	Atlas-SNP
ELMOD3	84173	hgsc.bcm.edu	37	2	85617579	85617579	+	Silent	SNP	C	C	T	rs17851663	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	92	70	117	0	0.76087	0	C|0.951;T|0.049	0.049	strong	.	ELMOD3	53	.	NM_032213	exon11	c.C1134T	p.V378V	GACTGTCGCCCTT	.	PASS	Atlas-SNP
INPP5B	3633	hgsc.bcm.edu	37	1	38329999	38329999	+	Missense_Mutation	SNP	C	C	G	rs41311191	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	84	40	75	0	0.47619	0	C|0.887;G|0.113	0.113	strong	.	INPP5B	76	.	NM_005540	exon23	c.G2611C	p.D871H	TCTCATCCAAATG	.	PASS	Atlas-SNP
RAB6C	84084	hgsc.bcm.edu	37	2	130738183	130738183	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	365	7	479	0	0.0191781	0	.	.	none	RAB6C,NS,carcinoma,+1,1	RAB6C	28	1	NM_032144	exon1	c.G495A	p.Q165Q	AAAGCAGCTCTTT	.	scavenged	Atlas-SNP
NR5A2	2494	hgsc.bcm.edu	37	1	200143281	200143281	+	Silent	SNP	C	C	T	rs1060060	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	78	47	74	0	0.602564	0	T|0.348;G|0.007	0.348	strong	NR5A2,NS,carcinoma,+1,1	NR5A2	83	1	NM_205860	exon8	c.C1569T	p.C523C	CCTGAACGGGGAT	.	PASS	Atlas-SNP
RBBP6	5930	hgsc.bcm.edu	37	16	24582299	24582299	+	Silent	SNP	C	C	G	rs7196736	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	146	64	117	0	0.438356	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
PIEZO1	9780	hgsc.bcm.edu	37	16	88782777	88782777	+	Silent	SNP	G	G	A	rs34352064	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	56	24	45	0	0.428571	0	G|0.995;A|0.005	0.005	strong	.	PIEZO1	79	.	NM_001142864	exon48	c.C7041T	p.D2347D	AGACTGGTCCGAG	.	PASS	Atlas-SNP
TAAR5	9038	hgsc.bcm.edu	37	6	132910612	132910612	+	Silent	SNP	G	G	A	rs3813355	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82	39	66	0	0.47561	0	G|0.343;A|0.657	0.657	strong	TAAR5,colon,carcinoma,0,1	TAAR5	53	1	NM_003967	exon1	c.C214T	p.L72L	GCAGCAGGAAGTT	.	PASS	Atlas-SNP
MAGEB10	139422	hgsc.bcm.edu	37	X	27839617	27839617	+	Missense_Mutation	SNP	G	G	A	rs12557898	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	39	38	28	0	0.974359	0	0|0.012;A|0.299	0.299	strong	.	MAGEB10	107	.	NM_182506	exon3	c.G194A	p.R65Q	GACTTCGGGAAGC	.	PASS	Atlas-SNP
NIN	51199	hgsc.bcm.edu	37	14	51202311	51202311	+	Missense_Mutation	SNP	G	G	C	rs2295847	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	65	34	83	0	0.523077	0	G|0.873;C|0.127	0.127	strong	.	NIN	475	.	NM_020921	exon28	c.C5800G	p.Q1934E	ATTCTTGTTCAAG	.	PASS	Atlas-SNP
MUC6	4588	hgsc.bcm.edu	37	11	1017773	1017773	+	Silent	SNP	G	G	A	rs57384288	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	678	99	538	28	0.146018	0.0520446	G|0.500;A|0.500	0.500	strong	MUC6,NS,carcinoma,0,1	MUC6	408	1	NM_005961	exon31	c.C5028T	p.S1676S	GGTCCCGCTGGTG	.	scavenged	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94	94	100	0	1	0	C|0.580;T|0.420	0.420	strong	.	PGLYRP3	55	.	NM_052891	exon3	c.G376A	p.G126S	CCTTACCTATCTT	.	PASS	Atlas-SNP
SLC9C1	285335	hgsc.bcm.edu	37	3	111918215	111918215	+	Missense_Mutation	SNP	C	C	T	rs28516377	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	60	23	64	0	0.383333	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
PCSK5	5125	hgsc.bcm.edu	37	9	78789900	78789900	+	Splice_Site	SNP	A	A	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	153	10	164	0	0.0653595	0	.	.	none	PCSK5_ENST00000545128,NS,carcinoma,0,3	PCSK5	329	3	NM_001190482	exon14	c.1757-2A>C	.	TTCTCAAGGTAAA	.	PASS	Atlas-SNP
PIWIL4	143689	hgsc.bcm.edu	37	11	94322353	94322353	+	Silent	SNP	G	G	A	rs11020846	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	176	30	155	0	0.170455	0	G|0.793;A|0.207	0.207	strong	.	PIWIL4	70	.	NM_152431	exon8	c.G981A	p.Q327Q	CTTTCAGAAGCGG	.	PASS	Atlas-SNP
SDK2	54549	hgsc.bcm.edu	37	17	71503636	71503636	+	Silent	SNP	T	T	C	rs9895895	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	106	41	77	0	0.386792	0	T|0.439;C|0.561	0.561	strong	.	SDK2	219	.	NM_001144952	exon2	c.A165G	p.P55P	CTCCAGTGGCCAG	.	PASS	Atlas-SNP
TEX14	56155	hgsc.bcm.edu	37	17	56690848	56690848	+	Silent	SNP	T	T	C	rs8077548	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	118	60	120	0	0.508475	0	T|0.835;C|0.165	0.165	strong	TEX14_ENST00000240361,NS,carcinoma,0,2	TEX14	343	2	NM_001201457	exon9	c.A957G	p.L319L	TTTCTCTAGGTCC	.	PASS	Atlas-SNP
FGF18	8817	hgsc.bcm.edu	37	5	170883734	170883734	+	Silent	SNP	G	G	A	rs34347344	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	41	15	46	0	0.365854	0	G|0.958;A|0.042	0.042	strong	.	FGF18	33	.	NM_003862	exon5	c.G549A	p.P183P	GCAGCCGGAGCTT	.	PASS	Atlas-SNP
UBE2Q2	92912	hgsc.bcm.edu	37	15	76136768	76136768	+	Missense_Mutation	SNP	C	C	T	rs72734531	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	31	68	0	0.407895	0	C|0.812;T|0.188	0.188	strong	.	UBE2Q2	26	.	NM_001145335	exon1	c.C74T	p.P25L	CTCCCCCGGGCCT	.	PASS	Atlas-SNP
PIK3AP1	118788	hgsc.bcm.edu	37	10	98411293	98411293	+	Silent	SNP	G	G	A	rs35668691	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	90	47	112	0	0.522222	0	G|0.975;A|0.025	0.025	strong	.	PIK3AP1	111	.	NM_152309	exon5	c.C828T	p.A276A	ATTCGCGGCATTG	.	PASS	Atlas-SNP
RHBG	57127	hgsc.bcm.edu	37	1	156347131	156347131	+	Missense_Mutation	SNP	G	G	A	rs2245623	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	188	184	198	1	0.978723	0.00505051	G|0.713;A|0.287	0.287	strong	.	RHBG	133	.	NM_020407	exon2	c.G227A	p.G76D	GCTTTGGCTTCCT	.	PASS	Atlas-SNP
GLIPR1L2	144321	hgsc.bcm.edu	37	12	75785100	75785100	+	Silent	SNP	C	C	T	rs11180483	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	128	59	127	0	0.460938	0	C|0.653;T|0.347	0.347	strong	.	GLIPR1L2	54	.	NM_152436	exon1	c.C204T	p.V68V	CGACGTCATTCCC	.	PASS	Atlas-SNP
TMEM132B	114795	hgsc.bcm.edu	37	12	125834095	125834095	+	Silent	SNP	C	C	A	rs1491893	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	115	54	119	0	0.469565	0	C|0.737;A|0.262	0.262	strong	.	TMEM132B	207	.	NM_052907	exon2	c.C150A	p.S50S	GGAGTCCTTTTTC	.	PASS	Atlas-SNP
UBAP2	55833	hgsc.bcm.edu	37	9	33998847	33998847	+	Missense_Mutation	SNP	T	T	C	rs149441020	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	16	11	25	0	0.6875	0	T|0.999;C|0.001	0.001	strong	.	UBAP2	82	.	NM_018449	exon3	c.A115G	p.M39V	GACGCATCTGTTC	.	PASS	Atlas-SNP
OR7G3	390883	hgsc.bcm.edu	37	19	9237554	9237554	+	Missense_Mutation	SNP	G	G	A	rs138008445	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	132	62	113	0	0.469697	0	G|0.995;A|0.005	0.005	strong	.	OR7G3	41	.	NM_001001958	exon1	c.C73T	p.P25S	GGATGGGCTGCAG	.	PASS	Atlas-SNP
UNC5C	8633	hgsc.bcm.edu	37	4	96166270	96166270	+	Silent	SNP	C	C	T	rs35120448	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49	19	55	0	0.387755	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
TIMM10B	26515	hgsc.bcm.edu	37	11	6502780	6502780	+	Silent	SNP	C	C	A	rs11555935	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	38	19	53	0	0.5	0	A|0.180;C|0.820;G|0.000;T|0.000	0.180	strong	.	.	.	.	NM_012192	exon1	c.C34A	p.R12R	CAACTGCGAAACG	.	PASS	Atlas-SNP
FOXO1	2308	hgsc.bcm.edu	37	13	41240299	41240299	+	Silent	SNP	C	C	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	11	5	3	0	0.454545	0	.	.	none	.	FOXO1	110	.	NM_002015	exon1	c.G51T	p.L17L	CCGGGGCAGCGGC	.	PASS	Atlas-SNP
GET4	51608	hgsc.bcm.edu	37	7	930608	930608	+	Silent	SNP	G	G	A	rs11543223	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	264	104	230	0	0.393939	0	G|0.921;A|0.079	0.079	strong	.	GET4	17	.	NM_015949	exon5	c.G510A	p.A170A	CTCAGCGGACGGG	.	PASS	Atlas-SNP
ALG14	199857	hgsc.bcm.edu	37	1	95538342	95538342	+	Missense_Mutation	SNP	C	C	A	rs139521179	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	29	58	0	0.47541	0	C|0.997;A|0.003	0.003	strong	.	ALG14	13	.	NM_144988	exon1	c.G113T	p.S38I	AAGATACTGAGAG	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	58	34	61	0	0.586207	0	G|0.833;A|0.167	0.167	strong	.	OR10H3	53	.	NM_013938	exon1	c.G878A	p.S293N	TTTTCAGTCTAAG	.	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-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	75	38	77	0	0.506667	0	T|0.001;G|0.251	0.251	strong	.	CEP72	53	.	NM_018140	exon9	c.A1525G	p.T509A	CACCACACACACA	.	PASS	Atlas-SNP
TPM1	7168	hgsc.bcm.edu	37	15	63351873	63351873	+	Silent	SNP	T	T	C	rs11558747	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	37	18	35	0	0.486486	0	T|0.951;C|0.049	0.049	strong	.	TPM1	59	.	NM_001018007	exon4	c.T486C	p.Y162Y	CAAATATGAAGAG	.	PASS	Atlas-SNP
GAREM	64762	hgsc.bcm.edu	37	18	29867091	29867091	+	Missense_Mutation	SNP	G	G	A	rs16962974	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	95	53	90	0	0.557895	0	G|0.936;A|0.064	0.064	strong	.	.	.	.	NM_022751	exon4	c.C1469T	p.A490V	GAAGTCGCACATT	.	PASS	Atlas-SNP
ME2	4200	hgsc.bcm.edu	37	18	48447462	48447462	+	Missense_Mutation	SNP	A	A	C	rs59409558	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	108	47	82	0	0.435185	0	A|0.991;C|0.009	0.009	strong	.	ME2	49	.	NM_001168335	exon10	c.A961C	p.N321H	ATTGCAAATCTTA	.	PASS	Atlas-SNP
COL24A1	255631	hgsc.bcm.edu	37	1	86591014	86591014	+	Silent	SNP	T	T	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	183	12	207	0	0.0655738	0	.	.	none	.	COL24A1	202	.	NM_152890	exon3	c.A1005G	p.K335K	CATTTCTTTGGCC	.	PASS	Atlas-SNP
C5orf20	140947	hgsc.bcm.edu	37	5	134782510	134782510	+	Missense_Mutation	SNP	T	T	C	rs12520809	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	49	49	55	0	1	0	C|0.631;N|0.000	0.631	strong	.	C5orf20	16	.	NM_130848	exon1	c.A289G	p.N97D	AAAGATTGGAGTT	.	PASS	Atlas-SNP
ZNF804A	91752	hgsc.bcm.edu	37	2	185801559	185801559	+	Missense_Mutation	SNP	A	A	G	rs35676856	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	126	63	114	0	0.5	0	A|0.947;G|0.053	0.053	strong	ZNF804A,NS,carcinoma,+1,1	ZNF804A	322	1	NM_194250	exon4	c.A1436G	p.D479G	AGCCAGACTTAAA	.	PASS	Atlas-SNP
JAG1	182	hgsc.bcm.edu	37	20	10637057	10637057	+	Silent	SNP	T	T	C	rs10485741	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	40	19	34	0	0.475	0	T|0.940;C|0.060	0.060	strong	.	JAG1	213	.	NM_000214	exon5	c.A744G	p.P248P	GTCACCTGGGAGT	.	PASS	Atlas-SNP
APBB3	10307	hgsc.bcm.edu	37	5	139940233	139940233	+	Silent	SNP	G	G	A	rs250431	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	76	69	1	1	0.0144928	G|0.389;A|0.611	0.611	strong	APBB3,NS,carcinoma,-1,1	APBB3	34	1	NM_006051	exon10	c.C1044T	p.H348H	AATGGGGTGTGCA	.	scavenged	Atlas-SNP
FLRT1	23769	hgsc.bcm.edu	37	11	63885287	63885287	+	Silent	SNP	C	C	T	rs947939	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	158	88	155	0	0.556962	0	C|0.896;T|0.104	0.104	strong	.	FLRT1	46	.	NM_013280	exon2	c.C1548T	p.Y516Y	TGCCTACGTAGCT	.	PASS	Atlas-SNP
CSF1	1435	hgsc.bcm.edu	37	1	110466466	110466466	+	Missense_Mutation	SNP	T	T	C	rs1058885	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	43	67	0	0.494253	0	T|0.587;C|0.413	0.413	strong	.	CSF1	40	.	NM_000757	exon6	c.T1223C	p.L408P	CATCACTGCGCCC	.	PASS	Atlas-SNP
TMEM173	340061	hgsc.bcm.edu	37	5	138857925	138857925	+	Missense_Mutation	SNP	C	C	G	rs78233829	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	36	92	0	0.418605	0	C|0.807;G|0.193	0.193	strong	.	TMEM173	19	.	NM_198282	exon6	c.G689C	p.G230A	TGGTCACCGGTCT	.	PASS	Atlas-SNP
SLC4A1AP	22950	hgsc.bcm.edu	37	2	27887034	27887034	+	Missense_Mutation	SNP	C	C	A	rs9678851	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72	36	105	0	0.5	0	C|0.590;A|0.410	0.410	strong	.	SLC4A1AP	63	.	NM_018158	exon1	c.C415A	p.P139T	CGCCCCCCGACAG	.	PASS	Atlas-SNP
NEIL3	55247	hgsc.bcm.edu	37	4	178256913	178256913	+	Missense_Mutation	SNP	C	C	G	rs7689099	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	238	113	204	0	0.47479	0	C|0.910;G|0.090	0.090	strong	.	NEIL3	89	.	NM_018248	exon3	c.C350G	p.P117R	CTTCTCCTGTTTT	.	PASS	Atlas-SNP
TPBG	7162	hgsc.bcm.edu	37	6	83075914	83075914	+	Silent	SNP	G	G	A	rs700494	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80	48	88	0	0.6	0	G|0.316;A|0.684	0.684	strong	.	TPBG	37	.	NM_001166392	exon2	c.G1236A	p.T412T	ATTAACGAACCTC	.	PASS	Atlas-SNP
DHX58	79132	hgsc.bcm.edu	37	17	40263400	40263400	+	Missense_Mutation	SNP	C	C	T	rs35118457	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	78	45	89	0	0.576923	0	C|0.957;T|0.043	0.043	strong	.	DHX58	39	.	NM_024119	exon4	c.G284A	p.R95Q	TGGCACCGGGCCA	.	PASS	Atlas-SNP
CXCL16	58191	hgsc.bcm.edu	37	17	4638563	4638563	+	Missense_Mutation	SNP	G	G	A	rs2277680	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	180	101	149	0	0.561111	0	G|0.576;A|0.424	0.424	strong	.	CXCL16	30	.	NM_022059	exon4	c.C599T	p.A200V	GGCCCAGCTGCCA	.	PASS	Atlas-SNP
SETMAR	6419	hgsc.bcm.edu	37	3	4358210	4358210	+	Silent	SNP	A	A	G	rs7647539	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	34	14	40	0	0.411765	0	A|0.558;G|0.442	0.442	strong	.	SETMAR	30	.	NM_006515	exon3	c.A1335G	p.R445R	CGTTCGACATTTG	.	PASS	Atlas-SNP
URGCP	55665	hgsc.bcm.edu	37	7	43917013	43917013	+	Silent	SNP	G	G	A	rs2232105	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	34	8	78	0	0.235294	0	G|0.529;A|0.471	0.471	strong	.	URGCP	170	.	NM_001077663	exon6	c.C2049T	p.H683H	TCGGACGTGCAGC	.	PASS	Atlas-SNP
TMEM132E	124842	hgsc.bcm.edu	37	17	32953258	32953258	+	Silent	SNP	G	G	A	rs4795954	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	68	35	57	0	0.514706	0	G|0.870;A|0.130	0.130	strong	.	TMEM132E	122	.	NM_207313	exon2	c.G180A	p.E60E	GCGGGAGGCGCGG	.	PASS	Atlas-SNP
HGSNAT	138050	hgsc.bcm.edu	37	8	43053062	43053062	+	Missense_Mutation	SNP	G	G	C	rs148632988	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	236	123	209	0	0.521186	0	G|0.995;C|0.005	0.005	strong	.	HGSNAT	85	.	NM_152419	exon17	c.G1693C	p.G565R	GTGAAGGGGCTGT	.	PASS	Atlas-SNP
CD40LG	959	hgsc.bcm.edu	37	X	135730555	135730555	+	Silent	SNP	T	T	C	rs1126535	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72	24	55	0	0.333333	0	0|0.032;C|0.165	0.165	strong	.	CD40LG	46	.	NM_000074	exon1	c.T148C	p.L50L	AGAAGGTTGGACA	.	PASS	Atlas-SNP
SGPL1	8879	hgsc.bcm.edu	37	10	72631626	72631626	+	Silent	SNP	C	C	T	rs865832	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	30	75	0	0.638298	0	C|0.828;T|0.172	0.172	strong	.	SGPL1	37	.	NM_003901	exon11	c.C942T	p.V314V	TCATGTCGACGCT	.	PASS	Atlas-SNP
LCTL	197021	hgsc.bcm.edu	37	15	66850204	66850204	+	Silent	SNP	A	A	G	rs16953566	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	26	73	0	0.38806	0	A|0.965;G|0.035	0.035	strong	.	LCTL	73	.	NM_207338	exon8	c.T778C	p.L260L	AGTTCAATGAAAT	.	PASS	Atlas-SNP
NT5E	4907	hgsc.bcm.edu	37	6	86199243	86199243	+	Missense_Mutation	SNP	T	T	C	rs2229524	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	74	33	68	0	0.445946	0	A|0.000;C|0.157;G|0.000;T|0.843	0.157	strong	.	NT5E	56	.	NM_001204813	exon6	c.T1136C	p.M379T	ATGAAATGTTCTG	.	PASS	Atlas-SNP
C6orf15	29113	hgsc.bcm.edu	37	6	31079894	31079894	+	Missense_Mutation	SNP	A	A	G	rs2233977	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	99	14	93	0	0.141414	0	A|0.825;G|0.175	0.175	strong	C6orf15,NS,carcinoma,-1,1	C6orf15	29	1	NM_014070	exon2	c.T242C	p.V81A	GCAGGCACGCTGA	.	PASS	Atlas-SNP
CD276	80381	hgsc.bcm.edu	37	15	73996101	73996101	+	Missense_Mutation	SNP	G	G	A	rs10083681	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	137	79	125	0	0.576642	0	G|0.813;A|0.187	0.187	strong	.	CD276	29	.	NM_001024736	exon5	c.G835A	p.A279T	AGCCTGGCACAGC	.	PASS	Atlas-SNP
HSPG2	3339	hgsc.bcm.edu	37	1	22157545	22157545	+	Silent	SNP	G	G	A	rs112494360	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	96	46	87	0	0.479167	0	A|0.024;C|0.000;G|0.976	0.024	strong	HSPG2,NS,carcinoma,0,1	HSPG2	311	1	NM_005529	exon85	c.C11601T	p.Y3867Y	GCACACGTAGCTG	.	PASS	Atlas-SNP
NRIP1	8204	hgsc.bcm.edu	37	21	16340289	16340289	+	Silent	SNP	C	C	T	rs2229741	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	131	83	83	0	0.633588	0	C|0.443;T|0.557	0.557	strong	NRIP1,NS,carcinoma,0,1	NRIP1	103	1	NM_003489	exon4	c.G225A	p.G75G	GCCAGACCCCTGA	.	PASS	Atlas-SNP
CUBN	8029	hgsc.bcm.edu	37	10	16979661	16979661	+	Silent	SNP	T	T	C	rs1801234	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	39	46	0	0.629032	0	T|0.475;C|0.525	0.525	strong	.	CUBN	515	.	NM_001081	exon39	c.A5856G	p.S1952S	CTTCCCTGAGATT	.	PASS	Atlas-SNP
KRT9	3857	hgsc.bcm.edu	37	17	39723990	39723990	+	Silent	SNP	T	T	A	rs3890472	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	26	15	30	0	0.576923	0	T|0.457;A|0.543	0.543	strong	KRT9,NS,adenoma,0,1	KRT9	78	1	NM_000226	exon7	c.A1407T	p.G469G	TCCAGCTCCGGAG	.	PASS	Atlas-SNP
ZNF853	54753	hgsc.bcm.edu	37	7	6656830	6656830	+	Missense_Mutation	SNP	G	G	A	rs2243563	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	32	15	38	0	0.46875	0	G|0.313;A|0.687	0.687	strong	ZNF853_ENST00000457543,rectum,carcinoma,0,2	ZNF853	32	2	NM_017560	exon2	c.G22A	p.G8R	ACTCCCGGGAATC	.	PASS	Atlas-SNP
LRRK2	120892	hgsc.bcm.edu	37	12	40742254	40742254	+	Silent	SNP	G	G	A	rs10878405	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110	53	104	0	0.481818	0	G|0.735;A|0.265	0.265	strong	.	LRRK2	763	.	NM_198578	exon43	c.G6324A	p.E2108E	GGTTGAGAAATTA	.	PASS	Atlas-SNP
SSTR4	6754	hgsc.bcm.edu	37	20	23017044	23017044	+	Silent	SNP	C	C	T	rs3746728	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	101	44	109	0	0.435644	0	C|0.669;T|0.331	0.331	strong	SSTR4,colon,carcinoma,0,2	SSTR4	83	2	NM_001052	exon1	c.C924T	p.P308P	CAACCCCATTCTC	.	PASS	Atlas-SNP
PROP1	5626	hgsc.bcm.edu	37	5	177422908	177422908	+	Silent	SNP	A	A	G	rs1135320	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	40	67	0	0.56338	0	A|0.580;G|0.420	0.420	strong	.	PROP1	28	.	NM_006261	exon1	c.T27C	p.A9A	CTTCTCAGCCTGG	.	PASS	Atlas-SNP
ARSI	340075	hgsc.bcm.edu	37	5	149677635	149677635	+	Silent	SNP	G	G	A	rs139203947	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	47	23	44	0	0.489362	0	G|0.999;A|0.001	0.001	strong	.	ARSI	65	.	NM_001012301	exon2	c.C852T	p.Y284Y	GAAACCGTAGCGC	.	PASS	Atlas-SNP
WASF3	10810	hgsc.bcm.edu	37	13	27250805	27250805	+	Missense_Mutation	SNP	G	G	T	rs139779405	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	69	34	72	0	0.492754	0	A|0.000;G|0.999;T|0.001	0.001	strong	.	WASF3	68	.	NM_006646	exon7	c.G660T	p.L220F	CAGGTTGTCTCAG	.	PASS	Atlas-SNP
HTR2C	3358	hgsc.bcm.edu	37	X	113965735	113965735	+	Missense_Mutation	SNP	G	G	C	rs6318	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	181	55	140	0	0.303867	0	0|0.015;C|0.215	0.215	strong	.	HTR2C	117	.	NM_000868	exon4	c.G68C	p.C23S	GGCAATGTGATAT	.	PASS	Atlas-SNP
KIAA0753	9851	hgsc.bcm.edu	37	17	6531648	6531648	+	Silent	SNP	A	A	G	rs2072149	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	221	111	227	0	0.502262	0	A|0.332;G|0.668	0.668	strong	.	KIAA0753	63	.	NM_014804	exon3	c.T507C	p.S169S	GGCACCAGAGCTG	.	PASS	Atlas-SNP
SIX4	51804	hgsc.bcm.edu	37	14	61180657	61180657	+	Missense_Mutation	SNP	T	T	G	rs3742636	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72	71	105	0	0.986111	0	T|0.345;G|0.655	0.655	strong	.	SIX4	69	.	NM_017420	exon3	c.A1814C	p.H605P	AGTGGATGCAGGC	.	PASS	Atlas-SNP
ZKSCAN2	342357	hgsc.bcm.edu	37	16	25258035	25258035	+	Silent	SNP	A	A	G	rs11649280	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	176	90	216	1	0.511364	0.00462963	A|0.696;G|0.304	0.304	strong	.	ZKSCAN2	90	.	NM_001012981	exon5	c.T1482C	p.N494N	ACTGAGATTCTGA	.	PASS	Atlas-SNP
TG	7038	hgsc.bcm.edu	37	8	133881996	133881996	+	Missense_Mutation	SNP	G	G	A	rs116340633	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	37	16	70	0	0.432432	0	G|0.992;A|0.008	0.008	strong	.	TG	416	.	NM_003235	exon3	c.G199A	p.G67S	AACGACGGCCGCT	.	PASS	Atlas-SNP
DHX9	1660	hgsc.bcm.edu	37	1	182845346	182845346	+	Silent	SNP	C	C	T	rs35533583	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	143	72	158	0	0.503497	0	C|0.976;T|0.024	0.024	strong	.	DHX9	114	.	NM_001357	exon17	c.C1977T	p.G659G	GCCTGGCTGGAAT	.	PASS	Atlas-SNP
TMEM169	92691	hgsc.bcm.edu	37	2	216964944	216964944	+	Silent	SNP	C	C	T	rs61732367	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	153	78	142	1	0.509804	0.00704225	C|0.987;T|0.013	0.013	strong	TMEM169,caecum,carcinoma,+1,1	TMEM169	46	1	NM_001142310	exon4	c.C573T	p.F191F	CATCTTCCTCGTG	.	scavenged	Atlas-SNP
RIPK2	8767	hgsc.bcm.edu	37	8	90784979	90784979	+	Missense_Mutation	SNP	T	T	C	rs2230801	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	80	44	86	0	0.55	0	T|0.922;C|0.078	0.078	strong	.	RIPK2	37	.	NM_003821	exon6	c.T776C	p.I259T	ATGATATACCTCA	.	PASS	Atlas-SNP
OR2L2	26246	hgsc.bcm.edu	37	1	248202412	248202412	+	Silent	SNP	C	C	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	126	7	81	0	0.0555556	0	.	.	none	OR2L2,NS,carcinoma,0,1	OR2L2	115	1	NM_001004686	exon1	c.C843T	p.T281T	CCTCACCCCAATG	.	scavenged	Atlas-SNP
SLC11A1	6556	hgsc.bcm.edu	37	2	219249013	219249013	+	Silent	SNP	C	C	T	rs2276631	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	101	53	89	0	0.524752	0	C|0.789;T|0.211	0.211	strong	.	SLC11A1	41	.	NM_000578	exon3	c.C198T	p.F66F	TGGCTTCCTCATG	.	PASS	Atlas-SNP
LDLRAP1	26119	hgsc.bcm.edu	37	1	25890189	25890189	+	Silent	SNP	A	A	G	rs28969504	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	37	19	67	0	0.513514	0	A|0.383;G|0.617	0.617	strong	.	LDLRAP1	28	.	NM_015627	exon7	c.A654G	p.T218T	GGAGACAGCTAAG	.	PASS	Atlas-SNP
C12orf77	196415	hgsc.bcm.edu	37	12	25148824	25148824	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	209	58	178	0	0.277512	0	.	.	none	.	C12orf77	18	.	NM_001101339	exon3	c.C324A	p.N108K	TTCCGTGTTCATA	.	PASS	Atlas-SNP
SGK223	0	hgsc.bcm.edu	37	8	8234077	8234077	+	Silent	SNP	G	G	C	rs4840952	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	77	37	67	0	0.480519	0	G|0.632;C|0.368	0.368	strong	.	.	.	.	NM_001080826	exon2	c.C1842G	p.A614A	CGAGGCGGCAGGC	.	PASS	Atlas-SNP
ENGASE	64772	hgsc.bcm.edu	37	17	77075673	77075673	+	Silent	SNP	A	A	G	rs3744185	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	46	17	67	0	0.369565	0	A|0.715;G|0.285	0.285	strong	ENGASE,caecum,adenoma,0,1	ENGASE	55	1	NM_001042573	exon4	c.A519G	p.P173P	TCCCCCAGTGGGC	.	PASS	Atlas-SNP
AASDH	132949	hgsc.bcm.edu	37	4	57219613	57219613	+	Silent	SNP	C	C	T	rs17086696	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82	32	101	0	0.390244	0	C|0.825;T|0.175	0.175	strong	.	AASDH	101	.	NM_181806	exon9	c.G1533A	p.P511P	CTCATCCGGGACT	.	PASS	Atlas-SNP
CEP85	64793	hgsc.bcm.edu	37	1	26582091	26582091	+	Missense_Mutation	SNP	G	G	A	rs3795686	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	104	46	102	0	0.442308	0	G|0.777;A|0.223	0.223	strong	.	CEP85	61	.	NM_022778	exon4	c.G638A	p.S213N	GAACCAGCACAAG	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9085004	9085004	+	Missense_Mutation	SNP	T	T	C	rs11085805	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94	45	91	0	0.478723	0	T|0.812;C|0.188	0.188	strong	MUC16_ENST00000397910,NS,carcinoma,+1,2	MUC16	4315	2	NM_024690	exon1	c.A6811G	p.T2271A	AATGAGTTGTCTT	.	PASS	Atlas-SNP
GK	2710	hgsc.bcm.edu	37	X	30686141	30686141	+	Silent	SNP	G	G	A	rs34795481	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	224	152	197	0	0.678571	0	G|0.953;A|0.047	0.047	strong	.	GK	95	.	NM_203391	exon3	c.G165A	p.Q55Q	GGAACAGGACCCT	.	PASS	Atlas-SNP
CELSR1	9620	hgsc.bcm.edu	37	22	46930107	46930107	+	Silent	SNP	C	C	T	rs8141744	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	174	87	166	0	0.5	0	C|0.794;T|0.206	0.206	strong	.	CELSR1	242	.	NM_014246	exon1	c.G2961A	p.V987V	GATGGTCACCTGG	.	PASS	Atlas-SNP
RBMXL3	139804	hgsc.bcm.edu	37	X	114424941	114424941	+	Missense_Mutation	SNP	G	G	A	rs62601530	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	149	41	99	0	0.275168	0	G|0.929;A|0.071	0.071	strong	.	RBMXL3	83	.	NM_001145346	exon1	c.G937A	p.A313T	TGCGGCGCTGCCC	.	PASS	Atlas-SNP
BPIFB1	92747	hgsc.bcm.edu	37	20	31894766	31894766	+	Silent	SNP	C	C	T	rs41311304	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	33	81	0	0.37931	0	C|0.965;T|0.035	0.035	strong	.	.	.	.	NM_033197	exon15	c.C1368T	p.F456F	GGGATTCGAGGCA	.	PASS	Atlas-SNP
PON3	5446	hgsc.bcm.edu	37	7	95025600	95025600	+	Silent	SNP	G	G	A	rs13226149	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	77	31	79	0	0.402597	0	G|0.723;A|0.277	0.277	strong	.	PON3	59	.	NM_000940	exon1	c.C63T	p.F21F	CGCCAGGAACATC	.	PASS	Atlas-SNP
MRPL28	10573	hgsc.bcm.edu	37	16	420179	420179	+	Silent	SNP	G	G	A	rs11557300	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	22	10	36	0	0.454545	0	G|0.916;C|0.000;A|0.083	0.083	strong	.	MRPL28	15	.	NM_006428	exon2	c.C40T	p.L14L	GCTGCAGCCGCTT	.	PASS	Atlas-SNP
CAMK1G	57172	hgsc.bcm.edu	37	1	209782343	209782343	+	Silent	SNP	A	A	G	rs11119314	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	111	41	122	0	0.369369	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
UGDH	7358	hgsc.bcm.edu	37	4	39512347	39512347	+	Silent	SNP	T	T	C	rs11544855	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	246	117	218	3	0.47561	0.0137615	T|0.904;C|0.096	0.096	strong	UGDH,caecum,carcinoma,-2,1	UGDH	52	1	NM_003359	exon4	c.A399G	p.P133P	CCGCACTGGAACT	.	scavenged	Atlas-SNP
TEX38	374973	hgsc.bcm.edu	37	1	47138819	47138819	+	Missense_Mutation	SNP	T	T	G	rs614486	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	41	63	0	0.539474	0	T|0.461;G|0.539	0.539	strong	.	.	.	.	NM_001145474	exon2	c.T312G	p.D104E	GTGGGATTTGGAC	.	PASS	Atlas-SNP
AP3B1	8546	hgsc.bcm.edu	37	5	77412011	77412011	+	Silent	SNP	A	A	G	rs42360	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	87	45	79	0	0.517241	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
CILP2	148113	hgsc.bcm.edu	37	19	19656615	19656615	+	Silent	SNP	C	C	T	rs61744761	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	195	101	184	0	0.517949	0	C|0.845;T|0.155	0.155	strong	.	CILP2	84	.	NM_153221	exon8	c.C3261T	p.G1087G	TGACGGCTTCTCC	.	PASS	Atlas-SNP
ENGASE	64772	hgsc.bcm.edu	37	17	77079576	77079576	+	Silent	SNP	A	A	G	rs61756761	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	90	44	122	0	0.488889	0	A|0.902;G|0.098	0.098	strong	ENGASE,NS,carcinoma,+1,1	ENGASE	55	1	NM_001042573	exon9	c.A1155G	p.R385R	GGGCCGACTGGAG	.	PASS	Atlas-SNP
SLC35G5	83650	hgsc.bcm.edu	37	8	11189616	11189616	+	Missense_Mutation	SNP	G	G	A	rs200495954		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55	6	103	0	0.109091	0	G|0.999;A|0.001	0.001	weak	AMAC1L2,right_upper_lobe,carcinoma,+1,1	.	.	1	NM_054028	exon1	c.G1001A	p.G334E	GGACAGGGAAGGT	.	scavenged	Atlas-SNP
PITX3	5309	hgsc.bcm.edu	37	10	103991381	103991381	+	Silent	SNP	G	G	A	rs2281983	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	96	94	88	0	0.979167	0	G|0.327;A|0.673	0.673	strong	.	PITX3	9	.	NM_005029	exon3	c.C285T	p.I95I	CACGGCGATCTCC	.	PASS	Atlas-SNP
ZCWPW2	152098	hgsc.bcm.edu	37	3	28520417	28520417	+	Missense_Mutation	SNP	T	T	A	rs1563656	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	155	75	142	0	0.483871	0	T|0.574;A|0.426	0.426	strong	.	ZCWPW2	49	.	NM_001040432	exon4	c.T605A	p.L202Q	CAAAACTACAAGG	.	PASS	Atlas-SNP
FLT4	2324	hgsc.bcm.edu	37	5	180043388	180043388	+	Silent	SNP	G	G	A	rs1130378	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	128	125	147	0	0.976562	0	G|0.751;A|0.249	0.249	strong	.	FLT4	356	.	NM_182925	exon23	c.C3198T	p.P1066P	GTAGTCGGGGTCT	.	PASS	Atlas-SNP
SGK1	6446	hgsc.bcm.edu	37	6	134495683	134495683	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	46	16	70	0	0.347826	0	.	.	none	SGK1_ENST00000367858,NS,lymphoid_neoplasm,0,2	SGK1	387	2	NM_001143676	exon4	c.C403G	p.Q135E	TCTTCTGAATAAA	.	PASS	Atlas-SNP
CLCC1	23155	hgsc.bcm.edu	37	1	109477406	109477406	+	Silent	SNP	C	C	T	rs150029224	byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	203	102	228	1	0.502463	0.00438596	C|1.000;T|0.000	0.000	strong	.	CLCC1	55	.	NM_001048210	exon11	c.G1542A	p.K514K	CTGGGCCTTTTCC	.	PASS	Atlas-SNP
TAS1R1	80835	hgsc.bcm.edu	37	1	6635306	6635306	+	Missense_Mutation	SNP	G	G	A	rs34160967	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	120	55	127	0	0.458333	0	G|0.871;A|0.129	0.129	strong	TAS1R1,caecum,carcinoma,0,1	TAS1R1	76	1	NM_138697	exon3	c.G1114A	p.A372T	TTCATGGCACACA	.	PASS	Atlas-SNP
SPHKAP	80309	hgsc.bcm.edu	37	2	228883029	228883029	+	Missense_Mutation	SNP	A	A	C	rs3811515	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	256	110	290	2	0.429688	0.00689655	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	.	scavenged	Atlas-SNP
TRIM22	10346	hgsc.bcm.edu	37	11	5717762	5717762	+	Silent	SNP	T	T	C	rs10838543	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	54	31	54	0	0.574074	0	T|0.595;C|0.405	0.405	strong	.	TRIM22	66	.	NM_001199573	exon2	c.T300C	p.H100H	GCACCATGGAAAA	.	PASS	Atlas-SNP
PKD1L1	168507	hgsc.bcm.edu	37	7	47879049	47879049	+	Missense_Mutation	SNP	G	G	A	rs76100363	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	67	46	92	0	0.686567	0	G|0.859;A|0.141	0.141	strong	PKD1L1,NS,carcinoma,0,1	PKD1L1	328	1	NM_138295	exon36	c.C5764T	p.R1922W	CCTTCCGGAAGCC	.	PASS	Atlas-SNP
LILRB3	11025	hgsc.bcm.edu	37	19	54721320	54721320	+	Missense_Mutation	SNP	C	C	G	rs1053002	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	213	115	255	0	0.539906	0	C|0.891;G|0.109	0.109	strong	LILRB3,NS,carcinoma,-2,1	LILRB3	67	1	NM_001081450	exon12	c.G1620C	p.Q540H	CACTGCCTGGGGG	.	PASS	Atlas-SNP
C6orf15	29113	hgsc.bcm.edu	37	6	31079264	31079264	+	Missense_Mutation	SNP	C	C	T	rs2233984	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	90	12	105	1	0.133333	0.00952381	C|0.921;T|0.079	0.079	strong	C6orf15,NS,carcinoma,-1,1	C6orf15	29	1	NM_014070	exon2	c.G872A	p.G291D	TTGATACCTGGGT	.	scavenged	Atlas-SNP
ATP12A	479	hgsc.bcm.edu	37	13	25266932	25266932	+	Silent	SNP	C	C	A	rs963984	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	29	88	0	0.408451	0	C|0.845;A|0.155	0.155	strong	.	ATP12A	172	.	NM_001185085	exon10	c.C1293A	p.V431V	CCAAGTCTTTGAC	.	PASS	Atlas-SNP
POTEC	388468	hgsc.bcm.edu	37	18	14542654	14542654	+	Silent	SNP	C	C	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	380	7	346	2	0.0184211	0.00578035	.	.	none	POTEC,NS,carcinoma,-1,5	POTEC	129	5	NM_001137671	exon1	c.G492T	p.T164T	CATGTCCGTGTCC	.	scavenged	Atlas-SNP
LAMA4	3910	hgsc.bcm.edu	37	6	112493894	112493894	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	100	41	109	0	0.41	0	.	.	none	.	LAMA4	227	.	NM_001105206	exon12	c.A1470T	p.E490D	AAGTGCTTCCTGG	.	PASS	Atlas-SNP
ACOT2	10965	hgsc.bcm.edu	37	14	74036370	74036370	+	Silent	SNP	G	G	T	rs60568739	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	44	20	20	0	0.454545	0	G|0.940;T|0.060	0.060	strong	.	ACOT2	24	.	NM_006821	exon1	c.G426T	p.L142L	GGGGCTGCTCTGG	.	PASS	Atlas-SNP
FRA10AC1	118924	hgsc.bcm.edu	37	10	95441272	95441272	+	Missense_Mutation	SNP	G	G	A	rs11187583	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	110	46	133	1	0.418182	0.0075188	G|0.902;A|0.098	0.098	strong	FRA10AC1_ENST00000371426,colon,carcinoma,-1,2	FRA10AC1	68	2	NM_145246	exon11	c.C752T	p.S251F	GCAGAAGATAATC	.	scavenged	Atlas-SNP
STK33	65975	hgsc.bcm.edu	37	11	8486310	8486310	+	Silent	SNP	C	C	A	rs1446464	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	290	151	308	1	0.52069	0.00324675	C|0.587;A|0.413	0.413	strong	STK33_ENST00000447869,NS,adenoma,0,2	STK33	147	2	NM_030906	exon5	c.G399T	p.A133A	GTCTGTCGCTTCA	.	PASS	Atlas-SNP
ZNF683	257101	hgsc.bcm.edu	37	1	26691174	26691174	+	Missense_Mutation	SNP	C	C	A	rs11247933	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	105	54	97	0	0.514286	0	C|0.728;A|0.272	0.272	strong	.	ZNF683	51	.	NM_173574	exon4	c.G863T	p.R288L	CCACCACGCTCCA	.	PASS	Atlas-SNP
GOLGA5	9950	hgsc.bcm.edu	37	14	93276654	93276654	+	Missense_Mutation	SNP	T	T	C	rs1040835	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	142	142	137	0	1	0	T|0.201;C|0.799	0.799	strong	.	GOLGA5	84	.	NM_005113	exon5	c.T1048C	p.F350L	CAGACTTTTCAGG	.	PASS	Atlas-SNP
ISG20L2	81875	hgsc.bcm.edu	37	1	156697056	156697056	+	Missense_Mutation	SNP	T	T	C	rs3795737	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	135	62	126	0	0.459259	0	T|0.877;C|0.123	0.123	strong	.	ISG20L2	43	.	NM_030980	exon1	c.A389G	p.N130S	TGGCTATTGATCT	.	PASS	Atlas-SNP
CRIPAK	285464	hgsc.bcm.edu	37	4	1389007	1389007	+	Silent	SNP	C	C	T	rs78871723	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	39	2	7	1	0.0512821	0.142857	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
PRSS1	5644	hgsc.bcm.edu	37	7	142460339	142460339	+	Missense_Mutation	SNP	G	G	A	rs200973660	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	286	35	377	0	0.122378	0	.	.	weak	.	PRSS1	68	.	NM_002769	exon4	c.G512A	p.C171Y	CTAAGTGTGAAGC	.	PASS	Atlas-SNP
CD300E	342510	hgsc.bcm.edu	37	17	72608834	72608834	+	Silent	SNP	G	G	A	rs579238	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	24	15	28	0	0.625	0	G|0.713;A|0.287	0.287	strong	.	CD300E	70	.	NM_181449	exon4	c.C576T	p.V192V	CCAGAAGACAGCA	.	PASS	Atlas-SNP
MBOAT7	79143	hgsc.bcm.edu	37	19	54687453	54687453	+	Silent	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	121	40	121	0	0.330579	0	.	.	none	.	MBOAT7	37	.	NM_001146082	exon5	c.C444T	p.S148S	CATCAGGGAGGGC	.	PASS	Atlas-SNP
GZMM	3004	hgsc.bcm.edu	37	19	549728	549728	+	Silent	SNP	C	C	G	rs58601458	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	51	25	67	0	0.490196	0	C|0.931;G|0.069	0.069	strong	.	GZMM	11	.	NM_005317	exon5	c.C711G	p.P237P	GCCTCCCGTGGCC	.	PASS	Atlas-SNP
GRM6	2916	hgsc.bcm.edu	37	5	178415983	178415983	+	Missense_Mutation	SNP	G	G	A	rs5019554	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	122	49	163	0	0.401639	0	A|0.008;G|0.992	0.008	strong	.	GRM6	149	.	NM_000843	exon6	c.C1307T	p.T436I	CCATCAGTGGGTT	.	PASS	Atlas-SNP
SUSD5	26032	hgsc.bcm.edu	37	3	33195284	33195284	+	Silent	SNP	G	G	A	rs61743511	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	62	29	55	0	0.467742	0	G|0.848;A|0.152	0.152	strong	SUSD5,NS,carcinoma,0,1	SUSD5	53	1	NM_015551	exon5	c.C840T	p.P280P	ATCTGCGGGGACA	.	PASS	Atlas-SNP
SYNGAP1	8831	hgsc.bcm.edu	37	6	33409006	33409006	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	118	11	70	0	0.0932203	0	.	.	none	.	SYNGAP1	202	.	NM_006772	exon12	c.G1970A	p.W657X	TGGAATGGGGTTC	.	PASS	Atlas-SNP
GEMIN4	50628	hgsc.bcm.edu	37	17	649505	649505	+	Missense_Mutation	SNP	T	T	A	rs4968104	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	70	41	64	0	0.585714	0	T|0.816;A|0.184	0.184	strong	GEMIN4_ENST00000319004,NS,carcinoma,0,4	GEMIN4	116	4	NM_015721	exon2	c.A1778T	p.E593V	CCCTGCTCTTCCA	.	PASS	Atlas-SNP
IL17RC	84818	hgsc.bcm.edu	37	3	9974809	9974809	+	Silent	SNP	G	G	A	rs76999397	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	61	30	57	0	0.491803	0	G|0.968;A|0.032	0.032	strong	IL17RC,NS,carcinoma,0,1	IL17RC	55	1	NM_153461	exon19	c.G1908A	p.A636A	TCACGCGCAGCGG	.	PASS	Atlas-SNP
TMEM135	65084	hgsc.bcm.edu	37	11	87020670	87020670	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	70	20	65	0	0.285714	0	.	.	none	.	TMEM135	40	.	NM_022918	exon10	c.T892G	p.F298V	GAAAACTTCCAGC	.	PASS	Atlas-SNP
C6orf15	29113	hgsc.bcm.edu	37	6	31079644	31079644	+	Silent	SNP	G	G	A	rs2233980	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83	71	76	0	0.855422	0	G|0.926;A|0.074	0.074	strong	.	C6orf15	29	.	NM_014070	exon2	c.C492T	p.P164P	AGCCTTGGGTGAG	.	PASS	Atlas-SNP
CHRM3	1131	hgsc.bcm.edu	37	1	240070944	240070944	+	Missense_Mutation	SNP	G	G	A	rs2067481	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	131	72	132	0	0.549618	0	G|0.990;A|0.010	0.010	strong	.	CHRM3	118	.	NM_000740	exon5	c.G193A	p.V65I	CATACCGTCTGGC	.	PASS	Atlas-SNP
ASPM	259266	hgsc.bcm.edu	37	1	197070707	197070707	+	Silent	SNP	G	G	A	rs41308365	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	40	39	60	0	0.975	0	A|0.300;G|0.700;T|0.000	0.300	strong	.	ASPM	444	.	NM_018136	exon18	c.C7674T	p.I2558I	TATTACGATAGAA	.	PASS	Atlas-SNP
WDR49	151790	hgsc.bcm.edu	37	3	167240215	167240215	+	Missense_Mutation	SNP	C	C	T	rs202225646	bycluster	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72	39	47	0	0.541667	0	.	.	weak	.	WDR49	188	.	NM_178824	exon12	c.G1606A	p.V536M	TTTCCACTAAATT	.	PASS	Atlas-SNP
NOP56	10528	hgsc.bcm.edu	37	20	2638579	2638579	+	Missense_Mutation	SNP	T	T	C	rs6753	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	73	36	74	0	0.493151	0	T|0.637;C|0.363	0.363	strong	NOP56,caecum,carcinoma,-1,1	NOP56	73	1	NM_006392	exon12	c.T1424C	p.M475T	AGGAGATGAGTGA	.	PASS	Atlas-SNP
PRMT6	55170	hgsc.bcm.edu	37	1	107599918	107599918	+	Missense_Mutation	SNP	C	C	T	rs2232016	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	95	32	83	0	0.336842	0	C|0.849;T|0.151	0.151	strong	.	PRMT6	55	.	NM_018137	exon1	c.C581T	p.A194V	TCATAGCCCCCAT	.	PASS	Atlas-SNP
SASH1	23328	hgsc.bcm.edu	37	6	148840980	148840980	+	Missense_Mutation	SNP	C	C	T	rs116958992	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	16	6	21	0	0.375	0	C|0.994;T|0.006	0.006	strong	.	SASH1	123	.	NM_015278	exon10	c.C1160T	p.S387F	CCCGCTCCCTCAC	.	PASS	Atlas-SNP
TULP4	56995	hgsc.bcm.edu	37	6	158870081	158870081	+	Silent	SNP	A	A	G	rs705956	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	56	26	50	2	0.464286	0.04	A|0.374;G|0.626	0.626	strong	TULP4,NS,carcinoma,+1,1	TULP4	137	1	NM_020245	exon4	c.A597G	p.R199R	CGGCAGAATGCTG	.	scavenged	Atlas-SNP
SERPINB10	5273	hgsc.bcm.edu	37	18	61585260	61585260	+	Missense_Mutation	SNP	T	T	C	rs724558	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82	45	87	0	0.548781	0	A|0.020;C|0.224	0.224	strong	SERPINB10,NS,carcinoma,0,1	SERPINB10	53	1	NM_005024	exon3	c.T296C	p.I99T	CAGAAATCCTCAA	.	PASS	Atlas-SNP
WNT7B	7477	hgsc.bcm.edu	37	22	46319203	46319203	+	Missense_Mutation	SNP	G	G	A	rs147287645		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	18	63	0	0.272727	0	G|1.000;A|0.000	0.000	weak	.	WNT7B	45	.	NM_058238	exon4	c.C583T	p.R195W	GCATCCGGTCCTC	.	PASS	Atlas-SNP
KCNB1	3745	hgsc.bcm.edu	37	20	47990250	47990250	+	Missense_Mutation	SNP	G	G	C	rs2229006	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	53	26	54	0	0.490566	0	G|0.986;C|0.014	0.014	strong	.	KCNB1	142	.	NM_004975	exon2	c.C1847G	p.T616S	CCCCCAGTCTTGC	.	PASS	Atlas-SNP
OR8G2	26492	hgsc.bcm.edu	37	11	124096277	124096277	+	Missense_Mutation	SNP	G	G	A	rs2466612	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	195	143	168	0	0.733333	0	G|0.888;A|0.112	0.112	strong	.	.	.	.	NM_001007249	exon1	c.G880A	p.V294I	ACTATTGTTGTGC	.	PASS	Atlas-SNP
SCRIB	23513	hgsc.bcm.edu	37	8	144895669	144895669	+	Silent	SNP	G	G	A	rs56748182	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	76	34	72	0	0.447368	0	G|0.941;A|0.059	0.059	strong	.	SCRIB	192	.	NM_015356	exon5	c.C474T	p.L158L	CTCCCGGAGCTCC	.	PASS	Atlas-SNP
NFATC3	4775	hgsc.bcm.edu	37	16	68225515	68225515	+	Silent	SNP	G	G	A	rs12598	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	108	108	91	0	1	0	G|0.945;A|0.055	0.055	strong	.	NFATC3	190	.	NM_173163	exon9	c.G2943A	p.T981T	AAGTACGGGCCAG	.	PASS	Atlas-SNP
C3	718	hgsc.bcm.edu	37	19	6713262	6713262	+	Missense_Mutation	SNP	G	G	A	rs1047286	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	66	26	54	0	0.393939	0	G|0.864;A|0.136	0.136	strong	.	C3	192	.	NM_000064	exon9	c.C941T	p.P314L	GCTCGGGGGTTCT	.	PASS	Atlas-SNP
KIAA1755	85449	hgsc.bcm.edu	37	20	36850988	36850988	+	Silent	SNP	C	C	T	rs35524973	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	30	15	25	0	0.5	0	A|0.000;C|0.971;T|0.029	0.029	strong	.	KIAA1755	145	.	NM_001029864	exon10	c.G2280A	p.R760R	CAGGCACCTGGTA	.	PASS	Atlas-SNP
ZNF211	10520	hgsc.bcm.edu	37	19	58152795	58152795	+	Missense_Mutation	SNP	C	C	T	rs11879465	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	40	19	41	0	0.475	0	C|0.792;T|0.208	0.208	strong	.	ZNF211	78	.	NM_001265597	exon5	c.C1136T	p.A379V	CTTATGCGTGCCC	.	PASS	Atlas-SNP
PPP2R3A	5523	hgsc.bcm.edu	37	3	135720540	135720540	+	Missense_Mutation	SNP	A	A	G	rs9814557	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	165	77	173	0	0.466667	0	A|0.801;G|0.199	0.199	strong	.	PPP2R3A	114	.	NM_002718	exon2	c.A200G	p.D67G	ATGCAGATCTGAA	.	PASS	Atlas-SNP
TIAM1	7074	hgsc.bcm.edu	37	21	32567589	32567589	+	Silent	SNP	G	G	C	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	50	20	50	0	0.4	0	.	.	none	.	TIAM1	522	.	NM_003253	exon14	c.C2526G	p.V842V	CTGAGTGACTTTT	.	PASS	Atlas-SNP
ZBTB41	360023	hgsc.bcm.edu	37	1	197168690	197168690	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	189	6	227	0	0.031746	0	.	.	none	ZBTB41,NS,carcinoma,0,1	ZBTB41	116	1	NM_194314	exon1	c.A914C	p.E305A	TCTTCTTCAGCAT	.	scavenged	Atlas-SNP
COX4I2	84701	hgsc.bcm.edu	37	20	30232673	30232673	+	Missense_Mutation	SNP	G	G	A	rs11907253	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	118	59	90	0	0.5	0	G|0.919;A|0.081	0.081	strong	.	COX4I2	18	.	NM_032609	exon5	c.G482A	p.R161H	CCTCCCGCTGGGA	.	PASS	Atlas-SNP
SUPT6H	6830	hgsc.bcm.edu	37	17	27014396	27014396	+	Silent	SNP	C	C	T	rs28753762	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	89	43	66	0	0.483146	0	C|0.898;T|0.102	0.102	strong	.	SUPT6H	165	.	NM_003170	exon23	c.C2913T	p.V971V	CGGGGTCGATGTC	.	PASS	Atlas-SNP
TNR	7143	hgsc.bcm.edu	37	1	175293629	175293629	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	163	2	181	0	0.0122699	0	.	.	none	TNR,colon,carcinoma,0,3	TNR	399	3	NM_003285	exon22	c.C3820T	p.R1274C	AAGGGCGTCCTTG	.	scavenged	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9059232	9059232	+	Missense_Mutation	SNP	T	T	C	rs12710265	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	149	84	152	0	0.563758	0	T|0.786;C|0.214	0.214	strong	.	MUC16	4315	.	NM_024690	exon3	c.A28214G	p.Q9405R	ACTGACTGTGGAA	.	PASS	Atlas-SNP
LLGL2	3993	hgsc.bcm.edu	37	17	73565171	73565171	+	Missense_Mutation	SNP	T	T	C	rs1671021	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	92	91	134	0	0.98913	0	T|0.486;C|0.514	0.514	strong	.	LLGL2	155	.	NM_004524	exon13	c.T1435C	p.F479L	GAGAACTTCAGTG	.	PASS	Atlas-SNP
RNMTL1	55178	hgsc.bcm.edu	37	17	685752	685752	+	Missense_Mutation	SNP	G	G	A	rs2249542	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	43	22	54	0	0.511628	0	G|0.824;A|0.175	0.175	strong	.	RNMTL1	25	.	NM_018146	exon1	c.G134A	p.G45E	CTTCCGGAGAGGT	.	PASS	Atlas-SNP
ICAM1	3383	hgsc.bcm.edu	37	19	10395683	10395683	+	Missense_Mutation	SNP	A	A	G	rs5498	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	86	44	57	0	0.511628	0	A|0.656;G|0.344	0.344	strong	.	ICAM1	32	.	NM_000201	exon6	c.A1405G	p.K469E	ACCCGCAAGGTGA	.	PASS	Atlas-SNP
CPB2	1361	hgsc.bcm.edu	37	13	46638826	46638826	+	Silent	SNP	G	G	A	rs2277440	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	116	41	84	0	0.353448	0	G|0.890;A|0.110	0.110	strong	CPB2,NS,carcinoma,0,1	CPB2	60	1	NM_001872	exon8	c.C753T	p.I251I	TGTTCCGATGCAA	.	PASS	Atlas-SNP
SLCO4A1	28231	hgsc.bcm.edu	37	20	61288355	61288355	+	Silent	SNP	G	G	T	rs3195701	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	31	19	65	0	0.612903	0	G|0.820;T|0.180	0.180	strong	SLCO4A1,caecum,carcinoma,0,1	SLCO4A1	65	1	NM_016354	exon2	c.G549T	p.G183G	CACGGGGTCGCTG	.	PASS	Atlas-SNP
DYSF	8291	hgsc.bcm.edu	37	2	71838597	71838597	+	Silent	SNP	C	C	A	rs2303606	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	38	26	49	0	0.684211	0	C|0.529;A|0.471	0.471	strong	.	DYSF	536	.	NM_001130982	exon39	c.C4104A	p.I1368I	TTAGATCCTGGCA	.	PASS	Atlas-SNP
ZNF385C	201181	hgsc.bcm.edu	37	17	40189847	40189847	+	Missense_Mutation	SNP	G	G	A	rs145907332	bycluster;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55	33	58	0	0.6	0	G|0.994;A|0.006	0.006	strong	.	ZNF385C	7	.	NM_001242704	exon2	c.C70T	p.R24W	GAGGCCGGGTGGG	.	PASS	Atlas-SNP
TUBGCP6	85378	hgsc.bcm.edu	37	22	50657008	50657008	+	Silent	SNP	C	C	T	rs111335098	bycluster;byfrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	114	61	127	0	0.535088	0	C|0.999;T|0.001	0.001	strong	.	TUBGCP6	132	.	NM_020461	exon22	c.G4863A	p.V1621V	CTTGCTCACGCAG	.	PASS	Atlas-SNP
USH2A	7399	hgsc.bcm.edu	37	1	216258194	216258194	+	Silent	SNP	G	G	T	rs56110889	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	89	88	81	0	0.988764	0	G|0.844;T|0.156	0.156	strong	.	USH2A	1168	.	NM_206933	exon25	c.C5013A	p.G1671G	GAGACAGCCCACA	.	PASS	Atlas-SNP
RNF213	57674	hgsc.bcm.edu	37	17	78319380	78319380	+	Silent	SNP	G	G	C	rs4890012	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	117	116	137	0	0.991453	0	G|0.447;C|0.553	0.553	strong	.	RNF213	766	.	NM_001256071	exon29	c.G7245C	p.P2415P	GATCCCGGTTATC	.	PASS	Atlas-SNP
TMEM17	200728	hgsc.bcm.edu	37	2	62733201	62733201	+	Missense_Mutation	SNP	A	A	T	rs78110679	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	72	28	109	0	0.388889	0	A|0.925;T|0.075	0.075	strong	.	TMEM17	19	.	NM_198276	exon1	c.T64A	p.S22T	GATTGGAATCACT	.	PASS	Atlas-SNP
CARD9	64170	hgsc.bcm.edu	37	9	139265088	139265088	+	Silent	SNP	C	C	T	rs59902911	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	105	57	123	0	0.542857	0	C|0.955;T|0.045	0.045	strong	.	CARD9	47	.	NM_052813	exon5	c.G693A	p.T231T	CTTCAGCGTGTGC	.	PASS	Atlas-SNP
SERPINB3	6317	hgsc.bcm.edu	37	18	61323012	61323012	+	Missense_Mutation	SNP	C	C	G	rs3180227	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	169	85	168	0	0.502959	0	C|0.858;G|0.142	0.142	strong	.	SERPINB3	90	.	NM_006919	exon8	c.G1052C	p.G351A	CCGAATCCTACTA	.	PASS	Atlas-SNP
LILRB4	11006	hgsc.bcm.edu	37	19	55179377	55179377	+	Missense_Mutation	SNP	T	T	G	rs149600113		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	167	7	215	4	0.0419162	0.0186047	.	.	weak	LILRB4,NS,carcinoma,0,1	LILRB4	86	1	NM_006847	exon12	c.T1254G	p.F418L	CAGCTTTACCCTC	.	scavenged	Atlas-SNP
BAZ1B	9031	hgsc.bcm.edu	37	7	72883898	72883898	+	Missense_Mutation	SNP	G	G	A	rs145043036	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	117	59	136	0	0.504274	0	G|0.999;A|0.001	0.001	strong	.	BAZ1B	147	.	NM_032408	exon9	c.C2815T	p.H939Y	AGTGATGGTTGAA	.	PASS	Atlas-SNP
ZFPM1	161882	hgsc.bcm.edu	37	16	88594567	88594567	+	Silent	SNP	C	C	T	rs35121729	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82	41	82	0	0.5	0	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	.	PASS	Atlas-SNP
MYOM1	8736	hgsc.bcm.edu	37	18	3176040	3176040	+	Missense_Mutation	SNP	C	C	G	rs8099021	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	77	39	100	0	0.506494	0	C|0.250;G|0.750	0.750	strong	.	MYOM1	192	.	NM_003803	exon6	c.G1022C	p.G341A	TCTTACCCATTAA	.	PASS	Atlas-SNP
RNF19B	127544	hgsc.bcm.edu	37	1	33402542	33402542	+	Silent	SNP	G	G	C	rs35756506	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	83	43	92	0	0.518072	0	G|0.947;C|0.053	0.053	strong	.	RNF19B	43	.	NM_153341	exon9	c.C2064G	p.P688P	GGAGCGGGGGGAG	.	PASS	Atlas-SNP
NUP210	23225	hgsc.bcm.edu	37	3	13379400	13379400	+	Silent	SNP	C	C	T	rs3773302	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	22	10	31	0	0.454545	0	C|0.416;T|0.584	0.584	strong	.	NUP210	182	.	NM_024923	exon26	c.G3489A	p.E1163E	CAGCACCTCCACC	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9083457	9083457	+	Missense_Mutation	SNP	C	C	T	rs17000886	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	71	30	73	0	0.422535	0	C|0.797;T|0.203	0.203	strong	.	MUC16	4315	.	NM_024690	exon1	c.G8358A	p.M2786I	TAGTGGCATCACA	.	PASS	Atlas-SNP
TRIM16	10626	hgsc.bcm.edu	37	17	15554504	15554504	+	Silent	SNP	G	G	A	rs4792642	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82	40	87	0	0.487805	0	G|0.746;A|0.254	0.254	strong	.	TRIM16	45	.	NM_006470	exon4	c.C420T	p.A140A	GCAGAAGGCAGAC	.	PASS	Atlas-SNP
CLHC1	130162	hgsc.bcm.edu	37	2	55436934	55436934	+	Missense_Mutation	SNP	G	G	A	rs9677948	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	57	37	54	0	0.649123	0	G|0.762;A|0.238	0.238	strong	.	.	.	.	NM_152385	exon6	c.C533T	p.A178V	GTGAGAGCATCTA	.	PASS	Atlas-SNP
CSE1L	1434	hgsc.bcm.edu	37	20	47685320	47685320	+	Silent	SNP	G	G	C	rs2227946	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	206	98	227	0	0.475728	0	G|0.784;C|0.216	0.216	strong	.	CSE1L	83	.	NM_001256135	exon7	c.G636C	p.L212L	TTCCCTGATCCTG	.	PASS	Atlas-SNP
PATE4	399968	hgsc.bcm.edu	37	11	125708293	125708293	+	Missense_Mutation	SNP	T	T	G	rs12224646	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	108	90	73	0	0.833333	0	T|0.874;G|0.126	0.126	strong	.	PATE4	10	.	NM_001144874	exon3	c.T268G	p.C90G	CTGTGCTGTGACA	.	PASS	Atlas-SNP
MYOM3	127294	hgsc.bcm.edu	37	1	24406535	24406535	+	Missense_Mutation	SNP	G	G	A	rs35446243	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	55	23	47	0	0.418182	0	G|0.869;A|0.131	0.131	strong	.	MYOM3	131	.	NM_152372	exon20	c.C2557T	p.P853S	GGCCTGGGGTGAC	.	PASS	Atlas-SNP
ENTPD7	57089	hgsc.bcm.edu	37	10	101451259	101451259	+	Missense_Mutation	SNP	T	T	C	rs11190245	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	88	52	71	0	0.590909	0	T|0.752;C|0.248	0.248	strong	.	ENTPD7	44	.	NM_020354	exon8	c.T827C	p.V276A	CCTCTGTCCTTCC	.	PASS	Atlas-SNP
NOTCH4	4855	hgsc.bcm.edu	37	6	32190390	32190390	+	Missense_Mutation	SNP	T	T	G	rs915894	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	156	155	153	0	0.99359	0	T|0.623;G|0.377	0.377	strong	.	NOTCH4	201	.	NM_004557	exon3	c.A349C	p.K117Q	CAAGCTTGGCCTG	.	PASS	Atlas-SNP
ZFHX3	463	hgsc.bcm.edu	37	16	72993706	72993706	+	Silent	SNP	G	G	A	rs62053191	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	104	45	102	0	0.432692	0	G|0.958;A|0.042	0.042	strong	.	ZFHX3	404	.	NM_006885	exon2	c.C339T	p.A113A	GTCGCTGGCGCTC	.	PASS	Atlas-SNP
IZUMO1	284359	hgsc.bcm.edu	37	19	49245518	49245518	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	129	31	134	0	0.24031	0	.	.	none	.	IZUMO1	30	.	NM_182575	exon7	c.A548C	p.E183A	TTTAACTCACAGT	.	PASS	Atlas-SNP
TNKS1BP1	85456	hgsc.bcm.edu	37	11	57081146	57081146	+	Missense_Mutation	SNP	G	G	C	rs12364724	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98	39	113	0	0.397959	0	G|0.949;C|0.051	0.051	strong	.	TNKS1BP1	148	.	NM_033396	exon5	c.C1016G	p.P339R	GCACTTGGAGCTG	.	PASS	Atlas-SNP
IL10RB	3588	hgsc.bcm.edu	37	21	34640788	34640788	+	Missense_Mutation	SNP	A	A	G	rs2834167	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	148	98	130	0	0.662162	0	A|0.728;G|0.272	0.272	strong	.	IL10RB	37	.	NM_000628	exon2	c.A139G	p.K47E	TTTGCCAAAGGGA	.	PASS	Atlas-SNP
MRTO4	51154	hgsc.bcm.edu	37	1	19583636	19583636	+	Silent	SNP	C	C	T	rs1126682	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	94	39	136	0	0.414894	0	C|0.842;T|0.158	0.158	strong	MRTO4,NS,carcinoma,0,1	MRTO4	17	1	NM_016183	exon4	c.C270T	p.H90H	CCTGCACCAGGTA	.	PASS	Atlas-SNP
CCDC6	8030	hgsc.bcm.edu	37	10	61552692	61552692	+	Missense_Mutation	SNP	G	G	T	rs1053266	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	103	42	115	0	0.407767	0	G|0.577;T|0.423	0.423	strong	CCDC6,NS,carcinoma,0,1	CCDC6	44	1	NM_005436	exon9	c.C1408A	p.P470T	AGGAGGGGTGCGC	.	PASS	Atlas-SNP
MICAL2	9645	hgsc.bcm.edu	37	11	12183846	12183846	+	Silent	SNP	C	C	T	rs28625145	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	82	43	82	0	0.52439	0	C|0.813;T|0.187	0.187	strong	.	MICAL2	114	.	NM_014632	exon3	c.C144T	p.N48N	CAGAAACTTTTAT	.	PASS	Atlas-SNP
TNFRSF13B	23495	hgsc.bcm.edu	37	17	16842991	16842991	+	Missense_Mutation	SNP	G	G	A	rs34562254	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	137	74	127	0	0.540146	0	G|0.865;A|0.135	0.135	strong	.	TNFRSF13B	34	.	NM_012452	exon5	c.C752T	p.P251L	GGGTCGGGGGTCC	.	PASS	Atlas-SNP
NLRC5	84166	hgsc.bcm.edu	37	16	57060340	57060340	+	Silent	SNP	T	T	C	rs34531240	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	98	34	87	0	0.346939	0	T|0.837;C|0.163	0.163	strong	.	NLRC5	186	.	NM_032206	exon5	c.T1485C	p.T495T	GCTGACTTCCTTC	.	PASS	Atlas-SNP
BIN1	274	hgsc.bcm.edu	37	2	127816632	127816632	+	Silent	SNP	G	G	A	rs2276579	bycluster;byfrequency;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	33	25	42	0	0.757576	0	G|0.886;A|0.114	0.114	strong	.	BIN1	85	.	NM_139345	exon11	c.C957T	p.A319A	CCCGCCGGCCGGC	.	PASS	Atlas-SNP
PTGS1	5742	hgsc.bcm.edu	37	9	125143973	125143973	+	Missense_Mutation	SNP	C	C	A	rs5789	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	43	24	49	0	0.55814	0	C|0.979;A|0.021	0.021	strong	.	PTGS1	84	.	NM_000962	exon7	c.C709A	p.L237M	GACAATCTGGAGC	.	PASS	Atlas-SNP
OR4N2	390429	hgsc.bcm.edu	37	14	20296226	20296226	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	426	7	369	3	0.0164319	0.00813008	.	.	none	OR4N2,right_upper_lobe,carcinoma,-1,2	OR4N2	125	2	NM_001004723	exon1	c.A619G	p.T207A	CTGATGACACTCC	.	scavenged	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1083293	1083293	+	Silent	SNP	T	T	C	rs7394853	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	52	52	52	0	1	0	T|0.705;C|0.295	0.295	strong	MUC2_ENST00000441003,NS,carcinoma,0,2	MUC2	614	2	NM_002457	exon16	c.T2193C	p.D731D	GGGGGATGTGGTC	.	PASS	Atlas-SNP
